Journal of Microbiology

Reviews

Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria: Yubin Yang, Hana Hyeon, Minju Joo, Kangseok Lee, Eunkyoung Shin; J. Microbiol. 2025;63(4):e2501027. Published online April 2, 2025; DOI: https://doi.org/10.71150/jm.2501027

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The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.

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Biofilm, resistance, and quorum sensing: The triple threat in bacterial pathogenesis
Mohammad Nazrul Islam Bhuiyan
The Microbe.2025; 9: 100578. CrossRef
Biofilm maturation in carbapenem-resistant Pseudomonas aeruginosa is regulated by the sRNA PA213 and its corresponding encoded small protein
Yongli Song, Jie Li, Yating Zhang, Lingge Su, Shuang Qin, Chunyan Wu, Guibo Song
International Journal of Antimicrobial Agents.2025; 66(6): 107625. CrossRef

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation: Jun Ren, So Hee Oh, Dokyun Na; J. Microbiol. 2025;63(3):e2501033. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501033

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Abstract PDF

Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef
Recombinase-Mediated Cassette Exchange-Based CRISPR Activation Screening Identifies Hyperosmotic Stress-Resistant Genes in Chinese Hamster Ovary Cells
Minhye Baek, Seokchan Kweon, Yujin Kim, Nathan E. Lewis, Jae Seong Lee, Gyun Min Lee
ACS Synthetic Biology.2025; 14(8): 3116. CrossRef

Journal Articles

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606: Kyeongmin Kim, Md Maidul Islam, Seunghyeok Bang, Jeongah Kim, Chung-Young Lee, Je Chul Lee, Minsang Shin; J. Microbiol. 2024;62(11):999-1012. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00182-5

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Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606^T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606^T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

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The H-NS homologues MvaT and MvaU repress CRISPR-Cas in Pseudomonas aeruginosa
Kira Céline Koonce, Jesper Juel Mauritzen, Ida Friberg Hitz, Emil Funk Vangsgaard, Elizabeth H. M. Putz, Anne Sofie Wajn, Frederik Hagelund Leth, Nina Molin Høyland-Kroghsbo
Philosophical Transactions of the Royal Society B: Biological Sciences.2025;[Epub] CrossRef
BaeR and H-NS control CRISPR-Cas-mediated immunity and virulence in Acinetobacter baumannii
Ting Yu, Jun Xie, Xinyue Huang, Jiayuan Huang, Guangyu Bao, Wenjie Yuan, Chengfeng Gao, Cuicui Liu, Jian Hu, Weixuan Yang, Guocai Li, Ryan McClure
mSystems.2025;[Epub] CrossRef

An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets: Minchang Jang, Joon Young Park, Gayeon Lee, Donghyuk Kim; J. Microbiol. 2024;62(12):1075-1088. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00181-6

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Transcriptional regulatory networks (TRNs) in bacteria are crucial for elucidating the mechanisms that regulate gene expression and cellular responses to environmental stimuli. These networks delineate the interactions between transcription factors (TFs) and their target genes, thereby uncovering the regulatory processes that modulate gene expression under varying environmental conditions. Analyzing TRNs offers valuable insights into bacterial adaptation, stress responses, and metabolic optimization from an evolutionary standpoint. Additionally, understanding TRNs can drive the development of novel antimicrobial therapies and the engineering of microbial strains for biofuel and bioproduct production. This protocol integrates advanced data analysis pipelines, including ChEAP, DEOCSU, and DESeq2, to analyze omics datasets that encompass genome-wide TF binding sites and transcriptome profiles derived from ChIP-exo and RNA-seq experiments. This approach minimizes both the time required and the risk of bias, making it accessible to non-expert users. Key steps in the protocol include preprocessing and peak calling from ChIP-exo data, differential expression analysis of RNA-seq data, and motif and regulon analysis. This method offers a comprehensive and efficient framework for TRN reconstruction across various bacterial strains, enhancing both the accuracy and reliability of the analysis while providing valuable insights for basic and applied research.

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ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim
Nucleic Acids Research.2025;[Epub] CrossRef

Review

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review: Chiranjib Chakraborty, Manojit Bhattacharya, Md Aminul Islam, Hatem Zayed, Elijah Ige Ohimain, Sang-Soo Lee, Prosun Bhattacharya, Kuldeep Dhama; J. Microbiol. 2024;62(5):337-354. Published online May 23, 2024; DOI: https://doi.org/10.1007/s12275-024-00138-9

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Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

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Phylogenetic analyses of the spread of Clade I MPOX in African and non-African nations
Chiranjib Chakraborty, Manojit Bhattacharya, Arpita Das, Ali S. Abdelhameed
Virus Genes.2025; 61(3): 265. CrossRef
Efficient and modular reverse genetics system for rapid generation of recombinant severe acute respiratory syndrome coronavirus 2
Sojung Bae, Jinjong Myoung
Journal of Microbiology.2025; 63(7): e2504015. CrossRef
Real-time malaria detection in the Amazon rainforest via drone-collected eDNA and portable qPCR
Yin Cheong Aden Ip, Luca Montemartini, Jia Jin Marc Chang, Andrea Desiderato, Nicolás D. Franco-Sierra, Christian Geckeler, Mailyn Adriana Gonzalez Herrera, Michele Gregorini, Meret Jucker, Steffen Kirchgeorg, Martina Lüthi, Elvira Mächler, Frederik Bendi
One Health.2025; 21: 101167. CrossRef
Development of a multiplex real-time PCR for the simultaneous detection of monkeypox virus clades I, II, and goatpox virus
Yongqiang Lin, Zijing Guo, Jinsong Chen, Xianwen Zhang, Long Zhou, Yanmin Li, Zhidong Zhang
Frontiers in Veterinary Science.2024;[Epub] CrossRef
Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2024; 34(12): 2506. CrossRef

Journal Articles

Vaccine Development for Severe Fever with Thrombocytopenia Syndrome Virus in Dogs: Seok-Chan Park, Da-Eun Jeong, Sun-Woo Han, Joon-Seok Chae, Joo-Yong Lee, Hyun-Sook Kim, Bumseok Kim, Jun-Gu Kang; J. Microbiol. 2024;62(4):327-335. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00119-y

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Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening viral zoonosis. The causative agent of this disease is the Dabie bandavirus, which is usually known as the SFTS virus (SFTSV). Although the role of vertebrates in SFTSV transmission to humans remains uncertain, some reports have suggested that dogs could potentially transmit SFTSV to humans. Consequently, preventive measures against SFTSV in dogs are urgently needed. In the present study, dogs were immunized three times at two-week intervals with formaldehyde-inactivated SFTSV with two types of adjuvants. SFTSV (KCD46) was injected into all dogs two weeks after the final immunization. Control dogs showed viremia from 2 to 4 days post infection (dpi), and displayed white pulp atrophy in the spleen, along with a high level of terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling assay (TUNEL) positive area. However, the inactivated SFTSV vaccine groups exhibited rare pathological changes and significantly reduced TUNEL positive areas in the spleen. Furthermore, SFTSV viral loads were not detected at any of the tested dpi. Our results indicate that both adjuvants can be safely used in combination with an inactivated SFTSV formulation to induce strong neutralizing antibodies. Inactivated SFTSV vaccines effectively prevent pathogenicity and viremia in dogs infected with SFTSV. In conclusion, our study highlighted the potential of inactivated SFTSV vaccination for SFTSV control in dogs.

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The immunogenicity and protection efficacy evaluation of mRNA vaccine candidate for severe fever with thrombocytopenia syndrome in mice
Da-Eun Jeong, Jack Yoon, Baek Kim, Jun-Gu Kang, Abdallah M. Samy
PLOS Neglected Tropical Diseases.2025; 19(4): e0012999. CrossRef
Efficient and modular reverse genetics system for rapid generation of recombinant severe acute respiratory syndrome coronavirus 2
Sojung Bae, Jinjong Myoung
Journal of Microbiology.2025; 63(7): e2504015. CrossRef
Current status of severe fever with thrombocytopenia syndrome in China (Review)
Hao Sun, Quanman Hu, Saiwei Lu, Yanyan Yang, Li Zhang, Jinzhao Long, Yuefei Jin, Haiyan Yang, Shuaiyin Chen, Guangcai Duan
International Journal of Molecular Medicine.2025; 56(5): 1. CrossRef
Domain-Specific Impacts of Spike Protein Mutations on Infectivity and Antibody Escape in SARS-CoV-2 Omicron BA.1
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef

Dynamics of Microbial Community Structure, Function and Assembly Mechanism with Increasing Stand Age of Slash Pine (Pinus elliottii) Plantations in Houtian Sandy Area, South China: Xiaoyang Zhang , Si-Yi Xiong , Xiukun Wu , Bei-Bei Zeng , Yang-Mei Mo , Zhi-Cheng Deng , Qi Wei , Yang Gao , Licao Cui , Jianping Liu , Haozhi Long; J. Microbiol. 2023;61(11):953-966. Published online November 29, 2023; DOI: https://doi.org/10.1007/s12275-023-00089-7

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Establishing slash pine plantations is the primary method for restoring sandification land in the Houtian area of South China. However, the microbial variation pattern with increasing stand age remains unclear. In this study, we investigated microbial community structure and function in bare sandy land and four stand age gradients, exploring ecological processes that determine their assembly. We did not observe a significant increase in the absolute abundance of bacteria or fungi with stand age. Bacterial communities were dominated by Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria; the relative abundance of Chloroflexi significantly declined while Proteobacteria and Acidobacteria significantly increased with stand age. Fungal communities showed succession at the genus level, with Pisolithus most abundant in soils of younger stands (1- and 6-year-old). Turnover of fungal communities was primarily driven by stochastic processes; both deterministic and stochastic processes influenced the assembly of bacterial communities, with the relative importance of stochastic processes gradually increasing with stand age. Bacterial and fungal communities showed the strongest correlation with the diameter at breast height, followed by soil available phosphorus and water content. Notably, there was a significant increase in the relative abundance of functional groups involved in nitrogen fixation and uptake as stand age increased. Overall, this study highlights the important effects of slash pine stand age on microbial communities in sandy lands and suggests attention to the nitrogen and phosphorus requirements of slash pine plantations in the later stages of sandy management.

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Assembly and co-occurrence pattern of microbial communities in bulk and rhizosphere soils of Pinus elliottii plantations on sandy lands in China
Haozhi Long, Si-Yi Xiong, Yang-Mei Mo, Bei-Bei Zeng, Bin-Xuan Shan, Ting Xiao, Yang Gao, Chaoyu Cui
Plant and Soil.2025; 511(1-2): 309. CrossRef
Assembly processes and networks of soil microbial communities along karst forest succession
Wanxia Peng, Min Song, Hu Du, Shanghua Jiang, Fuping Zeng, Huijun Chen, Tongqing Song
CATENA.2025; 248: 108574. CrossRef
Temporal dynamics of soil microbial symbioses in the root zone of wolfberry: deciphering the effects of biotic and abiotic factors on bacterial and fungal ecological networks
Mengyuan He, Qianqian Wang, Yiming Wang, Junhua Zhang
Frontiers in Plant Science.2025;[Epub] CrossRef
Forest Age and Soil Depth Mediate the Effects of Soil and Root Traits on Soil Microbial Community in Plantations
Yaxuan Chen, Qianyuan Liu, Yanmei Chen, Changqi Ai, Peipei Jiang
Ecology and Evolution.2025;[Epub] CrossRef
Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics
Bo Ram Kang, Soo Bin Kim, Jin-Kyung Hong, Seok Hyun Ahn, Jinwon Kim, Nayeon Lee, Tae Kwon Lee
Science of The Total Environment.2024; 957: 177724. CrossRef
The complex relationships between diatoms, bacterial communities, and dissolved organic matter: Effects of silicon concentration
Xiding Wang, Yang Liu, Yi Zhang, Peng Wu, Xudong Liu, Fangru Nan, Qi Liu, Junping Lv, Jia Feng, Shulian Xie
Algal Research.2024; 79: 103460. CrossRef

Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I: Dayeong Bae , Hana Hyeon , Eunkyoung Shin , Ji&# , Kangseok Lee; J. Microbiol. 2023;61(2):211-220. Published online February 22, 2023; DOI: https://doi.org/10.1007/s12275-023-00013-z

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RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity. Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication, at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the 5′-end (RNA I- 5) resulted in an approximately twofold increase in the steady-state levels of RNA I- 5 and the copy number of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These
results
indicate that RNA I- 5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5′-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5′-monophosphorylated end.

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Engineering an Escherichia coli based in vivo mRNA manufacturing platform
Edward Curry, George Muir, Jixin Qu, Zoltán Kis, Martyn Hulley, Adam Brown
Biotechnology and Bioengineering.2024; 121(6): 1912. CrossRef

Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV’s oncogenic role: Chunpeng Yu , Jian Li , Qun Li , Shuai Chang , Yufeng Cao , Hui Jiang , Lingling Xie , Gang Fan , Song Wang; J. Microbiol. 2022;60(11):1106-1112. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2371-x

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Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.

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Decoding codon usage in human papillomavirus type 59
Xiaochun Tan, Wenyi Zhou, Shunyou Jing, Weifeng Shen, Binbin Lu
Virus Genes.2025; 61(3): 313. CrossRef
Bioinformatics and system biology approach to discover the common pathogenetic processes between COVID-19 and chronic hepatitis B
Xiao Ma, Tengda Huang, Yujia Song, Hongyuan Pan, Ao Du, Xinyi Zhou, Yong Zeng, Kefei Yuan, Xiaosheng Tan
PLOS One.2025; 20(5): e0323708. CrossRef
Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics
Shuquan Su, Zhongran Ni, Tian Lan, Pengyao Ping, Jinling Tang, Zuguo Yu, Gyorgy Hutvagner, Jinyan Li
Scientific Reports.2025;[Epub] CrossRef
Conserved spatiotemporal expression landscape of dominant tRNA genes in human and mouse
Evan Y. Wu, Laura Landry
Biochemical and Biophysical Research Communications.2023; 681: 173. CrossRef
Evolution and diversity of nucleotide and dinucleotide composition in poxviruses
Cristian Molteni, Diego Forni, Rachele Cagliani, Ignacio G. Bravo, Manuela Sironi
Journal of General Virology .2023;[Epub] CrossRef
Krüppel-like factor 15 in liver diseases: Insights into metabolic reprogramming
Hao Chen, Lan-Lan Li, Yan Du
Frontiers in Pharmacology.2023;[Epub] CrossRef

Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale: Sarbjeet Niraula , Meaghan Rose , Woo-Suk Chang; J. Microbiol. 2022;60(10):986-997. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2363-x

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Microbial communities in the rhizosphere play a crucial role in determining plant growth and crop yield. A few studies have been performed to evaluate the diversity and co-occurrence patterns of rhizosphere microbiomes in soybean (Glycine max) at a regional scale. Here, we used a culture-independent
method
to compare the bacterial communities of the soybean rhizosphere between Nebraska (NE), a high-yield state, and Oklahoma (OK), a low-yield state. It is well known that the rhizosphere microbiome is a subset of microbes that ultimately get colonized by microbial communities from the surrounding bulk soil. Therefore, we hypothesized that differences in the soybean yield are attributed to the variations in the rhizosphere microbes at taxonomic, functional, and community levels. In addition, soil physicochemical properties were also evaluated from each sampling site for comparative study. Our result showed that distinct clusters were formed between NE and OK in terms of their soil physicochemical property. Among 3 primary nutrients (i.e., nitrogen, phosphorus, and potassium), potassium is more positively correlated with the high-yield state NE samples. We also attempted to identify keystone communities that significantly affected the soybean yield using co-occurrence network patterns. Network analysis revealed that communities formed distinct clusters in which members of modules having significantly positive correlations with the soybean yield were more abundant in NE than OK. In addition, we identified the most influential bacteria for the soybean yield in the identified modules. For instance, included are class Anaerolineae, family Micromonosporaceae, genus Plantomyces, and genus Nitrospira in the most complex module (ME9) and genus Rhizobium in ME23. This research would help to further identify a way to increase soybean yield in low-yield states in the U.S. as well as worldwide by reconstructing the microbial communities in the rhizosphere.

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Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems
Honglei Ren, Huilong Hong, Bire Zha, Sobhi F. Lamlom, Hongmei Qiu, Yongqiang Cao, Rujian Sun, Haorang Wang, Junkui Ma, Hengbin Zhang, Liping Sun, Qing Yang, Changjun Zhou, Xiulin Liu, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Kezhen Zhao, Rongqiang Yuan,
Microbiome.2025;[Epub] CrossRef
Impact of Bacterial Pustule Disease Occurrence on Bacterial and Fungal Communities Within Vegetable Soybean Plants
Choosak Khaengraeng, Wuttichai Mhuantong, Usawadee Chaiprom, Sawita Suwannarat, Nattakorn Kuncharoen, Nutjarin Haewou, Warapon Bunkoed, Tiyakhon Chatnaparat
Plant Pathology.2025; 74(5): 1228. CrossRef
A molecular conveyor belt-associated protein controls the rotational direction of the bacterial type 9 secretion system
Abhishek Trivedi, Jacob A. Miratsky, Emma C. Henderson, Abhishek Singharoy, Abhishek Shrivastava, Clay Fuqua
mBio.2025;[Epub] CrossRef
The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics
Benoit Renaud Martins, Viviane Radl, Krzysztof Treder, Dorota Michałowska, Karin Pritsch, Michael Schloter
FEMS Microbiology Ecology.2024;[Epub] CrossRef
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Yingying Liu, Dan Wu, Yongjun Kan, Li Zhao, Chang Jiang, Wensheng Pang, Juan Hu, Meilan Zhou
Eurasian Soil Science.2024; 57(3): 446. CrossRef
Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
Meiyan Jiang, Fei Yao, Yunshu Yang, Yang Zhou, Kai Hou, Yinyin Chen, Dongju Feng, Wei Wu
PeerJ.2023; 11: e15997. CrossRef
Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition
Wanling Wei, Dawei Guan, Mingchao Ma, Xin Jiang, Fenliang Fan, Fangang Meng, Li Li, Baisuo Zhao, Yubin Zhao, Fengming Cao, Huijun Chen, Jun Li
Frontiers in Microbiology.2023;[Epub] CrossRef

A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis: Ju-Hyung Lee , Soo-Jeong Kwon , Ji-Yoon Han , Sang-Hyun Cho , Yong-Joon Cho , Joo-Hong Park; J. Microbiol. 2022;60(2):215-223. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1649-3

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The mammalian intestinal tract contains trillions of bacteria. However, the genetic factors that allow gut symbiotic bacteria to occupy intestinal niches remain poorly understood. Here, we identified genetic determinants required for Bacteroides thetaiotaomicron colonization in the gut using transposon sequencing analysis. Transposon insertion in BT2391, which encodes a hybrid two-component system, increased the competitive fitness of B. thetaiotaomicron. The BT2391 mutant showed a growth advantage in a mucin-dependent manner and had an increased ability to adhere to mucus-producing cell lines. The increased competitive advantage of the BT2391 mutant was dependent on the BT2392–2395 locus containing susCD homologs. Deletion of BT2391 led to changes in the expression levels of B. thetaiotaomicron genes during gut colonization. However, colonization of the BT2391 mutant promoted DSS colitis in low-fiber diet-fed mice. These results indicate that BT2391 contributes to a sustainable symbiotic relationship by maintaining a balance between mucosal colonization and gut homeostasis.

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The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron
Ann-Sophie Rüttiger, Daniel Ryan, Luisella Spiga, Vanessa Lamm-Schmidt, Gianluca Prezza, Sarah Reichardt, Madison Langford, Lars Barquist, Franziska Faber, Wenhan Zhu, Alexander J. Westermann
Nature Communications.2025;[Epub] CrossRef
Effect of Lactobacillus plantarum BFS1243 on a female frailty model induced by fecal microbiota transplantation in germ-free mice
Sashuang Dong, Qi Zeng, Weimin He, Wei Cheng, Ling Zhang, Ruimin Zhong, Wen He, Xiang Fang, Hong Wei
Food & Function.2024; 15(8): 3993. CrossRef
A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides
Rong Gao, Ti Wu, Ann M. Stock, Michael T. Laub
mBio.2024;[Epub] CrossRef
Polysaccharides from Polygonatum cyrtonema Hua prevent depression-like behaviors in mice with chronic unpredictable mild stress through refining gut microbiota-lipopolysaccharide-paraventricular nucleus signal axis
Xinya Wang, Xueqing Wang, Feng Gao, Shaojie Yang, Yilan Zhen, Xuncui Wang, Guoqi Zhu
Heliyon.2024; 10(19): e38554. CrossRef
Metal Messengers: Communication in the Bacterial World through Transition-Metal-Sensing Two-Component Systems
Alexander Paredes, Chioma Iheacho, Aaron T. Smith
Biochemistry.2023; 62(16): 2339. CrossRef
Tang-Ping-San Decoction Remodel Intestinal Flora and Barrier to Ameliorate Type 2 Diabetes Mellitus in Rodent Model
Wen Yin, Si-Qi Zhang, Wen-Lin Pang, Xiao-Jiao Chen, Jing Wen, Jiong Hou, Cui Wang, Li-Yun Song, Zhen-Ming Qiu, Peng-Tao Liang, Jia-Li Yuan, Zhong-Shan Yang, Yao Bian
Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy.2022; Volume 15: 2563. CrossRef

Characterization of a novel phage depolymerase specific to Escherichia coli O157:H7 and biofilm control on abiotic surfaces: Do-Won Park , Jong-Hyun Park; J. Microbiol. 2021;59(11):1002-1009. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1413-0

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The increasing prevalence of foodborne diseases caused by Escherichia coli O157:H7 as well as its ability to form biofilms poses major threats to public health worldwide. With increasing concerns about the limitations of current disinfectant treatments, phage-derived depolymerases may be used as promising biocontrol agents. Therefore, in this study, the characterization, purification, and application of a novel phage depolymerase, Dpo10, specifically targeting the lipopolysaccharides of E. coli O157, was performed. Dpo10, with a molecular mass of 98 kDa, was predicted to possess pectate lyase activity via genome analysis and considered to act as a receptor- binding protein of the phage. We confirmed that the purified Dpo10 showed O-polysaccharide degrading activity only for the E. coli O157 strains by observing its opaque halo. Dpo10 maintained stable enzymatic activities across a wide range of temperature conditions under 55°C and mild basic pH. Notably, Dpo10 did not inhibit bacterial growth but significantly increased the complement-mediated serum lysis of E. coli O157 by degrading its O-polysaccharides. Moreover, Dpo10 inhibited the biofilm formation against E. coli O157 on abiotic polystyrene by 8-fold and stainless steel by 2.56 log CFU/coupon. This inhibition was visually confirmed via fieldemission scanning electron microscopy. Therefore, the novel depolymerase from E. coli siphophage exhibits specific binding and lytic activities on the lipopolysaccharide of E. coli O157 and may be used as a promising anti-biofilm agent against the E. coli O157:H7 strain.

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[PROTOCOL] Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems: Jin-Kyung Hong , Soo Bin Kim , Seok Hyun Ahn , Yongjoo Choi , Tae Kwon Lee; J. Microbiol. 2021;59(10):879-885. Published online September 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1443-7

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Flow cytometry is a promising tool used to identify the phenotypic features of bacterial communities in aquatic ecosystems by measuring the physical and chemical properties of cells based on their light scattering behavior and fluorescence. Compared to molecular or culture-based approaches, flow cytometry is suitable for the online monitoring of microbial water quality because of its relatively simple sample preparation process, rapid analysis time, and high-resolution phenotypic data. Advanced statistical techniques (e.g., denoising and binning) can be utilized to successfully calculate phenotypic diversity by processing the scatter data obtained from flow cytometry. These phenotypic diversities were well correlated with taxonomic-based diversity computed using nextgeneration 16S RNA gene sequencing. The protocol provided in this paper should be a useful guide for a fast and reliable flow cytometric monitoring of bacterial phenotypic diversity in aquatic ecosystems.

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Screening of small molecules attenuating biofilm formation of Acinetobacter baumannii by inhibition of ompA promoter activity: Seok Hyeon Na , Hyejin Jeon , Man Hwan Oh , Yoo Jeong Kim , Je Chul Lee; J. Microbiol. 2021;59(9):871-878. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1394-z

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Anti-virulence therapeutic strategies are promising alternatives against drug-resistant pathogens. Outer membrane protein A (OmpA) plays a versatile role in the pathogenesis and antimicrobial resistance of Acinetobacter baumannii. Therefore, OmpA is an innovative target for anti-virulence therapy against A. baumannii. This study aimed to develop a high-throughput screening (HTS) system to discover small molecules inhibiting the ompA promoter activity of A. baumannii and screen chemical compounds using the bacterial growth-based HTS system. The ompA promoter and open reading frame of nptI fusion plasmids that controlled the expression of nptI encoding resistance to kanamycin by the ompA promoter were constructed and then transformed into A. baumannii ATCC 17978. This reporter strain was applied to screen small molecules inhibiting the ompA promoter activity in a chemical library. Of the 7,520 chemical compounds, 15 exhibited ≥ 70% growth inhibition of the report strain cultured in media containing kanamycin. Three compounds inhibited the expression of ompA and OmpA in the outer membrane of A. baumannii ATCC 17978, which subsequently reduced biofilm formation. In conclusion, our reporter strain is useful for large-scale screening of small molecules inhibiting the ompA expression in A. baumannii. Hit compounds identified by the HTS system are promising scaffolds to develop novel therapeutics against A. baumannii.

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Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction: Matt N. Hicks , Sanjiva Gunasekara , Jose Serate , Jin Park , Pegah Mosharaf , Yue Zhou , Jin-Won Lee , Hwan Youn; J. Microbiol. 2017;55(10):816-822. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7266-x

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The Escherichia coli cAMP receptor protein (CRP) utilizes the helix-turn-helix motif for DNA binding. The CRP’s recognition helix, termed F-helix, includes a stretch of six amino acids (Arg180, Glu181, Thr182, Val183, Gly184, and Arg185) for direct DNA contacts. Arg180, Glu181 and Arg185 are known as important residues for DNA binding and specificity, but little has been studied for the other residues. Here we show that Gly184 is another F-helix residue critical for the transcriptional activation function of CRP. First, glycine was repeatedly selected at CRP position 184 for its unique ability to provide wild type-level transcriptional activation activity. To dissect the glycine requirement, wild type CRP and mutants G184A, G184F, G184S, and G184Y were purified and their in vitro DNA-binding activity was measured. G184A and G184F displayed reduced DNA binding, which may explain their low transcriptional activation activity. However, G184S and G184Y displayed apparently normal DNA affinity. Therefore, an additional factor is needed to account for the diminished transcriptional activation function in G184S and G184Y, and the best explanation is perturbations in their interaction with RNA polymerase. The fact that glycine is the smallest amino acid could not fully warrant its suitability, as shown in this study. We hypothesize that Gly184 fulfills the dual functions of DNA binding and RNA polymerase interaction by conferring conformational flexibility to the F-helix.

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cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans
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Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein
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Reviews

Plasmodium falciparum apicoplast and its transcriptional regulation through calcium signaling: Praveen Rai , Drista Sharma , Rani Soni , Nazia Khatoon , Bhaskar Sharma , Tarun Kumar Bhatt; J. Microbiol. 2017;55(4):231-236. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6525-1

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Malaria has been present since ancient time and remains a major global health problem in developing countries. Plas-modium falciparum belongs to the phylum Apicomplexan, largely contain disease-causing parasites and characterized by the presence of apicoplast. It is a very essential organelle of P. falciparum responsible for the synthesis of key mole-cules required for the growth of the parasite. Indispensable nature of apicoplast makes it a potential drug target. Calcium signaling is important in the establishment of malaria para-site inside the host. It has been involved in invasion and egress of merozoites during the asexual life cycle of the parasite. Calcium signaling also regulates apicoplast metabolism. There-fore, in this review, we will focus on the role of apicoplast in malaria biology and its metabolic regulation through Ca++ signaling.

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MINIREVIEW] Global transcriptional regulator TrmB family members in prokaryotes: Minwook Kim , Soyoung Park , Sung-Jae Lee; J. Microbiol. 2016;54(10):639-645. Published online September 30, 2016; DOI: https://doi.org/10.1007/s12275-016-6362-7

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Members of the TrmB family act as global transcriptional regulators for the activation or repression of sugar ABC transporters and central sugar metabolic pathways, including glycolytic, gluconeogenic, and other metabolic pathways, and also as chromosomal stabilizers in archaea. As a relatively newly classified transcriptional regulator family, there is limited experimental evidence for their role in Thermococcales, halophilic archaeon Halobacterium salinarum NRC1, and crenarchaea Sulfolobus strains, despite being one of the extending protein families in archaea. Recently, the protein structures of Pyrococcus furiosus TrmB and TrmBL2 were solved, and the transcriptomic data uncovered by microarray and ChIP-Seq were published. In the present review, recent evidence of the functional roles of TrmB family members in archaea is explained and extended to bacteria.

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Journal Article

Amino acid residues in the Ler protein critical for derepression of the LEE5 promoter in enteropathogenic E. coli: Su-Mi Choi , Jae-Ho Jeong , Hyon E. Choy , Minsang Shin; J. Microbiol. 2016;54(8):559-564. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6027-6

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Enteropathogenic E. coli causes attaching and effacing (A/E) intestinal lesions. The genes involved in the formation of A/E lesions are encoded within a chromosomal island comprising of five major operons, LEE1-5. The global regulator H-NS represses the expression of these operons. Ler, a H-NS homologue, counteracts the H-NS–mediated repression. Using a novel genetic approach, we identified the amino acid residues in Ler that are involved in the interaction with H-NS: I20 and L23 in the C-terminal portion of α-helix 3, and I42 in the following unstructured linker region.

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Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens
R. Christopher D. Furniss, Abigail Clements, William Margolin
Journal of Bacteriology.2018;[Epub] CrossRef

Reviews

MINIREVIEW] Transcriptional control of sexual development in Cryptococcus neoformans: Matthew E. Mead , Christina M. Hull; J. Microbiol. 2016;54(5):339-346. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6080-1

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Developmental processes are essential for the normal life cycles of many pathogenic fungi, and they can facilitate survival in challenging environments, including the human host. Sexual development of the human fungal pathogen Cryptococcus neoformans not only produces infectious particles (spores) but has also enabled the evolution of new disease-related traits such as drug resistance. Transcription factor networks are essential to the development and pathogenesis of C. neoformans, and a variety of sequence-specific DNA-binding proteins control both key developmental transitions and virulence by regulating the expression of their target genes. In this review we discuss the roles of known transcription factors that harbor important connections to both development and virulence. Recent studies of these transcription factors have identified a common theme in which metabolic, stress, and other responses that are required for sexual development appear to have been co-opted for survival in the human host, thus facilitating pathogenesis. Future work elucidating the connection between development and pathogenesis will provide vital insights into the evolution of complex traits in eukaryotes as well as mechanisms that may be used to combat fungal pathogens.

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Effect of a Mating Type Gene Editing in Lentinula edodes Using RNP/Nanoparticle Complex
Minseek Kim, Minji Oh, Ji-Hoon Im, Eun-Ji Lee, Hojin Ryu, Hyeon-Su Ro, Youn-Lee Oh
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Sinil Kim, Byeongsuk Ha, Minseek Kim, Hyeon-Su Ro
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The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi
Sheng Sun, Marco A. Coelho, Márcia David-Palma, Shelby J. Priest, Joseph Heitman
Annual Review of Genetics.2019; 53(1): 417. CrossRef
Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar
Poppy C. S. Sephton-Clark, Jose F. Muñoz, Elizabeth R. Ballou, Christina A. Cuomo, Kerstin Voelz, Aaron P. Mitchell
mSphere.2018;[Epub] CrossRef
Activation of the Mating Pheromone Response Pathway ofLentinula edodesby Synthetic Pheromones
Byeongsuk Ha, Sinil Kim, Minseek Kim, Hyeon-Su Ro
Mycobiology.2018; 46(4): 407. CrossRef

MINIREVIEW] Histone deacetylase-mediated morphological transition in Candida albicans: Jueun Kim , Ji-Eun Lee , Jung-Shin Lee; J. Microbiol. 2015;53(12):805-811. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5488-3

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Abstract

Candida albicans is the most common opportunistic fungal pathogen, which switches its morphology from single-cell yeast to filament through the various signaling pathways responding to diverse environmental cues. Various transcriptional factors such as Nrg1, Efg1, Brg1, Ssn6, and Tup1 are the key components of these signaling pathways. Since C. albicans can regulate its transcriptional gene expressions using common eukaryotic regulatory systems, its morphological transition by these signaling pathways could be linked to the epigenetic regulation by chromatin structure modifiers. Histone proteins, which are critical components of eukaryotic chromatin structure, can regulate the eukaryotic chromatin structure through their own modifications such as acetylation, methylation, phosphorylation and ubiquitylation. Recent studies revealed that various histone modifications, especially histone acetylation and deacetylation, participate in morphological transition of C. albicans collaborating with well-known transcription factors in the signaling pathways. Here, we review recent studies about chromatin-mediated morphological transition of C. albicans focusing on the interaction between transcription factors in the signaling pathways and histone deacetylases.

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Research Support, Non-U.S. Gov't

Transcriptional profiles of laccase genes in the brown rot fungus Postia placenta MAD-R-698: Hongde An , Dongsheng Wei , Tingting Xiao; J. Microbiol. 2015;53(9):606-615. Published online August 1, 2015; DOI: https://doi.org/10.1007/s12275-015-4705-4

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Abstract PDF

One of the laccase isoforms in the brown rot fungus Postia placenta is thought to contribute to the production of hydroxyl radicals, which play an important role in lignocellulose degradation. However, the presence of at least two laccase isoforms in this fungus makes it difficult to understand the details of this mechanism. In this study, we systematically investigated the transcriptional patterns of two laccase genes, Pplcc1 and Pplcc2, by quantitative PCR (qPCR) to better understand the mechanism. The qPCR results showed that neither of the two genes was expressed constitutively throughout growth in liquid culture or during the degradation of a woody substrate. Transcription of Pplcc1 was upregulated under nitrogen depletion and in response to a high concentration of copper in liquid culture, and during the initial colonization of intact aspen wafer. However, it was subject to catabolite repression by a high concentration of glucose. Transcription of Pplcc2 was upregulated by stresses caused by ferulic acid, 2, 6-dimethylbenzoic acid, and ethanol, and under osmotic stress in liquid culture. However, the transcription of Pplcc2 was downregulated upon contact with the woody substrate in solid culture. These results indicate that Pplcc1 and Pplcc2 are differentially regulated in liquid and solid cultures. Pplcc1 seems to play the major role in producing hydroxyl radicals and Pplcc2 in the stress response during the degradation of a woody substrate.

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Isolation, characterization and optimizations of laccase producer from soil: A comprehensive study of application of statistical approach to enhance laccase productivity in Myrothecium verrucaria NFCCI 4363
J.P. Jawale, V.S. Nandre, R.V. Latpate, M.V. Kulkarni, P.J. Doshi
Bioresource Technology Reports.2021; 15: 100751. CrossRef
Multicopper oxidase of Acinetobacter baumannii: Assessing its role in metal homeostasis, stress management and virulence
Kavleen Kaur, Harsimran Sidhu, Neena Capalash, Prince Sharma
Microbial Pathogenesis.2020; 143: 104124. CrossRef
Reference genes for accurate normalization of gene expression in wood-decomposing fungi
Jiwei Zhang, Hugh D. Mitchell, Lye Meng Markillie, Matthew J. Gaffrey, Galya Orr, Jonathan Schilling
Fungal Genetics and Biology.2019; 123: 33. CrossRef
Multicopper oxidases: Biocatalysts in microbial pathogenesis and stress management
Kavleen Kaur, Aarjoo Sharma, Neena Capalash, Prince Sharma
Microbiological Research.2019; 222: 1. CrossRef
Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses
Lianlian Yan, Ruiping Xu, Yinbing Bian, Hongxian Li, Yan Zhou
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Laccase induction by synthetic dyes in Pycnoporus sanguineus and their possible use for sugar cane bagasse delignification
Christian Hernández, Anne-Marie Farnet Da Silva, Fabio Ziarelli, Isabelle Perraud-Gaime, Beatriz Gutiérrez-Rivera, José Antonio García-Pérez, Enrique Alarcón
Applied Microbiology and Biotechnology.2017; 101(3): 1189. CrossRef
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Lixia Yang, Mu Peng, Syed Shah, Qiuyu Wang
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Molecular characterization of a novel thermostable laccase PPLCC2 from the brown rot fungus Postia placenta MAD-698-R
Hongde An, Tingting Xiao, Huan Fan, Dongsheng Wei
Electronic Journal of Biotechnology.2015; 18(6): 451. CrossRef

Journal Article

Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation: May Nyan Taw , Hae-In Lee , Sang-Ho Lee , Woo-Suk Chang; J. Microbiol. 2015;53(8):518-525. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5313-z

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Abstract

Bradyrhizobium japonicum is a Gram-negative soil bacterium that can fix nitrogen into ammonia by developing a symbiotic relationship with the soybean plant. MocR proteins make up a subfamily of GntR superfamily, one of the most widely distributed and prolific groups of the helix-turn-helix transcription factors. In this study, we constructed a mutant strain for mocR (blr6977) to investigate its role in cellular processes and symbiosis in B. japonicum. Although growth rate and morphology of the mutant were indistinguishable from those of the wild type, the mutant showed significant differences in motility and attachment (i.e., biofilm formation) from the wild type. The mutant displayed a decrease in biofilm formation, but was more motile than the wild type. The inactivation of mocR did not affect the number of nodules on soybean roots, but caused delayed nodulation. Delayed nodulation intrigued us to study competitiveness of the mutant infecting soybeans. The mutant was less competitive than the wild type, indicating that delayed nodulation might be due to competitiveness. Gene expressions of other MocR subfamily members were also compared between the wild type and mutant strains. None of the mocR-like genes examined in this study were differentially expressed between both strains.

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Wenxiu Zhu, Yuanhang Cheng, Yankun Zhang, Mingxin Li, Yue Teng, Yunqi Gu, Haisong Wang, Xiaodong Xia
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Prevalence and virulence of Vibrio parahaemolyticus isolated from clinical and environmental samples in Huzhou, China
Peng Zhang, Xiaofang Wu, Lei Ji, Wei Yan, Liping Chen, Zhonghao Lu, Deshun Xu, Yunfeng Zha, Dafang Xu, Fenfen Dong
BMC Genomics.2024;[Epub] CrossRef
The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135
Si‐Qiong Xu, Xiao Wang, Lu Xu, Ke‐Xin Wang, Yin‐Hu Jiang, Fu‐Yin Zhang, Qing Hong, Jian He, Shuang‐Jiang Liu, Ji‐Guo Qiu
Environmental Microbiology.2023; 25(3): 675. CrossRef
The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus
Yangyang Li, Weidong Sun, Quan Wang, Ying Yu, Ying Wan, Kai Zhou, Rong Guo, Xiangan Han, Zhaoguo Chen, Weihuan Fang, Wei Jiang
Microbial Pathogenesis.2022; 167: 105546. CrossRef
Biological and transcriptional studies reveal VmeL is involved in motility, biofilm formation and virulence in Vibrio parahaemolyticus
Peng-xuan Liu, Xiao-yun Zhang, Quan Wang, Yang-yang Li, Wei-dong Sun, Yu Qi, Kai Zhou, Xian-gan Han, Zhao-guo Chen, Wei-huan Fang, Wei Jiang
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PrbP modulates biofilm formation in Liberibacter crescens
Lei Pan, Christopher L. Gardner, Reagan Beliakoff, Danilo da Silva, Ran Zuo, Fernando A. Pagliai, Kaylie A. Padgett‐Pagliai, Marcelo L. Merli, Erol Bahadiroglu, Claudio F. Gonzalez, Graciela L. Lorca
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Haozhe Ruan, Haibo Yu, Jianzhong Xu
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Huihui Fu, Peng Jiang, Jin Zhao, Chunhui Wu
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The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism
Angela Tramonti, Caterina Nardella, Martino L. di Salvo, Stefano Pascarella, Roberto Contestabile
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Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene
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Research Support, Non-U.S. Gov'ts

Negative regulation of the vacuole-mediated resistance to K+ stress by a novel C2H2 zinc finger transcription factor encoded by aslA in Aspergillus nidulans: Dong Soo Park , Yeong Man Yu , Yong Jin Kim , Pil Jae Maeng; J. Microbiol. 2015;53(2):100-110. Published online January 28, 2015; DOI: https://doi.org/10.1007/s12275-015-4701-8

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Abstract

In fungi and plants, vacuoles function as a storage and sequestration vessel for a wide variety of ions and are responsible for cytosolic ion homeostasis and responses to ionic shock. In the filamentous fungus Aspergillus nidulans, however, little is known about the molecular genetic mechanisms of vacuolar biogenesis and function. In the present study, we analyzed the function of the aslA gene (AN5583) encoding a novel C2H2-type zinc finger transcription factor (TF) in relation to K+ stress resistance, vacuolar morphology, and vacuolar transporters. The mutant lacking aslA showed increased mycelial growth and decreased branching at high K+ concentrations. Deletion of aslA also caused elevated K+ stress-inducible expression of the genes, nhxA (AN2288), vnxA (AN6986), and vcxA (AN0471), encoding putative endosomal and vacuolar cation/H+ exchangers, as well as cpyA and vpsA genes encoding the proteins involved in vacuolar biogenesis. Interestingly, vacuolar fragmentation induced by K+ stress was alleviated by aslA deletion, resulting in persistence of unfragmented vacuoles. In the presence of bafilomycin, an inhibitor of vacuolar H+-ATPase, the mutant phenotype was suppressed in terms of growth rates and vacuolar morphology. These results together suggest that the C2H2- type zinc finger TF AslA attenuates the K+ stress-inducible expression of the genes encoding the ion pumps involved in vacuolar sequestration of K+ ions powered by vacuolar H+- ATPase, as well as the proteins that function in vacuolar biogenesis.

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The hyphae-specific C 2 H 2 transcription factor HscA regulates development, stress response, and mycotoxin production in Aspergillus species
Ye-Eun Son, Kyu-Hyun Kim, He-Jin Cho, Jae-Hyuk Yu, Hee-Soo Park, Aaron P. Mitchell
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Molecular circuit between Aspergillus nidulans transcription factors MsnA and VelB to coordinate fungal stress and developmental responses
Emmanouil Bastakis, Jennifer Gerke, Seyma Özkan, Rebekka Harting, Tanja Lienard, Christoph Sasse, Emmanouil S. Xylakis, Merle Aden, Anja Strohdiek, Gabriele Heinrich, Verena Grosse, Gerhard H. Braus, Zachary A. Lewis
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The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors
Xiaoyi Chen, Juan P. Moran Torres, Peter Jan Vonk, J. Mirjam A. Damen, Karli R. Reiding, Jan Dijksterhuis, Luis G. Lugones, Han A.B. Wösten
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Survival Factor A (SvfA) Contributes to Aspergillus nidulans Pathogenicity
Joo-Yeon Lim, Ye-Eun Jung, Hye-Eun Hwang, Cheol-Hee Kim, Nese Basaran-Akgul, Sri Harshini Goli, Steven P. Templeton, Hee-Moon Park
Journal of Fungi.2023; 9(2): 143. CrossRef
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Honghui Zhu, Junjian Situ, Tianfang Guan, Ziyuan Dou, Guanghui Kong, Zide Jiang, Pinggen Xi
International Journal of Molecular Sciences.2022; 23(5): 2733. CrossRef
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Rehab Abdelmonem Mohamed, Chong‐Tao Guo, Si‐Yuan Xu, Sheng‐Hua Ying, Ming‐Guang Feng
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The LAMMER Kinase, LkhA, Affects Aspergillus fumigatus Pathogenicity by Modulating Reproduction and Biosynthesis of Cell Wall PAMPs
Joo-Yeon Lim, Yeon Ju Kim, Seul Ah Woo, Jae Wan Jeong, Yu-Ri Lee, Cheol-Hee Kim, Hee-Moon Park
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Mannitol-1-phosphate dehydrogenase, MpdA, is required for mannitol production in vegetative cells and involved in hyphal branching, heat resistance of conidia and sexual development in Aspergillus nidulans
Joo-Yeon Lim, Seung-Hyun Jang, Hee-Moon Park
Current Genetics.2021; 67(4): 613. CrossRef
The putative C2H2 transcription factor RocA is a novel regulator of development and secondary metabolism in Aspergillus nidulans
Dong Chan Won, Yong Jin Kim, Da Hye Kim, Hee-Moon Park, Pil Jae Maeng
Journal of Microbiology.2020; 58(7): 574. CrossRef
Survival factor SvfA plays multiple roles in differentiation and is essential for completion of sexual development in Aspergillus nidulans
Joo-Yeon Lim, Eun-Hye Kang, Yun-Hee Park, Jun-Ho Kook, Hee-Moon Park
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Fungal oxylipins direct programmed developmental switches in filamentous fungi
Mengyao Niu, Breanne N. Steffan, Gregory J. Fischer, Nandhitha Venkatesh, Nicholas L. Raffa, Molly A. Wettstein, Jin Woo Bok, Claudio Greco, Can Zhao, Erwin Berthier, Ernst Oliw, David Beebe, Michael Bromley, Nancy P. Keller
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The Cys2His2 zinc finger protein Zfp1 regulates sexual reproduction and virulence in Cryptococcus neoformans
Cheng-Li Fan, Lian-Tao Han, Su-Ting Jiang, An-Ni Chang, Ze-Yang Zhou, Tong-Bao Liu
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Ling Sun, Xinyi Li, Haile Ma, Ronghai He, Prince O. Donkor
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The signal peptide peptidase SppA is involved in sterol regulatory element‐binding protein cleavage and hypoxia adaptation in Aspergillus nidulans
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ZNF1 Encodes a Putative C2H2 Zinc-Finger Protein Essential for Appressorium Differentiation by the Rice Blast Fungus Magnaporthe oryzae
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Transcription level analysis of intracellular Burkholderia pseudomallei illustrates the role of BPSL1502 during bacterial interaction with human lung epithelial cells: Teerasit Techawiwattanaboon , Tanachaporn Bartpho , Rasana Wongratanacheewin Sermswan , Sorujsiri Chareonsudjai; J. Microbiol. 2015;53(2):134-140. Published online January 28, 2015; DOI: https://doi.org/10.1007/s12275-015-4522-9

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Abstract

Melioidosis caused by Burkholderia pseudomallei is a globally important disease of increasing concern according to high
case
-fatality rate and epidemic spreading. The ability of B. pseudomallei to attach and invade host cells and subsequently survive intracellularly has stimulated many questions concerning the comprehension of bacterial pathogenesis progression. Transcription levels of intracellular B. pseudomallei genes in human lung epithelial cells were therefore analyzed using bioinformatic tools, RT-PCR and real time RT-PCR. Here, it is reported that the identification of bpsl1502, encoding B. pseudomallei SurE (stationary phase survival protein E) located in a global transcriptional regulation operon was accomplished. The up-regulation of B. pseudomallei SurE was demonstrated during intracellular survival of A549 cells at 12, 18, and 24 h post-infection. To investigate the role of this protein, a B. pseudomallei SurE defective mutant was constructed. The invasion and initial survival of the SurE mutants within the A549 cells were impaired. There was no difference, however, between the growth of B. pseudomallei SurE mutant as compared to the wild type in Luria-Bertani culture. These data suggest that SurE may assist B. pseudomallei host cells invade and facilitate early intracellular infection but is not crucial during the stationary growth phase. The identification of B. pseudomallei SurE provides more information of bacterial strategy during an early step of the pathogenesis process of melioidosis.

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Metabolomics Analysis of Bacterial PathogenBurkholderia thailandensisand Mammalian Host Cells in Co-culture
Nicole Aiosa, Anupama Sinha, Olakunle A. Jaiyesimi, Ricardo R. da Silva, Steven S. Branda, Neha Garg
ACS Infectious Diseases.2022; 8(8): 1646. CrossRef
In vitro passage alters virulence, immune activation and proteomic profiles of Burkholderia pseudomallei
Taksaon Duangurai, Onrapak Reamtong, Amporn Rungruengkitkun, Varintip Srinon, Usa Boonyuen, Direk Limmathurotsakul, Narisara Chantratita, Pornpan Pumirat
Scientific Reports.2020;[Epub] CrossRef
Burkholderia pseudomallei Biofilm Promotes Adhesion, Internalization and Stimulates Proinflammatory Cytokines in Human Epithelial A549 Cells
Chanikarn Kunyanee, Watcharaporn Kamjumphol, Suwimol Taweechaisupapong, Sakawrat Kanthawong, Suwin Wongwajana, Surasak Wongratanacheewin, Chariya Hahnvajanawong, Sorujsiri Chareonsudjai, R. Mark Wooten
PLOS ONE.2016; 11(8): e0160741. CrossRef
A predicted cation transporter protein, BPSS1228, is involved in intracellular behaviour ofBurkholderia pseudomalleiin a human lung epithelial cell line (A549)
Teerasit Techawiwattanaboon, Sorujsiri Chareonsudjai, Craig Winstanley
FEMS Microbiology Letters.2016; 363(23): fnw259. CrossRef
Environmental Free-Living Amoebae Isolated from Soil in Khon Kaen, Thailand, Antagonize Burkholderia pseudomallei
Parumon Noinarin, Pisit Chareonsudjai, Pinich Wangsomnuk, Surasak Wongratanacheewin, Sorujsiri Chareonsudjai, William C. Nierman
PLOS ONE.2016; 11(11): e0167355. CrossRef
Mechanisms of Disease: Host-Pathogen Interactions between Burkholderia Species and Lung Epithelial Cells
Jonathan David, Rachel E. Bell, Graeme C. Clark
Frontiers in Cellular and Infection Microbiology.2015;[Epub] CrossRef

Transcriptional Regulation of fksA, a β-1,3-Glucan Synthase Gene, by the APSES Protein StuA during Aspergillus nidulans Development: Bum-Chan Park , Yun-Hee Park , Soohyun Yi , Yu Kyung Choi , Eun-Hye Kang , Hee-Moon Park; J. Microbiol. 2014;52(11):940-947. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4517-y

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Abstract PDF

The temporal and spatial regulation of β-1,3-glucan synthesis plays an important role in morphogenesis during fungal growth and development. Northern blot analysis showed that the transcription of fksA, the gene encoding β-1,3-glucan synthase in Aspergillus nidulans, was cell-cycle-dependent and increased steadily over the duration of the vegetative period, but its overall expression during the asexual and sexual stages was fairly constant up until the time of transcription cessation. In an A. nidulans strain mutated in the eukaryotic bHLH-like APSES transcription factor stuA1, the transcriptional level of fksA, and consequently the content of alkali-insoluble cell wall β-glucan, significantly increased at the conidial chain formation and maturation stage. Electrophoretic mobility shift assays revealed that StuA was bound to StREs (StuA Response Elements) on the fksA promoter region. Promoter analysis with sGFP-fusion constructs also indicated the negative regulation of fksA expression by StuA, especially during asexual development. Taken together, these data suggest that StuA plays an important role in cell wall biogenesis during the development of A. nidulans, by controlling the transcription level of fksA.

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Transcription Factor TrStuA Regulates Vegetative Growth, Virulence, and Trichothecin Synthesis in Trichothecium roseum
Manli Sun, Zihan Meng, Yichen Yang, Yanan Li, Shutong Wang, Pengbo Dai
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Survival Factor A (SvfA) Contributes to Aspergillus nidulans Pathogenicity
Joo-Yeon Lim, Ye-Eun Jung, Hye-Eun Hwang, Cheol-Hee Kim, Nese Basaran-Akgul, Sri Harshini Goli, Steven P. Templeton, Hee-Moon Park
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Note] Identification of High-Specificity H-NS Binding Site in LEE5 Promoter of Enteropathogenic Esherichia coli (EPEC): Abhay Prasad Bhat , Minsang Shin , Hyon E. Choy; J. Microbiol. 2014;52(7):626-629. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3562-x

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Abstract PDF

Histone-like nucleoid structuring protein (H-NS) is a small but abundant protein present in enteric bacteria and is involved in compaction of the DNA and regulation of the transcription. Recent reports have suggested that H-NS binds to a specific AT rich DNA sequence than to intrinsically curved DNA in sequence independent manner. We detected two high-specificity H-NS binding sites in LEE5 promoter of EPEC centered at -110 and -138, which were close to the proposed consensus H-NS binding motif. To identify H-NS binding sequence in LEE5 promoter, we took a random mutagenesis approach and found the mutations at around -138 were specifically defective in the regulation byH-NS. It was concluded that H-NS exertsmaximumrepression via the specific sequence at around -138 and ubsequently contacts α subunit of RNAP through oligomerization.

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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands
Alejandro Piña-Iturbe, Isidora D. Suazo, Guillermo Hoppe-Elsholz, Diego Ulloa-Allendes, Pablo A. González, Alexis M. Kalergis, Susan M. Bueno
Genes.2020; 11(2): 142. CrossRef
Recent advances in genetic engineering tools based on synthetic biology
Jun Ren, Jingyu Lee, Dokyun Na
Journal of Microbiology.2020; 58(1): 1. CrossRef
Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens
R. Christopher D. Furniss, Abigail Clements, William Margolin
Journal of Bacteriology.2018;[Epub] CrossRef
Bacterial-Chromatin Structural Proteins Regulate the Bimodal Expression of the Locus of Enterocyte Effacement (LEE) Pathogenicity Island in Enteropathogenic Escherichia coli
Hervé Leh, Ahmad Khodr, Marie-Christine Bouger, Bianca Sclavi, Sylvie Rimsky, Stéphanie Bury-Moné, Susan Gottesman
mBio.2017;[Epub] CrossRef
Alternative Synthesis Route of Biocompatible Polyvinylpyrrolidone Nanoparticles and Their Effect on Pathogenic Microorganisms
Vedran Milosavljevic, Pavlina Jelinkova, Ana Maria Jimenez Jimenez, Amitava Moulick, Yazan Haddad, Hana Buchtelova, Sona Krizkova, Zbynek Heger, Lukas Kalina, Lukas Richtera, Pavel Kopel, Vojtech Adam
Molecular Pharmaceutics.2017; 14(1): 221. CrossRef
H-NS and RNA polymerase: a love–hate relationship?
Robert Landick, Joseph T Wade, David C Grainger
Current Opinion in Microbiology.2015; 24: 53. CrossRef
Effect of promoter-upstream sequence on σ38-dependent stationary phase gene transcription
Hyung-Ju Lim, Kwangsoo Kim, Minsang Shin, Jae-Ho Jeong, Phil Youl Ryu, Hyon E. Choy
Journal of Microbiology.2015; 53(4): 250. CrossRef

A Putative APSES Transcription Factor Is Necessary for Normal Growth and Development of Aspergillus nidulans: Ji-Yeon Lee , Lee-Han Kim , Ha-Eun Kim , Jae-Sin Park , Kap-Hoon Han , Dong-Min Han; J. Microbiol. 2013;51(6):800-806. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3100-2

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The nsdD gene encoding a GATA type transcription factor positively controls sexual development in Aspergillus nidulans. According to microarray data, 20 genes that were upregulated by deleting nsdD during various life cycle stages were randomly selected and deleted for functional analysis. None of the mutants showed apparent changes in growth or development compared with those of the wild-type except the AN3154 gene that encodes a putative APSES transcription factor and is an ortholog of Saccharomyces cerevisiae swi4. Deleting AN3154 resulted in retarded growth and development, and the gene was named rgdA (retared growth and development). The rgdA deletion mutant developed a reduced number of conidia even under favorable conditions for asexual development. The retarded growth and development was partially suppressed by the veA1 mutation. The conidial heads of the mutant aborted, showing reduced and irregular shaped phialides. Fruiting body development was delayed compared with that in the wild-type. The mutant did not respond to various nutritional or environmental factors that affected the development patterns. The rgdA gene was expressed at low levels throughout the life cycle and was not significantly affected by several regulators of sexual and asexual development such as nsdD, veA, stuA, or brlA. However, the rgdA gene affected brlA and abaA expression, which function as key regulators of asexual sporulation, suggesting that rgdA functions upstream of those genes.

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The analysis of transcriptomics reveals the function of TrPLD3 in the pathogenicity of Trichothecium roseum infecting apples
Xiao Li, Qianqian Zhang, Qili Liu, Xiaobin Xu, Jinzhu Li, Dandan Zhu, Yuanyuan Zong, Huali Xue, Yang Bi
Postharvest Biology and Technology.2025; 227: 113628. CrossRef
Putative APSES family transcription factor mbp1 plays an essential role in regulating cell wall synthesis in the agaricomycete Pleurotus ostreatus
Hayase Kojima, Moriyuki Kawauchi, Yuitsu Otsuka, Kim Schiphof, Kenya Tsuji, Akira Yoshimi, Chihiro Tanaka, Shigekazu Yano, Takehito Nakazawa, Yoichi Honda
Fungal Genetics and Biology.2024; 175: 103936. CrossRef
Regulators of the Asexual Life Cycle of Aspergillus nidulans
Ye-Eun Son, Jae-Hyuk Yu, Hee-Soo Park
Cells.2023; 12(11): 1544. CrossRef
Characterization of the mbsA Gene Encoding a Putative APSES Transcription Factor in Aspergillus fumigatus
Yong-Ho Choi, Sang-Cheol Jun, Min-Woo Lee, Jae-Hyuk Yu, Kwang-Soo Shin
International Journal of Molecular Sciences.2021; 22(7): 3777. CrossRef
The Putative APSES Transcription Factor RgdA Governs Growth, Development, Toxigenesis, and Virulence in Aspergillus fumigatus
Sang-Cheol Jun, Yong-Ho Choi, Min-Woo Lee, Jae-Hyuk Yu, Kwang-Soo Shin, Aaron P. Mitchell
mSphere.2020;[Epub] CrossRef
Analogous and Diverse Functions of APSES-Type Transcription Factors in the Morphogenesis of the Entomopathogenic Fungus Metarhizium rileyi
Caiyan Xin, Jinping Zhang, Siji Nian, Guangxi Wang, Zhongkang Wang, Zhangyong Song, Guangwei Ren, Ning-Yi Zhou
Applied and Environmental Microbiology.2020;[Epub] CrossRef
Distribution, evolution and expression ofGATA-TFsprovide new insights into their functions in light response and fruiting body development ofTolypocladium guangdongense
Chenghua Zhang, Gangzheng Wang, Wangqiu Deng, Taihui Li
PeerJ.2020; 8: e9784. CrossRef
Characterization of the APSES-family transcriptional regulators of Histoplasma capsulatum
Larissa V G Longo, Stephanie C Ray, Rosana Puccia, Chad A Rappleye
FEMS Yeast Research.2018;[Epub] CrossRef
Essential APSES Transcription Factors for Mycotoxin Synthesis, Fungal Development, and Pathogenicity in Aspergillus flavus
Guangshan Yao, Feng Zhang, Xinyi Nie, Xiuna Wang, Jun Yuan, Zhenhong Zhuang, Shihua Wang
Frontiers in Microbiology.2017;[Epub] CrossRef
Characterizing the nuclear proteome of Paracoccidioides spp.
Lucas Nojosa Oliveira, Luciana Casaletti, Sônia Nair Báo, Clayton Luiz Borges, Patrícia de Sousa Lima, Célia Maria de Almeida Soares
Fungal Biology.2016; 120(10): 1209. CrossRef
Isolation and Characterization of Two Methyltransferase Genes, AfuvipB and AfuvipC in Aspergillus fumigatus
Mohammed A. Abdo Elgabbar, Kap-Hoon Han
The Korean Journal of Mycology.2015; 43(1): 33. CrossRef
Depletion of ε-COP in the COPI Vesicular Coat Reduces Cleistothecium Production inAspergillus nidulans
Eun-Hye Kang, Eun-Jung Song, Jun Ho Kook, Hwan-Hee Lee, Bo-Ri Jeong, Hee-Moon Park
Mycobiology.2015; 43(1): 31. CrossRef
FgFlbD regulates hyphal differentiation required for sexual and asexual reproduction in the ascomycete fungus Fusarium graminearum
Hokyoung Son, Myung-Gu Kim, Suhn-Kee Chae, Yin-Won Lee
Journal of Microbiology.2014; 52(11): 930. CrossRef
Transcriptional regulation of fksA, a β-1,3-glucan synthase gene, by the APSES protein StuA during Aspergillus nidulans development
Bum-Chan Park, Yun-Hee Park, Soohyun Yi, Yu Kyung Choi, Eun-Hye Kang, Hee-Moon Park
Journal of Microbiology.2014; 52(11): 940. CrossRef

Experimental Phasing Using Zinc and Sulfur Anomalous Signals Measured at the Zinc Absorption Peak: Sangmin Lee , Min-Kyu Kim , Chang-Jun Ji , Jin-Won Lee , Sun-Shin Cha; J. Microbiol. 2013;51(5):639-643. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3412-2

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Abstract PDF: Iron is an essential transition metal required for bacterial growth and survival. Excess free iron can lead to the generation of reactive oxygen species that can cause severe damage to cellular functions. Cells have developed iron-sensing regulators to maintain iron homeostasis at the transcription level. The ferric uptake regulator (Fur) is an iron-responsive regulator that controls the expression of genes involved in iron homeostasis, bacterial virulence, stress resistance, and redox metabolism. Here, we report the expression, purification, crystallization, and phasing of the apo-form of Bacillus subtilis Fur (BsFur) in the absence of regulatory metal ions. Crystals were obtained by microbatch crystallization method at 295 K and diffraction data at a resolution of 2.6 Å was collected at the zinc peak wavelength (λ=1.2823 Å). Experimental phasing identified the positions of one zinc atom and four sulfur atoms of cysteine residues coordinating the zinc atom, indicating that the data contained a meaningful anomalous scattering originating from the ordered zinc-coordinating sulfur atoms, in spite of the small anomalous signals of sulfur atoms at the examined wavelength.

Functional Analysis of SGR4635-Induced Enhancement of Pigmented Antibiotic Production in Streptomyces lividans: Won-Jae Chi , Soon-Youl Lee , JaeHag Lee; J. Microbiol. 2011;49(5):828-833. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1100-7

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The Gram-positive mycelium-producing bacterium Streptomyces undergoes complex morphological differentiation after autolytic degradation of the vegetative mycelium. Cell-wall breakdown during growth stimulates cell development and secondary metabolite production by Streptomyces. N-acetylglucosamine (GlcNAc) produced by cell-wall lysis acts as a signal molecule, triggering the production of secondary metabolites in S. coelicolor A3(2). Here, we report that introduction of multiple copies of the GlcNAc-internalizing gene (sgr4635, encoding nagE2) of S. griseus activates actinorhodin and undecylprodigiosin production during the late growth of S. lividans in the absence of GlcNAc. Furthermore, the repressor-type transcriptional regulator DasR binds to two operator sites upstream of sgr4635. Our findings indicate that sgr4635 induces DasR-mediated antibiotic production by internalizing the GlcNAc accumulated from cell-wall lysis.

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Review

REVIEW] Transcriptional Regulatory Elements in Fungal Secondary Metabolism: Wenbing Yin , Nancy P. Keller; J. Microbiol. 2011;49(3):329-339. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-1009-1

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Abstract PDF

Filamentous fungi produce a variety of secondary metabolites of diverse beneficial and detrimental activities to humankind. The genes required for a given secondary metabolite are typically arranged in a gene cluster. There is considerable evidence that secondary metabolite gene regulation is, in part, by transcriptional control through hierarchical levels of transcriptional regulatory elements involved in secondary metabolite cluster regulation. Identification of elements regulating secondary metabolism could potentially provide a means of increasing production of beneficial metabolites, decreasing production of detrimental metabolites, aid in the identification of ‘silent’ natural products and also contribute to a broader understanding of molecular mechanisms by which secondary metabolites are produced. This review summarizes regulation of secondary metabolism associated with transcriptional regulatory elements from a broad view as well as the tremendous advances in discovery of cryptic or novel secondary metabolites by genomic mining.

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Cys-92, Cys-95, and the C-Terminal 12 Residues of the Vibrio harveyi Ferric Uptake Regulator (Fur) are Functionally Inessential: Kun Sun , Shuang Cheng , Min Zhang , Fang Wang , Li Sun; J. Microbiol. 2008;46(6):670-680. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0113-3

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Abstract PDF

Ferric uptake regulator (Fur) is a global regulator involved in multiple aspects of bacterial life. The gene encoding the Vibrio harveyi Fur (FurVh) was cloned from a pathogenic V. harveyi strain isolated from diseased fish. FurVh shares 77% overall sequence identity with the Escherichia coli Fur (FurEc) and could complement a mutant of FurEc. Like FurEc, FurVh possesses two cysteine residues at positions 92 and 95, yet unlike FurEc, in which these cysteine residues constitute part of the metal ion coordination site and hence are vital to the repressor activity, C92 and C95 of FurVh proved to be functionally inessential. Further study identified a Vibrio Fur signature sequence, which is preserved in all the ten Vibrio Fur proteins that have been discovered to date but in none of the non-vibrio Fur proteins. Site-directed and random mutation analyses of the signature residues, the cysteine residues, and seven highly charged amino acid residues indicated that D9, H32, C137, and K138 of FurVh are functionally important but D9, C137, and K138 can be replaced by more than one functional substitutes. Systematic deletion analysis demonstrated that the C-terminal 12 residues of FurVh are functionally inessential. These results (i) indicated that the activation mechanism, or certain aspects of which, of FurVh is possibly different from that of FurEc; and (ii) suggested that it is not very likely that the C-terminal 12 residues play any significant role in the activation or stability of FurVh; and (iii) provided insights into the potential function of the local structure involving C137 and K138.

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DNA Microarray-Based Global Transcriptional Profiling of Yersinia pestis in Multicellularity: Jingfu Qiu , Zhaobiao Guo , Haihong Liu , Dongsheng Zhou , Yanping Han , Ruifu Yang; J. Microbiol. 2008;46(5):557-563. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0140-0

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Abstract PDF: Yersinia pestis, the causative agent of plague, has a feature of forming multicellular aggregates at liquid-air interface around the wall of glass tube. In this study, we employed the whole-genome DNA microarray of Y. pestis to investigate the global transcriptional profile in multicellularity compared with that in its planktonic growth. A total of 177 genes were differentially expressed in Y. pestis during early stage of multicellular formation; Seventy genes of them were up-regulated while 107 down-regulated. In addition to a large number of genes encoding unknown functions, most of the induced genes encode cell envelope and transport/binding proteins. The up-regulation of amino acid biosynthesis, the differentially altered genes that are involved in virulence, and the cold shock protein genes were for the first time reported to be associated with the multicellular formation. Our results revealed the global gene expression of Y. pestis were changed in the formation of multicellularity, providing insights into the molecular mechanism of multicellular behaviour, which need investigating further.

Generation of Infectious Transcripts from Korean Strain and Mild Mottle Strain of Potato Virus X: Sun Hee Choi , Ki Hyun Ryu; J. Microbiol. 2008;46(5):502-507. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0078-2

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Full-length cDNAs of two different strains of Potato virus X (PVX-Kr and PVX-Mo) have been directly amplified by long template reverse transcription polymerase chain reaction (RT-PCR) using the 5’-end primer containing a SP6 or T7 RNA promoter sequence and the virus-specific 3’-end primer, and then constructed in plasmid vectors. Capped in vitro transcripts from cloned full-length cDNAs as well as those RTPCR amplicons proved to be infectious systemically on tobacco plants. Symptom expression on tobacco plants from PVX-Mo transcripts was faster and severer than that from PVX-Kr. In replication stability test of transcripts derived from PVX clones, progeny viruses showed stable replication according to sequencing through passages. This highly infectious transcript system from the full-length cDNA clones for PVX can be useful for recombinant molecules for functional analysis of viral proteins in plant-virus interaction study as well as for expression of foreign protein in planta.

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Validation of reference genes for quantifying changes in gene expression in virus-infected tobacco
Eseul Baek, Ju-Yeon Yoon, Peter Palukaitis
Virology.2017; 510: 29. CrossRef
Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: Apple chlorotic leaf spot virus as a case study
Fater Youssef, Armelle Marais, Chantal Faure, Pascal Gentit, Thierry Candresse
Virology Journal.2011;[Epub] CrossRef

The GntR-Type Regulators GtrA and GtrB Affect Cell Growth and Nodulation of Sinorhizobium meliloti: Yi Wang , Ai-Min Chen , Ai-Yuan Yu , Li Luo , Guan-Qiao Yu , Jia-Bi Zhu , Yan-Zhang Wang; J. Microbiol. 2008;46(2):137-145. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0145-0

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Abstract PDF

GntR-type transcriptional regulators are involved in the regulation of various biological processes in bacteria, but little is known about their functions in Sinorhizobium meliloti. Here, we identified two GntR-type transcriptional regulator genes, gtrA and gtrB, from S. meliloti strain 1021. Both the gtrA1 mutant and the gtrB1 mutant had lower growth rates and maximal cell yields on rich and minimal media, as well as lower cell motility on swimming plates, than did the wild-type strain. Both mutants were also symbiotically deficient. Alfalfa plants inoculated with wild-type strain 1021 formed pink elongated nodules on primary roots. In contrast, the plants inoculated with the gtrA1 and gtrB1 mutants formed relatively smaller, round, light pink nodules mainly on lateral roots. During the first 3~4 weeks post-inoculation, the plants inoculated with the gtrA1 and gtrB1 mutants were apparently stunted, with lower levels of nitrogenase activity, but there was a remarkable increase in the number of nodules compared to those inoculated with the wild-type strain. Moreover, the gtrA1 and gtrB1 mutants not only showed delayed nodulation, but also showed markedly reduced nodulation competition. These results demonstrated that both GtrA and GtrB affect cell growth and effective symbiosis of S. meliloti. Our work provides new insight into the functions of GntR-like transcriptional regulators.

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Investigation of Nitrogen Fixation Efficiency in Diverse Alfalfa Varieties Utilizing Sinorhizobium meliloti LL2
Yilin Han, Wenjuan Kang, Shangli Shi, Jian Guan, Yuanyuan Du, Fuqiang He, Baofu Lu, Ming Wang
Agronomy.2024; 14(11): 2732. CrossRef
The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus
Yangyang Li, Weidong Sun, Quan Wang, Ying Yu, Ying Wan, Kai Zhou, Rong Guo, Xiangan Han, Zhaoguo Chen, Weihuan Fang, Wei Jiang
Microbial Pathogenesis.2022; 167: 105546. CrossRef
Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion
Xiujuan Zhou, Bin Liu, Yanhong Liu, Chunlei Shi, Pina M. Fratamico, Lida Zhang, Dapeng Wang, Jianhua Zhang, Yan Cui, Ping Xu, Xianming Shi
BMC Genomics.2021;[Epub] CrossRef
Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation
May Nyan Taw, Hae-In Lee, Sang-Ho Lee, Woo-Suk Chang
Journal of Microbiology.2015; 53(8): 518. CrossRef
Directed Construction and Analysis of a Sinorhizobium meliloti pSymA Deletion Mutant Library
Svetlana N. Yurgel, Michael W. Mortimer, Jennifer T. Rice, Jodi L. Humann, Michael L. Kahn
Applied and Environmental Microbiology.2013; 79(6): 2081. CrossRef
PCR identification of Salmonella serogroups based on specific targets obtained by comparative genomics
Bin Liu, Lida Zhang, Xinna Zhu, Chunlei Shi, Jing Chen, Weibing Liu, Xiaohua He, Xianming Shi
International Journal of Food Microbiology.2011; 144(3): 511. CrossRef
Identification of a TRAP transporter for malonate transport and its expression regulated by GtrA from Sinorhizobium meliloti
Ai-Min Chen, Yong-Bao Wang, Sun Jie, Ai-Yuan Yu, Li Luo, Guan-Qiao Yu, Jia-Bi Zhu, Yan-Zhang Wang
Research in Microbiology.2010; 161(7): 556. CrossRef
Role of Quorum Sensing in Sinorhizobium meliloti -Alfalfa Symbiosis
Nataliya Gurich, Juan E. González
Journal of Bacteriology.2009; 191(13): 4372. CrossRef

Partial Purification of Factors for Differential Transcription of the rrnD Promoters for Ribosomal RNA Synthesis in Streptomyces coelicolor: Mi-Young Hahn , Jung-Hye Roe; J. Microbiol. 2007;45(6):534-540.; DOI: https://doi.org/2612 [pii]

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Abstract PDF: The Streptomyces coelicolor A3(2) genome contains six operons (rrnA to F) for ribosomal RNA synthesis. Transcription from rrnD occurs from four promoters (p1 to p4). We found that transcripts from the p1 and p3 promoters were most abundant in vivo in the early exponential phase. However, at later phases of exponential and stationary growth, transcripts from the p1 promoter decreased drastically, with the p3 and p4 transcripts constituting the major forms. Partially purified RNA polymerase supported transcription from the p3 and p4 promoters, whereas pure reconstituted RNA polymerase with core enzyme (E) and the major vegetative sigma factor sigmaHrdB (E.sigmaHrdB) did not. In order to assess any potential requirement for additional factor(s) that allow transcription from the p3 and p4 promoters, we fractionated a partially purified RNA polymerase preparation by denaturing gel filtration chromatography. We found that transcription from the p3 and p4 promoters required factor(s) of about 30-35 kDa in addition to RNAP holoenzyme (E.sigmaHrdB). Therefore, transcription from the p3 and p4 promoters, which contain a consensus -10 region but no -35 for sigmaHrdB recognition, are likely to be regulated by transcription factor(s) that modulate RNA polymerase holoenzyme activity in S. coelicolor.

Retracted Publication

Transcriptional Analysis of the DNA Polymerase Gene of Bombyx mori Parvo-like Virus (China Isolate): Yong-Jie Wang , Ke-Ping Chen , Qin Yao , Xu Han; J. Microbiol. 2007;45(2):139-145.; DOI: https://doi.org/2521 [pii]

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Abstract PDF: The Bombyx mori parvo-like virus (China isolate) DNA polymerase (BmDNV-3 dnapol) gene has been tentatively identified based on the presence of conserved motifs. In the present study, we perform a transcriptional analysis of the BmDNV-3 dnapol gene using the total RNA isolated from BmDNV-3 infected silkworm at different times. Northern blot analysis with a BmDNV-3 dnapol-specific riboprobe showed a major transcript of 3.3 kb. 5′-RACE revealed that the major transcription start point was located 20 nucleotides downstream of the TATA box. In a temporal expression analysis using differential RT-PCR, BmDNV-3 dnapol transcript was detected at low levels at 6 h.p.i., increased from 6 to 36 h.p.i., and remained fairly constant thereafter. Analysis of the predicted DNA polymerase sequence using neighborjoining and protein parsimony algorithms indicated that the predicted 1115-residue polypeptide contained five motifs associated with DNA polymerases synthetic activities and three additional motifs associated with polymerases possessing 3′ to 5′ exonuclease activity. The molecular phylogenetic analysis of this gene supported the placement of Bombyx mori parvo-like virus in a separate virus family.

Journal Article

Carbon Source-Dependent Regulation of the Schizosaccharomyces pombe pbh1 Gene: Su-Jung Kim , Nam-Chul Cho , In Wang Ryu , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2006;44(6):689-693.; DOI: https://doi.org/2454 [pii]

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Abstract PDF: Pbh1, from the fission yeast Schizosaccharomyces pombe, is a baculoviral inhibitor of apoptosis (IAP) repeat (BIR) domain-containing protein. Its unique encoding gene was previously found to be regulated by nitric oxide and nitrogen starvation. In the current work, the Pbh1-lacZ fusion gene was used to elucidate the transcriptional regulation of the pbh1 gene under various carbon sources. When fermentable carbon sources, such as glucose (at a low concentration of 0.2%), sucrose (2.0%) and lactose (2.0%), were the sole carbon source, the synthesis of β-galactosidase from the Pbh1-lacZ fusion gene was reasonably enhanced. However, the induction by these fermentable carbon sources was abolished in the Pap1-negative S. pombe cells, implying that this type of induction of the pbh1 gene is mediated by Pap1. Ethanol (2.0%), a nonfermentable carbon source, was also able to enhance the synthesis of β-galactosidase from the fusion gene in wild-type cells but not in Pap1-negative cells. The results indicate that the S. pombe pbh1 gene is up-regulated under metabolic oxidative stress in a Pap1-dependent manner.

Review

Rho-dependent Transcription Termination: More Questions than Answers: Sharmistha Banerjee , Jisha Chalissery , Irfan Bandey , Ranjan Sen; J. Microbiol. 2006;44(1):11-22.; DOI: https://doi.org/2342 [pii]

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Abstract PDF: Escherichia coli protein Rho is required for the factor-dependent transcription termination by an RNA polymerase and is essential for the viability of the cell. It is a homohexameric protein that recognizes and binds preferably to C-rich sites in the transcribed RNA. Once bound to RNA, it utilizes RNA-dependent ATPase activity and subsequently ATPase-dependent helicase activity to unwind RNA-DNA hybrids and release RNA from a transcribing elongation complex. Studies over the past few decades have highlighted Rho as a molecule and have revealed much of its mechanistic properties. The recently solved crystal structure could explain many of its physiological functions in terms of its structure. Despite all these efforts, many of the fundamental questions pertaining to Rho recognition sites, differential ATPase activity in response to different RNAs, translocation of Rho along the nascent transcript, interactions with elongation complex and finally unwinding and release of RNA remain obscure. In the present review we have attempted to summarize ‘the knowns’ and ‘the unknowns’ of the Rho protein revealed by the recent developments in this field. An attempt has also been made to understand the physiology of Rho in the light of its phylogeny.

Research Support, Non-U.S. Gov'ts

Transcriptional Regulation of the Schizosaccharomyces pombe Gene Encoding Glutathione S-Transferase I by a Transcription Factor Pap1: Hong-Gyum Kim , Byung-Chul Kim , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2004;42(4):353-356.; DOI: https://doi.org/2099 [pii]

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Abstract PDF: In a previous study, a gst gene was isolated from the fission yeast Schizosaccharomyces pombe. This gene was dubbed gst I, and was characterized using the gstI-lacZ fusion plasmid pYSH2000. In this work, four additional fusion plasmids, pYSHSD1, pYSHSD2, pYSHSD3 and pYSHSD4, were constructed, in order to carry (respectively) 770, 551, 358 and 151 bp upstream regions from the translational initiation point. The sequence responsible for induction by aluminum, mercury and hydrogen peroxide was located in the range between -1,088 and -770 bp upstream of the S. pombe gst I gene. The same region was identified to contain the nucleotide sequence responsible for regulation by Pap1, and has one putative Pap1 binding site, TTACGTAT, located in the range between -954 ~ -947 bp upstream of the gst I gene. Negatively acting sequences are located between -1,088 and -151 bp. These findings imply that the Pap1 protein is involved in basal and inducible transcription of the gst I gene in the fission yeast S. pombe.

Coregulation of lux Genes and Riboflavin Genes in Bioluminescent Bacteria of Photobacterium phosphoreum: Nack-Do Sung , Chan Yong Lee; J. Microbiol. 2004;42(3):194-199.; DOI: https://doi.org/2090 [pii]

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Abstract PDF: Investigation of the expression of the riboflavin (rib) genes, which are found immediately downstream of luxG in the lux operon in Photobacterium phosphoreum, provides more information relevant to the evolution of bioluminescence, as well as to the regulation of supply of flavin substrate for bacterial bioluminescence reactions. In order to answer the question of whether or not the transcriptions of lux and rib genes are integrated, a transcriptional termination assay was performed with P. phosphoreum DNA, containing the possible stem-loop structures, located in the intergenic region of luxF and luxE ([omega]_A), of luxG and ribE ([omega]_B), and downstream of ribA ([omega]_C). The expression of the CAT (Chloramphenicol Acetyl Transferase) reporter gene was remarkably decreased upon the insertion of the stem-loop structure ([omega]_C) into the strong lux promoter and the reporter gene. However, the insertion of the structure ([omega]_B) into the intergenic region of the lux and the rib genes caused no significant change in expression from the CAT gene. In addition, the single stranded DNA in the same region was protected by the P. phosphoreum mRNA from the S1 nuclease protection assay. These results suggest that lux genes and rib genes are part of the same operon in P. phosphoreum

Transcriptional Regulation of the Gene Encoding g-Glutamylcysteine Synthetase from the Fission Yeast Schizosaccharomyces pombe: Su-Jung Kim , Hong-Gyum Kim , Byung-Chul Kim , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2004;42(3):233-238.; DOI: https://doi.org/2083 [pii]

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Abstract PDF: Transcriptional regulation of the Schizosaccharomyces pombe [gamma]-glutamylcysteine synthetase (GCS) gene was examined using the two GCS-lacZ fusion plasmids pUGCS101 and pUGCS102, which harbor 607 bp and 447 bp upstream regions, respectively. The negatively-acting sequence was located in the -607 ~ -447 bp upstream region of the GCS gene. The upstream sequence responsible for induction by menadione (MD) and L-buthionine-(S, R)-sulfoximine (BSO) resides in the -607 ~ -447 bp region, whereas the sequence which codes for nitric oxide induction is located within the -447 bp region, measured from the translational initiation point. Carbon source-dependent regulation of the GCS gene appeared to be dependent on the nucleotide sequence within -447 bp region. The transcription factor Pap1 is involved in the induction of the GCS gene by MD and BSO, but not by nitric oxide. Induction of the GCS gene occurring due to low glucose concentration does not depend on the presence of Pap1. These data imply that induction by MD and BSO may be mediated by the Pap1 binding site, probably located in the -607 ~ -447 region, and also that the nitric oxide-mediated regulation of the S. pombe GCS gene may share a similar mechanism with its carbon-dependent induction.

Factors Influencing Preferential Utilization of RNA Polymerase Containing Sigma-38 in Stationary-Phase Gene Expression in Escherichia coli: Eun Young Kim , Min-Sang Shin , Joon Haeng Rhee , Hyon E. Choy; J. Microbiol. 2004;42(2):103-110.; DOI: https://doi.org/2037 [pii]

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Abstract PDF: In order to understand the molecular basis of selective expression of stationary-phase genes by RNA polymerase containing [sigma]^38 (E[sigma]^38) in Escherichia coli, we examined transcription from the stationaryphase promoters, katEP, bolAP, hdeABP, csgBAP, and mcbP, in vivo and in vitro. Although these promoters are preferentially recognized in vivo by E[sigma]^38, they are transcribed in vitro by both E[sigma]^38 and E[sigma]^70 containing the major exponential [sigma], [sigma]^70. In the presence of high concentrations of glutamate salts, however, only E[sigma]^38 was able to efficiently transcribe from these promoters, which supports the concept that the promoter selectivity of [sigma]^38 -containing RNA polymerase is observed only under specific reaction conditions. The examination of 6S RNA, which is encoded by the ssr1 gene in vivo, showed that it reduced E[sigma]^70 activity during the stationary phase, but this reduction of activity did not result in the elevation of E[sigma]^38 activity. Thus, the preferential expression of stationary-phase genes by E[sigma]^38 is unlikely the consequence of selective inhibition of E[sigma]^70 by 6S RNA.

Restriction and Transcription Maps of Mitochondrial DNA of Trimorphomyces papilionaceus: Jeoung, Won Jin , Hong, Soon Gyu , Kang, Young Won , Jung, Hack Sung; J. Microbiol. 1995;33(2):149-153.

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Abstract PDF: Mitochondrial DNA has been isolated from Trimorphomyces papilionaceus. By analyzing DNA fragments digested by restriction enzymes, a restriction site map has been constructured. The mtDNA of T. papilionaceus amounts to 48.5 kb in size and is circular in structure. Entire mitochondrial DNA was cloned in E coli plasmids and Northern blot hybridization was done using cloned and subcloned DNAs as probes. Based on hybridization results of mitochondrial RNA transcripts, a transcription map was prepared.

Role of chromatin structure in HMRE mediated transcriptional repression of the HSP82 heat shock gene: Lee, See Woo , Gross, Davis S.; J. Microbiol. 1996;34(1):40-48.

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Abstract PDF: We have examined the chromatin structure of the HMRE/HSP82 and HMRa/HSP82 allels using three complementary approaches : DNase I chromating footprinting, micrococcal nuclease (MNase) nucleosome-protected ladder assay, and an in vivo E. coli dam methylase accessibility assay. The footprinting results indicate that the promoter and silencer sequences are assembled into nucleoprotein complexes which exhibit no detectable change in structure, despite a 70-fold range in expression levels. In addition, the promoter region of the HMRa/HSP82 allele is cleaved randomly by MNase in all cases, indicating the absence of anonical nucleosomes over this region irrespective of SIR4 or heat-shock. Finally, no discernible difference in the accessibility of the HMRE/HSP82 locus to dam methylase in SIR4 vs. sir4 cells was seen, which again suggests that the chromatin structure of HMRE/HSP82 allele is identical regardless of SIR4. Altogether, our results indicate that in contrast to other observations of the silent mating-type loci, no discernible structural alteration is detected at either HMR/HSP82 allele regardless of SIR genetic background or transcriptional state of the gene.

Cloning and mulecular characterization of a nprX gene of bacillus subtilis NS15-4 encoding a neutral protease: Lee, Seung Hwan , Yoon, Ki Hong , Nam, Hee Sop , Oh, Tae Kwang , Lee, Seog Jae , Chae, Keon Sang; J. Microbiol. 1996;34(1):68-73.

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Abstract PDF: An nprX gene of Bacillus subtilis NS15-4 encoding a neutral protease was cloned and its molecular characteristics were analyzed. The complete nucleotide sequence indicated that there is an open reading frame (0RF) possibly encoding 521 amino acid polypeptide. The ORF used all codons expected two cysteine and a proline having a codon bias index (CBI) of 0.09 in Escherichia coli. There were homologous sequences to the consensus sequence of -35 and -10 regions of E. coli promoters and to a Shine-Dalgarno (SD) sequence located 25 bp downstream of a major transcription initiation site. Moreover, there were also five minor transcription initiation sites at 6. 7. 8. 14 and 15 nt downstream of the major site. Northern blot analysis revealed the presence of about 1.8 kb mRNA transcript in E. coli having the nprX gene. The nucleotide sequence was identified in GenBank to be a gene for a neutral protease of B. subtilis with six nucleotide difference in the ORF region. The flanking regions of the NprX ORF showed much more differences form those of other neutral protease genes except the nprE gene of B. subtilis, which has the most homology to the nprX gene, and of which the flanking regions were identical to those of the nprX gene.

Amino acid substitutions conferring cold-sensitive phenotype on the yeast MTF1 gene: Jang , Sei Heon; J. Microbiol. 1997;35(3):228-233.

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Abstract PDF: The MTF1 gene of Saccharomyces cerevisiae encodes a 43 kDa MITOCHONDRIAL RNA polymerase specificity factor which recognizes mitochondrial promoters to initiate correct transcription. To better understand structure-function of the MTF1 gene as well as the transcription mechanism of mitochondrial RNA polymerase, two cold-sensitive alleles of the MTF1 mutation were isolated by plasmid shuffling method after PCR-based random mutagenesis of the MTF1 gene. The mutation sites were analyzed by nucleotide sequencing. These cs phenotype mtf1 mutants were respiration competent on the nonfermentible glycerol medium at the permissive temperature, but incompetent at 13℃. The cs phenotype allele of the MTF1, yJH147, encoded an L146P replacement. The other cs allele, yJH148, contained K179E and K214M double replacements. Mutations in both alleles were in a region of Mtflp which is located between domains with amino acid sequence similarities to conserved regions 2 and 3 of bacterial s factors.

Mechanism of Transcriptional Activation of the Phosphate Regulon in Escherichi coli: Kozo Makino , Mitsuko Amemura , Soo-Ki Kim , Katsushi Yokoyama , Sigenobu Kimura; J. Microbiol. 1998;36(4):231-238.

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Abstract PDF: In Escherichia coli, at least 31 genes, which are involved in the roles related to the transport and assimilation of phosphate and phosphorus compounds, are induced by phosphate starvation. They constitute a single phosphate (pho) regulon, and are under the same physiological and genetic control (30, 36, 46). Proteins PhoB and PhoR, which are regulatory systems for the transcriptional regulation of the phogenes, belong to a large family of two-component regulatory systems that respond to a variety of environmental stimuli in bacteria (23, 24, 33, 39). PhoB is the transcriptional activator, which binds to the promoters of the pho genes (21, 22). PhoR is a transmembrane protein that modulates the activity of PhoB by promoting specific phosphorylation and dephosphorylation of PhoB in response to the phosphate signal in the medium (19, 21, 37, 50). The phosphorylation of PhoB protein occurs concurrently with the acquisition of the ability to activate transcription from the pho promoters (Fig. 1). In the absence of the PhoR functions, PhoB is phosphorylated independently of the phosphate levels by PhoM, a PhoR like protein (2, 3, 26), which was renamed CreC by Wanner (45). In this article, we describe our recent studies on the mechanism of the transcriptional regulation of the pho regulon.

Genetic Manipulation of Rhabdoviruses : New Insights to Virus Replication, Transcription and Assembly: Michael A. Whitt; J. Microbiol. 1998;36(1):1-8.

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Abstract PDF: Rhabdoviruses, together with the other members of the Rhabdoviridae family, are one of the most widely distributed groups of viruses in nature. Rhabdoviruses have been isolated from virtually all vertebrates, several different species of insects, as well as many plant (65). It is thought that insects were the original hosts for this group of viruses and that rhabdoviruses have since adapted to grow in both vertebrates and invertebrates. This adaptation undoubtedly contributed to one of the disdinguishing features of the prototypic rhabdovirus, vesicular stomatitis virus (VSV), namely the ability to replicate in most primary cell cultures and essentially all established mammalian cell lines, as well as a number of insect and amphibian cell lines. Because VSV has a broad host range, is relatively easy to grow and replicates to high titers in cell culture it has been used extensively as a model system to study many aspects of rhabdovirus entry (32, 69, 70), replication (3, 4) and assembly(36, 55, 58).

Identification of Critical Amino Acids in the Core RNA Polynerase Binding Region of Yease Mtflp: Yang, Jae Sub , Jang, Sei Heon; J. Microbiol. 1998;36(3):208-213.

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Abstract PDF: Yeast mitochondral RNA polymerase specificity factor encoded by the nuclear MTF1 gene is required for a selective transcription on nonanucleotide mitochondral promoter by core RNA polymerase. Although there is a little amino acid sequence similarity of Mtf1p with bacterial sigma factors, the mode of transcriptional initiation of mitochondrial RNA polymerase is identical to that of E. coli RNA polymerase. To study the interaction of mtf1p with core polymerase, we carried out region-directed random mutagenesis of the core binding domain with the pool of mutant oligonucleotide. Out of 4,000 transformants screened for petite phenotype on glycerol media by plasmid shuffling, six alleles of the MTF1 gene were isolated. The positions of amino acid replacements that resulted in mtf1 mutants were limited to amino acids 53-54 and 65-67. Among mutant forms of Mtf1p overproduced in E. coli, Mtf1p with either L53H or Y65Dmutation was unable to produce a selective transcript in run-off transcription reaction, suggesting that amino acids L53 and Y65 are crucial for promoter recognition and/or contact with core polymerase.

Regulation of Actin Gene Expression During the Differentiation of Naegleria gruberi: Misook Kim , JooHun Lee; J. Microbiol. 2001;39(1):42-48.

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Abstract PDF: The regulation of actin gene expression during the differentiation of Naegleria gruberi was examined. Actin mRNA concentration was maximal in amoebae and decreased rapidly after the initiation of differentiation. At 20 min after initiation, the concentration of actin mRNA decreased to 55% of the maximal value. The actin mRNA concentration decreased to the minimum at 80 min (15% of the maximum), and then began to increase slightly at the end of differentiation. This decrease of actin mRNA concentration was regulated by the repression of actin gene transcription based on nuclear runon transcription experiments. The rates of transcription of actin gene in nuclei prepared at 40 and 80 min after the initiation of differentiation were 50 and 28% of that of nuclei prepared at the beginning of differentiation, respectively. The addition of cycloheximide at the initiation of differentiation inhibited both the rapid decrease in the concentration of actin mRNA and the repression of actin gene transcription. These results suggest that the rapid decrease in the concentration of actin mRNA during the differentiation of N. gruberi is accomplished by the repression of actin gene transcription and this transcriptional regulation requires continuous protein synthesis during the differentiation.

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