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Microorganisms
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Transcriptional Regulation in Bacteria, 2nd Edition
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Transcriptional Regulation in Bacteria, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 6638

Special Issue Editor

Dr. Tomohiro Shimada

E-Mail Website
Guest Editor
School of Agriculture, Meiji University, Kawasaki, Japan
Interests: transcription factor; transcriptional regulation; genomic SELEX; RNA polymerase; sigma factor; Escherichia coli; genome regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The goal of research in the post-genomic era, now that the full extent of the genes encoded by microbial genomes is known, is to elucidate the whole mechanism by which microorganisms utilize genes through transcriptional regulation. Deciphering the genome sequence of microorganisms has revealed its gene set and the set of transcriptional regulators that regulate those genes, providing a complete overview of transcriptional regulation in microorganisms. The number of target genes depends on the function of the transcription factor; some single-target regulators target a single gene in the genome, while others are global regulators that target hundreds of genes. In some cases, these have been shown to cooperate or antagonize each other at hundreds or more sites on the genome, dynamically regulating gene transcription.

It has also become clear that transcription factors comprehensively regulate multiple genes involved in seemingly unrelated biological functions. Thus, analyses of transcriptional regulation reveal not only the molecular mechanisms of transcriptional regulation but also the functional network of genes, leading to the elucidation of new physiological mechanisms of microorganisms.

This Special Issue aims to collect recent studies on microorganisms, from detailed and precise studies on the transcriptional regulatory mechanisms of single genes, to studies on the genome regulatory networks of whole genes, to newly revealed microorganism mechanisms.

Dr. Tomohiro Shimada
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transcription
  • gene regulation
  • genome regulation
  • regulatory network
  • RNA polymerase
  • sigma factor
  • transcription factor
  • nucleoid

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Published Papers (6 papers)

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Research

16 pages, 1975 KB  
Article
MtrR Regulates a Major Lytic Transglycosylase (ltgA) Responsible for Peptidoglycan-Derived Cytotoxin Release and Autolysis in Neisseria gonorrhoeae
by Alaa I. Telchy, Tia Morgan, Kathleen T. Hackett, Ronald K. McMillan, Robert A. Nicholas, Joseph P. Dillard and Daniel Williams
Microorganisms 2026, 14(2), 474; https://doi.org/10.3390/microorganisms14020474 - 14 Feb 2026
Viewed by 542
Abstract
The multiple-transferable resistance protein (MtrR) is a transcriptional repressor of the mtrCDE-encoded drug efflux pump and Type IV pilus biosynthesis (pilM), and an activator of penicillin-binding protein 1 (ponA) expression in Neisseria gonorrhoeae. Previously published microarray data [...] Read more.
The multiple-transferable resistance protein (MtrR) is a transcriptional repressor of the mtrCDE-encoded drug efflux pump and Type IV pilus biosynthesis (pilM), and an activator of penicillin-binding protein 1 (ponA) expression in Neisseria gonorrhoeae. Previously published microarray data suggested that MtrR is also an activator of ltgA expression in the gonococcus. LtgA is a lytic transglycosylase responsible for approximately half of recycled peptidoglycan fragments and released peptidoglycan-derived cytotoxins, which cause ciliary damage and induce specific inflammatory responses. The fragments generated by LtgA during peptidoglycan remodeling can either be recognized by the permease AmpG for uptake into the bacterial cytoplasm and recycled for new cell wall growth and general metabolism or released into the external milieu. Therefore, we sought to define the capacity of MtrR to regulate LtgA expression in gonococci. We show that MtrR binds to the ltgA promoter region in a concentration-dependent manner, and that this binding results both in increased ltgA mRNA transcription and LtgA protein levels during exponential growth. Deletion of mtrR in N. gonorrhoeae decreased peptidoglycan monomer release from growing cells and increased autolysis. These results suggest that MtrR regulation of ltgA impacts peptidoglycan-derived cytotoxin release and autolysis in the gonococcus. This study suggests a central role of MtrR in coordinating aspects of the cellular envelope that may contribute to gonococcal pathogenesis. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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16 pages, 2804 KB  
Article
Transcription Factor HusR (YnfL) Is a Novel Regulator for Hydroxyurea Sensitivity in Escherichia coli K-12
by Ikki Kobayashi, Sousuke Imamura, Ken Okamoto and Tomohiro Shimada
Microorganisms 2026, 14(1), 134; https://doi.org/10.3390/microorganisms14010134 - 7 Jan 2026
Viewed by 549
Abstract
Understanding the functions of all genes and their biological mechanisms based on comprehensive genome regulation mechanisms is an important issue in life sciences. YnfL is an uncharacterized LysR family transcription factor in Escherichia coli. Genomic SELEX screening was performed to identify YnfL [...] Read more.
Understanding the functions of all genes and their biological mechanisms based on comprehensive genome regulation mechanisms is an important issue in life sciences. YnfL is an uncharacterized LysR family transcription factor in Escherichia coli. Genomic SELEX screening was performed to identify YnfL regulatory targets in the E. coli genome and reveal the function of YnfL. Nine loci on the E. coli genome were identified as regulatory targets of YnfL, and the target genes were involved in supplying DNA substrates and DNA repair. RT-qPCR analysis in vivo revealed that YnfL activates its target genes during the stationary phase. Tests for drug resistance that causes DNA damage revealed that ynfL deficiency increased abnormal cell filamentation and the appearance of anucleate cells in the presence of hydroxyurea. Furthermore, ynfL deficiency reduced cell survival under long-term nitrogen starvation conditions. In summary, we propose renaming ynfL to hydroxyurea sensitivity regulator (husR). These findings contribute to understanding DNA maintenance and long-term survival through transcriptional regulation. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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18 pages, 1419 KB  
Article
The Nucleoid-Associated Protein Fis Represses Type 3 Fimbriae to Modulate Biofilm and Adherence Formation in Klebsiella pneumoniae
by Santa Mejia-Ventura, Jorge Soria-Bustos, Fernando Chimal-Cázares, Gabriela Hernández-Martínez, Roberto Rosales-Reyes, Miguel A. De la Cruz, Jorge A. Yañez-Santos, Maria L. Cedillo, Gonzalo Castillo-Rojas, Dimitris Georgellis and Miguel A. Ares
Microorganisms 2025, 13(11), 2591; https://doi.org/10.3390/microorganisms13112591 - 13 Nov 2025
Viewed by 968
Abstract
The nucleoid-associated protein Fis functions as a global regulator that influences various cellular processes in Gram-negative bacteria. In this study, we examined the role of Fis in the transcriptional regulation of type 3 fimbriae in Klebsiella pneumoniae, a notable opportunistic pathogen associated [...] Read more.
The nucleoid-associated protein Fis functions as a global regulator that influences various cellular processes in Gram-negative bacteria. In this study, we examined the role of Fis in the transcriptional regulation of type 3 fimbriae in Klebsiella pneumoniae, a notable opportunistic pathogen associated with hospital-acquired infections. Our transcriptional analyses revealed that deleting the fis gene caused a significant upregulation of mrkA and mrkH, the genes responsible for the structure and regulation of type 3 fimbriae, respectively. Additionally, phenotypic assays demonstrated that the Δfis mutant exhibited enhanced biofilm formation and greater adherence to A549 lung epithelial cells compared to the wild-type strain. These effects were restored to wild-type levels in the cis-complemented strain. Electrophoretic mobility shift assays confirmed that Fis directly binds to the regulatory regions upstream of both mrkA and mrkH, indicating that repression occurs through direct interaction with the promoter. In summary, our findings show that Fis acts as a transcriptional repressor of mrkA and mrkH, thereby negatively regulating the expression of type 3 fimbriae, biofilm formation, and adherence. This study highlights Fis as a direct regulator of fimbrial expression and biofilm development in K. pneumoniae, deepening our understanding of its virulence regulatory network. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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25 pages, 6655 KB  
Article
Posttranscriptional 3′-Terminal Modifications of Escherichia coli RNA Fragments Evolved for Diversity Boosting
by Nikita M. Kamoldinov, Valery V. Panyukov, Nikolay P. Kolzhetsov, Natalia Y. Markelova, Konstantin S. Shavkunov, Uliana S. Shvyreva, Olga V. Alikina, Olga A. Glazunova, Iuliia A. Praslova and Olga N. Ozoline
Microorganisms 2025, 13(9), 2189; https://doi.org/10.3390/microorganisms13092189 - 19 Sep 2025
Viewed by 1305
Abstract
An emerging area of microbial biology focuses on oligonucleotides excised from functional RNAs and subsequently fulfilling an independent cellular role. Some of these products are subjected to modifications that may expand their functional inventory. Here, we applied a differential analysis of intra- and [...] Read more.
An emerging area of microbial biology focuses on oligonucleotides excised from functional RNAs and subsequently fulfilling an independent cellular role. Some of these products are subjected to modifications that may expand their functional inventory. Here, we applied a differential analysis of intra- and extracellular RNA fragments produced by wild-type Escherichia coli and its dps-null mutant and discovered leucine tRNA fragments with random 3′-terminal extensions among oligonucleotides with Dps-dependent secretion. We observed an exclusive intracellular enrichment of modified LeuT(VPQ) tRNA fragments compared to secretomes, with abundance level dependent on growth medium and the presence of competing bacteria. To assess the pervasiveness of this phenomenon, we developed a custom computational pipeline for detecting variable RNA termini in RNA-seq data. Beyond LeuT(VPQ) tRNA fragments, several other genomic loci yielded oligos with highly heterogeneous ends, indicating that terminal elongation, most prevalent in LeuT(VPQ), is not exclusive to these fragments. Ex vivo testing using synthetic LeuT(VPQ) analogs revealed their stimulatory effect on the persistence of multiple taxa in an artificial microbiome, which was attenuated by 3′-end elongation. We propose that non-template extensions may serve to broaden the spectrum of target molecules for elimination of unused mRNAs by an interference-like mechanism or to generate sequences absent from the E. coli genome as part of a primitive defense system. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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17 pages, 2653 KB  
Article
RcsB and H-NS Both Contribute to the Repression the Expression of the csgDEFG Operon
by Hiroshi Ogasawara, Azusa Tomioka and Yuki Kato
Microorganisms 2025, 13(8), 1829; https://doi.org/10.3390/microorganisms13081829 - 5 Aug 2025
Cited by 3 | Viewed by 1139
Abstract
Curli fimbriae are a major component of biofilm formation in Escherichia coli, and their expression is regulated by numerous transcription factors and small regulatory RNAs (sRNAs). The RcsD-RcsC-RcsB phosphorelay system, which is involved in the envelope stress response, plays a role in [...] Read more.
Curli fimbriae are a major component of biofilm formation in Escherichia coli, and their expression is regulated by numerous transcription factors and small regulatory RNAs (sRNAs). The RcsD-RcsC-RcsB phosphorelay system, which is involved in the envelope stress response, plays a role in this regulation. In this study, we report that DNase-I footprinting analysis revealed that the response regulator RcsB interacts with the −31 to +53 region of the promoter region of csgD, which encodes a major regulator of biofilm formation, and thus contributes to its transcriptional repression. Additionally, overexpression of RcsB or RcsB D56A that could not be phosphorylated by the histidine kinases RcsC and D both significantly reduced csgD expression and suppressed Curli formation. This indicates that the phosphorylation of RcsB has an insignificant impact on its affinity for its operator sites. Furthermore, we confirm that RcsB binds cooperatively to the csgD promoter region in the presence of the nucleoid-associated protein H-NS. Our study also confirms that RcsB positively regulates the expression of an sRNA, RprA, which is known to reduce mRNA csgD mRNA translation RprA via its binding to the 5′-untranslated region (UTR) of csgD. These findings indicate that, in E. coli, the RcsBCD system suppresses csgD expression through both direct transcriptional repression by the regulator RcsB and translational repression by the sRNA RprA. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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24 pages, 3042 KB  
Article
Integrated Transcriptomic and Proteomic Analyses Reveal CsrA-Mediated Regulation of Virulence and Metabolism in Vibrio alginolyticus
by Bing Liu, Huizhen Chen, Kai Sheng, Jianxiang Fang, Ying Zhang and Chang Chen
Microorganisms 2025, 13(7), 1516; https://doi.org/10.3390/microorganisms13071516 - 28 Jun 2025
Cited by 1 | Viewed by 1467
Abstract
Vibrio alginolyticus, a common Gram-negative opportunistic pathogen of marine animals and humans, is known for its rapid growth in organic-matter-rich environments. However, it remains unclear how it incorporates metabolic pathways in response to diverse carbon and nitrogen sources and rapidly alters gene [...] Read more.
Vibrio alginolyticus, a common Gram-negative opportunistic pathogen of marine animals and humans, is known for its rapid growth in organic-matter-rich environments. However, it remains unclear how it incorporates metabolic pathways in response to diverse carbon and nitrogen sources and rapidly alters gene expression. Increasing evidence suggests that post-transcriptional regulation by RNA-binding proteins and small RNAs (sRNAs) plays a crucial role in bacterial adaptation and metabolism. CsrA (carbon storage regulator A), a conserved post-transcriptional regulator in Gammaproteobacteria, is poorly characterized in Vibrio species. Using integrated transcriptomic and proteomic analyses, we found that CsrA alters the expression of 661 transcripts and 765 protein transcripts in V. alginolyticus, influencing key pathways including central carbon metabolism, amino acid metabolism and transport, quorum sensing, and bacterial secretion systems. Through directed CsrA-RNA EMSAs, we identified several direct mRNA targets of CsrA, including gltB, gcvP, aceE, and tdh, as well as secretion system components (tagH, tssL, yopD, and sctC). Notably, CsrA also directly regulates rraA, a key modulator of ribonuclease activity, suggesting a broader role in RNA metabolism. Our findings establish CsrA as a global regulator in V. alginolyticus, expanding the known targets of CsrA and providing new insights into its regulatory roles. Full article
(This article belongs to the Special Issue Transcriptional Regulation in Bacteria, 2nd Edition)
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