Journal of Microbiology

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Comparative genome analysis of enterohemorrhagic Escherichia coli ATCC 43894 and its pO157-cured strain 277: Se Kye Kim, Yong-Joon Cho, Carolyn J. Hovde, Sunwoo Hwang, Jonghyun Kim, Jang Won Yoon; J. Microbiol. 2025;63(12):e2511015. Published online December 31, 2025; DOI: https://doi.org/10.71150/jm.2511015

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Abstract PDF Supplementary Material: Enterohemorrhagic Escherichia coli (EHEC) O157:H7 ATCC 43894 (also known as EDL932) has been widely used as a reference strain for studying the pathophysiology of EHEC. To elucidate the role of a large virulence plasmid pO157 and its relationship with acid resistance, for example, both EHEC ATCC 43894 and its pO157-cured derivative strain 277 were well studied. However, it is unclear whether or not these two strains are isogenic and share the same genetic background. To address this question, we analyzed the whole genome sequences of ATCC 43894 and 277. As expected, three and two closed contigs were identified from ATCC 43894 and 277, respectively; two contigs shared in both strains were a chromosome and a small un-identified plasmid, and one contig found only in ATCC 43894 was pO157. Surprisingly, our pan-genome analyses of the two sequences revealed several genetic variations including frameshift, substitution, and deletion mutations. In particular, the deletion mutation of hdeD and gadE in ATCC 43894 was identified, and further PCR analysis also confirmed their deletion of a 2.5-kb fragment harboring hdeD, gadE, and mdtE in ATCC 43894. Taken together, our findings demonstrate that EHEC ATCC 43894 harbors genetic mutations affecting glutamate-dependent acid resistance system and imply that the pO157-cured EHEC 277 may not be isogenic to ATCC 43894. This is the first report that such genetic differences between both reference strains of EHEC should be considered in future studies on pathogenic E. coli.

Encapsulin protein MAV2054 enhances Mycobacterium avium virulence by promoting Cdc42-dependent epithelial cell invasion: Dong Ho Kim, I Jeong Jo, Min Ju Kang, Yi Seol Kim, Duyen Do Tran Huong, Kyungho Woo, Ho-Sung Park, Hwa-Jung Kim, Chul Hee Choi; J. Microbiol. 2025;63(11):e2506008. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2506008

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Abstract PDF: Mycobacterium avium complex (MAC) organisms are widespread environmental pathogens associated with chronic pulmonary infections. Although M. avium is known to invade epithelial cells, the molecular mechanisms underlying this process remain incompletely understood. In this study, we identified a novel role for MAVRS09815 (formerly MAV2054), a family 2A encapsulin nanocompartment shell protein, in mediating bacterial adhesion, epithelial cell invasion, and in vivo virulence. We engineered a recombinant M. smegmatis strain expressing MAV2054 (Ms_2054) and an M. avium MAV2054 deletion mutant (Δ2054). Ms_2054 exhibited enhanced epithelial invasion, whereas Δ2054 showed reduced intracellular survival. Recombinant MAV2054 protein was bound directly to human epithelial cells in a dose-dependent manner. Pretreatment of host cells with cytochalasin D or vinblastine significantly inhibited bacterial internalization, indicating that MAV2054-mediated invasion is cytoskeleton-dependent. Confocal and scanning electron microscopy revealed MAV2054-dependent membrane rearrangements during infection. Pull-down assays demonstrated that MAV2054 activates Cdc42, a key regulator of actin polymerization, with reduced activation observed in Δ2054-infected cells. In a murine intratracheal infection model, the Δ2054 exhibited significantly reduced bacterial burdens and lung inflammation compared to the wild type. These findings demonstrate that MAV2054 enhances M. avium virulence by promoting epithelial cell invasion through Cdc42-dependent cytoskeletal remodeling. This study reveals a previously unrecognized role for an encapsulin-like protein in host-pathogen interactions and highlights its potential as a therapeutic target in MAC infections.

Review

Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast: Phuong Hoang Nguyen Tran, Taek Soon Lee; J. Microbiol. 2025;63(3):e2501006. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501006

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Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.

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Peroxisome engineering in yeast: Advances, challenges, and prospects
Cuifang Ye, Xiaoqian Li, Tao Liu, Shiyu Li, Mengyu Zhang, Yao Zhao, Jintao Cheng, Guiling Yang, Peiwu Li
Biotechnology Advances.2026; 86: 108747. CrossRef
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Andrea M. Garza Elizondo, Ilenne del Valle Kessra, Erica Teixeira Prates, Evan Komp, Elise K. Phillips, Nandhini Ashok, Daniel A. Jacobson, Erin G. Webb, Yannick J. Bomble, William G. Alexander, Joanna Tannous, Chung-Jui Tsai, Wayne A. Parrott, Xiaohan Ya
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Journal Article

Genomic Characterization and Comparative Analysis of Streptococcus zhangguiae sp. nov. Isolated from the Respiratory Tract of Marmota Himalayana: Caixin Yang, Jiajia Ma, Huimin Zhou, Jing Yang, Ji Pu, Shan Lu, Dong Jin, Liyun Liu, Kui Dong, Jianguo Xu; J. Microbiol. 2024;62(11):951-963. Published online November 4, 2024; DOI: https://doi.org/10.1007/s12275-024-00177-2

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Abstract PDF: Two Gram-stain-positive, oxidase-negative, non-motile, facultative anaerobic, α-hemolytic, coccus-shaped bacteria (zg-86^T and zg-70) were isolated from the respiratory tracts of marmots (Marmota Himalayana) on the Qinghai-Tibet Plateau of China. Phylogenetic analysis of the 16S rRNA gene and 545 core genes revealed that these two strains belong to the Streptococcus genus. These strains were most closely related to Streptococcus respiraculi HTS25^T, Streptococcus cuniculi CCUG 65085^T, and Streptococcus marmotae HTS5^T. The average nucleotide identity (ANI) and digital DNA‒DNA hybridization (dDDH) were below the threshold for species delineation. The predominant cellular fatty acids (CFAs) in this novel species were C_16:0, C_18:0, and C_18:1ω9c, whereas the primary polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and an unknown phosphoglycolipid (PGL). The optimal growth conditions for the strains were 37 °C, pH 7.0, and 0.5% (w/v) NaCl on brain-heart infusion (BHI) agar supplemented with 5% defibrinated sheep blood. Comparative genomics analyses revealed the potential pathogenicity of strain zg-86^T through comparisons with suis subclade strains in terms of virulence factors, pathogen-host interactions (PHIs) and mobile genetic factors (MGEs). Based on the phenotypic characteristics and phylogenetic analyses, we propose that these two isolates represent novel species in the genus Streptococcus, for which the names Streptococcus zhangguiae sp. nov. (the type strain zg-86^T=GDMCC 1.1758^T=JCM 34273^T) is proposed.

Review

Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems: Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park; J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00172-7

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Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.

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Rapid and selective disruption of photosystem I in toxic cyanobacteria protects aquatic ecosystem health
Wonjae Kim, Yerim Park, Yongjun Son, Nayeon Yoo, Eui-Hwan Chung, Woojun Park
Journal of Hazardous Materials.2026; 501: 140736. CrossRef
Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont
Tzipora Peretz, Esther Cattan‐Tsaushu, Chiara Conti, Benyamin Rosental, Laura Steindler, Sarit Avrani
Environmental Microbiology.2025;[Epub] CrossRef
Public goods-mediated bacterial interplay in aquatic ecosystems
Yerim Park, Wonjae Kim, Jihye Bae, Woojun Park
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Horizontal Gene Transfer and Recombination in Cyanobacteriota
Devaki Bhaya, Gabriel Birzu, Eduardo P.C. Rocha
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Journal Articles

Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest: Mao Tian, Shiyu Wu, Wei Zhang, Gaosen Zhang, Xue Yu, Yujie Wu, Puchao Jia, Binglin Zhang, Tuo Chen, Guangxiu Liu; J. Microbiol. 2024;62(4):277-284. Published online March 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00108-1

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Abstract PDF: We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038(T), from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C(15:0) and iso-C(17:0). Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038(T) has the highest similarity with Spelaeicoccus albus DSM 26341( T) (96.02%). ZFBP1038(T) formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038(T) was 63.65 mol% and the genome size was 4.05 Mb. Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038(T) and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively. Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038(T) represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038(T) (= EE 014( T) = GDMCC 1.3024( T) = JCM 35335( T)).

LAMMER Kinase Governs the Expression and Cellular Localization of Gas2, a Key Regulator of Flocculation in Schizosaccharomyces pombe: Won-Hwa Kang , Yoon-Dong Park , Joo-Yeon Lim , Hee-Moon Park; J. Microbiol. 2024;62(1):21-31. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00097-7

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Abstract PDF: It was reported that LAMMER kinase in Schizosaccharomyces pombe plays an important role in cation-dependent and galactose-specific flocculation. Analogous to other flocculating yeasts, when cell wall extracts of the Δlkh1 strain were treated to the wild-type strain, it displayed flocculation. Gas2, a 1,3-β-glucanosyl transferase, was isolated from the EDTA-extracted cell-surface proteins in the Δlkh1 strain. While disruption of the gas2+ gene was not lethal and reduced the flocculation activity of the Δlkh1 strain, the expression of a secreted form of Gas2, in which the GPI anchor addition sequences had been removed, conferred the ability to flocculate upon the WT strain. The Gas2-mediated flocculation was strongly inhibited by galactose but not by glucose. Immunostaining analysis showed that the cell surface localization of Gas2 was crucial for the flocculation of fission yeast. In addition, we identified the regulation of mbx2+ expression by Lkh1 using RT-qPCR. Taken together, we found that Lkh1 induces asexual flocculation by regulating not only the localization of Gas2 but also the transcription of gas2+ through Mbx2.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region: Salman Khan , Chun Han , Awais Iqbal , Chao Guan , Changming Zhao; J. Microbiol. 2023;61(10):903-915. Published online November 23, 2023; DOI: https://doi.org/10.1007/s12275-023-00085-x

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Elevation gradients, often regarded as “natural experiments or laboratories”, can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen ( NH4 +-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_ 1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

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Distribution patterns of herbaceous rhizosphere bacterial and fungal diversities and their influencing factors along the elevational gradient in mountain ecosystems
Yuhang Wang, Kaiyang Qiu, Wangsuo Liu, Yanju Guo, Yi Yang, Jianping Li, Hongmei Wang, Jingjing Zhang, Panxing He, Yingzhong Xie
Applied Soil Ecology.2026; 217: 106573. CrossRef

Development of a Novel D‑Lactic Acid Production Platform Based on Lactobacillus saerimneri TBRC 5746: Kitisak Sansatchanon , Pipat Sudying , Peerada Promdonkoy , Yutthana Kingcha , Wonnop Visessanguan , Sutipa Tanapongpipat , Weerawat Runguphan , Kanokarn Kocharin; J. Microbiol. 2023;61(9):853-863. Published online September 14, 2023; DOI: https://doi.org/10.1007/s12275-023-00077-x

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D-Lactic acid is a chiral, three-carbon organic acid, that bolsters the thermostability of polylactic acid. In this study, we developed a microbial production platform for the high-titer production of D-lactic acid. We screened 600 isolates of lactic acid bacteria (LAB) and identified twelve strains that exclusively produced D-lactic acid in high titers. Of these strains, Lactobacillus saerimneri TBRC 5746 was selected for further development because of its homofermentative metabolism. We investigated the effects of high temperature and the use of cheap, renewable carbon sources on lactic acid production and observed a titer of 99.4 g/L and a yield of 0.90 g/g glucose (90% of the theoretical yield). However, we also observed L-lactic acid production, which reduced the product’s optical purity. We then used CRISPR/dCas9-assisted transcriptional repression to repress the two Lldh genes in the genome of L. saerimneri TBRC 5746, resulting in a 38% increase in D-lactic acid production and an improvement in optical purity. This is the first demonstration of CRISPR/dCas9-assisted transcriptional repression in this microbial host and represents progress toward efficient microbial production of D-lactic acid.

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Ultrasonic Treatment Enhanced Astaxanthin Production of Haematococcus pluvialis: Yun Hwan Park , Jaewon Park , Jeong Sik Choi , Hyun Soo Kim , Jong Soon Choi , Yoon-E Choi; J. Microbiol. 2023;61(6):633-639. Published online June 13, 2023; DOI: https://doi.org/10.1007/s12275-023-00053-5

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Abstract PDF

In this study, effects of ultrasonic treatment on Haematococcus pluvialis (H. pluvialis) were investigated. It has been confirmed that the ultrasonic stimulation acted as stress resources in the red cyst stage H. pluvialis cells containing astaxanthin,
result
ing in additional astaxanthin production. With the increase in production of astaxanthin, the average diameter of H. pluvialis cells increased accordingly. In addition, to determine how ultrasonic stimulation had an effect on the further biosynthesis of astaxanthin, genes related to astaxanthin synthesis and cellular ROS level were measured. As a result, it was confirmed that astaxanthin biosynthesis related genes and cellular ROS levels were increased, and thus ultrasonic stimulation acts as an oxidative stimulus. These results support the notion on the effect of the ultrasonic treatment, and we believe our novel approach based on the ultrasonic treatment would help to enhance the astaxanthin production from H. pluvialis.

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Yingjie Song, Zhangli Hu, Sizhao Liu, Shasha Luo, Ruimin He, Xinyan Yang, Shuang Li, Xuewei Yang, Yuxing An, Yinglin Lu
Journal of Agricultural and Food Chemistry.2025; 73(8): 4466. CrossRef
Multidimensional Characterization of the Physiological State of Hematococcuspluvialis Using Scanning Structured Illumination Super-Resolution Microscopy
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Transition between germination and dormancy for non-motile cells of Haematococcus pluvialis: dependence on nitrogen availability through metabolic flux of amino acids and nucleotides
Jing Li, Litao Zhang, Wenjie Yu, Feng Chen, Anatoly A. Tsygankov, Jianguo Liu
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Haematococcus pluvialis culture contaminated with chytrids: growth management and astaxanthin production
Zineb Mansouri, Ibtissam Lijassi, Ana Amorim, Aïcha El Aissami, Laila Rhazi, Imane Wahby
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Editorial

Editorial] Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation: Jin-Won Lee; J. Microbiol. 2023;61(3):273-276. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00036-6

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Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

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Journal Articles

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

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Reversible acetylation of ribosomal protein S1 serves as a smart switch for Salmonella to rapidly adapt to host stress
Yi-Lin Shen, Tian-Xian Liu, Lei Xu, Bang-Ce Ye, Ying Zhou
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Multi-Lasso Peptide-Based Synergistic Nanocomposite: A High-Stability, Broad-Spectrum Antimicrobial Agent with Potential for Combined Antibacterial Therapy
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Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish: Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae; J. Microbiol. 2022;60(6):576-584. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1604-3

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Three aerobic, Gram-negative, and rod-shaped bacterial strains, designated strains G4M1T, SM13T, and L12M9T, were isolated from the gut of Batillaria multiformis, Cellana toreuma, and Patinopecten yessoensis collected from the Yellow Sea in South Korea. All the strains grew optimally at 25°C, in the presence of 2% (w/v) NaCl, and at pH 7. These three strains, which belonged to the genus Polaribacter in the family Flavobacteriaceae, shared < 98.8% in 16S rRNA gene sequence and < 86.68% in whole-genome sequence with each other. Compared with the type strains of Polaribacter, isolates showed the highest sequence similarity to P. haliotis KCTC 52418T (< 98.68%), followed by P. litorisediminis KCTC 52500T (< 98.13%). All the strains contained MK-6 as their predominant menaquinone and iso-C15:0 as their major fatty acid. Moreover, all the strains had phosphatidylethanolamine as their polar lipid component. In addition, strain G4M1T had two unidentified lipids and three unidentified aminolipids, strain SM13T had three unidentified lipids and three unidentified aminolipids, and strain L12M9T had three unidentified lipids and one unidentified aminolipid. The DNA G + C contents of strains G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%, respectively. Based on phenotypic, phylogenetic, chemotaxonomic, and genotypic findings, strains G4M1T (= KCTC 82388T = DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T), and L12M9T (= KCTC 62751T = DSM 112374T) were classified into the genus Polaribacter as the type strains of novel species, for which the names Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., respectively, have been proposed.

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W. M. Lakshani Anuradha Wanasinghe, Wang Xin, Yuan Siliang, Dongru Qiu
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Isolation and characterization of Polaribacter sargassicola sp. nov. and Algibacter ulvanivorans sp. nov.: two novel species with ability to degrade algal polysaccharides
Jin Li, Aihua Mao, Chao Peng, Linhui Li, Binghan Li, Lijuan Zhou, Yan Xu, Mingqi Zhong, Zhong Hu
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Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
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Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013
Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon
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Aharon Oren, George Garrity
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Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
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Activity of Lactobacillus crispatus isolated from vaginal microbiota against Mycobacterium tuberculosis: Youngkyoung Lee , Hoonhee Seo , Sukyung Kim Abdur Rahim , Youjin Yoon , Jehee Jung , Saebim Lee , Chang Beom Ryu , Ho-Yeon Song; J. Microbiol. 2021;59(11):1019-1030. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1332-0

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Abstract PDF

Tuberculosis, an infectious disease, is caused by Mycobacterium tuberculosis. It remains a significant public health issue around the globe, causing about 1.8 million deaths every year. Drug-resistant M. tuberculosis, including multi-drug-resistant (MDR), extremely-drug-resistant (XDR), and totally drugresistant (TDR) M. tuberculosis, continues to be a threat to public health. In the case of antibiotic-resistant tuberculosis, the treatment effect of conventional antibiotics is low. Side effects caused by high doses over a long period are causing severe problems. To overcome these problems, there is an urgent need to develop a new anti-tuberculosis drug that is different from the existing compound-based antibiotics. Probiotics are defined as live microorganisms conferring health benefits. They can be potential therapeutic agents in this context as the effectiveness of probiotics against different infectious diseases has been well established. Here, we report that Lactobacillus crispatus PMC201 shows a promising effect on tuberculosis isolated from vaginal fluids of healthy Korean women. Lactobacillus crispatus PMC201 reduced M. tuberculosis H37Rv under co-culture conditions in broth and reduced M. tuberculosis H37Rv and XDR M. tuberculosis in macrophages. Lactobacillus crispatus PMC201 was not toxic to a guinea pig model and did not induce dysbiosis in a human intestinal microbial ecosystem simulator. Taken together, these
results
indicate that L. crispatus PMC201 can be a promising alternative drug candidate in the current tuberculosis drug regime. Further study is warranted to assess the in vivo efficacy and confirm the mode of action of L. crispatus PMC201.

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Effect of Probiotics Supplementation on Clinical, Humanistic, and Safety Outcomes in Patients With Tuberculosis: A Prospective Cohort Study in a Tertiary Healthcare Facility in South India
Tejaswini Baral, Varun Kumar Sudha Gururaj, Mohan K. Manu, Chandrashekar Udyavara Kudru, Jitendra Singh, Chiranjay Mukhopadhyay, Mahadev Rao, Kavitha Saravu, Sonal Sekhar Miraj
Journal of the American Nutrition Association.2026; 45(1): 44. CrossRef
Insights into Autophagy in Microbiome Therapeutic Approaches for Drug-Resistant Tuberculosis
Md Abdur Rahim, Hoonhee Seo, Indrajeet Barman, Mohammed Solayman Hossain, Md Sarower Hossen Shuvo, Ho-Yeon Song
Cells.2025; 14(7): 540. CrossRef
The potential role of probiotics and their bioactive compounds in the management of pulmonary tuberculosis
Hamed Memariani, Mojtaba Memariani, Seyed Ebrahim Eskandari, Abdolmajid Ghasemian, Ali Nour Neamatollahi
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Gut microbiota and tuberculosis infection: interaction and therapeutic potential
Yinghui Chai, Min Li, Xianping Deng, Congcong Ma, Nannan Zhou, Yanan Chen, Yushan Yao, Kang Li, Wenping Gong, Hong Lei
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Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice
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Hanieh Tajdozian, Hoonhee Seo, Yoonkyoung Jeong, Fatemeh Ghorbanian, Chae-eun Park, Faezeh Sarafraz, Md Abdur Rahim, Youngkyoung Lee, Sukyung Kim, Saebim Lee, Jung-Hyun Ju, Chul-Ho Kim, Ho-Yeon Song
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Mohammed Solayman Hossain, Hoonhee Seo, Md Abdur Rahim, Md Sarower Hossen Shuvo, Indrajeet Barman, Hokyoung Kim, Jinhyeon An, Sukyung Kim, Ho-Yeon Song
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Qiqi Zhuo, Xianyi Zhang, Kehong Zhang, Chan Chen, Zhen Huang, Yuzhong Xu
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Archana Pant, Bhabatosh Das, Gopalakrishnan Aneeshkumar Arimbasseri
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Roberto Arrigoni, Andrea Ballini, Skender Topi, Lucrezia Bottalico, Emilio Jirillo, Luigi Santacroce
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Fatemeh Ghorbanian, Hoonhee Seo, Hanieh Tajdozian, Youngkyoung Lee, MD Abdur Rahim, Sukyung Kim, Il-Yun Jung, Saebim Lee, Ho-Yeon Song
Polish Journal of Microbiology.2022; 71(4): 553. CrossRef

Salmonella Typhimurium ST313 isolated in Brazil revealed to be more invasive and inflammatory in murine colon compared to ST19 strains: Amanda Aparecida Seribelli , Tamara R. Machado Ribeiro , Patrick da Silva† , Isabela Mancini Martins , Felipe Pinheiro Vilela , Marta I. Cazentini Medeiros , Kamila Chagas Peronni , Wilson Araújo da Silva Junior , Cristiano Gallina Moreira , Juliana Pfrimer Falcão; J. Microbiol. 2021;59(9):861-870. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1082-z

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Salmonella Typhimurium (ST313) has caused an epidemic of invasive disease in sub-Saharan Africa and has been recently identified in Brazil. As the virulence of this ST is poorly understood, the present study aimed to (i) perform the RNAseq in vitro of S. Typhimurium STm30 (ST313) grown in Luria-Bertani medium at 37°C; (ii) compare it with the RNAseq of the S. Typhimurium SL1344 (ST19) and S. Typhimurium STm11 (ST19) strains under the same growing conditions; and (iii) examine the colonization capacity and expression of virulence genes and cytokines in murine colon. The STm30 (ST313) strain exhibited stronger virulence and was associated with a more inflammatory profile than the strains SL1344 (ST19) and STm11 (ST19), as demonstrated by transcriptome and in vivo assay. The expression levels of the hilA, sopD2, pipB, and ssaS virulence genes, other Salmonella pathogenicity islands SPI-1 and SPI-2 genes or effectors, and genes of the cytokines IL-1β, IFN-γ, TNF-α, IL-6, IL-17, IL-22, and IL-12 were increased during ST313 infection in C57BL/6J mice. In conclusion, S. Typhimurium STm30 (ST313) isolated from human feces in Brazil express higher levels of pathogenesis- related genes at 37°C and has stronger colonization and invasion capacity in murine colon due to its high expression levels of virulence genes, when compared with the S. Typhimurium SL1344 (ST19) and STm11 (ST19) strains. STm30 (ST313) also induces stronger expression of pro-inflammatory cytokines in this organ, suggesting that it causes more extensive tissue damage.

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Mina Rahiminejad, Maryam Montaseri, Mohammad Hashem Yousefi, Saeed Nazifi, Jeroen Wagemans, Saeid Hosseinzadeh
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Isabela Mancini Martins, Amanda Aparecida Seribelli, Tamara R. Machado Ribeiro, Patrick da Silva, Bruna Cardinali Lustri, Rodrigo T. Hernandes, Juliana Pfrimer Falcão, Cristiano Gallina Moreira
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Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi: Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2021;59(5):460-466. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-0513-1

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To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase- positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.

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In-silico study of molecular adaptations in halophilic Cas9
Anisha Debnath, Aveepsa Sengupta, Sujata Rudrapal, Ashutosh Kumar, Mamta Rani
Letters in Applied Microbiology.2025;[Epub] CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Role of melatonin in murine “restraint stress”-induced dysfunction of colonic microbiota: Rutao Lin , Zixu Wang , Jing Cao , Ting Gao , Yulan Dong , Yaoxing Chen; J. Microbiol. 2021;59(5):500-512. Published online February 25, 2021; DOI: https://doi.org/10.1007/s12275-021-0305-7

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Intestinal diseases caused by physiological stress have become a severe public health threat worldwide. Disturbances in the gut microbiota-host relationship have been associated with irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory and antioxidant effects. The objective of this study was to investigate the mechanisms by which MT-mediated protection mitigated stress-induced intestinal microbiota dysbiosis and inflammation. We successfully established a murine restraint stress model with and without MT supplementation. Mice subjected to restraint stress had significantly elevated corticosterone (CORT) levels, decreased MT levels in their plasma, elevated colonic ROS levels and increased bacterial abundance, including Bacteroides and Tyzzerella, in their colon tract, which led to elevated expression of Toll-like receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation with 20 mg/kg MT reversed the elevation of the plasma CORT levels, downregulated the colon ROS levels and inhibited the changes in the intestinal microbiota induced by restraint stress. These effects, in turn, inhibited the activities of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory reaction induced by restraint stress. Our results suggested that MT may mitigate “restraint stress”-induced colonic microbiota dysbiosis and intestinal inflammation by inhibiting the activation of the NF-κB pathway.

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Monthly distribution of ammonia-oxidizing microbes in a tropical bay: Tie-Qiang Mao , Yan-Qun Li , Hong-Po Dong , Wen-Na Yang , Li-Jun Hou; J. Microbiol. 2021;59(1):10-19. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0287-5

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Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing
methods
to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17– 20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17–20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.

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Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis: Ozan Ertekin , Meltem Kutnu , Aslı Aras Ta&# , Mustafa Demir , Ayten Yazgan Karata&# , Gülay Özcengiz; J. Microbiol. 2020;58(4):297-313. Published online January 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9064-0

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Bacilysin, as the simplest peptide antibiotic made up of only L-alanine and L-anticapsin, is produced and excreted by Bacillus subtilis under the control of quorum sensing. We analyzed bacilysin-nonproducing strain OGU1 which was obtained by bacA-targeted pMutin T3 insertion into the parental strain genome resulting in a genomic organization (bacA􍿁::lacZ::erm::bacABCDEF) to form an IPTG-inducible bac operon. Although IPTG induction provided 3- to 5-fold increment in the transcription of bac operon genes, no bacilysin activity was detectable in bioassays and inability of the OGU1 to form bacilysin was confirmed by UPLC-mass spectrometry analysis. Phenotypic analyses revealed the deficiencies in OGU1 with respect to colony pigmentation, spore coat proteins, spore resistance and germination, which could be rescued by external addition of bacilysin concentrate into its cultures. 2DE MALDI-TOF/MS and nanoLC-MS/MS were used as complementary approaches to compare cytosolic proteomes of OGU1. 2-DE identified 159 differentially expressed proteins corresponding to 121 distinct ORFs. In nanoLCMS/ MS, 76 proteins were differentially expressed in OGU1. Quantitative transcript analyses of selected genes validated the proteomic findings. Overall, the results pointed to the impact of bacilysin on expression of certain proteins of sporulation and morphogenesis; the members of mother cell compartment- specific σE and σK regulons in particular, quorum sensing and two component-global regulatory systems, peptide transport, stress response as well as CodY- and ScoCregulated proteins.

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Exploring Bacillus velezensis in a biomedical context: a systematic review
Eduarda Guimarães Sousa, Gabriela Munis Campos, Ludmila Silva Quaresma, Thaís Fernandes Mendonça Mota, Nédia de Castilhos Ghisi, Gabriel Camargos Gomes, Rhayane Cristina Viegas Santos, Beatriz Gamarano Rocha de Souza, Éric Guédon, Siomar de Castro Soares,
Academia Molecular Biology and Genomics.2025;[Epub] CrossRef
The direct regulatory effects of Bacilysin on the cellular physiology of Bacillus subtilis
Büşra Öztürk Baykal, Hadeel Waleed Abdulmalek AlJirjees, Can Holyavkin, Ayten Yazgan-Karataş
Annals of Microbiology.2025;[Epub] CrossRef
Biocontrol Ability of Strain Bacillus amyloliquefaciens SQ-2 against Table Grape Rot Caused by Aspergillus tubingensis
Suran Li, Shuangshuang Dai, Lei Huang, Yumeng Cui, Ming Ying
Journal of Agricultural and Food Chemistry.2024; 72(44): 24374. CrossRef
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Xin Zhao, Yang Zhai, Lin Wei, Fei Xia, Yuanru Yang, Yongjian Yi, Hongying Wang, Caisheng Qiu, Feng Wang, Liangbin Zeng
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Signatures of kin selection in a natural population of the bacteria Bacillus subtilis
Laurence J Belcher, Anna E Dewar, Chunhui Hao, Melanie Ghoul, Stuart A West
Evolution Letters.2023; 7(5): 315. CrossRef
Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis
Meltem Kutnu, Elif Tekin İşlerel, Nurcan Tunçbağ, Gülay Özcengiz
Integrative Biology.2022; 14(5): 99. CrossRef
Probiotic effects of the Bacillus velezensis GY65 strain in the mandarin fish, Siniperca chuatsi
Jiachuan Wang, Defeng Zhang, Yajun Wang, Zhijun Liu, Lijuan Liu, Cunbin Shi
Aquaculture Reports.2021; 21: 100902. CrossRef
Bacilysin within the Bacillus subtilis group: gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens
Catherine Nannan, Huong Quynh Vu, Annika Gillis, Simon Caulier, Thuy Thanh Thi Nguyen, Jacques Mahillon
Journal of Biotechnology.2021; 327: 28. CrossRef
Impact of spatial proximity on territoriality among human skin bacteria
Jhonatan A. Hernandez-Valdes, Lu Zhou, Marcel P. de Vries, Oscar P. Kuipers
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Evolution of a major bovine mastitic genotype (rpoB sequence type 10-2) of Staphylococcus aureus in cows: Dae-Sung Ko , Danil Kim , Eun-Kyung Kim , Jae-Hong Kim , Hyuk-Joon Kwon; J. Microbiol. 2019;57(7):587-596. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8699-1

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Staphylococcus aureus is the major pathogen leading to bovine mastitis globally while livestock-associated methicillin resistant S. aureus (LA-MRSA) has become a potential threat to public health. MRSA from bovine mastitis is not common but a methicillin susceptible S. aureus (MSSA) genotype, rpoB sequence type (RST)10-2 (RST10-2), is prevalent in Korea. To date, many genomic sequences from S. aureus have been elucidated, but the complete genome sequences of RST10-2 MSSA from bovine mastitis has never been reported. In this study, we determined the complete genome sequence of two RST10-2 MSSA that differ from each other in staphylococcal protein A and molecular prophage types [PMB64-1 (t2489/ mPPT0) and PMB81-4 (t127/mPPT1-2-3)] and conducted a comparative genomics study. The genomic sequences of PMB64-1 and PMB81-4 were more homologous to the representative human RST10-2 strains (MSSA476, MW2 etc.) compared to other RSTs. Most of them shared five common pseudogenes, along with high amino acid identity of four variable virulence genes that were identified in this study. However, PMB64-1 and PMB81-4 acquired different strainspecific pseudogenes and mobile genetic elements than the human strains. The unique pseudogene profile and high identity of the virulence genes were verified in RST10-2 field strains from bovine mastitis. Thus, bovine mastitic RST10-2 MSSA may have an evolutionary relationship with the human RST10- 2 community-associated (CA) MSSA and CA-MRSA strains but may have adapted to cows.

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International Journal of Molecular Sciences.2024; 25(4): 2430. CrossRef
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Eun-Jin Ha, Seung-Min Hong, Seung-Ji Kim, Sun-Min Ahn, Ho-Won Kim, Kang-Seuk Choi, Hyuk-Joon Kwon
Antibiotics.2023; 12(12): 1714. CrossRef
Genetic characterization of Staphylococcus aureus isolated from Norway rats in Boston, Massachusetts
Gracen R. Gerbig, Helen Piontkivska, Tara C. Smith, Ruairi White, Jean Mukherjee, Hayley Benson, Marieke Rosenbaum, Jessica H. Leibler
Veterinary Medicine and Science.2023; 9(1): 272. CrossRef
Rapid Screening and Comparison of Chimeric Lysins for Antibacterial Activity against Staphylococcus aureus Strains
Jin-Mi Park, Dae-Sung Ko, Hee-Soo Kim, Nam-Hyung Kim, Eun-Kyoung Kim, Young-Hye Roh, Danil Kim, Jae-Hong Kim, Kang-Seuk Choi, Hyuk-Joon Kwon
Antibiotics.2023; 12(4): 667. CrossRef
Comparative genomics of bovine mastitis-origin Staphylococcus aureus strains classified into prevalent human genotypes
Dae-Sung Ko, Nam-Hyung Kim, Eun-Kyung Kim, Eun-Jin Ha, Young-Hye Ro, Danil Kim, Kang-Seuk Choi, Hyuk-Joon Kwon
Research in Veterinary Science.2021; 139: 67. CrossRef

Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Aeromicrobium endophyticum sp. nov., an endophytic actinobacterium isolated from reed (Phragmites australis): Fei-Na Li , Shui-Lin Liao , Shao-Wei Liu , Tao Jin , Cheng-Hang Sun; J. Microbiol. 2019;57(9):725-731. Published online May 23, 2019; DOI: https://doi.org/10.1007/s12275-019-8705-7

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A Gram-staining-positive, motile and short-rod-shaped actinobacterium designated 9W16Y-2T was isolated from surface- sterilized leaves of reed (Phragmites australis) collected from Taklamakan Desert in Xinjiang Uygur Autonomous Region, China. Colonies were pale greenish yellow, circular, smooth, and convex. The 16S rRNA gene sequence of strain 9W16Y-2T exhibited highest sequence similarities with Aeromicrobium camelliae CGMCC 1.12942T (99.0%) and Aeromicrobium erythreum NRRL B-3381T (97.2%). Phylogenetic analyses based on 16S rRNA gene sequences and single-copy phylogenetic marker genes (pMGs) showed that strain 9W16Y- 2T belonged to the genus Aeromicrobium and formed a monophyletic clade with Aeromicrobium camelliae CGMCC 1.12942T. Furthermore, average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) clearly separated strain 9W16Y-2T from the other species of the genus Aeromicrobium with values below the thresholds for species delineation. The G+C content of the genomic DNA is 68.9 mol%. The diagnostic diamino acid of the cell-wall peptidoglycan was LLdiaminopimelic acid. The predominant menaquinone was MK-9(H4). The major fatty acids (> 10% of the total fatty acids) were C18:0 10-methyl (TBSA) (28.2%), C16:0 (21.0%), C16:0 2-OH (20.8%) and C18:1 ω9c (12.8%). The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenic, phenotypic and chemotaxonomic features, strain 9W16Y-2T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium endophyticum sp. nov. is proposed. The type strain is 9W16Y-2T (= CGMCC 1.13876T = JCM 33141T).

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Solibacillus palustris sp. nov., isolated from wetland soil of ecology park
Jung-Hun Jo, Soon-Youl Lee, Moon-Soo Rhee, Kang-Hyun Lee, Se-Yoon Chun, Wan-Taek Im
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Ruegeria spongiae sp. nov., isolated from Callyspongia elongata
Seung-Min Han, Jin-Sook Park
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Ramlibacter paludis sp. nov., isolated from wetland
Ji-Eun Lim, Jung-Hun Jo, Wan-Taek Im
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Paludibacterium denitrificans sp. nov., a Novel Denitrifying Bacterium Isolated from Activated Sludge
Ji Eun Lee, Gyu-Min Choi, Yong-Jae Lee, Sang-Mi Lee, Soon Youl Lee, Wan-Taek Im
Current Microbiology.2022;[Epub] CrossRef
Histidinibacterium aquaticum sp. nov., Isolated from Salt-Field Sea Water
Kyu-Hang Lee, Jin-Sook Park
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Renewed interests in the discovery of bioactive actinomycete metabolites driven by emerging technologies
Jenifer Ossai, Behnam Khatabi, S. Eric Nybo, Madan K. Kharel
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Tae-Gi Shin, Jin-Sook Park
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Junqin Li, Wenjing Lei, Jing Yang, Shan Lu, Dong Jin, Xin-He Lai, Sihui Zhang, Yanpeng Cheng, Fei Mi, Yuyuan Huang, Ji Pu, Kui Dong, Zhi Tian, Xiaomin Wu, Ying Huang, Suping Wang, Jianguo Xu
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Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation: Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha; J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8372-0

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The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

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Identification of trehalose as a compatible solute in different species of acidophilic bacteria: Pedro A. Galleguillos , Barry M. Grail , Kevin B. Hallberg , Cecilia S. Demergasso , D. Barrie Johnson; J. Microbiol. 2018;56(10):727-733. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8176-2

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The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response or adaptation to osmotic stress. In order to investigate the response to osmotic stress in these microorganisms, six species of acidophilic bacteria were grown at elevated osmotic strength in liquid media, and the compatible solutes synthesised were identified using ion chromatography and MALDI-TOF mass spectrometry. Trehalose was identified as one of, or the sole, compatible solute in all species and strains, apart from Acidithiobacillus thiooxidans where glucose and proline levels increased at elevated osmotic potentials. Several other potential compatible solutes were tentatively identified by MALDITOF analysis. The same compatible solutes were produced by these bacteria regardless of the salt used to produce the osmotic stress. The results correlate with data from sequenced genomes which confirm that many chemolithotrophic and heterotrophic acidophiles possess genes for trehalose synthesis. This is the first report to identify and quantify compatible solutes in acidophilic bacteria that have important roles in biomining technologies.

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Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism: Man-Young Jung , So-Jeong Kim , Jong-Geol Kim , Heeji Hong , Joo-Han Gwak , Soo-Je Park , Yang-Hoon Kim , Sung-Keun Rhee; J. Microbiol. 2018;56(5):365-371. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7451-6

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Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H+ and Na+ ions, respectively. Strain IRF9 harbored two different types of ATPases (Na+-dependent F-type ATPase and H+- dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions.

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Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China
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Proteome analysis reveals global response to deletion of mrflbA in Monascus ruber: Qingqing Yan , Zhouwei Zhang , Yishan Yang , Fusheng Chen , Yanchun Shao; J. Microbiol. 2018;56(4):255-263. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7425-8

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Monascus spp. are commonly used for a wide variety of applications in the food and pharmaceutical industries. In previous studies, the knock-out of mrflbA (a putative regulator of the G protein α subunit) in M. ruber led to autolysis of the mycelia, decreased pigmentation and lowered mycotoxin production. Therefore, we aimed to obtain a comprehensive overview of the underlying mechanism of mrflbA deletion at the proteome level. A two-dimensional gel electrophoresis analysis of mycelial proteins indicated that the abundance of 178 proteins was altered in the ΔmrflbA strain, 33 of which were identified with high confidence. The identified proteins are involved in a range of activities, including carbohydrate and amino acid metabolism, hyphal development and the oxidative stress response, protein modification, and the regulation of cell signaling. Consistent with these findings, the activity of antioxidative enzymes and chitinase was elevated in the supernatant of the ΔmrflbA strain. Furthermore, deletion of mrflbA resulted in the transcriptional reduction of secondary metabolites (pigment and mycotoxin). In short, the mutant phenotypes induced by the deletion of mrflbA were consistent with changes in the expression levels of associated proteins, providing direct evidence of the regulatory functions mediated by mrflbA in M. ruber.

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Histone deacetylase MrHos3 negatively regulates the production of citrinin and pigments in Monascus ruber
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Effects of diet type, developmental stage, and gut compartment in the gut bacterial communities of two Cerambycidae species (Coleoptera): Jeong Myeong Kim , Min-Young Choi , Jae-Woo Kim , Shin Ae Lee , Jae-Hyung Ahn , Jaekyeong Song , Seong-Hyun Kim , Hang-Yeon Weon; J. Microbiol. 2017;55(1):21-30. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6561-x

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The gut bacterial community of wood-feeding beetles has been examined for its role on plant digestion and biocontrol
method
development. Monochamus alternatus and Psacothea hilaris, both belonging to the subfamily Lamiinae, are woodfeeding beetles found in eastern Asia and Europe and generally considered as destructive pests for pine and mulberry trees, respectively. However, limited reports exist on the gut bacterial communities in these species. Here, we characterized gut bacterial community compositions in larva and imago of each insect species reared with host tree logs and artificial diets as food sources. High-throughput 454 pyrosequencing of bacterial 16S rRNA gene revealed 225 operational taxonomic units (OTUs) based on a 97% sequences similarity cutoff from 138,279 sequence reads, the majority of which were derived from Proteobacteria (48.2%), Firmicutes (45.5%), and Actinobacteria (5.2%). The OTU network analysis revealed 7 modules with densely connected OTUs in specific gut samples, in which the distributions of Lactococcus-, Kluyvera-, Serratia-, and Enterococcus-related OTUs were distinct between diet types or developmental stages of the host insects. The gut bacterial communities were separated on a detrended correspondence analysis (DCA) plot and by c-means fuzzy clustering analysis, according to diet type. The results from this study suggest that diet was the main determinant for gut bacterial community composition in the two beetles.

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Biosynthesis and uptake of glycine betaine as cold-stress response to low temperature in fish pathogen Vibrio anguillarum: Yue Ma , Qiyao Wang , Xiating Gao , Yuanxing Zhang; J. Microbiol. 2017;55(1):44-55. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6370-2

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Fish pathogen Vibrio anguillarum, a mesophile bacterium, is usually found in estuarine and marine coastal ecosystems worldwide that pose a constant stress to local organism by its fluctuation in salinity as well as notable temperature change. Though V. anguillarum is able to proliferate while maintain its pathogenicity under low temperature (5–18°C), so far, coldadaption molecular mechanism of the bacteria is unknown. In this study, V. anguillarum was found possessing a putative glycine betaine synthesis system, which is encoded by betABI and synthesizes glycine betaine from its precursor choline. Furthermore, significant up-regulation of the bet gene at the transcriptional level was noted in log phase in response to cold-stress. Moreover, the accumulation of betaine glycine was only found appearing at low growth temperatures, suggesting that response regulation of both synthesis system and transporter system are cold-dependent. Furthermore, in-frame deletion mutation in the two putative ABC transporters and three putative BCCT family transporters associated with glycine betaine uptake could not block cellular accumulation of betaine glycine in V. anguillarum under coldstress, suggesting the redundant feature in V. anguillarum betaine transporter system. These findings confirmed that glycine betaine serves as an effective cold stress protectant and highlighted an underappreciated facet of the acclimatization of V. anguillarum to cold environments.

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Surface Display Expression of Bacillus licheniformis Lipase in Escherichia coli Using Lpp’OmpA Chimera: Jae-Hyung Jo , Chan-Wook Han , Seung-Hwan Kim , Hyuk-Jin Kwon , Hyune-Hwan Lee; J. Microbiol. 2014;52(10):856-862. Published online August 27, 2014; DOI: https://doi.org/10.1007/s12275-014-4217-7

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The lipase from Bacillus licheniformis ATCC14580 was displayed on the cell surface of Escherichia coli using Lpp’OmpA as the anchoring protein. The expressed Lpp’OmpA-lipase fusion protein has a molecular weight of approximately 35 kDa, which was confirmed by SDS-PAGE and western blot analysis. The Lpp’OmpA-lipase fusion protein was located on the cell surface, as determined by immunofluorescence confocal microscopy and flow cytometry. The enzyme activity of the surface-displayed lipase showed clear halo around the colony. The cell surface-displayed lipase showed the highest activity of 248.12 ± 9.42 U/g (lyophilized cell) at the optimal temperature of 37°C and pH 8.0. The enzyme exhibited the highest activity toward the substrate p-nitrophenyl caprylate (C8). These results suggest that E. coli, which displayed the lipase on its surface, could be used as a whole cell biocatalyst.

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Identification and Characterization of Ectoine Biosynthesis Genes and Heterologous Expression of the ectABC Gene Cluster from Halomonas sp. QHL1, a Moderately Halophilic Bacterium Isolated from Qinghai Lake: Derui Zhu , Jian Liu , Rui Han , Guoping Shen , Qifu Long , Xiaoxing Wei , Deli Liu; J. Microbiol. 2014;52(2):139-147. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3389-5

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The moderately halophilic bacterium Halomonas sp. QHL1 was identified as a member of the genus Halomonas by 16S rRNA gene sequencing. HPLC analysis showed that strain QHL1 synthesizes ectoine in its cytoplasm. The genes involved in the ectoine biosynthesis pathway were identified on the chromosome in the order ectABC. Subsequently, the ectB gene from this strain was amplified by PCR, and the entire ectABC gene cluster (3,580 bp) was cloned using genome walking. Analysis showed that the ectA (579 bp), ectB (1269 bp), and ectC (390 bp) genes were organized in a single transcriptional unit and were predicted to encode three peptides of 21.2 kDa, 46.4 kDa, and 14.7 kDa, respectively. Two putative promoters, a δ70-dependent promoter and a δ38-controlled promoter, as well as several conserved motifs with unknown function were identified. Individual ectA, ectB, and ectC genes, and the entire ectABC gene cluster were inserted into the expression plasmid pET-28a(+) to generate the recombinant plasmids pET-28a(+)-ectA, pET-28a(+)-ectB, pET-28a(+)-ectC and pET-28a(+)-ectABC, respectively. Heterologous expression of these proteins in Escherichia coli BL21 (DE3) was confirmed by SDS-PAGE. The recombinant E. coli strain BL21 (pET-28a (+)-ectABC) displayed a higher salt tolerance than native E. coli cells but produced far less ectoine than the wild-type QHL1 strain.

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Parallel Gene Loss and Acquisition Among Strains of Different Brucella Species and Biovars: Zhijun Zhong , Yufei Wang , Jie Xu , Yanfen Chen , Yuehua Ke , Xiaoyan Zhou , Xitong Yuan , Dongsheng Zhou , Yi Yang , Ruifu Yang , Guangneng Peng , Hai Jiang , Jing Yuan , Hongbin Song , Buyun Cui , Liuyu Huang , Zeliang Chen; J. Microbiol. 2012;50(4):567-574. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2022-8

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The genus Brucella is divided into six species; of these, B. melitensis and B. abortus are pathogenic to humans, and B. ovis and B. neotomae are nonpathogenic to humans. The definition of gene loss and acquisition is essential for understanding Brucella’s ecology, evolutionary history, and host relationships. A DNA microarray containing unique genes of B. melitensis Type strain 16MT and B. abortus 9-941 was constructed and used to determine the gene contents of the representative strains of Brucella. Phylogenetic relationships were inferred from sequences of housekeeping genes. Gene loss and acquisition of different Brucella species were inferred. A total of 214 genes were found to be differentially distributed, and 173 of them were clustered into 15 genomic islands (GIs). Evidence of horizontal gene transfer was observed for 10 GIs. Phylogenetic analysis indicated that the 19 strains formed five clades, and some of the GIs had been lost or acquired independently among the different lineages. The derivation of Brucella lineages is concomitant with the parallel loss or acquisition of GIs, indicating a complex interaction between various Brucella species and hosts.

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Comparative Genomic Analysis of Bacteriophage EP23 Infecting Shigella sonnei and Escherichia coli: Ho-Won Chang , Kyoung-Ho Kim; J. Microbiol. 2011;49(6):927-934. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1577-0

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Abstract PDF: Bacteriophage EP23 that infects Escherichia coli and Shigella sonnei was isolated and characterized. The bacteriophage morphology was similar to members of the family Siphoviridae. The 44,077 bp genome was fully sequenced using 454 pyrosequencing. Comparative genomic and phylogenetic analyses showed that EP23 was most closely related to phage SO-1, which infects Sodalis glossinidius and phage SSL-2009a, which infects engineered E. coli. Genomic comparison indicated that EP23 and SO-1 were very similar with each other in terms of gene order and amino acid similarity, even though their hosts were separated in the level of genus. EP23 and SSL-2009a displayed high amino acid similarity between their genes, but there was evidence of several recombination events in SSL-2009a. The results of the comparative genomic analyses further the understanding of the evolution and relationship between EP23 and its bacteriophage relatives.

Comparative Analysis of the Genomes of Bombyx mandarina and Bombyx mori Nucleopolyhedroviruses: Yi-Peng Xu , Zheng-Pei Ye , Chang-Ying Niu , Yan-Yuan Bao , Wen-Bing Wang , Wei-De Shen , Chuan-Xi Zhang; J. Microbiol. 2010;48(1):102-110. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0197-4

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The Bombyx mandarina nucleopolyhedrovirus (BomaNPV) S1 strain can infect the silkworm, Bombyx mori, but is significantly less virulent than B. mori nucleopolyhedrovirus (BmNPV) T3 strain. The complete nucleotide sequence of the S1 strain of BomaNPV was determined and compared with the BmNPV T3 strain. The circular, double stranded DNA genome of the S1 strain was 126,770 nucleotides long (GenBank accession no. FJ882854), with a G+C content of 40.23%. The genome contained 133 potential ORFs. Most of the putative proteins were more than 96% identical to homologs in the BmNPV T3 strain, except for bro-a, lef-12, bro-c, and bro-d. Compared with the BmNPV T3 strain, however, this genome did not encode the bro-b and bro-e genes. In addition, hr1 lacked two repeat units, while hr2L, hr2R, hr3, hr4L, hr4R, and hr5 were similar to the corresponding hrs in the T3 strain. The sequence strongly suggested that BomaNPV and BmNPV are variants with each other, and supported the idea that baculovirus strain heterogeneity may often be caused by variation in the hrs and bro genes.

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Distribution and genetic diversity of Bombyx mori nucleopolyhedrovirus in mass-reared silkworms in Thailand
Jörg T. Wennmann, Sergei Senger, Birgit Ruoff, Johannes A. Jehle, Siripuk Suraporn
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Genomic Sequence Analysis of Bombyx mori Nucleopolyhedrovirus Isolated from Yunnan Sericulture Region, China
Yonghong Zhang, Feng Zhu, Yulan Shao, Zhenguo Su, Jing Ni, Xingrong Bai
Indian Journal of Microbiology.2021; 61(3): 383. CrossRef
Bombyx mori nucleopolyhedrovirus ptp and egt genes are dispensable for triggering enhanced locomotory activity and climbing behavior in Bombyx mandarina larvae
Ryuhei Kokusho, Susumu Katsuma
Journal of Invertebrate Pathology.2021; 183: 107604. CrossRef
Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain
Shota Fujimoto, Munetaka Kawamoto, Keisuke Shoji, Yutaka Suzuki, Susumu Katsuma, Masashi Iwanaga
Virus Genes.2020; 56(2): 249. CrossRef
Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori
Tieshan Feng, Ping Lin, Jiao Gong, Dong Cheng, Xi Yang, Quan Zhang, Tingcai Cheng
International Journal of Genomics.2019; 2019: 1. CrossRef
Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences
Jörg T. Wennmann, Jens Keilwagen, Johannes A. Jehle
Journal of General Virology.2018; 99(9): 1307. CrossRef
Bombyx mori nucleopolyhedrovirus actin rearrangement-inducing factor 1 enhances systemic infection in B. mori larvae
Susumu Katsuma, Toru Shimada, Ryuhei Kokusho, Sumio Sugano, Yutaka Suzuki, Yasue Koyano, Munetaka Kawamoto
Journal of General Virology.2015; 96(7): 1938. CrossRef
Complete genome sequence of the first non-Asian isolate of Bombyx mori nucleopolyhedrovirus
Daniel Mendes Pereira Ardisson-Araújo, Fernando Lucas Melo, Miguel de Souza Andrade, Rose Meire Costa Brancalhão, Sônia Nair Báo, Bergmann Morais Ribeiro
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Identification of a Conserved Non-Protein-Coding Genomic Element that Plays an Essential Role in Alphabaculovirus Pathogenesis
Irina Kikhno, Carmen San Martin
PLoS ONE.2014; 9(4): e95322. CrossRef
Analysis of the genomic sequence of Philosamia cynthia nucleopolyhedrin virus and comparison with Antheraea pernyinucleopolyhedrin virus
Heying Qian, Yuehua Zhang, Yejun Wu, Pingiang Sun, Shanying Zhu, Xijie Guo, Kun Gao, Anying Xu, Wenbing Wang
BMC Genomics.2013;[Epub] CrossRef
Genomic diversity of Bombyx mori nucleopolyhedrovirus strains
Yi-Peng Xu, Ruo-Lin Cheng, Yu Xi, Chuan-Xi Zhang
Genomics.2013; 102(1): 63. CrossRef
Genome Sequence of a Bombyx mori Nucleopolyhedrovirus Strain with Cubic Occlusion Bodies
Ruo-Lin Cheng, Yi-Peng Xu, Chuan-Xi Zhang
Journal of Virology.2012; 86(18): 10245. CrossRef
Identification of a new Bombyx mori nucleopolyhedrovirus and analysis of its bro gene family
Jing-Bo Zhou, Xing-Qi Li, Wanchai De-Eknamkul, Siripuk Suraporn, Jia-Ping Xu
Virus Genes.2012; 44(3): 539. CrossRef
A baculovirus isolated from wild silkworm encompasses the host ranges of Bombyx mori nucleopolyhedrosis virus and Autographa californica multiple nucleopolyhedrovirus in cultured cells
Yi-Peng Xu, Lin-Zhu Gu, Yi-Han Lou, Ruo-Lin Cheng, Hai-Jun Xu, Wen-Bing Wang, Chuan-Xi Zhang
Journal of General Virology .2012; 93(11): 2480. CrossRef
Genome of a Bombyx mori Nucleopolyhedrovirus Strain Isolated from India
Hai-Wei Fan, Xue-Chao Zhang, Yi-Peng Xu, Xiao-Wen Cheng, Chuan-Xi Zhang
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Complete Sequence, Analysis and Organization of the Orgyia leucostigma Nucleopolyhedrovirus Genome
David K. Thumbi, Robert J. M. Eveleigh, Christopher J. Lucarotti, Renée Lapointe, Robert I. Graham, Lillian Pavlik, Hilary A. M. Lauzon, Basil M. Arif
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Comparative analysis of budded virus infectivity of Bombyx mandarina and B. mori nucleopolyhedroviruses
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Jun-Qing Ge, Guo-Hui Gao, Yi-Peng Xu, Chuan-Xi Zhang
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Baculovirus: Molecular Insights on Their Diversity and Conservation
Solange Ana Belen Miele, Matías Javier Garavaglia, Mariano Nicolás Belaich, Pablo Daniel Ghiringhelli
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Identification of a novel functional nuclear localization signal in the protein encoded by open reading frame 47 of Bombyx mori nucleopolyhedrovirus
Zhong-Jian Guo, Dian-Xuan Wang, Qin Yao, Ke-Ping Chen, Chuan-Xi Zhang
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The Changes of Proteomes Components of Helicobacter pylori in Response to Acid Stress without Urea: Chunhong Shao , Qunye Zhang , Wei Tang , Wei Qu , Yabin Zhou , Yundong Sun , Han Yu , Jihui Jia; J. Microbiol. 2008;46(3):331-337. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-008-0062-x

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Abstract PDF

Acid stress is the most obvious challenge Helicobacter pylori encounters in human stomach. The urease system is the basic process used to maintain periplasmic and cytoplasmic pH near neutrality when H. pylori is exposed to acidic condition. However, since the urea concentration in gastric juice is approximately 1 mM, considered possibly insufficient to ensure the survival of H. pylori, it is postulated that additional mechanisms of pH homeostasis may contribute to the acid adaptation in H. pylori. In order to identify the acid-related proteins other than the urease system we have compared the proteome profiles of H. pylori strain 26695 exposed to different levels of external pH (7.4, 6.0, 5.0, 4.0, 3.0, and 2.0) for 30 min in the absence of urea using 2-DE. Differentially expressed proteins were identified by MALDI-TOF-TOF-MS analysis, which turned out to be 36 different proteins. The functions of these proteins included ammonia production, molecular chaperones, energy metabolism, cell envelope, response regulator and some proteins with unknown function. SOM analysis indicated that H. pylori responds to acid stress through multi-mechanisms involving many proteins, which depend on the levels of acidity the cells encounter.

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Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System
John T. Loh, Miranda V. Shum, Scott D. R. Jossart, Anne M. Campbell, Neha Sawhney, W. Hayes McDonald, Matthew B. Scholz, Mark S. McClain, Mark H. Forsyth, Timothy L. Cover, Victor J. Torres
Infection and Immunity.2021;[Epub] CrossRef
Proteomic analysis of Rhizobium freirei PRF 81T reveals the key role of central metabolic pathways in acid tolerance
Leandro Datola Tullio, Douglas Fabiano Gomes, Luciano Paulino Silva, Mariangela Hungria, Jesiane Stefania da Silva Batista
Applied Soil Ecology.2019; 135: 98. CrossRef
Acid‐regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Elizabeth A. Marcus, George Sachs, David R. Scott
Helicobacter.2018;[Epub] CrossRef
The histone‐like protein HU has a role in gene expression during the acid adaptation response in Helicobacter pylori
Alhejandra Álvarez, Héctor Toledo
Helicobacter.2017;[Epub] CrossRef
Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori
Stephan A. Müller, Sandy R. Pernitzsch, Sven-Bastiaan Haange, Peter Uetz, Martin von Bergen, Cynthia M. Sharma, Stefan Kalkhof
Journal of Proteomics.2015; 126: 34. CrossRef
Characterization of the Arginine Decarboxylase Gene (ORF HP0422, speA) Involved in Acid Tolerance in Helicobacter pylori
Manuel Valenzuela, Aníbal Cáceres, Oscar Almarza, Denisse Bravo, Sarita Soto, Oscar Cerda, Héctor Toledo
Helicobacter.2014; 19(3): 182. CrossRef
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen, Stefan Kalkhof
Journal of Proteomics.2013; 86: 27. CrossRef
Effect of gastric environment on Helicobacter pylori adhesion to a mucoadhesive polymer
Frederico Nogueira, Inês C. Gonçalves, M. Cristina L. Martins
Acta Biomaterialia.2013; 9(2): 5208. CrossRef
Analysis of Aztreonam-Inducing Proteome Changes in Nondividing Filamentous Helicobacter pylori
Chunhong Shao, Yabin Zhou, Yundong Sun, Hongyan Wang, Wei Qu, Han Yu, Chunyan Chen, Jihui Jia
Current Microbiology.2012; 65(1): 108. CrossRef
Identification of S-nitrosylation of proteins of Helicobacter pylori in response to nitric oxide stress
Wei Qu, Yabin Zhou, Yundong Sun, Ming Fang, Han Yu, Wenjuan Li, Zhifang Liu, Jiping Zeng, Chunyan Chen, Chengjiang Gao, Jihui Jia
The Journal of Microbiology.2011; 49(2): 251. CrossRef
Virulence factor cytotoxin-associated gene A in Helicobacter pylori is downregulated by interferon-γin vitro
Yinghui Zhao, Yabin Zhou, Yundong Sun, Ailian Yu, Han Yu, Wenjuan Li, Zhifang Liu, Jiping Zeng, Xi Li, Chunyan Chen, Jihui Jia
FEMS Immunology & Medical Microbiology.2011; 61(1): 76. CrossRef
Functional and structural aspects of helicobacter pylori acidic stress response factors
Giuseppe Zanotti, Laura Cendron
IUBMB Life.2010; 62(10): 715. CrossRef
Helicobacter pylori proteins response to nitric oxide stress
Wei Qu, Yabin Zhou, Chunhong Shao, Yundong Sun, Qunye Zhang, Chunyan Chen, Jihui Jia
The Journal of Microbiology.2009; 47(4): 486. CrossRef

Journal Article

Growth and Physiological Properties of Wild Type and Mutants of Halomonas subglaciescola DH-1 in Saline Environment: Hye Jeong Ryu , Yoo Jung Jeong , Doo Hyun Park; J. Microbiol. 2004;42(3):174-180.; DOI: https://doi.org/2093 [pii]

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Abstract PDF: A halophilic bacterium was isolated from fermented seafood. The 16S rDNA sequence identity between the isolate and Halomonas subglaciescola AJ306801 was above 95%. The isolate that did not grow in the condition without NaCl or in the condition with other sodium (Na^+) or chloride ions (Cl^-) instead of NaCl was named H. subglaciescola DH-1. Two mutants capable of growing without NaCl were obtained by random mutagenesis, of which their total soluble protein profiles were compared with those of the wild type by two-dimensional electrophoresis. The external compatible solutes (betaine and choline) and cell extract of the wild type did not function as osmoprotectants, and these parameters within the mutants did not enhance their growth in the saline environment. In the proton translocation test, rapid acidification of the reactant was not detected for the wild type, but it was detected for the mutant in the condition without NaCl. From these results, we derived the hypothesis that NaCl may be absolutely required for the energy metabolism of H. subglaciescola DH-1 but not for its osmoregulation, and the mutants may have another modified proton translocation system that is independent of NaCl, except for those mutants with an NaCl-dependent system.

Review

The Use of the Rare UUA Codon to Define "Expression Space" for Genes Involved in Secondary Metabolism, Development and Environmental Adaptation in Streptomyces: Keith F. Chater , Govind Chandra; J. Microbiol. 2008;46(1):1-11.; DOI: https://doi.org/10.1007/s12275-007-0233-1

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In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2~3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor-it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.

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Nguyen Huy Thuan, Dipesh Dhakal, Anaya Raj Pokhrel, Luan Luong Chu, Thi Thuy Van Pham, Anil Shrestha, Jae Kyung Sohng
Applied Microbiology and Biotechnology.2018; 102(10): 4355. CrossRef
Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters
Dimitris Kallifidas, Guangde Jiang, Yousong Ding, Hendrik Luesch
Microbial Cell Factories.2018;[Epub] CrossRef
In conditions of over-expression, WblI, a WhiB-like transcriptional regulator, has a positive impact on the weak antibiotic production of Streptomyces lividans TK24
Lan Yan, Qizhong Zhang, Marie-Joelle Virolle, Delin Xu, Dongsheng Zhou
PLOS ONE.2017; 12(3): e0174781. CrossRef
Tracking the Subtle Mutations Driving Host Sensing by the Plant Pathogen Streptomyces scabies
Samuel Jourdan, Isolde M. Francis, Benoit Deflandre, Rosemary Loria, Sébastien Rigali, Karen L. Visick
mSphere.2017;[Epub] CrossRef
Properties of Streptomyces albus J1074 mutant deficient in tRNALeu UAA gene bldA
Oksana Koshla, Maria Lopatniuk, Ihor Rokytskyy, Oleksandr Yushchuk, Yuriy Dacyuk, Victor Fedorenko, Andriy Luzhetskyy, Bohdan Ostash
Archives of Microbiology.2017; 199(8): 1175. CrossRef
Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis
Nestor Zaburannyi, Boyke Bunk, Josef Maier, Jörg Overmann, Rolf Müller, C. Vieille
Applied and Environmental Microbiology.2016; 82(6): 1945. CrossRef
Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation
Barbara Gorgoni, Luca Ciandrini, Matthew R. McFarland, M. Carmen Romano, Ian Stansfield
Nucleic Acids Research.2016; : gkw630. CrossRef
Overexpression of a pathway specific negative regulator enhances production of daunorubicin in bldA deficient Streptomyces peucetius ATCC 27952
Anaya Raj Pokhrel, Amit Kumar Chaudhary, Hue Thi Nguyen, Dipesh Dhakal, Tuoi Thi Le, Anil Shrestha, Kwangkyoung Liou, Jae Kyung Sohng
Microbiological Research.2016; 192: 96. CrossRef
Identification and engineering of regulation-related genes toward improved kasugamycin production
Chenchen Zhu, Qianjin Kang, Linquan Bai, Lin Cheng, Zixin Deng
Applied Microbiology and Biotechnology.2016; 100(4): 1811. CrossRef
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
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Nucleic Acids Research.2016; : gkw530. CrossRef
Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439
Jingxuan He, Briana Van Treeck, Han B. Nguyen, Charles E. Melançon
ACS Synthetic Biology.2016; 5(2): 125. CrossRef
The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5
Qing Yan, Benjamin Philmus, Cedar Hesse, Max Kohen, Jeff H. Chang, Joyce E. Loper
Frontiers in Microbiology.2016;[Epub] CrossRef
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Keith F. Chater
F1000Research.2016; 5: 2795. CrossRef
Changing Biosynthetic Profiles by Expressing bldA in Streptomyces Strains
Arne Gessner, Tanja Heitzler, Songya Zhang, Christine Klaus, Renato Murillo, Hanna Zhao, Stephanie Vanner, David L. Zechel, Andreas Bechthold
ChemBioChem.2015; 16(15): 2244. CrossRef
Genome Mining of Streptomyces sp. Tü 6176: Characterization of the Nataxazole Biosynthesis Pathway
Carolina Cano‐Prieto, Raúl García‐Salcedo, Marina Sánchez‐Hidalgo, Alfredo F. Braña, Hans‐Peter Fiedler, Carmen Méndez, José A. Salas, Carlos Olano
ChemBioChem.2015; 16(10): 1461. CrossRef
Identification of BagI as a positive transcriptional regulator of bagremycin biosynthesis in engineered Streptomyces sp. Tü 4128
Feng Liu, Dakui Xu, Yuchen Zhang, Yunxia Zhu, Jiang Ye, Huizhan Zhang
Microbiological Research.2015; 173: 18. CrossRef
Rifampicin-resistance, rpoB polymorphism and RNA polymerase genetic engineering
Pietro Alifano, Carla Palumbo, Daniela Pasanisi, Adelfia Talà
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Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning
Pavel V. Baranov, John F. Atkins, Martina M. Yordanova
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The Gene bldA, a Regulator of Morphological Differentiation and Antibiotic Production in Streptomyces
Stefanie Hackl, Andreas Bechthold
Archiv der Pharmazie.2015; 348(7): 455. CrossRef
Genetic and Proteomic Analyses of Pupylation in Streptomyces coelicolor
Corey L. Compton, Michael S. Fernandopulle, Rohith T. Nagari, Jason K. Sello, W. W. Metcalf
Journal of Bacteriology.2015; 197(17): 2747. CrossRef
c-di-GMP signalling and the regulation of developmental transitions in streptomycetes
Matthew J. Bush, Natalia Tschowri, Susan Schlimpert, Klas Flärdh, Mark J. Buttner
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Construction and development of a novel expression system of Streptomyces
Chengran Guan, Wenjing Cui, Xiaotian He, Xu Hu, Jun Xu, Guocheng Du, Jian Chen, Zhemin Zhou
Protein Expression and Purification.2015; 113: 17. CrossRef
Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism
Aurélie Guyet, Nadia Benaroudj, Caroline Proux, Myriam Gominet, Jean-Yves Coppée, Philippe Mazodier
BMC Microbiology.2014;[Epub] CrossRef
Thaxtomin A Production and Virulence Are Controlled by Several bld Gene Global Regulators in Streptomyces scabies
Dawn R. D. Bignell, Isolde M. Francis, Joanna K. Fyans, Rosemary Loria
Molecular Plant-Microbe Interactions®.2014; 27(8): 875. CrossRef
Developmental biology ofStreptomycesfrom the perspective of 100 actinobacterial genome sequences
Govind Chandra, Keith F. Chater
FEMS Microbiology Reviews.2014; 38(3): 345. CrossRef
The gamma-butyrolactone receptors BulR1 and BulR2 of Streptomyces tsukubaensis: tacrolimus (FK506) and butyrolactone synthetases production control
Zahra Salehi-Najafabadi, Carlos Barreiro, Antonio Rodríguez-García, Anthony Cruz, Gustavo E. López, Juan F. Martín
Applied Microbiology and Biotechnology.2014; 98(11): 4919. CrossRef
Gene networks regulating secondary metabolism in actinomycetes: Pleiotropic regulators
M. V. Rabyk, B. O. Ostash, V. O. Fedorenko
Cytology and Genetics.2014; 48(1): 55. CrossRef
Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei
M. Moutiez, J. Seguin, M. Fonvielle, P. Belin, I. B. Jacques, E. Favry, M. Arthur, M. Gondry
Nucleic Acids Research.2014; 42(11): 7247. CrossRef
Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?
Yuriy Rebets, Elke Brötz, Bogdan Tokovenko, Andriy Luzhetskyy
Journal of Industrial Microbiology and Biotechnology.2014; 41(2): 387. CrossRef
Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA
Barbara Gorgoni, Elizabeth Marshall, Matthew R. McFarland, M. Carmen Romano, Ian Stansfield
Biochemical Society Transactions.2014; 42(1): 160. CrossRef
Collismycin A biosynthesis in Streptomyces sp. CS40 is regulated by iron levels through two pathway-specific regulators
Natalia M. Vior, Carlos Olano, Ignacio García, Carmen Méndez, José A. Salas
Microbiology.2014; 160(3): 467. CrossRef
Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae
Matthew J. Bush, Maureen J. Bibb, Govind Chandra, Kim C. Findlay, Mark J. Buttner, Yves V. Brun
mBio.2013;[Epub] CrossRef
Pleiotropic regulatory genes bldA , adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin
Roman Makitrynskyy, Bohdan Ostash, Olga Tsypik, Yuriy Rebets, Emma Doud, Timothy Meredith, Andriy Luzhetskyy, Andreas Bechthold, Suzanne Walker, Victor Fedorenko
Open Biology.2013; 3(10): 130121. CrossRef
A Microbial Metagenome (Leucobactersp.) inCaenorhabditisWhole Genome Sequences
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Bioinformatics and Biology Insights.2013; 7: BBI.S11064. CrossRef
Molecular Regulation of Antibiotic Biosynthesis in Streptomyces
Gang Liu, Keith F. Chater, Govind Chandra, Guoqing Niu, Huarong Tan
Microbiology and Molecular Biology Reviews.2013; 77(1): 112. CrossRef
Towards a new science of secondary metabolism
Arryn Craney, Salman Ahmed, Justin Nodwell
The Journal of Antibiotics.2013; 66(7): 387. CrossRef
Recent advances in the biosynthesis of penicillins, cephalosporins and clavams and its regulation
Gulay Ozcengiz, Arnold L. Demain
Biotechnology Advances.2013; 31(2): 287. CrossRef
5S Clavam Biosynthesis Is Controlled by an Atypical Two-Component Regulatory System in Streptomyces clavuligerus
Thomas Kwong, Nathan J. Zelyas, Hui Cai, Kapil Tahlan, Annie Wong, Susan E. Jensen
Antimicrobial Agents and Chemotherapy.2012; 56(9): 4845. CrossRef
Interspecies modulation of bacterial development through iron competition and siderophore piracy
Matthew F. Traxler, Mohammad R. Seyedsayamdost, Jon Clardy, Roberto Kolter
Molecular Microbiology.2012; 86(3): 628. CrossRef
FK506 biosynthesis is regulated by two positive regulatory elements in Streptomyces tsukubaensis
Dušan Goranovič, Marko Blažič, Vasilka Magdevska, Jaka Horvat, Enej Kuščer, Tomaž Polak, Javier Santos-Aberturas, Miriam Martínez-Castro, Carlos Barreiro, Peter Mrak, Gregor Kopitar, Gregor Kosec, Štefan Fujs, Juan F Martín, Hrvoje Petković
BMC Microbiology.2012;[Epub] CrossRef
Evaluation of Streptomyces coelicolor A3(2) as a heterologous expression host for the cyanobacterial protein kinase C activator lyngbyatoxin A
Adam C. Jones, Sabine Ottilie, Alessandra S. Eustáquio, Daniel J. Edwards, Lena Gerwick, Bradley S. Moore, William H. Gerwick
The FEBS Journal.2012; 279(7): 1243. CrossRef
Signals and regulators that governStreptomycesdevelopment
Joseph R. McCormick, Klas Flärdh
FEMS Microbiology Reviews.2012; 36(1): 206. CrossRef
Three pathway-specific regulators control streptolydigin biosynthesis in Streptomyces lydicus
Cristina Gómez, Carlos Olano, Carmen Méndez, José A. Salas
Microbiology.2012; 158(10): 2504. CrossRef
Roles of fkbN in Positive Regulation and tcs7 in Negative Regulation of FK506 Biosynthesis in Streptomyces sp. Strain KCTC 11604BP
SangJoon Mo, Young Ji Yoo, Yeon Hee Ban, Sung-Kwon Lee, Eunji Kim, Joo-Won Suh, Yeo Joon Yoon
Applied and Environmental Microbiology.2012; 78(7): 2249. CrossRef
Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σBldN and a cognate anti‐sigma factor, RsbN
Maureen J. Bibb, Ágota Domonkos, Govind Chandra, Mark J. Buttner
Molecular Microbiology.2012; 84(6): 1033. CrossRef
tRNA accumulation and suppression of the bldA phenotype during development in Streptomyces coelicolor
B. M. Fredrik Pettersson, Leif A. Kirsebom
Molecular Microbiology.2011; 79(6): 1602. CrossRef
Novel Two-Component Systems Implied in Antibiotic Production in Streptomyces coelicolor
Ana Yepes, Sergio Rico, Antonio Rodríguez-García, Ramón I. Santamaría, Margarita Díaz, Ching-Hong Yang
PLoS ONE.2011; 6(5): e19980. CrossRef
The regulation of the secondary metabolism of Streptomyces: new links and experimental advances
Gilles P. van Wezel, Kenneth J. McDowall
Natural Product Reports.2011; 28(7): 1311. CrossRef
Strict regulation of morphological differentiation and secondary metabolism by a positive feedback loop between two global regulators AdpA and BldA in Streptomyces griseus
Akiyoshi Higo, Sueharu Horinouchi, Yasuo Ohnishi
Molecular Microbiology.2011; 81(6): 1607. CrossRef
The Level of AdpA Directly Affects Expression of Developmental Genes in Streptomyces coelicolor
Marcin Wolański, Rafał Donczew, Agnieszka Kois-Ostrowska, Paweł Masiewicz, Dagmara Jakimowicz, Jolanta Zakrzewska-Czerwińska
Journal of Bacteriology.2011; 193(22): 6358. CrossRef
SanG, a transcriptional activator, controls nikkomycin biosynthesis through binding to the sanN–sanO intergenic region in Streptomyces ansochromogenes
Xihong He, Rui Li, Yuanyuan Pan, Gang Liu, Huarong Tan
Microbiology .2010; 156(3): 828. CrossRef
Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina
Giuseppe Gallo, Giovanni Renzone, Rosa Alduina, Efthimia Stegmann, Tilmann Weber, Anna Eliasson Lantz, Jette Thykaer, Fabio Sangiorgi, Andrea Scaloni, Anna Maria Puglia
PROTEOMICS.2010; 10(7): 1336. CrossRef
Adaptation of the Highly Productive T7 Expression System to Streptomyces lividans
François-Xavier Lussier, François Denis, François Shareck
Applied and Environmental Microbiology.2010; 76(3): 967. CrossRef
Autoregulation of hpdR and its effect on CDA biosynthesis in Streptomyces coelicolor
Haihua Yang, Yang An, Linqi Wang, Shuli Zhang, Yue Zhang, Yuqing Tian, Gang Liu, Huarong Tan
Microbiology .2010; 156(9): 2641. CrossRef
Regulation of the Biosynthesis of the Macrolide Antibiotic Spiramycin in Streptomyces ambofaciens
Fatma Karray, Emmanuelle Darbon, Hoang Chuong Nguyen, Josette Gagnat, Jean-Luc Pernodet
Journal of Bacteriology.2010; 192(21): 5813. CrossRef
Moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity
Bohdan Ostash, Suzanne Walker
Natural Product Reports.2010; 27(11): 1594. CrossRef
Morphological differentiation and clavulanic acid formation are affected in a Streptomyces clavuligerus adpA-deleted mutant
M. T. Lopez-Garcia, I. Santamarta, P. Liras
Microbiology.2010; 156(8): 2354. CrossRef
Quantitative Proteome Analysis of Streptomyces coelicolor Nonsporulating Liquid Cultures Demonstrates a Complex Differentiation Process Comparable to That Occurring in Sporulating Solid Cultures
Angel Manteca, Hye R. Jung, Veit Schwämmle, Ole N. Jensen, Jesus Sanchez
Journal of Proteome Research.2010; 9(9): 4801. CrossRef
Genetically Engineered Lipopeptide Antibiotics Related to A54145 and Daptomycin with Improved Properties
Kien T. Nguyen, Xiaowei He, Dylan C. Alexander, Chen Li, Jian-Qiao Gu, Carmela Mascio, Andrew Van Praagh, Larry Mortin, Min Chu, Jared A. Silverman, Paul Brian, Richard H. Baltz
Antimicrobial Agents and Chemotherapy.2010; 54(4): 1404. CrossRef
Genes essential for morphological development and antibiotic production in Streptomyces coelicolor are targets of BldD during vegetative growth
Chris D. Den Hengst, Ngat T. Tran, Maureen J. Bibb, Govind Chandra, Brenda K. Leskiw, Mark J. Buttner
Molecular Microbiology.2010; 78(2): 361. CrossRef
The complex extracellular biology ofStreptomyces
Keith F. Chater, Sandor Biró, Kye Joon Lee, Tracy Palmer, Hildgund Schrempf
FEMS Microbiology Reviews.2010; 34(2): 171. CrossRef
Streptomyces scabies 87-22 Contains a Coronafacic Acid-Like Biosynthetic Cluster That Contributes to Plant–Microbe Interactions
Dawn R. D. Bignell, Ryan F. Seipke, José C. Huguet-Tapia, Alan H. Chambers, Ronald J. Parry, Rosemary Loria
Molecular Plant-Microbe Interactions®.2010; 23(2): 161. CrossRef
Characterization of γ-Butyrolactone Autoregulatory Signaling Gene Homologs in the Angucyclinone Polyketide WS5995B ProducerStreptomyces acidiscabies
Frank G. Healy, Kevin P. Eaton, Prajit Limsirichai, Joel F. Aldrich, Alaina K. Plowman, Russell R. King
Journal of Bacteriology.2009; 191(15): 4786. CrossRef
The pleiotropic regulator AdpA‐L directly controls the pathway‐specific activator of nikkomycin biosynthesis in Streptomyces ansochromogenes
Yuanyuan Pan, Gang Liu, Haihua Yang, Yuqing Tian, Huarong Tan
Molecular Microbiology.2009; 72(3): 710. CrossRef
The SmpB-tmRNA Tagging System Plays Important Roles in Streptomyces coelicolor Growth and Development
Chunzhong Yang, John R. Glover, Christophe Herman
PLoS ONE.2009; 4(2): e4459. CrossRef
Deciphering Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin and Generation of Glycosylated Derivatives
Carlos Olano, Cristina Gómez, María Pérez, Martina Palomino, Antonio Pineda-Lucena, Rodrigo J. Carbajo, Alfredo F. Braña, Carmen Méndez, José A. Salas
Chemistry & Biology.2009; 16(10): 1031. CrossRef
Extracellular signalling, translational control, two repressors and an activator all contribute to the regulation of methylenomycin production inStreptomyces coelicolor
Sean O'Rourke, Andreas Wietzorrek, Kay Fowler, Christophe Corre, Greg L. Challis, Keith F. Chater
Molecular Microbiology.2009; 71(3): 763. CrossRef
Evolutionary flux of potentially bldA-dependent Streptomyces genes containing the rare leucine codon TTA
Govind Chandra, Keith F. Chater
Antonie van Leeuwenhoek.2008; 94(1): 111. CrossRef
novE and novG act as positive regulators of novobiocin biosynthesis
Volker Dangel, Alessandra S. Eustáquio, Bertolt Gust, Lutz Heide
Archives of Microbiology.2008; 190(5): 509. CrossRef
SarA influences the sporulation and secondary metabolism inStreptomyces coelicolorM145
Xijun Ou, Bo Zhang, Lin Zhang, Kai Dong, Chun Liu, Guoping Zhao, Xiaoming Ding
Acta Biochimica et Biophysica Sinica.2008; 40(10): 877. CrossRef

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