Journal of Microbiology

Journal Articles

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

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake: Yabing Gu, Junsheng Li, Zhenghua Liu, Min Zhang, Zhaoyue Yang, Huaqun Yin, Liyuan Chai, Delong Meng, Nengwen Xiao; J. Microbiol. 2024;62(10):829-843. Published online October 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00171-8

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Abstract: The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH₄⁺-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Review

Temperature Matters: Bacterial Response to Temperature Change: Seongjoon Moon , Soojeong Ham , Juwon Jeong , Heechan Ku , Hyunhee Kim , Changhan Lee; J. Microbiol. 2023;61(3):343-357. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00031-x

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Abstract

Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.

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Microalgal-bacterial consortia for the treatment of livestock wastewater: Removal of pollutants, interaction mechanisms, influencing factors, and prospects for application
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Laser NIR Irradiation Enhances Antimicrobial Photodynamic Inactivation of Biofilms of Staphylococcus aureus
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O. V. Gunar, N. G. Sakhno, O. S. Tyncherova
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Molecular insights and functional analysis of isocitrate dehydrogenase in two gram-negative pathogenic bacteria
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The transcriptional response to low temperature is weakly conserved across the Enterobacteriaceae
Johnson Hoang, Daniel M. Stoebel, Sarah L. Svensson
mSystems.2024;[Epub] CrossRef
A newly isolated strain for poly(3-hydroxybutyrate) production under anaerobic conditions and the key enzyme analysis
Rui Ma, Ji Li, R.D. Tyagi, Xiaolei Zhang
Chemical Engineering Journal.2024; 496: 154200. CrossRef
Construction of a tertiary model and uncertainty analysis for the effect of time, temperature, available chlorine concentration of slightly acidic electrolyzed water on salmonella enteritidis and background total bacteria counts on chicken
Yao Zang, Yitian Zang, Qiang Zhang, Guosheng Zhang, Jie Hu, Renxin Liu, Mingming Tu, Wenduo Qiao, Mengzhen Hu, Boya Fu, Dengqun Shu, Yanjiao Li, Xianghui Zhao
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A riboswitch-controlled TerC family transporter Alx tunes intracellular manganese concentration in Escherichia coli at alkaline pH
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Journal Articles

Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus: Sung&# , Mi&# , Hyun&# , Kae Kyoung Kwon; J. Microbiol. 2023;61(2):175-187. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00022-y

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Abstract

Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. ( MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. ( MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.

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An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023
Sara D. Lawhon, Claire R. Burbick, Trinity Krueger, Elena Ruiz-Reyes, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Core promoter mutation of nucleotides A1762T and G1764A of hepatitis B virus increases core promoter transactivation by hepatocyte nuclear factor 1: Mi So Seong , Hyeon Jeong Hwang , Eun Ah Jang , Jeong Ah Jang , Wah Wah Aung , Yi Yi Kyaw , JaeHun Cheong; J. Microbiol. 2022;60(10):1039-1047. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-1675-1

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Abstract

Hepatitis B virus (HBV) infection highly increases the risk for liver cirrhosis and hepatocellular carcinoma (HCC). The clinical manifestation of HBV infection is determined by the mutual interplay of the viral genotype, host genetic factors, mode of transmission, adaptive mutations, and environmental factors. Core promoter activation plays a critical role in the pre-genomic RNA transcription of HBV for HBV replication. The mutations of core promoter have been implicated in HCC development. We had obtained HBV genes from Myanmar HBV infectants and identified gene variations at the core promoter region. For measuring the relative transactivation activity on core promoter, we prepared the core-promoter reporter construct. Both of A1762T and G1764A mutation were consistently found in the HBV genes with hepatocellular carcinoma. The A1762T/G1764A mutation was corresponding to K130M/V131I of HBx protein. We prepared the core promoter- luciferase reporter construct containing the double A1762T/G1764A mutation and the K130M/V131I HBx protein expression construct. The A1762T/G1764A mutation highly was responsive to core promoter transactivation by HBx, regardless of HBx mutation. The A1762T/G1764A mutation newly created hepatocyte nuclear factor 1 (HNF1) responsive element. Ectopic expression of HNF1 largely increased the HBV core promoter containing A1762T/G1764A mutation. In addition, hepatic rich fatty acid, palmitic acid and oleic acid, increased K130M/V131I HBx level by core promoter activation. These results provide biological properties and clinical significance of specific HBV core promoter mutants related with HCC development.

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A Survey of HBV Core/Pre-Core Mutations in Iraqi Patients with Chronic Hepatitis
Abdulhussain Kadhim Jwaziri, Maryam Esghaei, Mohammad Hadi Karbalaie Niya, Hadi Sayah, Mohammad Hossein Razizadeh, Ali Gholami, Leila Mousavizadeh, Hossein Keyvani
Hepatitis Monthly.2023;[Epub] CrossRef
The A1762T/G1764A mutations enhance HBV replication by alternating viral transcriptome
Danli Yang, Jun Zou, Guiwen Guan, Xiaoyu Feng, Ting Zhang, Guixin Li, Hui Liu, Huiling Zheng, Jingyuan Xi, Guangxin Yu, Lizhong Dai, Fengmin Lu, Xiangmei Chen
Journal of Medical Virology.2023;[Epub] CrossRef
Clinical application value of hepatitis B virus basal core promoter 1762/1764 and GGTII and GGT in patients with HBV-DNA-positive primary liver cancer
Shunhua Qiu, Lifen Jin, Dan Yang, Dewen Zhang
Medicine.2023; 102(43): e35699. CrossRef

Effects of rehydration on physiological and transcriptional responses of a water-stressed rhizobium: Jie Zhu , Xin Jiang , Dawei Guan , Yaowei Kang , Li Li , Fengming Cao , Baisuo Zhao , Mingchao Ma , Ji Zhao , Jun Li; J. Microbiol. 2022;60(1):31-46. Published online November 26, 2021; DOI: https://doi.org/10.1007/s12275-022-1325-7

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Abstract

As a microsymbiont of soybean, Bradyrhizobium japonicum plays an important role in symbiotic nitrogen fixation and sustainable agriculture. However, the survival of B. japonicum cells under water-deplete (e.g., drought) and water-replete (e.g., flood) conditions is a major concern affecting their nitrogen-fixing ability by establishing the symbiotic relationship with the host. In this study, we isolated a water stress tolerant rhizobium from soybean root nodules and tested its survival under water-deplete conditions. The rhizobium was identified as Bradyrhizobium japonicum and named strain 5038. Interestingly, both plate counting and live/dead fluorescence staining assays indicate that a number of viable but non-culturable cells exist in the culture medium upon the rehydration process which could cause dilution stress. Bradyrhizobium japonicum 5038 cells increased production of exopolysaccharide (EPS) and trehalose when dehydrated, suggesting that protective responses were stimulated. As expected, cells reduced their production upon the subsequent rehydration. To examine differential gene expression of B. japonicum 5038 when exposed to water-deplete and subsequent waterreplete conditions, whole-genome transcriptional analysis was performed under 10% relative humidity (RH), and subsequent 100% RH, respectively. A total of 462 differentially expressed genes (DEGs, > 2.0-fold) were identified under the 10% RH condition, while 3,776 genes showed differential expression during the subsequent rehydration (100% RH) process. Genes involved in signal transduction, inorganic ion transport, energy production and metabolisms of carbohydrates, amino acids, and lipids were far more up-regulated than downregulated in the 10% RH condition. Notably, trehalose biosynthetic genes (otsAB, treS, and treYZ), genes ligD, oprB, and a sigma factor rpoH were significantly induced by 10% RH. Under the subsequent 100% RH condition, genes involved in transcription, translation, cell membrane regulation, replication and repair, and protein processing were highly up-regulated. Interestingly, most of 10%-RH inducible genes displayed rehydration-repressed, except three genes encoding heat shock (Hsp20) proteins. Therefore, this study provides molecular evidence for the switch of gene expression of B. japonicum cells when encountered the opposite water availability from water-deplete to water-replete conditions.

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Microbiological Research.2024; 288: 127886. CrossRef
Plant–Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought
Nataliya Loiko, M. Nazrul Islam
Agronomy.2024; 14(9): 1949. CrossRef
Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress
Huimin Ju, Jian Zhang, Yiyang Zou, Feiyang Xie, Xiaoyu Tang, Si Zhang, Jie Li
Environmental Research.2024; 250: 118469. CrossRef
Effect of Nitrogen Application and Cutting Frequency on the Yield and Forage Quality of Alfalfa in Seasonal Cultivation
Kun Zhang, Chenyuan Zhai, Yonglong Li, Yan Li, Hui Qu, Yixin Shen
Agriculture.2023; 13(5): 1063. CrossRef
Profound Change in Soil Microbial Assembly Process and Co-occurrence Pattern in Co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 on Soybean
Yubin Zhao, Dawei Guan, Xu Liu, Gui-Feng Gao, Fangang Meng, Bingqiang Liu, Pengfei Xing, Xin Jiang, Mingchao Ma, Fengming Cao, Li Li, Jun Li
Frontiers in Microbiology.2022;[Epub] CrossRef

Review

Prokaryotic DNA methylation and its functional roles: Hoon Je Seong , Sang-Wook Han , Woo Jun Sul; J. Microbiol. 2021;59(3):242-248. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0674-y

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Abstract

DNA methylation is known as a universal mechanism of epigenetic regulation in all kingdoms of life. Particularly, given that prokaryotes lack key elements such as histones and nucleosomes that can structurally modify DNA, DNA methylation is considered a major epigenetic regulator in these organisms. However, because DNA methylation studies have focused primarily on eukaryotes, the mechanism of prokaryotic DNA methylation has been less studied than in eukaryotes. DNA methylation in prokaryotes plays an important role in regulating not only the host defense system, but also the cell cycle, gene expression, and virulence that can respond directly to the environment. Recent advances in sequencing techniques capable of detecting methylation signals have allowed for the characterization of prokaryotic genome-wide epigenetic regulation. In this review, we describe representative examples of cellular events regulated by DNA methylation in prokaryotes, from early studies to current applications.

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Journal Article

A comprehensive in silico analysis of sortase superfamily: Adeel Malik , Seung Bum Kim; J. Microbiol. 2019;57(6):431-443. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8545-5

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Abstract

Sortases are cysteine transpeptidases that assemble surface proteins and pili in their cell envelope. Encoded by all Grampositive bacteria, few Gram-negative bacteria and archaea, sortases are currently divided into six classes (A-F). Due to the steep increase in bacterial genome data in recent years, the number of sortase homologues have also escalated rapidly. In this study, we used protein sequence similarity networks to explore the taxonomic diversity of sortases and also to evaluate the current classification of these enzymes. The resultant data suggest that sortase classes A, B, and D predominate in Firmicutes and classes E and F are enriched in Actinobacteria, whereas class C is distributed in both Firmicutes and Actinobacteria except Streptomyces family. Sortases were also observed in various Gram-negatives and euryarchaeota, which should be recognized as novel classes of sortases. Motif analysis around the catalytic cysteine was also performed and suggested that the residue at 2nd position from cysteine may help distinguish various sortase classes. Moreover, the sequence analysis indicated that the catalytic arginine is highly conserved in almost all classes except sortase F in which arginine is replaced by asparagine in Actinobacteria. Additionally, class A sortases showed higher structural variation as compared to other sortases, whereas inter-class comparisons suggested structures of class C and D2 exhibited best similarities. A better understanding of the residues highlighted in this study should be helpful in elucidating their roles in substrate binding and the sortase function, and successively could help in the development of strong sortase inhibitors.

Citations

Citations to this article as recorded by

Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase
José Jesús Gallego-Parrilla, Emmanuele Severi, Govind Chandra, Tracy Palmer
Microbiology .2024;[Epub] CrossRef
Sortases: structure, mechanism, and implications for protein engineering
Jeanine F. Amacher, John M. Antos
Trends in Biochemical Sciences.2024; 49(7): 596. CrossRef
A unique binding mode of P1′ Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage
Brandon A. Vogel, Jadon M. Blount, Hanna M. Kodama, Noah J. Goodwin-Rice, Devin J. Andaluz, Sophie N. Jackson, John M. Antos, Jeanine F. Amacher
RSC Chemical Biology.2024; 5(1): 30. CrossRef
Advances and challenges in drug design against dental caries: application of in silico approaches
Zhongxin Chen, Xinyao Zhao, Hanyu Zheng, Yufei Wang, Linglin Zhang
Journal of Pharmaceutical Analysis.2024; : 101161. CrossRef
Rolling down the pilus formation of gram-positive bacteria: underlining the importance of Sortase C as a drug target
Himanshi Kain, Ena Gupta, Prashant Sharma, Akanksha Haldiya, Vijay Kumar Srivastava, Ravi Ranjan Kumar Neeraj, Pradeep Sharma, S. L. Kothari, Sandip Patil, Shaowei Dong, Anupam Jyoti, Sanket Kaushik
Biofouling.2024; : 1. CrossRef
GPApred: The first computational predictor for identifying proteins with LPXTG-like motif using sequence-based optimal features
Adeel Malik, Watshara Shoombuatong, Chang-Bae Kim, Balachandran Manavalan
International Journal of Biological Macromolecules.2023; 229: 529. CrossRef
Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes
Melody Gao, D. Alex Johnson, Isabel M. Piper, Hanna M. Kodama, Justin E. Svendsen, Elise Tahti, Frederick Longshore‐Neate, Brandon Vogel, John M. Antos, Jeanine F. Amacher
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Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities
Jordan D. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, Isabel M. Piper, Justin E. Svendsen, D. Alex Johnson, Brandon A. Vogel, John M. Antos, Michael J. Harms, Jeanine F. Amacher
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SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information
Adeel Malik, Sathiyamoorthy Subramaniyam, Chang-Bae Kim, Balachandran Manavalan
Computational and Structural Biotechnology Journal.2022; 20: 165. CrossRef
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Kira S. Makarova, Yuri I. Wolf, Svetlana Karamycheva, Eugene V. Koonin
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Sorting out the Superbugs: Potential of Sortase A Inhibitors among Other Antimicrobial Strategies to Tackle the Problem of Antibiotic Resistance
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Chemoenzymatic Semisynthesis of Proteins
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Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium
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BMC Genomics.2020;[Epub] CrossRef
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Applied and Environmental Microbiology.2019;[Epub] CrossRef

Review

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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Abstract

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.

Citations

Citations to this article as recorded by

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
Journal of Fungi.2024; 10(12): 866. CrossRef
Current Perspectives on Uniparental Mitochondrial Inheritance in Cryptococcus neoformans
Amber R. Matha, Xiaorong Lin
Pathogens.2020; 9(9): 743. CrossRef
Investigation of Mating Pheromone–Pheromone Receptor Specificity in Lentinula edodes
Sinil Kim, Byeongsuk Ha, Minseek Kim, Hyeon-Su Ro
Genes.2020; 11(5): 506. CrossRef
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

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

Flavobacterium aquaticum sp. nov., a Member of the Bacteroidetes Isolated from a Freshwater Reservoir: Siwon Lee , Jungnam Lee , Tae-Young Ahn; J. Microbiol. 2013;51(3):283-288. Published online April 26, 2013; DOI: https://doi.org/10.1007/s12275-013-2293-8

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Abstract: A novel bacterial strain, designated ARSA-111T, was isolated from a freshwater reservoir in Cheonan, Korea. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavobacterium of phylum Bacteroidetes. The 16S rRNA gene sequence of strain ARSA-111T showed a high degree of sequence similarity to those of Flavobacteium cheonanense KACC 14972T (97.3%), F. aquatile JCM 20475T (97.1%), and other type strains of the genus Flavobacterium (＜97.0%). The phylogenetic tree and network analysis (i.e. median-joining) based on 16S rRNA gene sequences showed that strain ARSA-111T is most closely related to F. aquatile JCM 20475T. DNA-DNA hybridization experiment revealed ＜70% of genomic relatedness among strain ARSA-111T, F. aquatile JCM 20475T and F. cheonanense KACC 14972T. The isolate had iso-C15:1, iso-C15:0, and iso-C15:0 3-OH as predominant cellular fatty acids and MK-6 as a predominant menaquinone. The genomic DNA G+C content of the isolate was 35.6 mol%. On the basis of these data, strain ARSA-111T is considered to be a novel species of the genus Flavobacterium, for which the name Flavobacterium aquaticum sp. nov. is proposed. The type strain is strain ARSA-111T (=KACC 14973T =KCTC 23185T = JCM 17070T).

Dynamical Analysis of Yeast Protein Interaction Network During the Sake Brewing Process: Mitra Mirzarezaee , Mehdi Sadeghi , Babak N. Araabi; J. Microbiol. 2011;49(6):965-973. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1194-y

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1 Scopus

Abstract: Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

Cyanobacterial Hybrid Kinase Sll0043 Regulates Phototaxis by Suppressing Pilin and Twitching Motility Protein: Bong-Jeong Shin , Jeehyun Oh , Sungsoo Kang , Young-Ho Chung , Young Mok Park , Young Hwan Kim , Seungil Kim , Jong Bhak , Jong-Soon Choi; J. Microbiol. 2008;46(3):300-308. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0212-6

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8 Scopus

Abstract: The unicellular cyanobacterium Synechocystis sp. PCC 6803 glides toward a light source through the interplay of positive phototaxis genes and proteins. In genetic analysis, the complete disruption of the hybrid sensory kinase sll0043 produced negative phototaxis. Furthermore, Sll0043 was found to be a hub protein by in silico prediction of protein-protein interaction, in which Sll0043 was predominantly linked to seven two-component proteins with high confidence. To understand the regulation and networking of positive phototaxis proteins, the proteomic profile of the sll0043 mutant was compared to that of wild-type. In the sll0043 mutant, 18 spots corresponding to 15 unique proteins were altered by 1.3 to 59 fold; the spots were identified by 2-DE/MALDI-MS analysis. Down-regulated proteins in the sll0043 null-mutant included chaperonins, superoxide dismutase, and phycocyanin β-subunit. In contrast, nine proteins involved in photosynthesis, translation, regulatory function, and other functions were up-regulated. In particular, a twitching motility protein (PilT1) was induced over 2-fold in sll0043 mutant. Moreover, semiquantitative and quantitative RT-PCR analysis revealed that pilin (pilA1), pili motor (pilT1), and pili switch gene (pilT2) were significantly increased in sll0043 mutant. These results suggest that the hybrid kinase Sll0043 regulates positive phototaxis by suppressing the expression of pili biosynthesis and regulatory genes and through the interplay with positive phototaxis/motility two-component proteins.

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