1
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Rodriguez A, Diehl JD, Wright GS, Bonar CD, Lundgren TJ, Moss MJ, Li J, Milenkovic T, Huber PW, Champion MM, Emrich SJ, Clark PL. Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production. Proc Natl Acad Sci U S A 2024; 121:e2405510121. [PMID: 39190361 PMCID: PMC11388325 DOI: 10.1073/pnas.2405510121] [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: 03/16/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications.
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Affiliation(s)
- Anabel Rodriguez
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Jacob D. Diehl
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Gabriel S. Wright
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Christopher D. Bonar
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Taylor J. Lundgren
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - McKenze J. Moss
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN46556
| | - Tijana Milenkovic
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Paul W. Huber
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Matthew M. Champion
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
| | - Scott J. Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN37996
| | - Patricia L. Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN46556
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2
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Cooper C, Legood S, Wheat RL, Forrest D, Sharma P, Haycocks JRJ, Grainger DC. H-NS is a bacterial transposon capture protein. Nat Commun 2024; 15:7137. [PMID: 39164300 PMCID: PMC11335895 DOI: 10.1038/s41467-024-51407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/05/2024] [Indexed: 08/22/2024] Open
Abstract
The histone-like nucleoid structuring (H-NS) protein is a DNA binding factor, found in gammaproteobacteria, with functional equivalents in diverse microbes. Universally, such proteins are understood to silence transcription of horizontally acquired genes. Here, we identify transposon capture as a major overlooked function of H-NS. Using genome-scale approaches, we show that H-NS bound regions are transposition "hotspots". Since H-NS often interacts with pathogenicity islands, such targeting creates clinically relevant phenotypic diversity. For example, in Acinetobacter baumannii, we identify altered motility, biofilm formation, and interactions with the human immune system. Transposon capture is mediated by the DNA bridging activity of H-NS and, if absent, more ubiquitous transposition results. Consequently, transcribed and essential genes are disrupted. Hence, H-NS directs transposition to favour evolutionary outcomes useful for the host cell.
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Affiliation(s)
- Charles Cooper
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Simon Legood
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Rachel L Wheat
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - David Forrest
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Prateek Sharma
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - David C Grainger
- School of Biosciences, University of Birmingham, Birmingham, UK.
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3
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Schumacher MA, Singh RR, Salinas R. Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp. Nucleic Acids Res 2024; 52:7354-7366. [PMID: 38832628 PMCID: PMC11229321 DOI: 10.1093/nar/gkae459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Rajiv R Singh
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
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4
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Hustmyer CM, Landick R. Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression. Mol Microbiol 2024; 122:81-112. [PMID: 38847475 PMCID: PMC11260248 DOI: 10.1111/mmi.15283] [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: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
DNA in bacterial chromosomes is organized into higher-order structures by DNA-binding proteins called nucleoid-associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and can either increase or decrease gene expression. To understand the mechanisms by which BCPs alter transcription, one must consider both steric effects and the topological forces that arise when DNA deviates from its fully relaxed double-helical structure. Transcribing RNAP creates DNA negative (-) supercoils upstream and positive (+) supercoils downstream whenever RNAP and DNA are unable to rotate freely. This (-) and (+) supercoiling generates topological forces that resist forward translocation of DNA through RNAP unless the supercoiling is constrained by BCPs or relieved by topoisomerases. BCPs also may enhance topological stress and overall can either inhibit or aid transcription. Here, we review current understanding of how RNAP, BCPs, and DNA topology interplay to control gene expression.
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Affiliation(s)
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison
- Department of Bacteriology, University of Wisconsin-Madison
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5
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Manisha Y, Srinivasan M, Jobichen C, Rosenshine I, Sivaraman J. Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens. Biol Rev Camb Philos Soc 2024; 99:837-863. [PMID: 38217090 DOI: 10.1111/brv.13047] [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: 10/20/2021] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.
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Affiliation(s)
- Yadav Manisha
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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6
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Park J, Kim JJ, Ryu JK. Mechanism of phase condensation for chromosome architecture and function. Exp Mol Med 2024; 56:809-819. [PMID: 38658703 PMCID: PMC11059216 DOI: 10.1038/s12276-024-01226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/26/2024] Open
Abstract
Chromosomal phase separation is involved in a broad spectrum of chromosome organization and functional processes. Nonetheless, the intricacy of this process has left its molecular mechanism unclear. Here, we introduce the principles governing phase separation and its connections to physiological roles in this context. Our primary focus is contrasting two phase separation mechanisms: self-association-induced phase separation (SIPS) and bridging-induced phase separation (BIPS). We provide a comprehensive discussion of the distinct features characterizing these mechanisms and offer illustrative examples that suggest their broad applicability. With a detailed understanding of these mechanisms, we explore their associations with nucleosomes and chromosomal biological functions. This comprehensive review contributes to the exploration of uncharted territory in the intricate interplay between chromosome architecture and function.
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Affiliation(s)
- Jeongveen Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Jeong-Jun Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea.
- Institute of Applied Physics of Seoul National University, Seoul, 08826, South Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, 08826, South Korea.
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7
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Figueroa-Bossi N, Fernández-Fernández R, Kerboriou P, Bouloc P, Casadesús J, Sánchez-Romero MA, Bossi L. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin. Nat Commun 2024; 15:2787. [PMID: 38555352 PMCID: PMC10981669 DOI: 10.1038/s41467-024-47114-w] [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: 10/09/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
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Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Rocío Fernández-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Patricia Kerboriou
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France.
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8
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Lukose B, Maruno T, Faidh M, Uchiyama S, Naganathan A. Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS. Nucleic Acids Res 2024; 52:2157-2173. [PMID: 38340344 PMCID: PMC10954469 DOI: 10.1093/nar/gkae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Environmentally regulated gene expression is critical for bacterial survival under stress conditions, including extremes in temperature, osmolarity and nutrient availability. Here, we dissect the thermo- and osmo-responsory behavior of the transcriptional repressor H-NS, an archetypal nucleoid-condensing sensory protein, ubiquitous in enterobacteria that infect the mammalian gut. Through experiments and thermodynamic modeling, we show that H-NS exhibits osmolarity, temperature and concentration dependent self-association, with a highly polydisperse native ensemble dominated by monomers, dimers, tetramers and octamers. The relative population of these oligomeric states is determined by an interplay between dimerization and higher-order oligomerization, which in turn drives a competition between weak homo- versus hetero-oligomerization of protein-protein and protein-DNA complexes. A phosphomimetic mutation, Y61E, fully eliminates higher-order self-assembly and preserves only dimerization while weakening DNA binding, highlighting that oligomerization is a prerequisite for strong DNA binding. We further demonstrate the presence of long-distance thermodynamic connectivity between dimerization and oligomerization sites on H-NS which influences the binding of the co-repressor Cnu, and switches the DNA binding mode of the hetero-oligomeric H-NS:Cnu complex. Our work thus uncovers important organizational principles in H-NS including a multi-layered thermodynamic control, and provides a molecular framework broadly applicable to other thermo-osmo sensory proteins that employ similar mechanisms to regulate gene expression.
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Affiliation(s)
- Bincy Lukose
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Mohammed A Faidh
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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9
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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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10
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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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11
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Groisman EA, Choi J. Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes. Bioessays 2023; 45:e2300062. [PMID: 37533411 PMCID: PMC10530229 DOI: 10.1002/bies.202300062] [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: 04/09/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Horizontal gene transfer advances bacterial evolution. To benefit from horizontally acquired genes, enteric bacteria must overcome silencing caused when the widespread heat-stable nucleoid structuring (H-NS) protein binds to AT-rich horizontally acquired genes. This ability had previously been ascribed to both anti-silencing proteins outcompeting H-NS for binding to AT-rich DNA and RNA polymerase initiating transcription from alternative promoters. However, we now know that pathogenic Salmonella enterica serovar Typhimurium and commensal Escherichia coli break down H-NS when this silencer is not bound to DNA. Curiously, both species use the same protease - Lon - to destroy H-NS in distinct environments. Anti-silencing proteins promote the expression of horizontally acquired genes without binding to them by displacing H-NS from AT-rich DNA, thus leaving H-NS susceptible to proteolysis and decreasing H-NS amounts overall. Conserved amino acid sequences in the Lon protease and H-NS cleavage site suggest that diverse bacteria degrade H-NS to exploit horizontally acquired genes.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT, 06516, USA
| | - Jeongjoon Choi
- Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
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12
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Beard S, Moya-Beltrán A, Silva-García D, Valenzuela C, Pérez-Acle T, Loyola A, Quatrini R. Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology. Front Microbiol 2023; 14:1271138. [PMID: 37817747 PMCID: PMC10561277 DOI: 10.3389/fmicb.2023.1271138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.
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Affiliation(s)
- Simón Beard
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ana Moya-Beltrán
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Danitza Silva-García
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Cesar Valenzuela
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Tomás Pérez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Alejandra Loyola
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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13
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Hespanhol JT, Nóbrega-Silva L, Bayer-Santos E. Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001376. [PMID: 37552221 PMCID: PMC10482370 DOI: 10.1099/mic.0.001376] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Bacteria live in complex polymicrobial communities and are constantly competing for resources. The type VI secretion system (T6SS) is a widespread antagonistic mechanism used by Gram-negative bacteria to gain an advantage over competitors. T6SSs translocate toxic effector proteins inside target prokaryotic cells in a contact-dependent manner. In addition, some T6SS effectors can be secreted extracellularly and contribute to the scavenging scarce metal ions. Bacteria deploy their T6SSs in different situations, categorizing these systems into offensive, defensive and exploitative. The great variety of bacterial species and environments occupied by such species reflect the complexity of regulatory signals and networks that control the expression and activation of the T6SSs. Such regulation is tightly controlled at the transcriptional, posttranscriptional and posttranslational level by abiotic (e.g. pH, iron) or biotic (e.g. quorum-sensing) cues. In this review, we provide an update on the current knowledge about the regulatory networks that modulate the expression and activity of T6SSs across several species, focusing on systems used for interbacterial competition.
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Affiliation(s)
- Julia Takuno Hespanhol
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Luize Nóbrega-Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
| | - Ethel Bayer-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-900, Brazil
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14
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Getz LJ, Brown JM, Sobot L, Chow A, Mahendrarajah J, Thomas N. Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus. Nucleic Acids Res 2023; 51:6156-6171. [PMID: 37158250 PMCID: PMC10325908 DOI: 10.1093/nar/gkad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/23/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Pathogenic Vibrio species account for 3-5 million annual life-threatening human infections. Virulence is driven by bacterial hemolysin and toxin gene expression often positively regulated by the winged helix-turn-helix (wHTH) HlyU transcriptional regulator family and silenced by histone-like nucleoid structural protein (H-NS). In the case of Vibrio parahaemolyticus, HlyU is required for virulence gene expression associated with type 3 Secretion System-1 (T3SS1) although its mechanism of action is not understood. Here, we provide evidence for DNA cruciform attenuation mediated by HlyU binding to support concomitant virulence gene expression. Genetic and biochemical experiments revealed that upon HlyU mediated DNA cruciform attenuation, an intergenic cryptic promoter became accessible allowing for exsA mRNA expression and initiation of an ExsA autoactivation feedback loop at a separate ExsA-dependent promoter. Using a heterologous E. coli expression system, we reconstituted the dual promoter elements which revealed that HlyU binding and DNA cruciform attenuation were strictly required to initiate the ExsA autoactivation loop. The data indicate that HlyU acts to attenuate a transcriptional repressive DNA cruciform to support T3SS1 virulence gene expression and reveals a non-canonical extricating gene regulation mechanism in pathogenic Vibrio species.
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Affiliation(s)
- Landon J Getz
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Justin M Brown
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Lauren Sobot
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Alexandra Chow
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Jastina Mahendrarajah
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Nikhil A Thomas
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
- Department of Medicine, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
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15
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Fitzgerald DM, Stringer AM, Smith C, Lapierre P, Wade JT. Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites. mBio 2023; 14:e0253522. [PMID: 37067422 PMCID: PMC10294691 DOI: 10.1128/mbio.02535-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of, genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert and hence are tolerated as genomic "noise." IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of nonregulatory, intragenic binding sites for transcription factors and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon M. Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne M. Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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16
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Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade JT. Genome-wide mapping of the Escherichia coli PhoB regulon reveals many transcriptionally inert, intragenic binding sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527549. [PMID: 36798257 PMCID: PMC9934606 DOI: 10.1101/2023.02.07.527549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of the Escherichia coli transcription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert, and hence are tolerated as genomic "noise". IMPORTANCE Recent studies have revealed large numbers of transcription factor binding sites within the genes of bacteria. The function, if any, of the vast majority of these binding sites has not been investigated. Here, we map the binding of the transcription factor PhoB across the Escherichia coli genome, revealing that the majority of PhoB binding sites are within genes. We show that PhoB binding sites within genes are not associated with regulation of the overlapping genes. Indeed, our data suggest that bacteria tolerate the presence of large numbers of non-regulatory, intragenic binding sites for transcription factors, and that these binding sites are not under selective pressure.
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Affiliation(s)
- Devon Fitzgerald
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Anne Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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17
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The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions. Int J Mol Sci 2022; 23:ijms232415536. [PMID: 36555178 PMCID: PMC9779718 DOI: 10.3390/ijms232415536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.
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18
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Erkelens AM, Qin L, van Erp B, Miguel-Arribas A, Abia D, Keek HGJ, Markus D, Cajili MKM, Schwab S, Meijer WJJ, Dame R. The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues. Nucleic Acids Res 2022; 50:12166-12185. [PMID: 36408910 PMCID: PMC9757077 DOI: 10.1093/nar/gkac1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.
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Affiliation(s)
| | | | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Helena G J Keek
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Dorijn Markus
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Wilfried J J Meijer
- Correspondence may also be addressed to Wilfried J.J. Meijer. Tel: +34 91 196 4539;
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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19
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Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut. Proc Natl Acad Sci U S A 2022; 119:e2210239119. [PMID: 36161931 DOI: 10.1073/pnas.2210239119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer drives bacterial evolution. To confer new properties, horizontally acquired genes must overcome gene silencing by nucleoid-associated proteins, such as the heat-stable nucleoid structuring (H-NS) protein. Enteric bacteria possess proteins that displace H-NS from foreign genes, form nonfunctional oligomers with H-NS, and degrade H-NS, raising the question of whether any of these mechanisms play a role in overcoming foreign gene silencing in vivo. To answer this question, we mutagenized the hns gene and identified a variant specifying an H-NS protein that binds foreign DNA and silences expression of the corresponding genes, like wild-type H-NS, but resists degradation by the Lon protease. Critically, Escherichia coli expressing this variant alone fails to produce curli, which are encoded by foreign genes and required for biofilm formation, and fails to colonize the murine gut. Our findings establish that H-NS proteolysis is a general mechanism of derepressing foreign genes and essential for colonization of mammalian hosts.
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20
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Sadoon AA, Oliver WF, Wang Y. Revisiting the Temperature Dependence of Protein Diffusion inside Bacteria: Validity of the Stokes-Einstein Equation. PHYSICAL REVIEW LETTERS 2022; 129:018101. [PMID: 35841576 DOI: 10.1103/physrevlett.129.018101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Although the transport and mixing of proteins and other molecules inside bacteria rely on the diffusion of molecules, many aspects of the molecular diffusion in bacterial cytoplasm remain unclear or controversial, including how the diffusion-temperature relation follows the Stokes-Einstein equation. In this study, we applied single-particle tracking photoactivated localization microscopy to investigate the diffusion of histonelike nucleoid structuring (HNS) proteins and free dyes in bacterial cytoplasm at different temperatures. Although the diffusion of HNS proteins in both live and dead bacteria increased at higher temperatures and appeared to follow the Arrhenius equation, the diffusion of free dyes decreased at higher temperatures, questioning the previously proposed theories based on superthermal fluctuations. To understand the measured diffusion-temperature relations, we developed an alternative model, in which the bacterial cytoplasm is considered as a polymeric network or mesh. In our model, the Stokes-Einstein equation remains valid, while the polymeric network contributes a significant term to the viscosity experienced by the molecules diffusing in bacterial cytoplasm. Our model was successful in predicting the diffusion-temperature relations for both HNS proteins and free dyes in bacteria. In addition, we systematically examined the predicted diffusion-temperature relations with different parameters in the model, and predicted the possible existence of phase transitions.
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Affiliation(s)
- Asmaa A Sadoon
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Department of Physics, University of Thi-Qar, Nassiriya 64001, Iraq
| | - William F Oliver
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
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21
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Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments. iScience 2022; 25:104429. [PMID: 35669520 PMCID: PMC9162952 DOI: 10.1016/j.isci.2022.104429] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the structures, arrangements of DNA-binding domains (DBDs), and positions of DBD-DNA contacts in linear and bridged filaments are uncertain. To characterize the H-NS DBD contacts that silence transcription by RNA polymerase, we combined ·OH footprinting, molecular dynamics, statistical modeling, and DBD mapping using a chemical nuclease (Fe2+-EDTA) tethered to the DBDs (TEN-map). We find that H-NS DBDs contact DNA at indistinguishable locations in bridged or linear filaments and that the DBDs vary in orientation and position with ∼10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged H-NS switching. Linear filaments able to inhibit only transcription initiation switch to bridged filaments able to inhibit both initiation and elongation using the same irregularly spaced DNA contacts.
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22
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Dombach JL, Quintana JLJ, Allgood SC, Nagy TA, Gustafson DL, Detweiler CS. A small molecule that disrupts S. Typhimurium membrane voltage without cell lysis reduces bacterial colonization of mice. PLoS Pathog 2022; 18:e1010606. [PMID: 35687608 PMCID: PMC9223311 DOI: 10.1371/journal.ppat.1010606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022] Open
Abstract
As pathogenic bacteria become increasingly resistant to antibiotics, antimicrobials with mechanisms of action distinct from current clinical antibiotics are needed. Gram-negative bacteria pose a particular problem because they defend themselves against chemicals with a minimally permeable outer membrane and with efflux pumps. During infection, innate immune defense molecules increase bacterial vulnerability to chemicals by permeabilizing the outer membrane and occupying efflux pumps. Therefore, screens for compounds that reduce bacterial colonization of mammalian cells have the potential to reveal unexplored therapeutic avenues. Here we describe a new small molecule, D66, that prevents the survival of a human Gram-negative pathogen in macrophages. D66 inhibits bacterial growth under conditions wherein the bacterial outer membrane or efflux pumps are compromised, but not in standard microbiological media. The compound disrupts voltage across the bacterial inner membrane at concentrations that do not permeabilize the inner membrane or lyse cells. Selection for bacterial clones resistant to D66 activity suggested that outer membrane integrity and efflux are the two major bacterial defense mechanisms against this compound. Treatment of mammalian cells with D66 does not permeabilize the mammalian cell membrane but does cause stress, as revealed by hyperpolarization of mitochondrial membranes. Nevertheless, the compound is tolerated in mice and reduces bacterial tissue load. These data suggest that the inner membrane could be a viable target for anti-Gram-negative antimicrobials, and that disruption of bacterial membrane voltage without lysis is sufficient to enable clearance from the host.
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Affiliation(s)
- Jamie L. Dombach
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (JLD); (CSD)
| | - Joaquin LJ Quintana
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Samual C. Allgood
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Toni A. Nagy
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Daniel L. Gustafson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (JLD); (CSD)
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23
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Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Sci Rep 2022; 12:6868. [PMID: 35477739 PMCID: PMC9046306 DOI: 10.1038/s41598-022-10827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022] Open
Abstract
Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
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24
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Forrest D, Warman EA, Erkelens AM, Dame RT, Grainger DC. Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity. Nat Commun 2022; 13:1149. [PMID: 35241653 PMCID: PMC8894471 DOI: 10.1038/s41467-022-28747-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli. Bacteria use specific silencing proteins to prevent spurious transcription of horizontally acquired DNA. Here, Forrest et al. describe differences in silencing strategies between E. coli and Bacillus subtilis, driven by the respective specificities of the silencing protein and the RNA polymerase in each organism.
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Affiliation(s)
- David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Emily A Warman
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.
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25
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Gurung JM, Amer AAA, Chen S, Diepold A, Francis MS. Type III secretion by Yersinia pseudotuberculosis is reliant upon an authentic N-terminal YscX secretor domain. Mol Microbiol 2022; 117:886-906. [PMID: 35043994 PMCID: PMC9303273 DOI: 10.1111/mmi.14880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
YscX was discovered as an essential part of the Yersinia type III secretion system about 20 years ago. It is required for substrate secretion and is exported itself. Despite this central role, its precise function and mode of action remains unknown. In order to address this knowledge gap, this present study refocused attention on YscX to build on the recent advances in the understanding of YscX function. Our experiments identified a N-terminal secretion domain in YscX promoting its secretion, with the first five codons constituting a minimal signal capable of promoting secretion of the signalless β-lactamase reporter. Replacing the extreme YscX N-terminus with known secretion signals of other Ysc-Yop substrates revealed that the YscX N-terminal segment contains non-redundant information needed for YscX function. Further, both in cis deletion of the YscX N-terminus in the virulence plasmid and ectopic expression of epitope tagged YscX variants again lead to stable YscX production but not type III secretion of Yop effector proteins. Mislocalisation of the needle components, SctI and SctF, accompanied this general defect in Yops secretion. Hence, a coupling exists between YscX secretion permissiveness and the assembly of an operational secretion system.
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Affiliation(s)
- Jyoti M Gurung
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Ayad A A Amer
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Shiyun Chen
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan, China
| | - Andreas Diepold
- Max Planck Institute for Terrestrial Microbiology, Department of Ecophysiology, Marburg, Germany
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
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26
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Duan Y, Liu S, Gao Y, Zhang P, Mao D, Luo Y. Macrolides mediate transcriptional activation of the msr(E)-mph(E) operon through histone-like nucleoid-structuring protein (HNS) and cAMP receptor protein (CRP). J Antimicrob Chemother 2021; 77:391-399. [PMID: 34747464 DOI: 10.1093/jac/dkab395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The msr(E)-mph(E) operon exists widely in diverse species of bacteria and msr(E) and mph(E) genes confer high resistance to macrolides. We aimed to explore whether macrolides regulate the transcription of the operon. METHODS Antibiotic resistance genes in clinical isolates of Klebsiella pneumoniae were analysed by WGS. The transcription of the msr(E)-mph(E) operon was investigated by quantitative PCR. Construction of enhanced green fluorescent protein (eGFP) reporter plasmids, gene knockout and complementation experiments were used to further explore the induction mechanism of macrolides for the operon. Sequence analysis was finally used to investigate whether the operon exists widely in diverse species of bacteria. RESULTS We originally found that the treatment of a pandrug-resistant isolate of K. pneumoniae (KP1517) with macrolides obviously up-regulated the msr(E)-mph(E) operon, which was further confirmed in another nine clinical isolates of K. pneumoniae. The induction mechanism of macrolides for the operon was partly elucidated. Macrolides could activate the operon promoter, and the J10/J35 regions (J10: 5'-AGTTATCAT-3'; J35: 5'-TTGTCT-3') of the promoter were determined. Histone-like nucleoid-structuring protein (HNS) and cAMP receptor protein (CRP) were involved in the erythromycin-mediated activation of the operon promoter. The 476 strains of bacteria carrying the msr(E)-mph(E) operon currently in the NCBI database are mainly Acinetobacter baumannii (158; 33%), K. pneumoniae (95; 20%), Escherichia coli (26; 5%) and Proteus mirabilis (25; 5%). They were mainly isolated from human clinical samples (287; 60%) and had a wide geographical distribution. CONCLUSIONS Macrolides could activate transcription of the msr(E)-mph(E) operon through HNS and CRP in K. pneumoniae and E. coli, and this might occur in diverse species of bacteria.
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Affiliation(s)
- Yitao Duan
- College of Environmental Science and Engineering, Nankai University, Tianjin, China.,Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuangqing Liu
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuting Gao
- College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Peng Zhang
- College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Luo
- College of Environmental Science and Engineering, Nankai University, Tianjin, China.,State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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27
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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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28
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Zhao X, Remington JM, Schneebeli ST, Arold ST, Li J. Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament. J Phys Chem Lett 2021; 12:7878-7884. [PMID: 34382809 PMCID: PMC9346976 DOI: 10.1021/acs.jpclett.1c01710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The histone-like nucleoid structuring (H-NS) protein controls the expression of hundreds of genes in Gram-positive bacteria through its capability to coat and condense DNA. This mechanism requires the formation of superhelical H-NS protein filaments that are sensitive to temperature and salinity, allowing H-NS to act as an environment sensor. We use multiscale modeling and simulations to obtain detailed insights into the mechanism of H-NS filament's sensitivity to environmental changes. Through the simulations of the superhelical H-NS filament, we reveal how different environments induce heterogeneity of H-NS monomers. Further, we observe that transient self-association within the H-NS filament creates temperature-inducible strain and might mildly oppose DNA binding. We also probe different H-NS-DNA complex architectures and show that complexation enhances the stability of both DNA and H-NS superhelices. Overall, our results provide unprecedented molecular insights into the environmental sensing and DNA interactions of a prototypical nucleoid-structuring bacterial protein filament.
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Affiliation(s)
- Xiaochuan Zhao
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Jacob M. Remington
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Severin T. Schneebeli
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Stefan T. Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Jianing Li
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
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29
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Zhao X, Yang F, Wang Y, Zhang Y. hns mRNA downregulates the expression of galU and attenuates the motility of Salmonella enterica serovar Typhi. Int J Med Microbiol 2021; 311:151525. [PMID: 34340061 DOI: 10.1016/j.ijmm.2021.151525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 10/20/2022] Open
Abstract
Recently, multiple bifunctional RNAs have been discovered, which can both be translated into proteins and play regulatory roles. hns encodes the global gene silencing factor H-NS, which is widespread in Gram-negative bacteria. This study reported that hns mRNA of Salmonella enterica serovar Typhi (S. Typhi) was a bifunctional RNA that could act as an antisense RNA downregulating the expression of galU, the coding gene of uridine triphosphate-glucose-1-phosphate uridylyltransferase, and attenuating bacterial motility. galU, which is located at the opposite strand of hns, was identified to have a long 3'-untranslated region that overlapped with hns and could be processed to produce short RNA fragments. The overexpression of hns mRNA inhibited the expression of galU. The deletion of galU attenuated the motility of S. Typhi, while the complementation of galU nearly restored the phenotype. Overexpressing hns mRNA in the wild-type strain of S. Typhi inhibited the motility and the expression of flagellar genes, while overexpressing hns mRNA in the galU-deletion mutant did not influence bacterial motility. In conclusion, hns mRNA has been identified to be a new bifunctional RNA that attenuates the motility of S. Typhi by downregulating the expression of galU.
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Affiliation(s)
- Xin Zhao
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210006, China.
| | - Fanfan Yang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Yurou Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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30
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Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli. J Bacteriol 2021; 203:e0010921. [PMID: 33972351 DOI: 10.1128/jb.00109-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a "stringent" RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli's ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.
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31
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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32
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Liu X, Lin S, Liu T, Zhou Y, Wang W, Yao J, Guo Y, Tang K, Chen R, Benedik MJ, Wang X. Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella. Nucleic Acids Res 2021; 49:3427-3440. [PMID: 33693785 PMCID: PMC8034616 DOI: 10.1093/nar/gkab137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/20/2022] Open
Abstract
Lateral gene transfer (LGT) plays a key role in shaping the genome evolution and environmental adaptation of bacteria. Xenogeneic silencing is crucial to ensure the safe acquisition of LGT genes into host pre-existing regulatory networks. We previously found that the host nucleoid structuring protein (H-NS) silences prophage CP4So at warm temperatures yet enables this prophage to excise at cold temperatures in Shewanella oneidensis. However, whether H-NS silences other genes and how bacteria modulate H-NS to regulate the expression of genes have not been fully elucidated. In this study, we discovered that the H-NS silences many LGT genes and the xenogeneic silencing of H-NS relies on a temperature-dependent phosphorylation at warm temperatures in S. oneidensis. Specifically, phosphorylation of H-NS at Ser42 is critical for silencing the cold-inducible genes including the excisionase of CP4So prophage, a cold shock protein, and a stress-related chemosensory system. By contrast, nonphosphorylated H-NS derepresses the promoter activity of these genes/operons to enable their expression at cold temperatures. Taken together, our results reveal that the posttranslational modification of H-NS can function as a regulatory switch to control LGT gene expression in host genomes to enable the host bacterium to react and thrive when environmental temperature changes.
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Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Visser EWA, Miladinovic J, Milstein JN. An Ultrastable and Dense Single-Molecule Click Platform for Sensing Protein-Deoxyribonucleic Acid Interactions. SMALL METHODS 2021; 5:e2001180. [PMID: 34928085 DOI: 10.1002/smtd.202001180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/29/2021] [Indexed: 06/14/2023]
Abstract
An ultrastable, highly dense single-molecule assay ideal for observing protein-DNA interactions is demonstrated. Stable click tethered particle motion leverages next generation click-chemistry to achieve an ultrahigh density of surface tethered reporter particles, and has low non-specific interactions, is stable at elevated temperatures to at least 45 °C, and is compatible with Mg2+ , an important ionic component of many regulatory protein-DNA interactions. Prepared samples remain stable, with little degradation, for >6 months in physiological buffers. These improvements enable the authors to study previously inaccessible sequence and temperature-dependent effects on DNA binding by the bacterial protein, histone-like nucleoid-structuring protein, a global transcriptional regulator found in Escherichia coli. This greatly improved assay can directly be translated to accelerate existing tethered particle-based, single-molecule biosensing applications.
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Affiliation(s)
- Emiel W A Visser
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands
| | - Jovana Miladinovic
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Joshua N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON M5S 1A1, Canada
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34
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Ageorges V, Monteiro R, Leroy S, Burgess CM, Pizza M, Chaucheyras-Durand F, Desvaux M. Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation. FEMS Microbiol Rev 2021; 44:314-350. [PMID: 32239203 DOI: 10.1093/femsre/fuaa008] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
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Affiliation(s)
- Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Via Fiorentina 1, 53100 Siena, Italy
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | | | - Frédérique Chaucheyras-Durand
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Lallemand Animal Nutrition SAS, F-31702 Blagnac Cedex, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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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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Abstract
Cholera is a potentially lethal disease that is endemic in much of the developing world. Vibrio cholerae, the bacterium underlying the disease, infects humans utilizing proteins encoded on horizontally acquired genetic material. Here, we provide evidence that TsrA, a Vibrionaceae-specific protein, plays a critical role in regulating these genetic elements and is essential for V. cholerae virulence in a mouse intestinal model. Pathogenic strains of Vibrio cholerae require careful regulation of horizontally acquired virulence factors that are largely located on horizontally acquired genomic islands (HAIs). While TsrA, a Vibrionaceae-specific protein, is known to regulate the critical HAI virulence genes toxT and ctxA, its broader function throughout the genome is unknown. Here, we find that deletion of tsrA results in genomewide expression patterns that heavily correlate with those seen upon deletion of hns, a widely conserved bacterial protein that regulates V. cholerae virulence. This correlation is particularly strong for loci on HAIs, where all differentially expressed loci in the ΔtsrA mutant are also differentially expressed in the Δhns mutant. Correlation between TsrA and H-NS function extends to in vivo virulence phenotypes where deletion of tsrA compensates for the loss of ToxR activity in V. cholerae and promotes wild-type levels of mouse intestinal colonization. All in all, we find that TsrA broadly controls V. cholerae infectivity via repression of key HAI virulence genes and many other targets in the H-NS regulon. IMPORTANCE Cholera is a potentially lethal disease that is endemic in much of the developing world. Vibrio cholerae, the bacterium underlying the disease, infects humans utilizing proteins encoded on horizontally acquired genetic material. Here, we provide evidence that TsrA, a Vibrionaceae-specific protein, plays a critical role in regulating these genetic elements and is essential for V. cholerae virulence in a mouse intestinal model.
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Fitzgerald S, Kary SC, Alshabib EY, MacKenzie KD, Stoebel D, Chao TC, Cameron ADS. Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration. Nucleic Acids Res 2020; 48:10184-10198. [PMID: 32894292 PMCID: PMC7544231 DOI: 10.1093/nar/gkaa709] [Citation(s) in RCA: 5] [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: 04/29/2020] [Revised: 08/07/2020] [Accepted: 08/23/2020] [Indexed: 12/27/2022] Open
Abstract
H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here, we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. Each clade is composed exclusively of either chromosome-encoded or plasmid-encoded proteins. On chromosomes, stpA and newly discovered hlpP are core genes in specific genera, whereas hfp and newly discovered hlpC are sporadically distributed. Six clades of H-NS plasmid proteins (Hpp) exhibit ancient and dedicated associations with plasmids, including three clades with fidelity for plasmid incompatibility groups H, F or X. A proliferation of H-NS homologs in Erwiniaceae includes the first observation of potentially co-dependent H-NS forms. Conversely, the observed diversification of oligomerization domains may facilitate stable co-existence of divergent homologs in a genome. Transcriptomic and proteomic analysis in Salmonella revealed regulatory crosstalk and hierarchical control of H-NS homologs. We also discovered that H-NS is both a repressor and activator of Salmonella Pathogenicity Island 1 gene expression, and both regulatory modes are restored by Sfh (HppH) in the absence of H-NS.
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Affiliation(s)
- Stephen Fitzgerald
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Stefani C Kary
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ebtihal Y Alshabib
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Keith D MacKenzie
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Daniel M Stoebel
- Department of Biology, Harvey Mudd College, Claremont, CA 91711, USA
| | - Tzu-Chiao Chao
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute of Environmental Change and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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Cristofalo M, Marrano CA, Salerno D, Corti R, Cassina V, Mammola A, Gherardi M, Sclavi B, Cosentino Lagomarsino M, Mantegazza F. Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers. Biochim Biophys Acta Gen Subj 2020; 1864:129725. [PMID: 32891648 DOI: 10.1016/j.bbagen.2020.129725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment. METHODS We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding. RESULTS In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively. CONCLUSIONS We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG. GENERAL SIGNIFICANCE Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.
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Affiliation(s)
- M Cristofalo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - C A Marrano
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - D Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - R Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - V Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - A Mammola
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - M Gherardi
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - B Sclavi
- Université Pierre et Marie Curie, Institut de Biologie Paris Seine, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - M Cosentino Lagomarsino
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - F Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy.
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Liu Z, Feng J, Yu B, Ma Q, Liu B. The functional determinants in the organization of bacterial genomes. Brief Bioinform 2020; 22:5892344. [PMID: 32793986 DOI: 10.1093/bib/bbaa172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial genomes are now recognized as interacting intimately with cellular processes. Uncovering organizational mechanisms of bacterial genomes has been a primary focus of researchers to reveal the potential cellular activities. The advances in both experimental techniques and computational models provide a tremendous opportunity for understanding these mechanisms, and various studies have been proposed to explore the organization rules of bacterial genomes associated with functions recently. This review focuses mainly on the principles that shape the organization of bacterial genomes, both locally and globally. We first illustrate local structures as operons/transcription units for facilitating co-transcription and horizontal transfer of genes. We then clarify the constraints that globally shape bacterial genomes, such as metabolism, transcription and replication. Finally, we highlight challenges and opportunities to advance bacterial genomic studies and provide application perspectives of genome organization, including pathway hole assignment and genome assembly and understanding disease mechanisms.
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Affiliation(s)
| | | | - Bin Yu
- College of Mathematics and Physics, Qingdao University of Science and Technology
| | - Qin Ma
- Department of Biomedical Informatics, the Ohio State University
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Warman EA, Singh SS, Gubieda AG, Grainger DC. A non-canonical promoter element drives spurious transcription of horizontally acquired bacterial genes. Nucleic Acids Res 2020; 48:4891-4901. [PMID: 32297955 PMCID: PMC7229825 DOI: 10.1093/nar/gkaa244] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 01/18/2023] Open
Abstract
RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Further elements, and gene regulatory proteins, are needed to recruit RNA polymerase to the -10 sequence. Hence, -10 elements cannot function in isolation. Many horizontally acquired genes also have a high AT-content. Consequently, sequences that resemble the -10 element occur frequently. As a result, foreign genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognizes such sequences. Here, we identify a non-canonical promoter element that plays a key role. The sequence, itself a short AT-tract, resides 5 base pairs upstream of otherwise cryptic -10 elements. The AT-tract alters DNA conformation and enhances contacts between the DNA backbone and RNA polymerase.
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Affiliation(s)
- Emily A Warman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Shivani S Singh
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alicia G Gubieda
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David C Grainger
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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41
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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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42
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Chaparian RR, Tran MLN, Miller Conrad LC, Rusch DB, van Kessel JC. Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. Nucleic Acids Res 2020; 48:171-183. [PMID: 31745565 PMCID: PMC7145609 DOI: 10.1093/nar/gkz1089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/15/2019] [Accepted: 11/18/2019] [Indexed: 01/03/2023] Open
Abstract
Bacteria coordinate cellular behaviors using a cell-cell communication system termed quorum sensing. In Vibrio harveyi, the master quorum sensing transcription factor LuxR directly regulates >100 genes in response to changes in population density. Here, we show that LuxR derepresses quorum sensing loci by competing with H-NS, a global transcriptional repressor that oligomerizes on DNA to form filaments and bridges. We first identified H-NS as a repressor of bioluminescence gene expression, for which LuxR is a required activator. In an hns deletion strain, LuxR is no longer necessary for transcription activation of the bioluminescence genes, suggesting that the primary role of LuxR is to displace H-NS to derepress gene expression. Using RNA-seq and ChIP-seq, we determined that H-NS and LuxR co-regulate and co-occupy 28 promoters driving expression of 63 genes across the genome. ChIP-PCR assays show that as autoinducer concentration increases, LuxR protein accumulates at co-occupied promoters while H-NS protein disperses. LuxR is sufficient to evict H-NS from promoter DNA in vitro, which is dependent on LuxR DNA binding activity. From these findings, we propose a model in which LuxR serves as a counter-silencer at H-NS-repressed quorum sensing loci by disrupting H-NS nucleoprotein complexes that block transcription.
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Affiliation(s)
| | - Minh L N Tran
- Department of Chemistry, San Jose State University, San Jose, CA, USA
| | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
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Sadoon AA, Khadka P, Freeland J, Gundampati RK, Manso RH, Ruiz M, Krishnamurthi VR, Thallapuranam SK, Chen J, Wang Y. Silver Ions Caused Faster Diffusive Dynamics of Histone-Like Nucleoid-Structuring Proteins in Live Bacteria. Appl Environ Microbiol 2020; 86:e02479-19. [PMID: 31953329 PMCID: PMC7054089 DOI: 10.1128/aem.02479-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The antimicrobial activity and mechanism of silver ions (Ag+) have gained broad attention in recent years. However, dynamic studies are rare in this field. Here, we report our measurement of the effects of Ag+ ions on the dynamics of histone-like nucleoid-structuring (H-NS) proteins in live bacteria using single-particle-tracking photoactivated localization microscopy (sptPALM). It was found that treating the bacteria with Ag+ ions led to faster diffusive dynamics of H-NS proteins. Several techniques were used to understand the mechanism of the observed faster dynamics. Electrophoretic mobility shift assay on purified H-NS proteins indicated that Ag+ ions weaken the binding between H-NS proteins and DNA. Isothermal titration calorimetry confirmed that DNA and Ag+ ions interact directly. Our recently developed sensing method based on bent DNA suggested that Ag+ ions caused dehybridization of double-stranded DNA (i.e., dissociation into single strands). These evidences led us to a plausible mechanism for the observed faster dynamics of H-NS proteins in live bacteria when subjected to Ag+ ions: Ag+-induced DNA dehybridization weakens the binding between H-NS proteins and DNA. This work highlighted the importance of dynamic study of single proteins in live cells for understanding the functions of antimicrobial agents in bacteria.IMPORTANCE As so-called "superbug" bacteria resistant to commonly prescribed antibiotics have become a global threat to public health in recent years, noble metals, such as silver, in various forms have been attracting broad attention due to their antimicrobial activities. However, most of the studies in the existing literature have relied on the traditional bioassays for studying the antimicrobial mechanism of silver; in addition, temporal resolution is largely missing for understanding the effects of silver on the molecular dynamics inside bacteria. Here, we report our study of the antimicrobial effect of silver ions at the nanoscale on the diffusive dynamics of histone-like nucleoid-structuring (H-NS) proteins in live bacteria using single-particle-tracking photoactivated localization microscopy. This work highlights the importance of dynamic study of single proteins in live cells for understanding the functions of antimicrobial agents in bacteria.
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Affiliation(s)
- Asmaa A Sadoon
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
- Microelectronics-Photonics Graduate Program, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Physics, University of Thi Qar, Thi Qar, Iraq
| | - Prabhat Khadka
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
| | - Jack Freeland
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ryan H Manso
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Mason Ruiz
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | | | | | - Jingyi Chen
- Microelectronics-Photonics Graduate Program, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, USA
- Microelectronics-Photonics Graduate Program, University of Arkansas, Fayetteville, Arkansas, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
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Rihtar E, Žgur Bertok D, Podlesek Z. The Uropathogenic Specific Protein Gene usp from Escherichia coli and Salmonella bongori is a Novel Member of the TyrR and H-NS Regulons. Microorganisms 2020; 8:E330. [PMID: 32111072 PMCID: PMC7142922 DOI: 10.3390/microorganisms8030330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
The Escherichia coli PAIusp is a small pathogenicity island encoding usp, for the uropathogenic specific protein (Usp), a genotoxin and three associated downstream imu1-3 genes that protect the producer against its own toxin. Bioinformatic analysis revealed the presence of the PAIusp also in publically available Salmonella bongori and Salmonella enterica subps. salamae genome sequences. PAIusp is in all examined sequences integrated within the aroP-pdhR chromosomal intergenic region. The focus of this work was identification of the usp promoter and regulatory elements controlling its activity. We show that, in both E. coli and S. bongori, the divergent TyrR regulated P3 promoter of the aroP gene, encoding an aromatic amino acid membrane transporter, drives usp transcription while H-NS acts antagonistically repressing expression. Our results show that the horizontally acquired PAIusp has integrated into the TyrR regulatory network and that environmental factors such as aromatic amino acids, temperature and urea induce usp expression.
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Affiliation(s)
- Erik Rihtar
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
- National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Darja Žgur Bertok
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
| | - Zdravko Podlesek
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
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45
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Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nat Rev Genet 2019; 21:227-242. [DOI: 10.1038/s41576-019-0185-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
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46
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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: 27] [Impact Index Per Article: 5.4] [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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Magán A, Amman F, El-Isa F, Hartl N, Shamovsky I, Nudler E, Schroeder R, Sedlyarova N. iRAPs curb antisense transcription in E. coli. Nucleic Acids Res 2019; 47:10894-10905. [PMID: 31535128 PMCID: PMC6847712 DOI: 10.1093/nar/gkz791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 01/27/2023] Open
Abstract
RNA polymerase-binding RNA aptamers (RAPs) are natural RNA elements that control transcription in cis by directly contacting RNA polymerase. Many RAPs inhibit transcription by inducing Rho-dependent termination in Escherichia coli. Here, we studied the role of inhibitory RAPs (iRAPs) in modulation of antisense transcription (AT) using in silico and in vivo approaches. We revisited the antisense transcriptome in cells with impaired AT regulators (Rho, H-NS and RNaseIII) and searched for the presence of RAPs within antisense RNAs. Many of these RAPs were found at key genomic positions where they terminate AT. By exploring the activity of several RAPs both in a reporter system and in their natural genomic context, we confirmed their significant role in AT regulation. RAPs coordinate Rho activity at the antisense strand and terminate antisense transcripts. In some cases, they stimulated sense expression by alleviating ongoing transcriptional interference. Essentially, our data postulate RAPs as key determinants of Rho-mediated AT regulation in E. coli.
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Affiliation(s)
- Andrés Magán
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Fabian Amman
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
- Institute for Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Fatinah El-Isa
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Natascha Hartl
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Renée Schroeder
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Nadezda Sedlyarova
- Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
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48
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Bossi L, Ratel M, Laurent C, Kerboriou P, Camilli A, Eveno E, Boudvillain M, Figueroa-Bossi N. NusG prevents transcriptional invasion of H-NS-silenced genes. PLoS Genet 2019; 15:e1008425. [PMID: 31589608 PMCID: PMC6797219 DOI: 10.1371/journal.pgen.1008425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/17/2019] [Accepted: 09/16/2019] [Indexed: 01/02/2023] Open
Abstract
Evolutionarily conserved NusG protein enhances bacterial RNA polymerase processivity but can also promote transcription termination by binding to, and stimulating the activity of, Rho factor. Rho terminates transcription upon anchoring to cytidine-rich motifs, the so-called Rho utilization sites (Rut) in nascent RNA. Both NusG and Rho have been implicated in the silencing of horizontally-acquired A/T-rich DNA by nucleoid structuring protein H-NS. However, the relative roles of the two proteins in H-NS-mediated gene silencing remain incompletely defined. In the present study, a Salmonella strain carrying the nusG gene under the control of an arabinose-inducible repressor was used to assess the genome-wide response to NusG depletion. Results from two complementary approaches, i) screening lacZ protein fusions generated by random transposition and ii) transcriptomic analysis, converged to show that loss of NusG causes massive upregulation of Salmonella pathogenicity islands (SPIs) and other H-NS-silenced loci. A similar, although not identical, SPI-upregulated profile was observed in a strain with a mutation in the rho gene, Rho K130Q. Surprisingly, Rho mutation Y80C, which affects Rho's primary RNA binding domain, had either no effect or made H-NS-mediated silencing of SPIs even tighter. Thus, while corroborating the notion that bound H-NS can trigger Rho-dependent transcription termination in vivo, these data suggest that H-NS-elicited termination occurs entirely through a NusG-dependent pathway and is less dependent on Rut site binding by Rho. We provide evidence that through Rho recruitment, and possibly through other still unidentified mechanisms, NusG prevents pervasive transcripts from elongating into H-NS-silenced regions. Failure to perform this function causes the feedforward activation of the entire Salmonella virulence program. These findings provide further insight into NusG/Rho contribution in H-NS-mediated gene silencing and underscore the importance of this contribution for the proper functioning of a global regulatory response in growing bacteria. The complete set of transcriptomic data is freely available for viewing through a user-friendly genome browser interface.
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Affiliation(s)
- Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, France
| | - Mathilde Ratel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, France
| | - Camille Laurent
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, France
| | - Patricia Kerboriou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, France
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States of America
| | - Eric Eveno
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, France
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49
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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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50
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Tungtur S, Schwingen KM, Riepe JJ, Weeramange CJ, Swint-Kruse L. Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors. Protein Sci 2019; 28:1806-1818. [PMID: 31351028 DOI: 10.1002/pro.3695] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022]
Abstract
To bridge biological and biochemical disciplines, the relationship between in vitro protein biochemical function and in vivo activity must be established. Such studies can (a) help determine whether properties measured in simple, dilute solutions extrapolate to the complex in vivo conditions and (b) illuminate cryptic biological factors that are new avenues for study. We have explored the in vivo-in vitro relationship for chimeras built from LacI/GalR transcription regulators. In prior studies of individual chimeras, amino acid changes that altered in vitro DNA binding affinity exhibited correlated changes in in vivo transcription repression. However, discrepancies arose when the two datasets were compared to each other: Although their DNA binding domains were identical and their in vitro binding affinities spanned the same range, their in vivo repression ranges differed by >50-fold. Here, we determined that the presence of endogenous ligand for one chimera further exacerbated the offset, but that different abilities to simultaneously bind and "loop" two DNA operators resolves the discrepancy. Indeed, results suggest that the lac operon can be looped by even weakly interacting repressor dimers. For looping-competent repressors, we measured in vitro binding to the secondary operator. Surprisingly, this was largely insensitive to amino acid changes in the repressor protein, which reflects altered specificity; this supports the emerging view that the locations of specificity determining positions can be unique to each protein homolog. In aggregate, this work illustrates how a comparative approach can enrich understanding of the in vivo-in vitro relationship and suggest unexpected avenues for future study.
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Affiliation(s)
- Sudheer Tungtur
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Kristen M Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Joshua J Riepe
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Chamitha J Weeramange
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
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