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Tanudjaja E, Hoshi N, Yamamoto K, Ihara K, Furuta T, Tsujii M, Ishimaru Y, Uozumi N. Two Trk/Ktr/HKT-type potassium transporters, TrkG and TrkH, perform distinct functions in Escherichia coli K-12. J Biol Chem 2022; 299:102846. [PMID: 36586436 PMCID: PMC9898762 DOI: 10.1016/j.jbc.2022.102846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli K-12 possesses two versions of Trk/Ktr/HKT-type potassium ion (K+) transporters, TrkG and TrkH. The current paradigm is that TrkG and TrkH have largely identical characteristics, and little information is available regarding their functional differences. Here, we show using cation uptake experiments with K+ transporter knockout mutants that TrkG and TrkH have distinct ion transport activities and physiological roles. K+-transport by TrkG required Na+, whereas TrkH-mediated K+ uptake was not affected by Na+. An aspartic acid located five residues away from a critical glycine in the third pore-forming region might be involved in regulation of Na+-dependent activation of TrkG. In addition, we found that TrkG but not TrkH had Na+ uptake activity. Our analysis of K+ transport mutants revealed that TrkH supported cell growth more than TrkG; however, TrkG was able to complement loss of TrkH-mediated K+ uptake in E. coli. Furthermore, we determined that transcription of trkG in E. coli was downregulated but not completely silenced by the xenogeneic silencing factor H-NS (histone-like nucleoid structuring protein or heat-stable nucleoid-structuring protein). Taken together, the transport function of TrkG is clearly distinct from that of TrkH, and TrkG seems to have been accepted by E. coli during evolution as a K+ uptake system that coexists with TrkH.
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Affiliation(s)
- Ellen Tanudjaja
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Naomi Hoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | | | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masaru Tsujii
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yasuhiro Ishimaru
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.
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2
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Im H, Lee JH, Choi SH. Independent Component Analysis Identifies the Modulons Expanding the Transcriptional Regulatory Networks of Enterohemorrhagic Escherichia coli. Front Microbiol 2022; 13:953404. [PMID: 35814713 PMCID: PMC9263587 DOI: 10.3389/fmicb.2022.953404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 01/19/2023] Open
Abstract
The elucidation of the transcriptional regulatory networks (TRNs) of enterohemorrhagic Escherichia coli (EHEC) is critical to understand its pathogenesis and survival in the host. However, the analyses of current TRNs are still limited to comprehensively understand their target genes generally co-regulated under various conditions regardless of the genetic backgrounds. In this study, independent component analysis (ICA), a machine learning-based decomposition method, was used to decompose the large-scale transcriptome data of EHEC into the modulons, which contain the target genes of several TRNs. The locus of enterocyte effacement (LEE) and the Shiga toxin (Stx) modulons mainly consisted of the Ler regulon and the Stx prophage genes, respectively, confirming that ICA properly grouped the co-regulated major virulence genes of EHEC. Further investigation revealed that the LEE modulon contained the hypothetical Z0395 gene as a novel member of the Ler regulon, and the Stx modulon contained the thi and cus locus genes in addition to the Stx prophage genes. Correspondingly, the Stx prophage genes were also regulated by thiamine and copper ions known to control the thi and cus locus genes, respectively. The modulons effectively clustered the genes co-regulated regardless of the growth conditions and the genetic backgrounds of EHEC. The changed activities of the individual modulons successfully explained the differential expressions of the virulence and survival genes during the course of infection in bovines. Altogether, these results suggested that ICA of the large-scale transcriptome data can expand and enhance the current understanding of the TRNs of EHEC.
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Affiliation(s)
- Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Ju-Hoon Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
- *Correspondence: Ju-Hoon Lee,
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
- Sang Ho Choi,
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3
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Lato DF, Zeng Q, Golding GB. Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites. Genome 2022; 65:287-299. [DOI: 10.1139/gen-2021-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic reorganization, like rearrangements and inversions, influence how genetic information is organized within bacterial genomes. Inversions in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies investigating the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome wide perspective on naturally occurring inversions and their post adaptation impact on gene expression. Here we use bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within <i>Escherichia coli</i>. We observed differences in gene expression between homologous inverted and non-inverted genes, even after long term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with nearly two thirds (71%) of differentially expressed inverted genes having 9.4-85.6 fold higher gene expression. The identified inversions had more overlap than expected with nucleoid associated protein binding sites, which assist in genomic gene expression regulation. Some inversions can drastically impact gene expression even between different strains of <i>E.coli</i>, and could provide a mechanism for the diversification of genetic content through controlled expression changes.
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Affiliation(s)
| | - Qing Zeng
- McMaster University, Department of Biology, Hamilton, Ontario, Canada,
| | - G. Brian Golding
- McMaster University, Department of Biology, 1280 Main Street West, Hamilton, Ontario, Canada, L8S 4K1,
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4
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Long-Distance Effects of H-NS Binding in the Control of hilD Expression in the Salmonella SPI1 Locus. J Bacteriol 2021; 203:e0030821. [PMID: 34424033 DOI: 10.1128/jb.00308-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Typhimurium utilizes a type three secretion system (T3SS) carried on the Salmonella pathogenicity island 1 (SPI1) to invade intestinal epithelial cells and induce inflammatory diarrhea. HilA activates expression of the T3SS structural genes. Expression of hyper invasion locus A (hilA) is controlled by the transcription factors HilD, HilC, and RtsA, which act in a complex feed-forward regulatory loop. The nucleoid-associated protein H-NS is a xenogeneic silencer that has a major effect on SPI1 expression. In this work, we use genetic techniques to show that disruptions of the chromosomal region surrounding hilD have a cis effect on H-NS-mediated repression of the hilD promoter; this effect occurs asymmetrically over ∼4 kb spanning the prgH-hilD intergenic region. CAT cassettes inserted at various positions in this region are also silenced in relation to the proximity to the hilD promoter. We identify a putative H-NS nucleation site, and its mutation results in derepression of the locus. Furthermore, we genetically show that HilD abrogates H-NS-mediated silencing to activate the hilD promoter. In contrast, H-NS-mediated repression of the hilA promoter, downstream of hilD, is through its control of HilD, which directly activates hilA transcription. Likewise, activation of the prgH promoter, although in a region silenced by H-NS, is strictly dependent on HilA. In summary, we propose a model in which H-NS nucleates within the hilD promoter region to polymerize and exert its repressive effect. Thus, H-NS-mediated repression of SPI1 is primarily through the control of hilD expression, with HilD capable of overcoming H-NS to autoactivate. IMPORTANCE Members of the foodborne pathogen Salmonella rely on a type III secretion system to invade intestinal epithelial cells and initiate infection. This system was acquired through horizontal gene transfer, essentially creating the Salmonella genus. Expression of this critical virulence factor is controlled by a complex regulatory network. The nucleoid protein H-NS is a global repressor of horizontally acquired genomic loci. Here, we identify the critical site of H-NS regulation in this system and show that alterations to the DNA over a surprisingly large region affect this regulation, providing important information regarding the mechanism of H-NS action.
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5
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Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa A, Bowring N, Boyle A, Ubbink M, Dove S, Dame R. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res 2021; 49:10770-10784. [PMID: 34520554 PMCID: PMC8501957 DOI: 10.1093/nar/gkab793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amanda M Erkelens
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew M Lippa
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Bowring
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Aimee L Boyle
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Simon L Dove
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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6
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Son B, Patterson-West J, Arroyo-Mendoza M, Ramachandran R, Iben J, Zhu J, Rao V, Dimitriadis E, Hinton D. A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing. Nucleic Acids Res 2021; 49:9229-9245. [PMID: 34365505 PMCID: PMC8450097 DOI: 10.1093/nar/gkab678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleoid Associated Proteins (NAPs) organize the bacterial chromosome within the nucleoid. The interaction of the NAP H-NS with DNA also represses specific host and xenogeneic genes. Previously, we showed that the bacteriophage T4 early protein MotB binds to DNA, co-purifies with H-NS/DNA, and improves phage fitness. Here we demonstrate using atomic force microscopy that MotB compacts the DNA with multiple MotB proteins at the center of the complex. These complexes differ from those observed with H-NS and other NAPs, but resemble those formed by the NAP-like proteins CbpA/Dps and yeast condensin. Fluorescent microscopy indicates that expression of motB in vivo, at levels like that during T4 infection, yields a significantly compacted nucleoid containing MotB and H-NS. motB overexpression dysregulates hundreds of host genes; ∼70% are within the hns regulon. In infected cells overexpressing motB, 33 T4 late genes are expressed early, and the T4 early gene repEB, involved in replication initiation, is up ∼5-fold. We postulate that MotB represents a phage-encoded NAP that aids infection in a previously unrecognized way. We speculate that MotB-induced compaction may generate more room for T4 replication/assembly and/or leads to beneficial global changes in host gene expression, including derepression of much of the hns regulon.
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Affiliation(s)
- Bokyung Son
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Patterson-West
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James R Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jingen Zhu
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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7
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Ishihama A, Shimada T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS Microbiol Rev 2021; 45:6312496. [PMID: 34196371 DOI: 10.1093/femsre/fuab032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.
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Affiliation(s)
- Akira Ishihama
- Hosei University, Research Institute for Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
| | - Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
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8
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Patterson-West J, Tai CH, Son B, Hsieh ML, Iben JR, Hinton DM. Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA. Viruses 2021; 13:v13010084. [PMID: 33435393 PMCID: PMC7827196 DOI: 10.3390/v13010084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
The bacteriophage T4 early gene product MotB binds tightly but nonspecifically to DNA, copurifies with the host Nucleoid Associated Protein (NAP) H-NS in the presence of DNA and improves T4 fitness. However, the T4 transcriptome is not significantly affected by a motB knockdown. Here we have investigated the phylogeny of MotB and its predicted domains, how MotB and H-NS together interact with DNA, and how heterologous overexpression of motB impacts host gene expression. We find that motB is highly conserved among Tevenvirinae. Although the MotB sequence has no homology to proteins of known function, predicted structure homology searches suggest that MotB is composed of an N-terminal Kyprides-Onzonis-Woese (KOW) motif and a C-terminal DNA-binding domain of oligonucleotide/oligosaccharide (OB)-fold; either of which could provide MotB’s ability to bind DNA. DNase I footprinting demonstrates that MotB dramatically alters the interaction of H-NS with DNA in vitro. RNA-seq analyses indicate that expression of plasmid-borne motB up-regulates 75 host genes; no host genes are down-regulated. Approximately 1/3 of the up-regulated genes have previously been shown to be part of the H-NS regulon. Our results indicate that MotB provides a conserved function for Tevenvirinae and suggest a model in which MotB functions to alter the host transcriptome, possibly by changing the association of H-NS with the host DNA, which then leads to conditions that are more favorable for infection.
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Affiliation(s)
- Jennifer Patterson-West
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.P.-W.); (B.S.); (M.-L.H.)
| | - Chin-Hsien Tai
- Center for Cancer Research, Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Bokyung Son
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.P.-W.); (B.S.); (M.-L.H.)
| | - Meng-Lun Hsieh
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.P.-W.); (B.S.); (M.-L.H.)
| | - James R. Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Deborah M. Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.P.-W.); (B.S.); (M.-L.H.)
- Correspondence: ; Tel.: +1-301-496-9885
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9
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Zhao X, Shahul Hameed UF, Kharchenko V, Liao C, Huser F, Remington JM, Radhakrishnan AK, Jaremko M, Jaremko Ł, Arold ST, Li J. Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins. eLife 2021; 10:57467. [PMID: 33410747 PMCID: PMC7817174 DOI: 10.7554/elife.57467] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 01/06/2021] [Indexed: 12/02/2022] Open
Abstract
The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less nuclear magnetic resonance spectroscopy, and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS-mediated environmental sensing and suggested that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
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Affiliation(s)
- Xiaochuan Zhao
- Department of Chemistry, The University of Vermont, Burlington, United States
| | - Umar F Shahul Hameed
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Vladlena Kharchenko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Chenyi Liao
- Department of Chemistry, The University of Vermont, Burlington, United States
| | - Franceline Huser
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Jacob M Remington
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Anand K Radhakrishnan
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, United States
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10
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Hurtado-Escobar GA, Grépinet O, Raymond P, Abed N, Velge P, Virlogeux-Payant I. H-NS is the major repressor of Salmonella Typhimurium Pef fimbriae expression. Virulence 2020; 10:849-867. [PMID: 31661351 PMCID: PMC6844306 DOI: 10.1080/21505594.2019.1682752] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fimbriae play an important role in adhesion and are therefore essential for the interaction of bacteria with the environments they encounter. Most of them are expressed in vivo but not in vitro, thus making difficult the full characterization of these fimbriae. Here, we characterized the silencing of plasmid-encoded fimbriae (Pef) expression, encoded by the pef operon, in the worldwide pathogen Salmonella Typhimurium. We demonstrated that the nucleoid-associated proteins H-NS and Hha, and their respective paralogs StpA and YdgT, negatively regulate at pH 5.1 and pH 7.1 the transcription of the pef operon. Two promoters, PpefB and PpefA, direct the transcription of this operon. All the nucleoid-associated proteins silence the PpefB promoter and H-NS also targets the PpefA promoter. While Hha and YdgT are mainly considered as acting primarily through H-NS to modulate gene transcription, our results strongly suggest that Hha and YdgT silence pef transcription at acidic pH either by interacting with StpA or independently of H-NS and StpA. We also confirmed the previously described post-transcriptional repression of Pef fimbriae by CsrA titration via the fim mRNA and CsrB and CsrC sRNA. Finally, among all these regulators, H-NS clearly appeared as the major repressor of Pef expression. These results open new avenues of research to better characterize the regulation of these bacterial adhesive proteins and to clarify their role in the virulence of pathogens.
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Affiliation(s)
| | | | | | - Nadia Abed
- ISP, INRA, Université de Tours, Nouzilly, France
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11
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Yamanaka Y, Watanabe H, Yamauchi E, Miyake Y, Yamamoto K. Measurement of the Promoter Activity in Escherichia coli by Using a Luciferase Reporter. Bio Protoc 2020; 10:e3500. [PMID: 33654727 DOI: 10.21769/bioprotoc.3500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/02/2022] Open
Abstract
The reporter system is widely used technique for measuring promoter activity in bacterial cells. Until now, a number of reporter system have been developed, but the bioluminescent reporter constructed from the bacterial luciferase genes is one of the useful systems for measuring in vivo dynamics of gene expression. The introduced bioluciferase lux reporter enables easy, fast, and sensitive measurement of the promoter activity without cell lysis because the substrates of bioluminescent reaction are synthesized inside the bacterial cell, thereby allowing low-cost experiments. This protocol describes a high throughput technique to measure the promoter activity in Escherichia coli K-12 using the lux reporter system.
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Affiliation(s)
- Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan.,Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Erika Yamauchi
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Yukari Miyake
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan.,Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan
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12
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Qin L, Erkelens AM, Ben Bdira F, Dame RT. The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins. Open Biol 2019; 9:190223. [PMID: 31795918 PMCID: PMC6936261 DOI: 10.1098/rsob.190223] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns- phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.
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Affiliation(s)
- L. Qin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. M. Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - F. Ben Bdira
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - R. T. Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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13
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Pfeifer E, Hünnefeld M, Popa O, Frunzke J. Impact of Xenogeneic Silencing on Phage-Host Interactions. J Mol Biol 2019; 431:4670-4683. [PMID: 30796986 PMCID: PMC6925973 DOI: 10.1016/j.jmb.2019.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.
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Affiliation(s)
- Eugen Pfeifer
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Ovidiu Popa
- Heinrich Heine Universität Düsseldorf, Institute for Quantitative and Theoretical Biology, 40223 Düsseldorf, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
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14
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Kapshikar RM, Gowrishankar J. Direct inhibition of transcription in vitro by the isolated N-terminal domain of the Escherichia coli nucleoid-associated protein H-NS and by its paralogue Hha. MICROBIOLOGY-SGM 2019; 165:463-474. [PMID: 30724731 DOI: 10.1099/mic.0.000780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
H-NS is an abundant nucleoid-associated protein in the enterobacteria that mediates both chromatin compaction and transcriptional silencing of numerous genes, especially those that have been acquired by horizontal transfer or that are involved in virulence functions. With two dimerization domains (N-terminal and central) and a C-terminal DNA-binding domain, the 15 kDa H-NS polypeptide can assemble as long polymeric filaments on DNA, and mutations in any of the three domains confer a dominant-negative phenotype in vivo by a subunit-poisoning mechanism. Here we confirm that several of these mutants [L26P, I119T and a truncation beyond residue 92(Δ93)] are also dominant-negative in vitro, in that they reverse the inhibition imposed by native H-NS in two different transcription assay formats (initiation+elongation, or elongation alone). On the other hand, another dominant-negative truncation mutant Δ64 (which possesses only the protein's N-terminal domain) per se completely and unexpectedly inhibited transcription in both assay formats. The Hha protein, which is a paralogue of H-NS and resembles its isolated N-terminal domain, also behaved like Δ64 as an inhibitor of transcription in vitro. We propose that under certain growth conditions, Escherichia coli RNA polymerase may be the direct inhibitory target of Hha, and that this effect is experimentally mimicked by the isolated N-terminal domain of H-NS.
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Affiliation(s)
- Rajvardhan M Kapshikar
- 1Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,2Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - J Gowrishankar
- 1Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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15
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Boudreau BA, Hron DR, Qin L, van der Valk RA, Kotlajich MV, Dame RT, Landick R. StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments. Nucleic Acids Res 2018; 46:5525-5546. [PMID: 29718386 PMCID: PMC6009659 DOI: 10.1093/nar/gky265] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/12/2018] [Accepted: 04/03/2018] [Indexed: 11/22/2022] Open
Abstract
In enterobacteria, AT-rich horizontally acquired genes, including virulence genes, are silenced through the actions of at least three nucleoid-associated proteins (NAPs): H-NS, StpA and Hha. These proteins form gene-silencing nucleoprotein filaments through direct DNA binding by H-NS and StpA homodimers or heterodimers. Both linear and bridged filaments, in which NAPs bind one or two DNA segments, respectively, have been observed. Hha can interact with H-NS or StpA filaments, but itself lacks a DNA-binding domain. Filaments composed of H-NS alone can inhibit transcription initiation and, in the bridged conformation, slow elongating RNA polymerase (RNAP) by promoting backtracking at pause sites. How the other NAPs modulate these effects of H-NS is unknown, despite evidence that they help regulate subsets of silenced genes in vivo (e.g. in pathogenicity islands). Here we report that Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20°C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37°C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, we report that both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments. Together, these observations indicate that Hha and StpA can affect H-NS-mediated gene regulation by stimulating bridging of H-NS/DNA filaments.
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Affiliation(s)
- Beth A Boudreau
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Daniel R Hron
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Liang Qin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Matthew V Kotlajich
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
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16
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Yamanaka Y, Winardhi RS, Yamauchi E, Nishiyama SI, Sowa Y, Yan J, Kawagishi I, Ishihama A, Yamamoto K. Dimerization site 2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation. J Biol Chem 2018; 293:9496-9505. [PMID: 29695505 DOI: 10.1074/jbc.ra117.001425] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/20/2018] [Indexed: 11/06/2022] Open
Abstract
The bacterial nucleoid-associated protein H-NS is a DNA-binding protein, playing a major role in gene regulation. To regulate transcription, H-NS silences genes, including horizontally acquired foreign genes. Escherichia coli H-NS is 137 residues long and consists of two discrete and independent structural domains: an N-terminal oligomerization domain and a C-terminal DNA-binding domain, joined by a flexible linker. The N-terminal oligomerization domain is composed of two dimerization sites, dimerization sites 1 and 2, which are both required for H-NS oligomerization, but the exact role of dimerization site 2 in gene silencing is unclear. To this end, we constructed a whole set of single amino acid substitution variants spanning residues 2 to 137. Using a well-characterized H-NS target, the slp promoter of the glutamic acid-dependent acid resistance (GAD) cluster promoters, we screened for any variants defective in gene silencing. Focusing on the function of dimerization site 2, we analyzed four variants, I70C/I70A and L75C/L75A, which all could actively bind DNA but are defective in gene silencing. Atomic force microscopy analysis of DNA-H-NS complexes revealed that all of these four variants formed condensed complexes on DNA, whereas WT H-NS formed rigid and extended nucleoprotein filaments, a conformation required for gene silencing. Single-molecule stretching experiments confirmed that the four variants had lost the ability to form stiffened filaments. We conclude that dimerization site 2 of H-NS plays a key role in the formation of rigid H-NS nucleoprotein filament structures required for gene silencing.
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Affiliation(s)
- Yuki Yamanaka
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan.,the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and
| | - Ricksen S Winardhi
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Erika Yamauchi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - So-Ichiro Nishiyama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Yoshiyuki Sowa
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Jie Yan
- the Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore, and.,the Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Ikuro Kawagishi
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Akira Ishihama
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan.,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
| | - Kaneyoshi Yamamoto
- From the Department of Frontier Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan, .,the Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Koganei, Tokyo 184-0003, Japan
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17
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van der Valk RA, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT. Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity. eLife 2017; 6:e27369. [PMID: 28949292 PMCID: PMC5647153 DOI: 10.7554/elife.27369] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator in Gram-negative bacteria and is believed to be a crucial player in bacterial chromatin organization via its DNA-bridging activity. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically, it is unclear how functional modulation of H-NS by such factors is achieved. Here, we show that a diverse spectrum of H-NS modulators alter the DNA-bridging activity of H-NS. Changes in monovalent and divalent ion concentrations drive an abrupt switch between a bridging and non-bridging DNA-binding mode. Similarly, synergistic and antagonistic co-regulators modulate the DNA-bridging efficiency. Structural studies suggest a conserved mechanism: H-NS switches between a 'closed' and an 'open', bridging competent, conformation driven by environmental cues and interaction partners.
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Affiliation(s)
| | - Jocelyne Vreede
- Computational ChemistryVan ‘t Hoff Institute for Molecular Sciences, University of AmsterdamAmsterdamNetherlands
| | - Liang Qin
- Leiden Institute of ChemistryLeiden UniversityLeidenNetherlands
| | | | - Andreas Hofmann
- Institute for Theoretical PhysicsUniversity of HeidelbergHeidelbergGermany
| | - Nora Goosen
- Leiden Institute of ChemistryLeiden UniversityLeidenNetherlands
| | - Remus T Dame
- Leiden Institute of ChemistryLeiden UniversityLeidenNetherlands
- Centre for Microbial Cell BiologyLeiden UniversityLeidenNetherlands
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18
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Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain. Clin Sci (Lond) 2017; 130:1165-77. [PMID: 27252403 DOI: 10.1042/cs20160024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/15/2016] [Indexed: 02/03/2023]
Abstract
The mechanisms used by bacterial pathogens to regulate the expression of their genes, especially their virulence genes, have been the subject of intense investigation for several decades. Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. Themes that have emerged include the importance of horizontal gene transfer to the evolution of pathogens, the need to impose regulatory discipline upon these imported genes and the important roles played by factors normally associated with the organization of genome architecture as regulatory principles in the control of virulence gene expression. Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process.
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19
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Abstract
The H-NS family of DNA-binding proteins is the subject of intense study due to its important roles in the regulation of horizontally acquired genes critical for virulence, antibiotic resistance, and metabolism. Xenogeneic silencing proteins, typified by the H-NS protein of Escherichia coli, specifically target and downregulate expression from AT-rich genes by selectively recognizing specific structural features unique to the AT-rich minor groove. In doing so, these proteins facilitate bacterial evolution; enabling these cells to engage in horizontal gene transfer while buffering potential any detrimental fitness consequences that may result from it. Xenogeneic silencing and counter-silencing explain how bacterial cells can evolve effective gene regulatory strategies in the face of rampant gene gain and loss and it has extended our understanding of bacterial gene regulation beyond the classic operon model. Here we review the structures and mechanisms of xenogeneic silencers as well as their impact on bacterial evolution. Several H-NS-like proteins appear to play a role in facilitating gene transfer by other mechanisms including by regulating transposition, conjugation, and participating in the activation of virulence loci like the locus of enterocyte effacement pathogenicity island of pathogenic strains of E. coli. Evidence suggests that the critical determinants that dictate whether an H-NS-like protein will be a silencer or will perform a different function do not lie in the DNA-binding domain but, rather, in the domains that control oligomerization. This suggests that H-NS-like proteins are transcription factors that both recognize and alter the shape of DNA to exert specific effects that include but are not limited to gene silencing.
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20
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Abstract
The H-NS (heat-stable nucleoid structuring) protein affects both nucleoid compaction and global gene regulation. H-NS appears to act primarily as a silencer of AT-rich genetic material acquired by horizontal gene transfer. As such, it is key in the regulation of most genes involved in virulence and in adaptation to new environmental niches. Here we review recent progress in understanding the biochemistry of H-NS and how xenogeneic silencing affects bacterial evolution. We highlight the strengths and weaknesses of some of the models proposed in H-NS-mediated nucleoprotein complex formation. Based on recent single-molecule studies, we also propose a novel mode of DNA compaction by H-NS termed intrabridging to explain over two decades of observations of the H-NS molecule.
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Affiliation(s)
- Kamna Singh
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada;
| | - Joshua N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Ontario L5L 1C6, Canada.,Department of Physics, University of Toronto, Ontario M5S 1A7, Canada
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21
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Wan B, Zhang Q, Tao J, Zhou A, Yao YF, Ni J. Global transcriptional regulation by H-NS and its biological influence on the virulence of Enterohemorrhagic Escherichia coli. Gene 2016; 588:115-23. [PMID: 27173635 DOI: 10.1016/j.gene.2016.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
As a global transcriptional regulator, H-NS, the histone-like nucleoid-associated DNA-binding and bridging protein, plays a wide range of biological roles in bacteria. In order to determine the role of H-NS in regulating gene transcription and further find out the biological significance of this protein in Enterohemorrhagic Escherichia coli (EHEC), we conducted transcriptome analysis of hns mutant by RNA sequencing. A total of 983 genes were identified to be regulated by H-NS in EHEC. 213 and 770 genes were down-regulated and up-regulated in the deletion mutant of hns, respectively. Interestingly, 34 of 97 genes on virulence plasmid pO157 were down-regulated by H-NS. Although the deletion mutant of hns showed a decreased survival rate in macrophage compared with the wild type strain, it exhibited the higher ability to colonize mice gut and became more virulent to BALB/c mice. The BALB/c mice infected with the deletion mutant of hns showed a lower survival rate, and a higher bacterial burden in the gut, compared with those infected with wild type strain, especially when the gut microbiota was not disturbed by antibiotic administration. These findings suggest that H-NS plays an important role in virulence of EHEC by interacting with host gut microbiota.
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Affiliation(s)
- Baoshan Wan
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiufen Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Tao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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22
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Zhai Y, He Z, Kang Y, Yu H, Wang J, Du P, Zhang Z, Hu S, Gao Z. Complete nucleotide sequence of pH11, an IncHI2 plasmid conferring multi-antibiotic resistance and multi-heavy metal resistance genes in a clinical Klebsiella pneumoniae isolate. Plasmid 2016; 86:26-31. [PMID: 27101788 DOI: 10.1016/j.plasmid.2016.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 11/17/2022]
Abstract
The complete 284,628bp sequence of pH11, an IncHI2 plasmid, was determined through single-molecule, real-time (SMRT) sequencing. Harbored by a clinical Klebsiella pneumoniae strain H11, and isolated in Beijing, this plasmid contains multiple antibiotic resistance genes, including catA2, aac(6')-Ib, strB, strA, dfrA19, blaTEM-1, blaSHV-12, sul1, qacE delta 1, ereA, arr2, and aac3. The aac(6')-Ib is carried by a class I integron. Plasmid pH11 also carries several genes associated with resistance to heavy metals, such as tellurium, mercury, cobalt, zinc, nickel, copper, lead and cadmium. This plasmid exhibits numerous characteristics, including HipBA and RelBE toxin-antitoxin systems, two major transfer (Tra) regions closely related to those of Salmonella enterica serovar plasmid pRH-R27, a type II restriction modification system (EcoRII R-M system), several methyltransferases and methylases and genes encoding Hha and StpA. These characteristics suggest that pH11 may adapt to various hosts and environments. Multiple insertion sequence elements, transposases, recombinases, resolvases and integrases are scattered throughout pH11. The presence of these genes may indicate that horizontal gene transfer occurs frequently in pH11 and thus may facilitate the dissemination of antimicrobial resistance determinants. Our data suggest that pH11 is a chimera gradually assembled through the integration of different horizontally acquired DNA segments via transposition or homologous recombination.
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Affiliation(s)
- Yao Zhai
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haiying Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianfeng Wang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Zhao Zhang
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China.
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23
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Fukui N, Oshima T, Ueda T, Ogasawara N, Tobe T. Gene Activation through the Modulation of Nucleoid Structures by a Horizontally Transferred Regulator, Pch, in Enterohemorrhagic Escherichia coli. PLoS One 2016; 11:e0149718. [PMID: 26901318 PMCID: PMC4764244 DOI: 10.1371/journal.pone.0149718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/04/2016] [Indexed: 11/19/2022] Open
Abstract
The horizontally transferred chromosomal segments, which are the main source of genetic diversity among bacterial pathogens, are bound by the nucleoid protein H-NS, resulting in the formation of a nucleoprotein complex and the silencing of gene expression. The de-silencing or activation of virulence genes necessary for the colonization of enterohemorrhagic Escherichia coli is achieved mainly by the action of two regulators, Pch and Ler, which are encoded by horizontally transferred elements. Although Ler has been shown to activate transcription by counteracting H-NS silencing, the mechanism for Pch is poorly understood. We show here that Pch activates the LEE1 promoter and also enhances the Ler-mediated activation of other LEE promoters. Transcriptional activation was completely dependent on repression by the H-NS/StpA/Hha/YdgT complex, indicating that Pch-derived activation was achieved by alleviating H-NS-mediated silencing. Expression of pch reduced the binding of H-NS at LEE1 promoter and altered the nucleoprotein complex. Furthermore, in vitro reconstruction of the protein-DNA complex on LEE1 promoter DNA confirmed the exclusive effect of Pch on H-NS binding. These results demonstrated that Pch is another anti-silencing regulator and a modulator of H-NS-containing nucleoprotein complexes. Thus, the anti-silencing mechanism plays a key role in the coordinated regulation of virulence genes in EHEC.
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Affiliation(s)
- Naoki Fukui
- Department of Biomedical Informatics, Graduate School of Medicine Osaka University, 1-7 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Taku Oshima
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan
| | - Takeshi Ueda
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan
| | - Toru Tobe
- Department of Biomedical Informatics, Graduate School of Medicine Osaka University, 1-7 Yamadaoka, Suita, Osaka, 565-0871, Japan
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24
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Higashi K, Tobe T, Kanai A, Uyar E, Ishikawa S, Suzuki Y, Ogasawara N, Kurokawa K, Oshima T. H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PLoS Genet 2016; 12:e1005796. [PMID: 26789284 PMCID: PMC4720273 DOI: 10.1371/journal.pgen.1005796] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 12/20/2015] [Indexed: 01/06/2023] Open
Abstract
Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches. Horizontal gene transfer among bacteria is the major means of acquiring genetic diversity and has been a central factor in bacterial evolution. The expression of horizontally transferred genes could potentially be optimized to permit the host bacteria to expand their habitat. The results of our study suggest that DNA regions bound by the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes, have been conserved during Escherichia coli evolution. Interestingly, H-NS-bound regions have evolved faster than H-NS-unbound regions, but only in gene regulatory and coding regions. We show that DNA sequence substitutions in H-NS-bound regions actually alter the regulation of gene expression in different E. coli strains. Thus, our results support the hypothesis that H-NS accelerates the diversification of the regulation of horizontally transferred genes such that their selective expression could potentially allow E. coli strains to adapt to new habitats.
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Affiliation(s)
- Koichi Higashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Toru Tobe
- Department of Biomedical Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- * E-mail: (TT); (KK); (TO)
| | - Akinori Kanai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Ebru Uyar
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Kurokawa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
- * E-mail: (TT); (KK); (TO)
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
- * E-mail: (TT); (KK); (TO)
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Solórzano C, Srikumar S, Canals R, Juárez A, Paytubi S, Madrid C. Hha has a defined regulatory role that is not dependent upon H-NS or StpA. Front Microbiol 2015; 6:773. [PMID: 26284052 PMCID: PMC4519777 DOI: 10.3389/fmicb.2015.00773] [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: 03/26/2015] [Accepted: 07/14/2015] [Indexed: 11/13/2022] Open
Abstract
The Hha family of proteins is involved in the regulation of gene expression in enterobacteria by forming complexes with H-NS-like proteins. Whereas several amino acid residues of both proteins participate in the interaction, some of them play a key role. Residue D48 of Hha protein is essential for the interaction with H-NS, thus the D48N substitution in Hha protein abrogates H-NS/Hha interaction. Despite being a paralog of H-NS protein, StpA interacts with HhaD48N with higher affinity than with the wild type Hha protein. To analyze whether Hha is capable of acting independently of H-NS and StpA, we conducted transcriptomic analysis on the hha and stpA deletion strains and the hhaD48N substitution strain of Salmonella Typhimurium using a custom microarray. The results obtained allowed the identification of 120 genes regulated by Hha in an H-NS/StpA-independent manner, 38% of which are horizontally acquired genes. A significant number of the identified genes are involved in functions related to cell motility, iron uptake, and pathogenicity. Thus, motility assays, siderophore detection and intra-macrophage replication assays were performed to confirm the transcriptomic data. Our findings point out the importance of Hha protein as an independent regulator in S. Typhimurium, highlighting a regulatory role on virulence.
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Affiliation(s)
- Carla Solórzano
- Departament de Microbiologia, Universitat de Barcelona Barcelona, Spain
| | | | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Antonio Juárez
- Departament de Microbiologia, Universitat de Barcelona Barcelona, Spain ; Institut de Bioenginyeria de Catalunya, Parc Científic de Barcelona Barcelona, Spain
| | - Sonia Paytubi
- Departament de Microbiologia, Universitat de Barcelona Barcelona, Spain
| | - Cristina Madrid
- Departament de Microbiologia, Universitat de Barcelona Barcelona, Spain
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Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli. G3-GENES GENOMES GENETICS 2015; 5:605-14. [PMID: 25701587 PMCID: PMC4390576 DOI: 10.1534/g3.114.016139] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins. Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal position on the efficiency of these global regulators. Here we show for the first time that genome position can affect transcription activity of a promoter regulated by the histone-like nucleoid-structuring protein (H-NS), a global regulator of bacterial transcription and genome organization. We have used as a local reporter of H-NS activity the level of expression of a fluorescent reporter protein under control of an H-NS−regulated promoter (Phns) at different sites along the genome. Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS. This modulation of gene expression moreover depends on the growth phase and the growth rate of the cells, reflecting the changes taking place in the relative abundance of different nucleoid proteins and the inherent heterogeneous organization of the nucleoid. Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene’s position during evolution.
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van der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic Looping: A Key Principle of Chromatin Organization. J Mol Microbiol Biotechnol 2015; 24:344-59. [DOI: 10.1159/000368851] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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H-NS and RNA polymerase: a love-hate relationship? Curr Opin Microbiol 2015; 24:53-9. [PMID: 25638302 DOI: 10.1016/j.mib.2015.01.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/24/2014] [Accepted: 01/10/2015] [Indexed: 01/23/2023]
Abstract
Histone-like nucleoid structuring (H-NS) protein is a component of bacterial chromatin and influences gene expression both locally and on a global scale. Although H-NS is broadly considered a silencer of transcription, the mechanisms by which H-NS inhibits gene expression remain poorly understood. Here we discuss recent advances in the context of a 'love-hate' relationship between H-NS and RNA polymerase, in which these factors recognise similar DNA sequences but interfere with each other's activity. Understanding the complex relationship between H-NS and RNA polymerase may unite the multiple models that have been proposed to describe gene silencing by H-NS.
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Kotlajich MV, Hron DR, Boudreau BA, Sun Z, Lyubchenko YL, Landick R. Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria. eLife 2015; 4. [PMID: 25594903 PMCID: PMC4337669 DOI: 10.7554/elife.04970] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/15/2015] [Indexed: 11/13/2022] Open
Abstract
Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria.
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Affiliation(s)
- Matthew V Kotlajich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Daniel R Hron
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Beth A Boudreau
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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Yamanaka Y, Oshima T, Ishihama A, Yamamoto K. Characterization of the YdeO regulon in Escherichia coli. PLoS One 2014; 9:e111962. [PMID: 25375160 PMCID: PMC4222967 DOI: 10.1371/journal.pone.0111962] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/09/2014] [Indexed: 11/23/2022] Open
Abstract
Enterobacteria are able to survive under stressful conditions within animals, such as acidic conditions in the stomach, bile salts during transfer to the intestine and anaerobic conditions within the intestine. The glutamate-dependent (GAD) system plays a major role in acid resistance in Escherichia coli, and expression of the GAD system is controlled by the regulatory cascade consisting of EvgAS > YdeO > GadE. To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites. All of the seven operons identified by ChIP-chip as being potentially regulated by YdeO were confirmed as being under the direct control of YdeO using RT-qPCR, EMSA, DNaseI-footprinting and reporter assays. Within this YdeO regulon, we identified four stress-response transcription factors, DctR, NhaR, GadE, and GadW and enzymes for anaerobic respiration. Both GadE and GadW are involved in regulation of the GAD system and NhaR is an activator for the sodium/proton antiporter gene. In conjunction with co-transcribed Slp, DctR is involved in protection against metabolic endoproducts under acidic conditions. Taken all together, we suggest that YdeO is a key regulator of E. coli survival in both acidic and anaerobic conditions.
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Affiliation(s)
- Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Taku Oshima
- Graduate School of Information Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Akira Ishihama
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Kaneyoshi Yamamoto
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
- Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan
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Dorman CJ. H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria. Plasmid 2014; 75:1-11. [DOI: 10.1016/j.plasmid.2014.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
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Sharma VK, Casey TA. Determining the relative contribution and hierarchy of hha and qseBC in the regulation of flagellar motility of Escherichia coli O157:H7. PLoS One 2014; 9:e85866. [PMID: 24465756 PMCID: PMC3897532 DOI: 10.1371/journal.pone.0085866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/06/2013] [Indexed: 11/18/2022] Open
Abstract
In recent studies, we demonstrated that a deletion of hha caused increased secretion of locus of enterocyte encoded adherence proteins and reduced motility of enterohemorrhagic Escherichia coli (EHEC) O157:H7. In addition to the importance of hha in positive regulation of motility, a two-component quorum sensing pathway encoded by the qseBC genes has been shown to activate bacterial motility in response to mammalian stress hormones epinephrine and norepinephrine as well as bacterially produced autoinducer-3. In this study, we compared regulatory contribution and hierarchy of hha, a member of the Hha/YmoA family of nucleoid-associated proteins, to that of qseBC in the expression of EHEC O157:H7 motility. Since norepinephrine affects motility of EHEC O157:H7 through a qseBC-encoded two-component quorum sensing signaling, we also determined whether the hha-mediated regulation of motility is affected by norepinephrine and whether this effect is qseBC dependent. We used single (Δhha or ΔqseC) and double (Δhha ΔqseC) deletion mutants to show that hha exerts a greater positive regulatory effect in comparison to qseBC on the expression of motility by EHEC O157:H7. We also show that Hha is hierarchically superior in transcriptional regulation of motility than QseBC because transcription of qseC was significantly reduced in the hha deletion mutant compared to that in the parental and the hha-complemented mutant strains. These results suggest that hha regulates motility of EHEC O157:H7 directly as well as indirectly by controlling the transcription of qseBC.
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Affiliation(s)
- Vijay K. Sharma
- Food Safety and Enteric Pathogens Research Unit, United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, United States of America
- * E-mail:
| | - Thomas A. Casey
- Food Safety and Enteric Pathogens Research Unit, United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, United States of America
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