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Baglivo I, Malgieri G, Roop RM, Barton IS, Wang X, Russo V, Pirone L, Pedone EM, Pedone PV. MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Mol Microbiol 2024. [PMID: 38619026 DOI: 10.1111/mmi.15261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roy Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
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2
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Barton IS, Ren Z, Cribb CB, Pitzer JE, Baglivo I, Martin DW, Wang X, Roop RM. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio 2023; 14:e0220123. [PMID: 37847580 PMCID: PMC10746212 DOI: 10.1128/mbio.02201-23] [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: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression. Brucella and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in Brucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in Brucella and related bacteria.
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Affiliation(s)
- Ian S. Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Connor B. Cribb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniel W. Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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3
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Bleem A, Prosswimmer T, Chen R, Hady TF, Li J, Bryers JD, Daggett V. Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells. Sci Rep 2023; 13:9272. [PMID: 37286572 PMCID: PMC10247742 DOI: 10.1038/s41598-023-36343-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
Uropathogenic Escherichia coli account for the largest proportion of nosocomial infections in the United States. Nosocomial infections are a major source of increased costs and treatment complications. Many infections are biofilm associated, rendering antibiotic treatments ineffective or cause additional complications (e.g., microbiome depletion). This work presents a potentially complementary non-antibiotic strategy to fight nosocomial infections by inhibiting the formation of amyloid fibrils, a proteinaceous structural reinforcement known as curli in E. coli biofilms. Despite extensive characterization of the fibrils themselves and their associated secretion system, mechanistic details of curli assembly in vivo remain unclear. We hypothesized that, like other amyloid fibrils, curli polymerization involves a unique secondary structure termed "α-sheet". Biophysical studies herein confirmed the presence of α-sheet structure in prefibrillar species of CsgA, the major component of curli, as it aggregated. Binding of synthetic α-sheet peptides to the soluble α-sheet prefibrillar species inhibited CsgA aggregation in vitro and suppressed amyloid fibril formation in biofilms. Application of synthetic α-sheet peptides also enhanced antibiotic susceptibility and dispersed biofilm-resident bacteria for improved uptake by phagocytic cells. The ability of synthetic α-sheet peptides to reduce biofilm formation, improve antibiotic susceptibility, and enhance clearance by macrophages has broad implications for combating biofilm-associated infections.
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Affiliation(s)
- Alissa Bleem
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tatum Prosswimmer
- Molecular Engineering Program, University of Washington, Seattle, WA, 98195, USA
| | - Ruying Chen
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Surgery and Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Thomas F Hady
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jinzheng Li
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - James D Bryers
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Surgery and Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
- Molecular Engineering Program, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
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4
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Núncio ASP, Webber B, Pottker ES, Cardoso B, Esposito F, Fontana H, Lincopan N, Girardello R, Pilotto F, dos Santos LR, Rodrigues LB. Genomic characterization of multidrug-resistant Salmonella Heidelberg E2 strain isolated from chicken carcass in southern Brazil. Int J Food Microbiol 2022; 379:109863. [DOI: 10.1016/j.ijfoodmicro.2022.109863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/09/2022] [Accepted: 07/27/2022] [Indexed: 10/16/2022]
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5
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Ma R, Liu Y, Gan J, Qiao H, Ma J, Zhang Y, Bu Y, Shao S, Zhang Y, Wang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3777-3798. [PMID: 35325196 PMCID: PMC9023278 DOI: 10.1093/nar/gkac180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - Haoxian Qiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiabao Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifan Bu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qiyao Wang
- To whom correspondence should be addressed. Tel: +86 21 64253306; Fax: +86 21 64253306;
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6
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Zhou J, Hong SH. Establishing Efficient Bisphenol A Degradation by Engineering Shewanella oneidensis. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c03324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiacheng Zhou
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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7
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Khan S, McWhorter AR, Moyle TS, Chousalkar KK. Refrigeration of eggs influences the virulence of Salmonella Typhimurium. Sci Rep 2021; 11:18026. [PMID: 34504138 PMCID: PMC8429434 DOI: 10.1038/s41598-021-97135-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
Salmonella Typhimurium is a human pathogen associated with eggs and egg-derived products. In Australia, it is recommended that eggs should be refrigerated to prevent condensation that can enhance bacterial penetration across the eggshell. Except for the United States, the guidelines on egg refrigeration are not prescriptive. In the current study, in-vitro and in-vivo experiments were conducted to understand the role of egg storage temperatures (refrigerated vs ambient) on bacterial load and the virulence genes expression of Salmonella Typhimurium. The in-vitro egg study showed that the load of Salmonella Typhimurium significantly increased in yolk and albumen stored at 25 °C. The gene expression study showed that ompR, misL, pefA, spvA, shdA, bapA, and csgB were significantly up-regulated in the egg yolk stored at 5 °C and 25 °C for 96 h; however, an in-vivo study revealed that mice infected with egg yolk stored at 25 °C, developed salmonellosis from day 3 post-infection (p.i.). Mice fed with inoculated egg yolk, albumen, or eggshell wash stored at refrigerated temperature did not show signs of salmonellosis during the period of the experiment. Data obtained in this study highlighted the importance of egg refrigeration in terms of improving product safety.
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Affiliation(s)
- Samiullah Khan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Andrea R McWhorter
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Talia S Moyle
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Kapil K Chousalkar
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia.
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8
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Kirthika P, Senevirathne A, Jawalagatti V, Park S, Lee JH. Deletion of the lon gene augments expression of Salmonella Pathogenicity Island (SPI)-1 and metal ion uptake genes leading to the accumulation of bactericidal hydroxyl radicals and host pro-inflammatory cytokine-mediated rapid intracellular clearance. Gut Microbes 2020; 11:1695-1712. [PMID: 32567462 PMCID: PMC7524146 DOI: 10.1080/19490976.2020.1777923] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 02/03/2023] Open
Abstract
In the present study, we characterized the involvement of Lon protease in bacterial virulence and intracellular survival in Salmonella under abiotic stress conditions resembling the conditions of a natural infection. Wild type (JOL401) and the lon mutant (JOL909) Salmonella Typhimurium were exposed to low temperature, pH, osmotic, and oxidative stress conditions and changes in gene expression profiles related to virulence and metal ion uptake were investigated. Expression of candidate genes invF and hilC of Salmonella Pathogenicity Island (SPI)-1 and sifA and sseJ of SPI-2 revealed that Lon protease controls SPI-1 genes and not SPI-2 genes under all stress conditions tested. The lon mutant exhibited increased accumulation of hydroxyl (OH·) ions that lead to cell damage due to oxidative stress. This oxidative damage can also be linked to an unregulated influx of iron due to the upregulation of ion channel genes such as fepA in the lon mutant. The deletion of lon from the Salmonella genome causes oxidative damage and increased expression of virulence genes. It also prompts the secretion of host pro-inflammatory cytokines leading to early clearance of the bacteria from host cells. We conclude that poor bacterial recovery from mice infected with the lon mutant is a result of disrupted bacterial intracellular equilibrium and rapid activation of cytokine expression leading to bacterial lysis.
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Affiliation(s)
- Perumalraja Kirthika
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Republic of Korea
| | - Amal Senevirathne
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Republic of Korea
| | | | - SungWoo Park
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Republic of Korea
| | - John Hwa Lee
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Republic of Korea
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9
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Salmonella expresses foreign genes during infection by degrading their silencer. Proc Natl Acad Sci U S A 2020; 117:8074-8082. [PMID: 32209674 DOI: 10.1073/pnas.1912808117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The heat-stable nucleoid structuring (H-NS, also referred to as histone-like nucleoid structuring) protein silences transcription of foreign genes in a variety of Gram-negative bacterial species. To take advantage of the products encoded in foreign genes, bacteria must overcome the silencing effects of H-NS. Because H-NS amounts are believed to remain constant, overcoming gene silencing has largely been ascribed to proteins that outcompete H-NS for binding to AT-rich foreign DNA. However, we report here that the facultative intracellular pathogen Salmonella enterica serovar Typhimurium decreases H-NS amounts 16-fold when inside macrophages. This decrease requires both the protease Lon and the DNA-binding virulence regulator PhoP. The decrease in H-NS abundance reduces H-NS binding to foreign DNA, allowing transcription of foreign genes, including those required for intramacrophage survival. The purified Lon protease degraded free H-NS but not DNA-bound H-NS. By displacing H-NS from DNA, the PhoP protein promoted H-NS proteolysis, thereby de-repressing foreign genes-even those whose regulatory sequences are not bound by PhoP. The uncovered mechanism enables a pathogen to express foreign virulence genes during infection without the need to evolve binding sites for antisilencing proteins at each foreign gene.
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10
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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11
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Gawade P, Gunjal G, Sharma A, Ghosh P. Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics 2019; 112:1264-1272. [PMID: 31356968 DOI: 10.1016/j.ygeno.2019.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.
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Affiliation(s)
- Priyanka Gawade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Gaurav Gunjal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Anamika Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
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12
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Große C, Poehlein A, Blank K, Schwarzenberger C, Schleuder G, Herzberg M, Nies DH. The third pillar of metal homeostasis inCupriavidus metalliduransCH34: preferences are controlled by extracytoplasmic function sigma factors. Metallomics 2019; 11:291-316. [DOI: 10.1039/c8mt00299a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
InC. metallidurans, a network of 11 extracytoplasmic function sigma factors forms the third pillar of metal homeostasis acting in addition to the metal transportome and metal repositories as the first and second pillar.
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Affiliation(s)
- Cornelia Große
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory
- Georg-August-University Göttingen, Grisebachstr. 8
- 37077 Göttingen
- Germany
| | - Kathrin Blank
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Claudia Schwarzenberger
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Grit Schleuder
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Martin Herzberg
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
| | - Dietrich H. Nies
- Molecular Microbiology
- Martin-Luther-University Halle-Wittenberg
- Kurt-Mothes-Str. 3
- 06099 Halle (Saale)
- Germany
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13
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Klauck G, Serra DO, Possling A, Hengge R. Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm. Open Biol 2018; 8:180066. [PMID: 30135237 PMCID: PMC6119863 DOI: 10.1098/rsob.180066] [Citation(s) in RCA: 48] [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: 04/17/2018] [Accepted: 07/18/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli, this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σS (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.
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Affiliation(s)
- Gisela Klauck
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Diego O Serra
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Alexandra Possling
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin 10115, Germany
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14
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Wade JT, Grainger DC. Waking the neighbours: disruption of H-NS repression by overlapping transcription. Mol Microbiol 2018; 108:221-225. [PMID: 29473964 DOI: 10.1111/mmi.13939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2018] [Indexed: 11/30/2022]
Abstract
The histone-like nucleoid structuring (H-NS) protein and its analogues bind large stretches of horizontally acquired AT-rich DNA in a broad range of bacterial species. Binding by H-NS silences the promoters within such DNA that would otherwise deplete the cellular pool of RNA polymerase. Selective de-repression can occur when sequence-specific DNA-binding proteins locally disrupt H-NS function; this mechanism is important for the regulation of many virulence genes. In this issue of Molecular Microbiology, Rangarajan and Schnetz show that when transcription from a neighbouring region invades an H-NS-bound locus, it can disrupt local H-NS repression. Moreover, they show that de-repression occurs in a dose-dependent manner, and they demonstrate a natural example of this in Escherichia coli. This finding has important implications for H-NS function and its impact on genome evolution.
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Affiliation(s)
- Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - David C Grainger
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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