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Sikora F, Budja LVP, Milojevic O, Ziemniewicz A, Dudys P, Görke B. Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon. Mol Microbiol 2024; 122:11-28. [PMID: 38770591 DOI: 10.1111/mmi.15280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
The rpoN operon, an important regulatory hub in Enterobacteriaceae, includes rpoN encoding sigma factor σ54, hpf involved in ribosome hibernation, rapZ regulating glucosamine-6-phosphate levels, and two genes encoding proteins of the nitrogen-related phosphotransferase system. Little is known about regulatory mechanisms controlling the abundance of these proteins. This study employs transposon mutagenesis and chemical screens to dissect the complex expression of the rpoN operon. We find that envelope stress conditions trigger read-through transcription into the rpoN operon from a promoter located upstream of the preceding lptA-lptB locus. This promoter is controlled by the envelope stress sigma factor E and response regulator PhoP is required for its full response to a subset of stress signals. σE also stimulates ptsN-rapZ-npr expression using an element downstream of rpoN, presumably by interfering with mRNA processing by RNase E. Additionally, we identify a novel promoter in the 3' end of rpoN that directs transcription of the distal genes in response to ethanol. Finally, we show that translation of hpf and ptsN is individually regulated by the RNA chaperone Hfq, perhaps involving small RNAs. Collectively, our work demonstrates that the rpoN operon is subject to complex regulation, integrating signals related to envelope stress and carbon source quality.
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Affiliation(s)
- Florian Sikora
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Lara Veronika Perko Budja
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Olja Milojevic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Amelia Ziemniewicz
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Przemyslaw Dudys
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Boris Görke
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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2
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Zhu Y, Dou Q, Du L, Wang Y. QseB/QseC: a two-component system globally regulating bacterial behaviors. Trends Microbiol 2023:S0966-842X(23)00046-X. [PMID: 36849330 DOI: 10.1016/j.tim.2023.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
QseB/QseC is a two-component system that is involved in the regulation of multiple bacterial behaviors by regulating quorum sensing, bacterial pathogenicity, and antibiotic resistance. Thus, QseB/QseC could provide a target for new antibiotic development. Recently, QseB/QseC has been found to confer survival advantages to environmental bacteria under stress conditions. The molecular mechanistic understanding of QseB/QseC has become an active area of research and revealed some emerging themes, including a deeper understanding of QseB/QseC regulation in different pathogens and environmental bacteria, the functional difference of QseB/QseC among species, and the possibility of analyzing QseB/QseC evolution. Here, we discuss the progression of QseB/QseC studies and describe several unresolved issues and future directions. Resolving these issues is among the challenges of future QseB/QseC studies.
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Affiliation(s)
- Yuxiang Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qin Dou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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3
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Ogawa A, Kojima F, Miyake Y, Yoshimura M, Ishijima N, Iyoda S, Sekine Y, Yamanaka Y, Yamamoto K. Regulation of constant cell elongation and Sfm pili synthesis in Escherichia coli via two active forms of FimZ orphan response regulator. Genes Cells 2022; 27:657-674. [PMID: 36057789 DOI: 10.1111/gtc.12982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/21/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
Escherichia coli (E. coli) has multiple copies of the chaperone-usher (CU) pili operon in five fimbria groups: CU pili, curli, type IV pili, type III secretion pili, and type IV secretion pili. Commensal E. coli K-12 contains 12 CU pili operons. Among these operons, Sfm is expressed by the sfmACDHF operon. Transcriptome analyses, reporter assays, and chromatin immunoprecipitation PCR analyses reported that FimZ directly binds to and activates the sfmA promoter, transcribing sfmACDHF. In addition, FimZ regularly induces constant cell elongation in E. coli, which is required for F-type ATPase function. The bacterial two-hybrid system showed a specific interaction between FimZ and the α subunit of the cytoplasmic F1 domain of F-type ATPase. Studies performed using mutated FimZs have revealed two active forms, I and II. Active form I is required for constant cell elongation involving amino acid residues K106 and D109. Active form II additionally required D56, a putative phosphorylation site, to activate the sfmA promoter. The chromosomal fimZ was hardly expressed in parent strain but functioned in phoB and phoP double-gene knockout strains. These insights may help to understand bacterial invasion restricted host environments by the sfm γ-type pili.
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Affiliation(s)
- Ayano Ogawa
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Fumika Kojima
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Yukari Miyake
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Miho Yoshimura
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Nozomi Ishijima
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Nippon Dental University School of Dentistry, Tokyo, Japan
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4
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Lin WY, Lee YJ, Yu PH, Tsai YL, She PY, Li TS, Liaw SJ. The QseEF Two-Component System-GlmY Small RNA Regulatory Pathway Controls Swarming in Uropathogenic Proteus mirabilis. Int J Mol Sci 2022; 23:ijms23010487. [PMID: 35008912 PMCID: PMC8745638 DOI: 10.3390/ijms23010487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial sensing of environmental signals through the two-component system (TCS) plays a key role in modulating virulence. In the search for the host hormone-sensing TCS, we identified a conserved qseEGF locus following glmY, a small RNA (sRNA) gene in uropathogenic Proteus mirabilis. Genes of glmY-qseE-qseG-qseF constitute an operon, and QseF binding sites were found in the glmY promoter region. Deletion of glmY or qseF resulted in reduced swarming motility and swarming-related phenotypes relative to the wild-type and the respective complemented strains. The qseF mutant had decreased glmYqseEGF promoter activity. Both glmY and qseF mutants exhibited decreased flhDC promoter activity and mRNA level, while increased rcsB mRNA level was observed in both mutants. Prediction by TargetRNA2 revealed cheA as the target of GlmY. Then, construction of the translational fusions containing various lengths of cheA 5′UTR for reporter assay and site-directed mutagenesis were performed to investigate the cheA-GlmY interaction in cheA activation. Notably, loss of glmY reduced the cheA mRNA level, and urea could inhibit swarming in a QseF-dependent manner. Altogether, this is the first report elucidating the underlying mechanisms for modulation of swarming motility by a QseEF-regulated sRNA GlmY, involving expression of cheA, rcsB and flhDC in uropathogenic P. mirabilis.
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Affiliation(s)
- Wen-Yuan Lin
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan; (W.-Y.L.); (Y.-L.T.); (P.-Y.S.); (T.-S.L.)
| | - Yuan-Ju Lee
- Department of Urology, National Taiwan University Hospital, Taipei 10002, Taiwan;
| | - Ping-Hung Yu
- Department of Nursing, National Taichung University of Science and Technology, Taichung City 404348, Taiwan;
| | - Yi-Lin Tsai
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan; (W.-Y.L.); (Y.-L.T.); (P.-Y.S.); (T.-S.L.)
| | - Pin-Yi She
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan; (W.-Y.L.); (Y.-L.T.); (P.-Y.S.); (T.-S.L.)
| | - Tzung-Shian Li
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan; (W.-Y.L.); (Y.-L.T.); (P.-Y.S.); (T.-S.L.)
| | - Shwu-Jen Liaw
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan; (W.-Y.L.); (Y.-L.T.); (P.-Y.S.); (T.-S.L.)
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan
- Correspondence: ; Tel.: +886-02-23123456 (ext. 6911)
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6
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Regulatory small RNA, Qrr2 is expressed independently of sigma factor-54 and can function as the sole Qrr sRNA to control quorum sensing in Vibrio parahaemolyticus. J Bacteriol 2021; 204:e0035021. [PMID: 34633869 DOI: 10.1128/jb.00350-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial cells alter gene expression in response to changes in population density in a process called quorum sensing (QS). In Vibrio harveyi, LuxO, a low cell density activator of sigma factor-54 (RpoN), is required for transcription of five non-coding regulatory sRNAs, Qrr1-Qrr5, which each repress translation of the master QS regulator LuxR. Vibrio parahaemolyticus, the leading cause of bacterial seafood-borne gastroenteritis, also contains five Qrr sRNAs that control OpaR (the LuxR homolog), controlling capsule polysaccharide (CPS), motility, and metabolism. We show that in a ΔluxO deletion mutant, opaR was de-repressed and CPS and biofilm were produced. However, in a ΔrpoN mutant, opaR was repressed, no CPS was produced, and less biofilm production was observed compared to wild type. To determine why opaR was repressed, expression analysis in ΔluxO showed all five qrr genes were repressed, while in ΔrpoN the qrr2 gene was significantly de-repressed. Reporter assays and mutant analysis showed Qrr2 sRNA can act alone to control OpaR. Bioinformatics analysis identified a sigma-70 (RpoD) -35 -10 promoter overlapping the canonical sigma-54 (RpoN) -24 -12 promoter in the qrr2 regulatory region. The qrr2 sigma-70 promoter element was also present in additional Vibrio species indicating it is widespread. Mutagenesis of the sigma-70 -10 promoter site in the ΔrpoN mutant background, resulted in repression of qrr2. Analysis of qrr quadruple deletion mutants, in which only a single qrr gene is present, showed that only Qrr2 sRNA can act independently to regulate opaR. Mutant and expression data also demonstrated that RpoN and the global regulator, Fis, act additively to repress qrr2. Our data has uncovered a new mechanism of qrr expression and shows that Qrr2 sRNA is sufficient for OpaR regulation. Importance The quorum sensing non-coding sRNAs are present in all Vibrio species but vary in number and regulatory roles among species. In the Harveyi clade, all species contain five qrr genes, and in V. harveyi these are transcribed by sigma-54 and are additive in function. In the Cholerae clade, four qrr genes are present, and in V. cholerae the qrr genes are redundant in function. In V. parahaemolyticus, qrr2 is controlled by two overlapping promoters. In an rpoN mutant, qrr2 is transcribed from a sigma-70 promoter that is present in all V. parahaemolyticus strains and in other species of the Harveyi clade suggesting a conserved mechanism of regulation. Qrr2 sRNA can function as the sole Qrr sRNA to control OpaR.
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7
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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8
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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9
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Piattelli E, Peltier J, Soutourina O. Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection. Genes (Basel) 2020; 11:E1209. [PMID: 33081172 PMCID: PMC7602753 DOI: 10.3390/genes11101209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria.
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Affiliation(s)
- Emma Piattelli
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
| | - Johann Peltier
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, 75015 Paris, France
| | - Olga Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
- Institut Universitaire de France, CEDEX 05, 75231 Paris, France
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10
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Khan MA, Durica‐Mitic S, Göpel Y, Heermann R, Görke B. Small RNA-binding protein RapZ mediates cell envelope precursor sensing and signaling in Escherichia coli. EMBO J 2020; 39:e103848. [PMID: 32065419 PMCID: PMC7073468 DOI: 10.15252/embj.2019103848] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein RapZ cooperates with small RNAs (sRNAs) GlmY and GlmZ to regulate the glmS mRNA in Escherichia coli. Enzyme GlmS synthesizes glucosamine-6-phosphate (GlcN6P), initiating cell envelope biosynthesis. GlmZ activates glmS expression by base-pairing. When GlcN6P is ample, GlmZ is bound by RapZ and degraded through ribonuclease recruitment. Upon GlcN6P depletion, the decoy sRNA GlmY accumulates through a previously unknown mechanism and sequesters RapZ, suppressing GlmZ decay. This circuit ensures GlcN6P homeostasis and thereby envelope integrity. In this work, we identify RapZ as GlcN6P receptor. GlcN6P-free RapZ stimulates phosphorylation of the two-component system QseE/QseF by interaction, which in turn activates glmY expression. Elevated GlmY levels sequester RapZ into stable complexes, which prevents GlmZ decay, promoting glmS expression. Binding of GlmY also prevents RapZ from activating QseE/QseF, generating a negative feedback loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. We reveal a multifunctional sRNA-binding protein that dynamically engages into higher-order complexes for metabolite signaling.
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Affiliation(s)
- Muna A Khan
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Svetlana Durica‐Mitic
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Ralf Heermann
- Microbiology and Wine ResearchInstitute for Molecular PhysiologyJohannes Gutenberg‐University MainzMainzGermany
| | - Boris Görke
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
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11
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Mutations Reducing In Vitro Susceptibility to Novel LpxC Inhibitors in Pseudomonas aeruginosa and Interplay of Efflux and Nonefflux Mechanisms. Antimicrob Agents Chemother 2019; 64:AAC.01490-19. [PMID: 31658970 DOI: 10.1128/aac.01490-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/22/2019] [Indexed: 11/20/2022] Open
Abstract
Upregulated expression of efflux pumps, lpxC target mutations, LpxC protein overexpression, and mutations in fabG were previously shown to mediate single-step resistance to the LpxC inhibitor CHIR-090 in P. aeruginosa Single-step selection experiments using three recently described LpxC inhibitors (compounds 2, 3, and 4) and mutant characterization showed that these mechanisms affect susceptibility to additional novel LpxC inhibitors. Serial passaging of P. aeruginosa wild-type and efflux pump-defective strains using the LpxC inhibitor CHIR-090 or compound 1 generated substantial shifts in susceptibility and underscored the interplay of efflux and nonefflux mechanisms. Whole-genome sequencing of CHIR-090 passage mutants identified efflux pump overexpression, fabG mutations, and novel mutations in fabF1 and in PA4465 as determinants of reduced susceptibility. Two new lpxC mutations, encoding A214V and G208S, that reduce susceptibility to certain LpxC inhibitors were identified in these studies, and we show that these and other target mutations differentially affect different LpxC inhibitor scaffolds. Lastly, the combination of target alteration (LpxCA214V) and upregulated expression of LpxC was shown to be tolerated in P. aeruginosa and could mediate significant decreases in susceptibility.
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Reprogramming of gene expression in Escherichia coli cultured on pyruvate versus glucose. Mol Genet Genomics 2019; 294:1359-1371. [PMID: 31363904 DOI: 10.1007/s00438-019-01597-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/22/2019] [Indexed: 12/30/2022]
Abstract
Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional expression profiles and actual mechanisms they use to regulate gene expression to control particular biological pathways. To learn more about the specific contribution of sRNAs to the global regulatory network controlling the Escherichia coli central carbon metabolism (CCM), we employed microarray analysis and compared transcriptome profiles of E. coli cells grown on two alternative minimal media supplemented with either pyruvate or glucose, respectively. Microarray analysis revealed that utilization of these alternative carbon sources led to profound differences in gene expression affecting all major gene clusters associated with CCM as well as expression of several known (CyaR, RyhB, GcvB and RyeA) and putative (C0652) sRNAs. To assess the impact of transcriptional reprogramming of gene expression on E. coli protein abundance, we also employed two-dimensional protein gel electrophoresis. Our experimental data made it possible to determine the major pathways for pyruvate assimilation when it is used as a sole carbon source and reveal the impact of other key processes (i.e., energy production, molecular transport and cell resistance to stress) associated with the CCM in E. coli. Moreover, some of these processes were apparently controlled by GcvB, RyhB and CyaR at the post-transcriptional level, thus indicating the complexity and interconnection of the regulatory networks that control CCM in bacteria.
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Abstract
Many bacterial small RNAs (sRNAs) are processed resulting in variants with roles potentially distinct from the primary sRNAs. In Enterobacteriaceae sRNA GlmZ activates expression of glmS by base-pairing when the levels of glucosamine-6-phosphate (GlcN6P) are low. GlmS synthesizes GlcN6P, which is required for cell envelope biosynthesis. When dispensable, GlmZ is cleaved by RNase E in the base-pairing sequence. Processing requires protein RapZ, which binds GlmZ and recruits RNase E by interaction. Cleavage is counteracted by the homologous sRNA GlmY, which accumulates upon GlcN6P scarcity and sequesters RapZ. Here, we report a novel role for a processed sRNA. We observed that processing of GlmZ is never complete in vivo. Even upon RapZ overproduction, a fraction of GlmZ remains full-length, while the 5' cleavage product (GlmZ*) accumulates. GlmZ* retains all elements required for RapZ binding. Accordingly, GlmZ* can displace full-length GlmZ from RapZ and counteract processing in vitro. To mimic GlmZ* in vivo, sRNA chimeras were employed consisting of foreign 3' ends including a terminator fused to the 3' end of GlmZ*. In vitro, these chimeras perform indistinguishable from GlmZ*. Expression of the chimeras in vivo inhibited processing of endogenous GlmZ, causing moderate upregulation of GlmS synthesis. Hence, accumulation of GlmZ* prevents complete GlmZ turnover. This mechanism may serve to adjust a robust glmS basal expression level that is buffered against fluctuations in RapZ availability.
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Affiliation(s)
- Svetlana Durica-Mitic
- a Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Boris Görke
- a Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
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Klein G, Raina S. Regulated Assembly of LPS, Its Structural Alterations and Cellular Response to LPS Defects. Int J Mol Sci 2019; 20:ijms20020356. [PMID: 30654491 PMCID: PMC6358824 DOI: 10.3390/ijms20020356] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 12/21/2022] Open
Abstract
Distinguishing feature of the outer membrane (OM) of Gram-negative bacteria is its asymmetry due to the presence of lipopolysaccharide (LPS) in the outer leaflet of the OM and phospholipids in the inner leaflet. Recent studies have revealed the existence of regulatory controls that ensure a balanced biosynthesis of LPS and phospholipids, both of which are essential for bacterial viability. LPS provides the essential permeability barrier function and act as a major virulence determinant. In Escherichia coli, more than 100 genes are required for LPS synthesis, its assembly at inner leaflet of the inner membrane (IM), extraction from the IM, translocation to the OM, and in its structural alterations in response to various environmental and stress signals. Although LPS are highly heterogeneous, they share common structural elements defining their most conserved hydrophobic lipid A part to which a core polysaccharide is attached, which is further extended in smooth bacteria by O-antigen. Defects or any imbalance in LPS biosynthesis cause major cellular defects, which elicit envelope responsive signal transduction controlled by RpoE sigma factor and two-component systems (TCS). RpoE regulon members and specific TCSs, including their non-coding arm, regulate incorporation of non-stoichiometric modifications of LPS, contributing to LPS heterogeneity and impacting antibiotic resistance.
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Affiliation(s)
- Gracjana Klein
- Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Satish Raina
- Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.
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Abstract
Small regulatory RNAs are now recognized as key regulators of gene expression in bacteria. They accumulate under specific conditions, most often because their synthesis is directly controlled by transcriptional regulators, including but not limited to alternative sigma factors and response regulators of two-component systems. In turn, small RNAs regulate, mostly at the posttranscriptional level, expression of multiple genes, among which are genes encoding transcriptional regulators. Small RNAs are thus embedded in mixed regulatory circuits combining transcriptional and posttranscriptional controls, and whose properties are discussed here.
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Göpel Y, Görke B. Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli. PLoS Genet 2018; 14:e1007547. [PMID: 30040820 PMCID: PMC6075780 DOI: 10.1371/journal.pgen.1007547] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/03/2018] [Accepted: 07/08/2018] [Indexed: 01/26/2023] Open
Abstract
Histidine kinase QseE and response regulator QseF compose a two-component system in Enterobacteriaceae. In Escherichia coli K-12 QseF activates transcription of glmY and of rpoE from Sigma 54-dependent promoters by binding to upstream activating sequences. Small RNA GlmY and RpoE (Sigma 24) are important regulators of cell envelope homeostasis. In pathogenic Enterobacteriaceae QseE/QseF are required for virulence. In enterohemorrhagic E. coli QseE was reported to sense the host hormone epinephrine and to regulate virulence genes post-transcriptionally through employment of GlmY. The qseEGF operon contains a third gene, qseG, which encodes a lipoprotein attached to the inner leaflet of the outer membrane. Here, we show that QseG is essential and limiting for activity of QseE/QseF in E. coli K-12. Metabolic 32P-labelling followed by pull-down demonstrates that phosphorylation of the receiver domain of QseF in vivo requires QseE as well as QseG. Accordingly, QseG acts upstream and through QseE/QseF by stimulating activity of kinase QseE. 32P-labelling also reveals an additional phosphorylation in the QseF C-terminus of unknown origin, presumably at threonine/serine residue(s). Pulldown and two-hybrid assays demonstrate interaction of QseG with the periplasmic loop of QseE. A mutational screen identifies the Ser58Asn exchange in the periplasmic loop of QseE, which decreases interaction with QseG and concomitantly lowers QseE/QseF activity, indicating that QseG activates QseE by interaction. Finally, epinephrine is shown to have a moderate impact on QseE activity in E. coli K-12. Epinephrine slightly stimulates QseF phosphorylation and thereby glmY transcription, but exclusively during stationary growth and this requires both, QseE and QseG. Our data reveal a three-component signaling system, in which the phosphorylation state of QseE/QseF is governed by interaction with lipoprotein QseG in response to a signal likely derived from the cell envelope.
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Affiliation(s)
- Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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Barvík I, Rejman D, Panova N, Šanderová H, Krásný L. Non-canonical transcription initiation: the expanding universe of transcription initiating substrates. FEMS Microbiol Rev 2017; 41:131-138. [PMID: 27799279 DOI: 10.1093/femsre/fuw041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.
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Affiliation(s)
- Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Natalya Panova
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Šanderová
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
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Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions. mSystems 2017; 2:mSystems00024-17. [PMID: 28766584 PMCID: PMC5527300 DOI: 10.1128/msystems.00024-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/06/2017] [Indexed: 12/23/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) bacteria are a diverse group of pathogens that cause moderate to severe diarrhea in young children in developing countries. EPEC isolates can be further subclassified as typical EPEC (tEPEC) isolates that contain the bundle-forming pilus (BFP) or as atypical EPEC (aEPEC) isolates that do not contain BFP. Comparative genomics studies have recently highlighted the considerable genomic diversity among EPEC isolates. In the current study, we used RNA sequencing (RNA-Seq) to characterize the global transcriptomes of eight tEPEC isolates representing the identified genomic diversity, as well as one aEPEC isolate. The global transcriptomes were determined for the EPEC isolates under conditions of laboratory growth that are known to induce expression of virulence-associated genes. The findings demonstrate that unique genes of EPEC isolates from diverse phylogenomic lineages contribute to variation in their global transcriptomes. There were also phylogroup-specific differences in the global transcriptomes, including genes involved in iron acquisition, which had significant differential expression in the EPEC isolates belonging to phylogroup B2. Also, three EPEC isolates from the same phylogenomic lineage (EPEC8) had greater levels of similarity in their genomic content and exhibited greater similarities in their global transcriptomes than EPEC from other lineages; however, even among closely related isolates there were isolate-specific differences among their transcriptomes. These findings highlight the transcriptional variability that correlates with the previously unappreciated genomic diversity of EPEC. IMPORTANCE Recent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC isolates during growth under in vitro virulence-inducing conditions. This study addressed biological variation among isolates of a single pathovar in an effort to demonstrate that while each of these isolates is considered an EPEC isolate, there is significant transcriptional diversity among members of this pathovar. Future studies should consider whether this previously undescribed transcriptional variation may play a significant role in isolate-specific variability of EPEC clinical presentations.
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Novel DNA Binding and Regulatory Activities for σ 54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017; 199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
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Genetic and Mechanistic Analyses of the Periplasmic Domain of the Enterohemorrhagic Escherichia coli QseC Histidine Sensor Kinase. J Bacteriol 2017; 199:JB.00861-16. [PMID: 28138098 DOI: 10.1128/jb.00861-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/23/2017] [Indexed: 12/23/2022] Open
Abstract
The histidine sensor kinase (HK) QseC senses autoinducer 3 (AI-3) and the adrenergic hormones epinephrine and norepinephrine. Upon sensing these signals, QseC acts through three response regulators (RRs) to regulate the expression of virulence genes in enterohemorrhagic Escherichia coli (EHEC). The QseB, QseF, and KdpE RRs that are phosphorylated by QseC constitute a tripartite signaling cascade having different and overlapping targets, including flagella and motility, the type three secretion system encoded by the locus of enterocyte effacement (LEE), and Shiga toxin. We modeled the tertiary structure of QseC's periplasmic sensing domain and aligned the sequences from 12 different species to identify the most conserved amino acids. We selected eight amino acids conserved in all of these QseC homologues. The corresponding QseC site-directed mutants were expressed and still able to autophosphorylate; however, four mutants demonstrated an increased basal level of phosphorylation. These mutants have differential flagellar, motility, LEE, and Shiga toxin expression phenotypes. We selected four mutants for more in-depth analyses and found that they differed in their ability to phosphorylate QseB, KdpE, and QseF. This suggests that these mutations in the periplasmic sensing domain affected the region downstream of the QseC signaling cascade and therefore can influence which pathway QseC regulates.IMPORTANCE In the foodborne pathogen EHEC, QseC senses AI-3, epinephrine, and norepinephrine, increases its autophosphorylation, and then transfers its phosphate to three RRs: QseB, QseF, and KdpE. QseB controls expression of flagella and motility, KdpE controls expression of the LEE region, and QseF controls the expression of Shiga toxin. This tripartite signaling pathway must be tightly controlled, given that flagella and the type three secretion system (T3SS) are energetically expensive appendages and Shiga toxin expression leads to bacterial cell lysis. Our data suggest that mutations in the periplasmic sensing loop of QseC differentially affect the expression of the three arms of this signaling cascade. This suggests that these point mutations may change QseC's phosphotransfer preferences for its RRs.
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Klein G, Stupak A, Biernacka D, Wojtkiewicz P, Lindner B, Raina S. Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective. J Biol Chem 2016; 291:22999-23019. [PMID: 27629414 DOI: 10.1074/jbc.m116.748954] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
The RpoE σ factor is essential for the viability of Escherichia coli RpoE regulates extracytoplasmic functions including lipopolysaccharide (LPS) translocation and some of its non-stoichiometric modifications. Transcription of the rpoE gene is positively autoregulated by EσE and by unknown mechanisms that control the expression of its distally located promoter(s). Mapping of 5' ends of rpoE mRNA identified five new transcriptional initiation sites (P1 to P5) located distal to EσE-regulated promoter. These promoters are activated in response to unique signals. Of these P2, P3, and P4 defined major promoters, recognized by RpoN, RpoD, and RpoS σ factors, respectively. Isolation of trans-acting factors, in vitro transcriptional and gel retardation assays revealed that the RpoN-recognized P2 promoter is positively regulated by a QseE/F two-component system and NtrC activator, whereas the RpoD-regulated P3 promoter is positively regulated by a Rcs system in response to defects in LPS core biosynthesis, overproduction of certain lipoproteins, and the global regulator CRP. Strains synthesizing Kdo2-LA LPS caused up to 7-fold increase in the rpoEP3 activity, which was abrogated in Δ(waaC rcsB). Overexpression of a novel 73-nucleotide sRNA rirA (RfaH interacting RNA) generated by the processing of 5' UTR of the waaQ mRNA induces the rpoEP3 promoter activity concomitant with a decrease in LPS content and defects in the O-antigen incorporation. In the presence of RNA polymerase, RirA binds LPS regulator RfaH known to prevent premature transcriptional termination of waaQ and rfb operons. RirA in excess could titrate out RfaH causing LPS defects and the activation of rpoE transcription.
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Affiliation(s)
- Gracjana Klein
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Anna Stupak
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Daria Biernacka
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Pawel Wojtkiewicz
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Buko Lindner
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, 23845 Borstel, Germany
| | - Satish Raina
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
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Khan MA, Göpel Y, Milewski S, Görke B. Two Small RNAs Conserved in Enterobacteriaceae Provide Intrinsic Resistance to Antibiotics Targeting the Cell Wall Biosynthesis Enzyme Glucosamine-6-Phosphate Synthase. Front Microbiol 2016; 7:908. [PMID: 27379045 PMCID: PMC4908143 DOI: 10.3389/fmicb.2016.00908] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/27/2016] [Indexed: 11/17/2022] Open
Abstract
Formation of glucosamine-6-phosphate (GlcN6P) by enzyme GlcN6P synthase (GlmS) represents the first step in bacterial cell envelope synthesis. In Escherichia coli, expression of glmS is controlled by small RNAs (sRNAs) GlmY and GlmZ. GlmZ activates the glmS mRNA by base-pairing. When not required, GlmZ is bound by adapter protein RapZ and recruited to cleavage by RNase E inactivating the sRNA. The homologous sRNA GlmY activates glmS indirectly. When present at high levels, GlmY sequesters RapZ by an RNA mimicry mechanism suppressing cleavage of GlmZ. The interplay of both sRNAs is believed to adjust GlmS synthesis to the needs of the cell, i.e., to achieve GlcN6P homeostasis. Bacilysin (tetaine) and Nva-FMDP are dipeptide antibiotics that impair cell envelope synthesis by inhibition of enzyme GlmS through covalent modification. However, although taken up efficiently, these antibiotics are less active against E. coli for reasons unknown so far. Here we show that the GlmY/GlmZ circuit provides resistance. Inhibition of GlmS causes GlcN6P deprivation leading to activation of GlmY and GlmZ, which in turn trigger glmS overexpression in a dosage-dependent manner. Mutation of glmY or glmZ disables this response and renders the bacteria highly susceptible to GlmS inhibitors. Thus, E. coli compensates inhibition of GlmS by increasing its synthesis through the GlmY/GlmZ pathway. This mechanism is also operative in Salmonella indicating that it is conserved in Enterobacteriaceae possessing these sRNAs. As GlmY apparently responds to GlcN6P, co-application of a non-metabolizable GlcN6P analog may prevent activation of the sRNAs and thereby increase the bactericidal activity of GlmS inhibitors against wild-type bacteria. Initial experiments using glucosamine-6-sulfate support this possibility. Thus, GlcN6P analogs might be considered for co-application with GlmS inhibitors in combined therapy to treat infections caused by pathogenic Enterobacteriaceae.
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Affiliation(s)
- Muna A. Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BiocenterVienna, Austria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BiocenterVienna, Austria
| | - Slawomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of TechnologyGdańsk, Poland
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BiocenterVienna, Austria
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Interkingdom Chemical Signaling in Enterohemorrhagic Escherichia coli O157:H7. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 874:201-13. [DOI: 10.1007/978-3-319-20215-0_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Bonocora RP, Smith C, Lapierre P, Wade JT. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. PLoS Genet 2015; 11:e1005552. [PMID: 26425847 PMCID: PMC4591121 DOI: 10.1371/journal.pgen.1005552] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription. There are two families of σ factor: σ70 and σ54. Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences, in association with RNA polymerase, in a transcriptionally inactive state. We have determined positions in the Escherichia coli genome that are bound by σ54, the archetypal member of the σ54 family. Surprisingly, we identified 135 binding sites for σ54, a huge increase over the number of previously described sites. Our data suggest that there are more than 250 σ54 sites in total. Strikingly, most σ54 binding sites are located inside genes, whereas only one intragenic σ54 binding site has previously been described. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved in other bacterial species. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this notion, we identify three σ54 promoters in E. coli that are located inside genes but drive transcription of unusual mRNAs for the neighboring genes.
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Affiliation(s)
- Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail:
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Martínez-Chavarría LC, Vadyvaloo V. Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective. Front Microbiol 2015; 6:956. [PMID: 26441890 PMCID: PMC4585118 DOI: 10.3389/fmicb.2015.00956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022] Open
Abstract
Yersinia pestis, responsible for causing fulminant plague, has evolved clonally from the enteric pathogen, Y. pseudotuberculosis, which in contrast, causes a relatively benign enteric illness. An ~97% nucleotide identity over 75% of their shared protein coding genes is maintained between these two pathogens, leaving much conjecture regarding the molecular determinants responsible for producing these vastly different disease etiologies, host preferences and transmission routes. One idea is that coordinated production of distinct factors required for host adaptation and virulence in response to specific environmental cues could contribute to the distinct pathogenicity distinguishing these two species. Small non-coding RNAs that direct posttranscriptional regulation have recently been identified as key molecules that may provide such timeous expression of appropriate disease enabling factors. Here the burgeoning field of small non-coding regulatory RNAs in Yersinia pathogenesis is reviewed from the viewpoint of adaptive colonization, virulence and divergent evolution of these pathogens.
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Affiliation(s)
- Luary C Martínez-Chavarría
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México Mexico
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA USA
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Papenfort K, Vanderpool CK. Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 2015; 39:362-78. [PMID: 25934124 DOI: 10.1093/femsre/fuv016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA Department of Biology I, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Global analysis of posttranscriptional regulation by GlmY and GlmZ in enterohemorrhagic Escherichia coli O157:H7. Infect Immun 2015; 83:1286-95. [PMID: 25605763 DOI: 10.1128/iai.02918-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a significant human pathogen and is the cause of bloody diarrhea and hemolytic-uremic syndrome. The virulence repertoire of EHEC includes the genes within the locus of enterocyte effacement (LEE) that are largely organized in five operons, LEE1 to LEE5, which encode a type III secretion system, several effectors, chaperones, and regulatory proteins. In addition, EHEC also encodes several non-LEE-encoded effectors and fimbrial operons. The virulence genes of this pathogen are under a large amount of posttranscriptional regulation. The small RNAs (sRNAs) GlmY and GlmZ activate the translation of glucosamine synthase (GlmS) in E. coli K-12, and in EHEC they destabilize the 3' fragments of the LEE4 and LEE5 operons and promote translation of the non-LEE-encoded effector EspFu. We investigated the global changes of EHEC gene expression governed by GlmY and GlmZ using RNA sequencing and gene arrays. This study extends the known effects of GlmY and GlmZ regulation to show that they promote expression of the curli adhesin, repress the expression of tryptophan metabolism genes, and promote the expression of acid resistance genes and the non-LEE-encoded effector NleA. In addition, seven novel EHEC-specific sRNAs were identified using RNA sequencing, and three of them--sRNA56, sRNA103, and sRNA350--were shown to regulate urease, fimbria, and the LEE, respectively. These findings expand the knowledge of posttranscriptional regulation in EHEC.
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Caswell CC, Oglesby-Sherrouse AG, Murphy ER. Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles. Front Cell Infect Microbiol 2014; 4:151. [PMID: 25389522 PMCID: PMC4211561 DOI: 10.3389/fcimb.2014.00151] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
Small RNA molecules (sRNAs) are now recognized as key regulators controlling bacterial gene expression, as sRNAs provide a quick and efficient means of positively or negatively altering the expression of specific genes. To date, numerous sRNAs have been identified and characterized in a myriad of bacterial species, but more recently, a theme in bacterial sRNAs has emerged: the presence of more than one highly related sRNAs produced by a given bacterium, here termed sibling sRNAs. Sibling sRNAs are those that are highly similar at the nucleotide level, and while it might be expected that sibling sRNAs exert identical regulatory functions on the expression of target genes based on their high degree of relatedness, emerging evidence is demonstrating that this is not always the case. Indeed, there are several examples of bacterial sibling sRNAs with non-redundant regulatory functions, but there are also instances of apparent regulatory redundancy between sibling sRNAs. This review provides a comprehensive overview of the current knowledge of bacterial sibling sRNAs, and also discusses important questions about the significance and evolutionary implications of this emerging class of regulators.
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Affiliation(s)
- Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD Regional College of Veterinary Medicine, Virginia Tech Blacksburg, VA, USA
| | - Amanda G Oglesby-Sherrouse
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD, USA ; Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, MD, USA
| | - Erin R Murphy
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine Athens, OH, USA
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Papenfort K, Vogel J. Small RNA functions in carbon metabolism and virulence of enteric pathogens. Front Cell Infect Microbiol 2014; 4:91. [PMID: 25077072 PMCID: PMC4098024 DOI: 10.3389/fcimb.2014.00091] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Enteric pathogens often cycle between virulent and saprophytic lifestyles. To endure these frequent changes in nutrient availability and composition bacteria possess an arsenal of regulatory and metabolic genes allowing rapid adaptation and high flexibility. While numerous proteins have been characterized with regard to metabolic control in pathogenic bacteria, small non-coding RNAs have emerged as additional regulators of metabolism. Recent advances in sequencing technology have vastly increased the number of candidate regulatory RNAs and several of them have been found to act at the interface of bacterial metabolism and virulence factor expression. Importantly, studying these riboregulators has not only provided insight into their metabolic control functions but also revealed new mechanisms of post-transcriptional gene control. This review will focus on the recent advances in this area of host-microbe interaction and discuss how regulatory small RNAs may help coordinate metabolism and virulence of enteric pathogens.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University Princeton, NJ, USA
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg Würzburg, Germany
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Göpel Y, Khan MA, Görke B. Ménage à trois: post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic. RNA Biol 2014; 11:433-42. [PMID: 24667238 PMCID: PMC4152352 DOI: 10.4161/rna.28301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In Escherichia coli, small RNAs GlmY and GlmZ feedback control synthesis of glucosamine-6-phosphate (GlcN6P) synthase GlmS, a key enzyme required for synthesis of the cell envelope. Both small RNAs are highly similar, but only GlmZ is able to activate the glmS mRNA by base-pairing. Abundance of GlmZ is controlled at the level of decay by RNase adaptor protein RapZ. RapZ binds and targets GlmZ to degradation by RNase E via protein–protein interaction. GlmY activates glmS indirectly by protecting GlmZ from degradation. Upon GlcN6P depletion, GlmY accumulates and sequesters RapZ in an RNA mimicry mechanism, thus acting as an anti-adaptor. As a result, this regulatory circuit adjusts synthesis of GlmS to the level of its enzymatic product, thereby mediating GlcN6P homeostasis. The interplay of RNase adaptor proteins and anti-adaptors provides an elegant means how globally acting RNases can be re-programmed to cleave a specific transcript in response to a cognate stimulus.
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Affiliation(s)
- Yvonne Göpel
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Muna A Khan
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Boris Görke
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
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Abstract
UNLABELLED Remodeling of the host cytoskeleton is a common strategy employed by bacterial pathogens. Although there is vigorous investigation of the cell biology underlying these bacterially mediated cytoskeleton modifications, knowledge of the plasticity and dynamics of the bacterial signaling networks that regulate the expression of genes necessary for these phenotypes is lacking. Enterohemorrhagic Escherichia coli attaches to enterocytes, forming pedestal-like structures. Pedestal formation requires the expression of the locus-of-enterocyte-effacement (LEE) and espFu genes. The LEE encodes a molecular syringe, a type III secretion system (T3SS) used by pathogens to translocate effectors such as EspFu into the host cell. By using a combination of genetic, biochemical, and cell biology approaches, we show that pedestal formation relies on posttranscriptional regulation by two small RNAs (sRNAs), GlmY and GlmZ. The GlmY and GlmZ sRNAs are unique; they have extensive secondary structures and work in concert. Although these sRNAs may offer unique insights into RNA and posttranscriptional biology, thus far, only one target and one mechanism of action (exposure of the ribosome binding site from the glmS gene to promote its translation) has been described. Here we uncovered new targets and two different molecular mechanisms of action of these sRNAs. In the case of EspFu expression, they promote translation by cleavage of the transcript, while in regard to the LEE, they promote destabilization of the mRNA. Our findings reveal that two unique sRNAs act in concert through different molecular mechanisms to coordinate bacterial attachment to mammalian cells. IMPORTANCE Pathogens evolve by horizontal acquisition of pathogenicity islands. We describe here how two sRNAs, GlmY and GlmZ, involved in cellular metabolism and cellular architecture, through the posttranscriptional control of GlmS (the previously only known target of GlmY and GlmZ), which controls amino sugar synthesis, have been coopted to modulate the expression of virulence. These sRNAs quickly allow for plasticity in gene expression in order for enterohemorrhagic Escherichia coli to fine-tune the expression of its complex type III secretion machinery and its effectors to promote bacterial attachment and subsequent actin rearrangement on host cells. Pedestal formation is a very dynamic process. Many of the genes necessary for pedestal formation are located within the same operon to evolutionarily guarantee that they are inherited together. However, it is worth noting that within these operons, several genes need to yield more proteins than others and that these differences cannot be efficiently regulated at the transcriptional level.
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Das C, Dutta A, Rajasingh H, Mande SS. Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling. Gut Pathog 2013; 5:28. [PMID: 24079299 PMCID: PMC3849742 DOI: 10.1186/1757-4749-5-28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/14/2013] [Indexed: 01/13/2023] Open
Abstract
Background Three pathogenicity islands, viz. SPI-1 (Salmonella pathogenicity island 1), SPI-2 (Salmonella pathogenicity island 2) and T6SS (Type VI Secretion System), present in the genome of Salmonella typhimurium have been implicated in the virulence of the pathogen. While the regulation of SPI-1 and SPI-2 (both encoding components of the Type III Secretion System - T3SS) are well understood, T6SS regulation is comparatively less studied. Interestingly, inter-connections among the regulatory elements of these three virulence determinants have also been suggested to be essential for successful infection. However, till date, an integrated view of gene regulation involving the regulators of these three secretion systems and their cross-talk is not available. Results In the current study, relevant regulatory information available from literature have been integrated into a single Boolean network, which portrays the dynamics of T3SS (SPI-1 and SPI-2) and T6SS mediated virulence. Some additional regulatory interactions involving a two-component system response regulator YfhA have also been predicted and included in the Boolean network. These predictions are aimed at deciphering the effects of osmolarity on T6SS regulation, an aspect that has been suggested in earlier studies, but the mechanism of which was hitherto unknown. Simulation of the regulatory network was able to recreate in silico the experimentally observed sequential activation of SPI-1, SPI-2 and T6SS. Conclusions The present study integrates relevant gene regulatory data (from literature and our prediction) into a single network, representing the cross-communication between T3SS (SPI-1 and SPI-2) and T6SS. This holistic view of regulatory interactions is expected to improve the current understanding of pathogenesis of S. typhimurium.
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Affiliation(s)
- Chandrani Das
- Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune 411013, Maharashtra, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune 411013, Maharashtra, India
| | - Hannah Rajasingh
- Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune 411013, Maharashtra, India.,Present address: Novartis Healthcare Pvt. Ltd., #6 Raheja Mindspace, Hitec-city, Hyderabad 500081, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune 411013, Maharashtra, India
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Zaprasis A, Hoffmann T, Wünsche G, Flórez LA, Stülke J, Bremer E. Mutational activation of the RocR activator and of a crypticrocDEFpromoter bypass loss of the initial steps of proline biosynthesis inBacillus subtilis. Environ Microbiol 2013; 16:701-17. [DOI: 10.1111/1462-2920.12193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Adrienne Zaprasis
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Guido Wünsche
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Lope A. Flórez
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Jörg Stülke
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
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Göpel Y, Papenfort K, Reichenbach B, Vogel J, Görke B. Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Genes Dev 2013; 27:552-64. [PMID: 23475961 DOI: 10.1101/gad.210112.112] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bacterial small RNAs (sRNAs) are well established to regulate diverse cellular processes, but how they themselves are regulated is less understood. Recently, we identified a regulatory circuit wherein the GlmY and GlmZ sRNAs of Escherichia coli act hierarchically to activate mRNA glmS, which encodes glucosamine-6-phosphate (GlcN6P) synthase. Although the two sRNAs are highly similar, only GlmZ is a direct activator that base-pairs with the glmS mRNA, aided by protein Hfq. GlmY, however, does not bind Hfq and activates glmS indirectly by protecting GlmZ from RNA cleavage. This complex regulation feedback controls the levels of GlmS protein in response to its product, GlcN6P, a key metabolite in cell wall biosynthesis. Here, we reveal the molecular basis for the regulated turnover of GlmZ, identifying RapZ (RNase adaptor protein for sRNA GlmZ; formerly YhbJ) as a novel type of RNA-binding protein that recruits the major endoribonuclease RNase E to GlmZ. This involves direct interaction of RapZ with the catalytic domain of RNase E. GlmY binds RapZ through a secondary structure shared by both sRNAs and therefore acts by molecular mimicry as a specific decoy for RapZ. Thus, in analogy to regulated proteolysis, RapZ is an adaptor, and GlmY is an anti-adaptor in regulated turnover of a regulatory small RNA.
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Affiliation(s)
- Yvonne Göpel
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, D-37077 Göttingen, Germany
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Expanding control in bacteria: interplay between small RNAs and transcriptional regulators to control gene expression. Curr Opin Microbiol 2013; 16:125-32. [PMID: 23415757 DOI: 10.1016/j.mib.2012.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/21/2012] [Accepted: 12/29/2012] [Indexed: 11/20/2022]
Abstract
Small regulatory RNAs (sRNAs) are now considered as major post-transcriptional regulators of gene expression in bacteria. Their importance is related to their variety in probably all bacterial species as well as to the extreme diversity of physiological functions of their target genes. An increasing amount of data point to an intimate connection between sRNAs and transcriptional regulatory networks to control multiple functions as important as motility or group behavior. The resulting mixed circuits unravel novel regulatory links and their properties are just starting to be characterized.
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Xiao J, Chen T, Yang M, Zhang Y, Wang Q. Identification of qseEGF genetic locus and its roles in controlling hemolytic activity and invasion in fish pathogen Edwardsiella tarda. Lett Appl Microbiol 2012; 55:91-8. [PMID: 22694092 DOI: 10.1111/j.1472-765x.2012.03260.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The aims of this study were to reveal the roles of the gene locus qseEGF in the pathogenesis of Edwardsiella tarda. METHODS AND RESULTS Genome sequencing of fish pathogen E. tarda EIB202 reveals that the gene locus qseEGF, which encodes a novel two-component system QseEF, were located in E. tarda. The transcription of qseE, qseF and qseG was firstly characterized to be cotranscribed by reverse-transcribed PCR (RT-PCR). The mutant strains ΔqseE, ΔqseF and ΔqseG were constructed with in-frame deletion strategy. Compared with the wild type, all of the mutants showed attenuated virulence and impaired intracellular survival capabilities. Deletion in qseE, qseF and qseG resulted in different effects on hemolysin production in E. tarda. qRT-PCR results indicated that QseEF played a role in regulation of secretion systems, which in turn affected the virulence of E. tarda. CONCLUSIONS The results manifested that QseEF system affected the virulence in E. tarda EIB202 by controlling the secretion system and hemolysin production. QseE, QseG and QseF in E. tarda serve for the physiological fitness and pathogenesis related to the bacterial survival in macrophage and in vivo of fish. SIGNIFICANCE AND IMPACT The present results suggested that the important role of two-component system QseEF in regulation of E. tarda pathogenesis and its potential for attenuated live vaccine construction.
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Affiliation(s)
- Jingfan Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Kawada-Matsuo M, Mazda Y, Oogai Y, Kajiya M, Kawai T, Yamada S, Miyawaki S, Oho T, Komatsuzawa H. GlmS and NagB regulate amino sugar metabolism in opposing directions and affect Streptococcus mutans virulence. PLoS One 2012; 7:e33382. [PMID: 22438919 PMCID: PMC3306399 DOI: 10.1371/journal.pone.0033382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 02/14/2012] [Indexed: 11/18/2022] Open
Abstract
Streptococcus mutans is a cariogenic pathogen that produces an extracellular polysaccharide (glucan) from dietary sugars, which allows it to establish a reproductive niche and secrete acids that degrade tooth enamel. While two enzymes (GlmS and NagB) are known to be key factors affecting the entrance of amino sugars into glycolysis and cell wall synthesis in several other bacteria, their roles in S. mutans remain unclear. Therefore, we investigated the roles of GlmS and NagB in S. mutans sugar metabolism and determined whether they have an effect on virulence. NagB expression increased in the presence of GlcNAc while GlmS expression decreased, suggesting that the regulation of these enzymes, which functionally oppose one another, is dependent on the concentration of environmental GlcNAc. A glmS-inactivated mutant could not grow in the absence of GlcNAc, while nagB-inactivated mutant growth was decreased in the presence of GlcNAc. Also, nagB inactivation was found to decrease the expression of virulence factors, including cell-surface protein antigen and glucosyltransferase, and to decrease biofilm formation and saliva-induced S. mutans aggregation, while glmS inactivation had the opposite effects on virulence factor expression and bacterial aggregation. Our results suggest that GlmS and NagB function in sugar metabolism in opposing directions, increasing and decreasing S. mutans virulence, respectively.
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Affiliation(s)
- Miki Kawada-Matsuo
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yusuke Mazda
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department of Orthodontics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mikihito Kajiya
- Department of Immunology, The Forsyth Institute, Boston, Massachusetts, United States of America
| | - Toshihisa Kawai
- Department of Immunology, The Forsyth Institute, Boston, Massachusetts, United States of America
| | - Sakuo Yamada
- Department of Microbiology, Kawasaki Medical School, Okayama, Japan
- Department of Clinical Nutrition, Kawasaki Medical Welfare, Okayama, Japan
| | - Shouichi Miyawaki
- Department of Orthodontics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takahiko Oho
- Department of Preventive Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- * E-mail:
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Göpel Y, Görke B. Rewiring two-component signal transduction with small RNAs. Curr Opin Microbiol 2011; 15:132-9. [PMID: 22197250 DOI: 10.1016/j.mib.2011.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/24/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
Abstract
Bacterial two-component systems (TCSs) and small regulatory RNAs (sRNAs) form densely interconnected networks that integrate and transduce information from the environment into fine-tuned changes of gene expression. Many TCSs control target genes indirectly through regulation of sRNAs, which in turn regulate gene expression by base-pairing with mRNAs or targeting a protein. Conversely, sRNAs may control TCS synthesis, thereby recruiting the TCS regulon to other regulatory networks. Several TCSs control expression of multiple homologous sRNAs providing the regulatory networks with further flexibility. These sRNAs act redundantly, additively or hierarchically on targets. The regulatory speed of sRNAs and their unique features in gene regulation make them ideal players extending the flexibility, dynamic range or timing of TCS signaling.
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Affiliation(s)
- Yvonne Göpel
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany
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Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a003798. [PMID: 20980440 DOI: 10.1101/cshperspect.a003798] [Citation(s) in RCA: 538] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Small RNA regulators (sRNAs) have been identified in a wide range of bacteria and found to play critical regulatory roles in many processes. The major families of sRNAs include true antisense RNAs, synthesized from the strand complementary to the mRNA they regulate, sRNAs that also act by pairing but have limited complementarity with their targets, and sRNAs that regulate proteins by binding to and affecting protein activity. The sRNAs with limited complementarity are akin to eukaryotic microRNAs in their ability to modulate the activity and stability of multiple mRNAs. In many bacterial species, the RNA chaperone Hfq is required to promote pairing between these sRNAs and their target mRNAs. Understanding the evolution of regulatory sRNAs remains a challenge; sRNA genes show evidence of duplication and horizontal transfer but also could be evolved from tRNAs, mRNAs or random transcription.
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Francke C, Groot Kormelink T, Hagemeijer Y, Overmars L, Sluijter V, Moezelaar R, Siezen RJ. Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics 2011; 12:385. [PMID: 21806785 PMCID: PMC3162934 DOI: 10.1186/1471-2164-12-385] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 08/01/2011] [Indexed: 02/06/2023] Open
Abstract
Background Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. Results We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. Conclusion Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm.
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Affiliation(s)
- Christof Francke
- TI Food and Nutrition, P,O,Box 557, 6700AN Wageningen, The Netherlands.
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Chen Y, Indurthi DC, Jones SW, Papoutsakis ET. Small RNAs in the genus Clostridium. mBio 2011; 2:e00340-10. [PMID: 21264064 PMCID: PMC3025663 DOI: 10.1128/mbio.00340-10] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 01/03/2011] [Indexed: 11/20/2022] Open
Abstract
The genus Clostridium includes major human pathogens and species important to cellulose degradation, the carbon cycle, and biotechnology. Small RNAs (sRNAs) are emerging as crucial regulatory molecules in all organisms, but they have not been investigated in clostridia. Research on sRNAs in clostridia is hindered by the absence of a systematic method to identify sRNA candidates, thus delegating clostridial sRNA research to a hit-and-miss process. Thus, we wanted to develop a method to identify potential sRNAs in the Clostridium genus to open up the field of sRNA research in clostridia. Using comparative genomics analyses combined with predictions of rho-independent terminators and promoters, we predicted sRNAs in 21 clostridial genomes: Clostridium acetobutylicum, C. beijerinckii, C. botulinum (eight strains), C. cellulolyticum, C. difficile, C. kluyveri (two strains), C. novyi, C. perfringens (three strains), C. phytofermentans, C. tetani, and C. thermocellum. Although more than one-third of predicted sRNAs have Shine-Dalgarno (SD) sequences, only one-sixth have a start codon downstream of SD sequences; thus, most of the predicted sRNAs are noncoding RNAs. Quantitative reverse transcription-PCR (Q-RT-PCR) and Northern analysis were employed to test the presence of a randomly chosen set of sRNAs in C. acetobutylicum and several C. botulinum strains, leading to the confirmation of a large fraction of the tested sRNAs. We identified a conserved, novel sRNA which, together with the downstream gene coding for an ATP-binding cassette (ABC) transporter gene, responds to the antibiotic clindamycin. The number of predicted sRNAs correlated with the physiological function of the species (high for pathogens, low for cellulolytic, and intermediate for solventogenic), but not with 16S rRNA-based phylogeny.
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Affiliation(s)
- Yili Chen
- Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, Newark, Delaware, USA
- Department of Chemical Engineering, Colburn Laboratory, University of Delaware, Newark, Delaware, USA; and
| | - Dinesh C. Indurthi
- Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, Newark, Delaware, USA
- Department of Chemical Engineering, Colburn Laboratory, University of Delaware, Newark, Delaware, USA; and
| | - Shawn W. Jones
- Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, Newark, Delaware, USA
- Department of Chemical Engineering, Colburn Laboratory, University of Delaware, Newark, Delaware, USA; and
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Eleftherios T. Papoutsakis
- Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, Newark, Delaware, USA
- Department of Chemical Engineering, Colburn Laboratory, University of Delaware, Newark, Delaware, USA; and
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
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Göpel Y, Lüttmann D, Heroven AK, Reichenbach B, Dersch P, Görke B. Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae. Nucleic Acids Res 2010; 39:1294-309. [PMID: 20965974 PMCID: PMC3045617 DOI: 10.1093/nar/gkq986] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small RNAs GlmY and GlmZ compose a cascade that feedback-regulates synthesis of enzyme GlmS in Enterobacteriaceae. Here, we analyzed the transcriptional regulation of glmY/glmZ from Yersinia pseudotuberculosis, Salmonella typhimurium and Escherichia coli, as representatives for other enterobacterial species, which exhibit similar promoter architectures. The GlmY and GlmZ sRNAs of Y. pseudotuberculosis are transcribed from σ54-promoters that require activation by the response regulator GlrR through binding to three conserved sites located upstream of the promoters. This also applies to glmY/glmZ of S. typhimurium and glmY of E. coli, but as a difference additional σ70-promoters overlap the σ54-promoters and initiate transcription at the same site. In contrast, E. coli glmZ is transcribed from a single σ70-promoter. Thus, transcription of glmY and glmZ is controlled by σ54 and the two-component system GlrR/GlrK (QseF/QseE) in Y. pseudotuberculosis and presumably in many other Enterobacteria. However, in a subset of species such as E. coli this relationship is partially lost in favor of σ70-dependent transcription. In addition, we show that activity of the σ54-promoter of E. coli glmY requires binding of the integration host factor to sites upstream of the promoter. Finally, evidence is provided that phosphorylation of GlrR increases its activity and thereby sRNA expression.
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Affiliation(s)
- Yvonne Göpel
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany
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Reading NC, Rasko D, Torres AG, Sperandio V. A transcriptome study of the QseEF two-component system and the QseG membrane protein in enterohaemorrhagic Escherichia coli O157 : H7. MICROBIOLOGY-SGM 2010; 156:1167-1175. [PMID: 20056703 DOI: 10.1099/mic.0.033027-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
QseE is a sensor kinase that responds to epinephrine, sulfate and phosphate. QseE constitutes a two-component signalling system together with the QseF sigma(54)-dependent response regulator. Encoded within the same operon as qseEF is the qseG gene, which encodes a membrane protein involved in the translocation of a type III secretion effector protein of enterohaemorrhagic Escherichia coli (EHEC) into epithelial cells. The qseEGF genes also form an operon with the glnB gene, which encodes the E. coli nitrogen sensor PII protein. Here we report a transcriptome analysis comparing qseE, qseF andqseG single mutants with the wild-type strain. This study revealed that the proteins encoded by these genes play a modest but significant role in iron uptake. Although QseEFG regulate genes involved in nitrogen utilization, these proteins do not play a notable role in nitrogen metabolism. In addition, QseEFG regulate transcription of the rcsBC and phoPQ two-component systems, linking several signal transduction pathways. The similarity of the microarray profiles of these mutants also indicates that these proteins work together. These data indicate that QseEFG are involved in the regulation of virulence and metabolism in EHEC.
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Affiliation(s)
- Nicola C Reading
- Department of Microbiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9048, USA
| | - David Rasko
- Department of Microbiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9048, USA
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
| | - Vanessa Sperandio
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9048, USA.,Department of Microbiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9048, USA
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