1
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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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2
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Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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3
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Åberg A, Gideonsson P, Bhat A, Ghosh P, Arnqvist A. Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori. Nucleic Acids Res 2024; 52:5572-5595. [PMID: 38499492 PMCID: PMC11162790 DOI: 10.1093/nar/gkae188] [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: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
Adaptation to variations in pH is crucial for the ability of Helicobacter pylori to persist in the human stomach. The acid responsive two-component system ArsRS, constitutes the global regulon that responds to acidic conditions, but molecular details of how transcription is affected by the ArsR response regulator remains poorly understood. Using a combination of DNA-binding studies, in vitro transcription assays, and H. pylori mutants, we demonstrate that phosphorylated ArsR (ArsR-P) forms an active protein complex that binds DNA with high specificity in order to affect transcription. Our data showed that DNA topology is key for DNA binding. We found that AT-rich DNA sequences direct ArsR-P to specific sites and that DNA-bending proteins are important for the effect of ArsR-P on transcription regulation. The repression of sabA transcription is mediated by ArsR-P with the support of Hup and is affected by simple sequence repeats located upstream of the sabA promoter. Here stochastic events clearly contribute to the fine-tuning of pH-dependent gene regulation. Our results reveal important molecular aspects for how ArsR-P acts to repress transcription in response to acidic conditions. Such transcriptional control likely mediates shifts in bacterial positioning in the gastric mucus layer.
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Affiliation(s)
- Anna Åberg
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Pär Gideonsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Abhayprasad Bhat
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Prachetash Ghosh
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Anna Arnqvist
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
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4
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Keshavam CC, Naz S, Gupta A, Sanyal P, Kochar M, Gangwal A, Sangwan N, Kumar N, Tyagi E, Goel S, Singh NK, Sowpati DT, Khare G, Ganguli M, Raze D, Locht C, Basu-Modak S, Gupta M, Nandicoori VK, Singh Y. The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein. J Biol Chem 2023; 299:105364. [PMID: 37865319 PMCID: PMC10665949 DOI: 10.1016/j.jbc.2023.105364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.
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Affiliation(s)
| | - Saba Naz
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Aanchal Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyadarshini Sanyal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India
| | - Manisha Kochar
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Nitika Sangwan
- Department of Zoology, University of Delhi, Delhi, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Delhi, India
| | - Ekta Tyagi
- Department of Zoology, University of Delhi, Delhi, India
| | - Simran Goel
- Department of Zoology, University of Delhi, Delhi, India
| | | | | | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dominique Raze
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | | | - Meetu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
| | - Vinay Kumar Nandicoori
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India; Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India.
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5
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Boulas I, Bruno L, Rimsky S, Espeli O, Junier I, Rivoire O. Assessing in vivo the impact of gene context on transcription through DNA supercoiling. Nucleic Acids Res 2023; 51:9509-9521. [PMID: 37667073 PMCID: PMC10570042 DOI: 10.1093/nar/gkad688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023] Open
Abstract
Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.
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Affiliation(s)
- Ihab Boulas
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Lisa Bruno
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Sylvie Rimsky
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Gulliver, ESPCI, CNRS, Université PSL, Paris, France
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6
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Kato F, Yamaguchi Y, Inouye K, Matsuo K, Ishida Y, Inouye M. A novel gyrase inhibitor from toxin-antitoxin system expressed by Staphylococcus aureus. FEBS J 2023; 290:1502-1518. [PMID: 36148483 DOI: 10.1111/febs.16634] [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: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
Abstract
Toxin-antitoxin (TA) systems consist of a toxin inhibiting essential cellular functions (such as DNA, RNA and protein synthesis), and its cognate antitoxin neutralizing the toxicity. Recently, we identified a TA system termed TsbA/TsbT in the Staphylococcus aureus genome. The induction of the tsbT gene in Escherichia coli halted both DNA and RNA synthesis, reduced supercoiled plasmid and resulted in increasingly relaxed DNA. These results suggested that DNA gyrase was the target of TsbT. In addition, TsbT inhibited both E. coli and S. aureus DNA gyrase activity and induced linearization of plasmid DNA in vitro. Taken together, these results demonstrate that the TsbT toxin targets DNA gyrase in vivo. Site-directed mutagenesis experiments showed that the E27 and D37 residues in TsbT are critical for toxicity. Secondary structure prediction combining the analysis of vacuum-ultraviolet circular-dichroism spectroscopy and neural network method demonstrated that the 22nd-32nd residues of TsbT form an α-helix structure, and that the E27 residue is located around the centre of the α-helix segment. These findings give new insights not only into S. aureus TA systems, but also into bacterial toxins targeting DNA topoisomerases.
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Affiliation(s)
- Fuminori Kato
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Yoshihiro Yamaguchi
- Department of Biology and Geosciences, Graduate School of Sciences, Osaka City University, Japan
| | - Keiko Inouye
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yojiro Ishida
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Masayori Inouye
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
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7
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Cordeiro TFVB, Gontijo MTP, Jorge GP, Brocchi M. EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes. Microorganisms 2022; 10:microorganisms10101945. [PMID: 36296221 PMCID: PMC9610160 DOI: 10.3390/microorganisms10101945] [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: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022] Open
Abstract
Genomic compaction is an essential characteristic of living organisms. Nucleoid-associated proteins (NAPs) are a group of small proteins that play crucial roles in chromosome architecture and affect DNA replication, transcription, and recombination by imposing topological alterations in genomic DNA, thereby modulating global gene expression. EbfC/YbaB was first described as a DNA-binding protein of Borrelia burgdorferi that regulates the expression of surface lipoproteins with roles in virulence. Further studies indicated that this protein binds specifically and non-specifically to DNA and colocalises with nucleoids in this bacterium. The data showed that this protein binds to DNA as a homodimer, although it can form other organised structures. Crystallography analysis indicated that the protein possesses domains responsible for protein–protein interactions and forms a “tweezer” structure probably involved in DNA binding. Moreover, sequence analysis revealed conserved motifs that may be associated with dimerisation. Structural analysis also showed that the tridimensional structure of EbfC/YbaB is highly conserved within the bacterial domain. The DNA-binding activity was observed in different bacterial species, suggesting that this protein can protect DNA during stress conditions. These findings indicate that EbfC/YbaB is a broadly distributed NAP. Here, we present a review of the existing data on this NAP.
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8
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Qian J, Xu W, Dunlap D, Finzi L. Single-molecule insights into torsion and roadblocks in bacterial transcript elongation. Transcription 2021; 12:219-231. [PMID: 34719335 PMCID: PMC8632135 DOI: 10.1080/21541264.2021.1997315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
During transcription, RNA polymerase (RNAP) translocates along the helical template DNA while maintaining high transcriptional fidelity. However, all genomes are dynamically twisted, writhed, and decorated by bound proteins and motor enzymes. In prokaryotes, proteins bound to DNA, specifically or not, frequently compact DNA into conformations that may silence genes by obstructing RNAP. Collision of RNAPs with these architectural proteins, may result in RNAP stalling and/or displacement of the protein roadblock. It is important to understand how rapidly transcribing RNAPs operate under different levels of supercoiling or in the presence of roadblocks. Given the broad range of asynchronous dynamics exhibited by transcriptional complexes, single-molecule assays, such as atomic force microscopy, fluorescence detection, optical and magnetic tweezers, etc. are well suited for detecting and quantifying activity with adequate spatial and temporal resolution. Here, we summarize current understanding of the effects of torsion and roadblocks on prokaryotic transcription, with a focus on single-molecule assays that provide real-time detection and readout.
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Affiliation(s)
- Jin Qian
- Emory University, Atlanta, GA, USA
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9
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Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise. Proc Natl Acad Sci U S A 2021; 118:2021941118. [PMID: 34290140 DOI: 10.1073/pnas.2021941118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcription initiation is highly regulated by promoter sequence, transcription factors, and ligands. All known transcription inhibitors, an important class of antibiotics, act in initiation. To understand regulation and inhibition, the biophysical mechanisms of formation and stabilization of the "open" promoter complex (OC), of synthesis of a short RNA-DNA hybrid upon nucleotide addition, and of escape of RNA polymerase (RNAP) from the promoter must be understood. We previously found that RNAP forms three different OC with λPR promoter DNA. The 37 °C RNAP-λPR OC (RPO) is very stable. At lower temperatures, RPO is less stable and in equilibrium with an intermediate OC (I3). Here, we report step-by-step rapid quench-flow kinetic data for initiation and growth of the RNA-DNA hybrid at 25 and 37 °C that yield rate constants for each step of productive nucleotide addition. Analyzed together, with previously published data at 19 °C, our results reveal that I3 and not RPO is the productive initiation complex at all temperatures. From the strong variations of rate constants and activation energies and entropies for individual steps of hybrid extension, we deduce that contacts of RNAP with the bubble strands are disrupted stepwise as the hybrid grows and translocates. Stepwise disruption of RNAP-strand contacts is accompanied by stepwise bubble collapse, base stacking, and duplex formation, as the hybrid extends to a 9-mer prior to disruption of upstream DNA-RNAP contacts and escape of RNAP from the promoter.
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10
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Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M. Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling. Nat Commun 2020; 11:2905. [PMID: 32518228 PMCID: PMC7283360 DOI: 10.1038/s41467-020-16724-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/19/2020] [Indexed: 01/26/2023] Open
Abstract
Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging of near-native, unlabeled E. coli cells by soft X-ray tomography, we show that HU remodels nucleoids by promoting the formation of a dense condensed core surrounded by less condensed isolated domains. Nucleoid remodeling during cell growth and environmental adaptation correlate with pH and ionic strength controlled molecular switch that regulated HUαα dependent intermolecular DNA bundling. Through crystallographic and solution-based studies we show that these effects mechanistically rely on HUαα promiscuity in forming multiple electrostatically driven multimerization interfaces. Changes in DNA bundling consequently affects gene expression globally, likely by constrained DNA supercoiling. Taken together our findings unveil a critical function of HU–DNA interaction in nucleoid remodeling that may serve as a general microbial mechanism for transcriptional regulation to synchronize genetic responses during the cell cycle and adapt to changing environments. HU is among the most conserved and abundant nucleoid-associated proteins in eubacteria. Here the authors investigate the role of histone-like proteins (HU) in the 3D organization of the bacteria DNA and show via soft X-ray tomography the process of nucleoid remodeling.
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Affiliation(s)
- Soumya G Remesh
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Subhash C Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Axel A Ekman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carolyn A Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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11
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Yousuf M, Iuliani I, Veetil RT, Seshasayee A, Sclavi B, Cosentino Lagomarsino M. Early fate of exogenous promoters in E. coli. Nucleic Acids Res 2020; 48:2348-2356. [PMID: 31960057 PMCID: PMC7049719 DOI: 10.1093/nar/gkz1196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023] Open
Abstract
Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.
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Affiliation(s)
- Malikmohamed Yousuf
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ilaria Iuliani
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
- School of Life science, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru 560064, Karnataka, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Bianca Sclavi
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Université, Campus Pierre and Marie Curie, 4 Place Jussieu, 75005 Paris, France
- CNRS, UMR7238, 4 Place Jussieu, 75005 Paris, France
- Current Affiliation: IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20143 Milan, Italy
- Current Affiliation: Physics Department, University of Milan, and I.N.F.N., Via Celoria 16, 20133 Milan, Italy
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12
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Kawalek A, Wawrzyniak P, Bartosik AA, Jagura-Burdzy G. Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes. Microorganisms 2020; 8:E105. [PMID: 31940850 PMCID: PMC7022226 DOI: 10.3390/microorganisms8010105] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.
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Affiliation(s)
| | | | | | - Grazyna Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (A.K.); (P.W.); (A.A.B.)
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13
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Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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14
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Kawalek A, Bartosik AA, Glabski K, Jagura-Burdzy G. Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif. Nucleic Acids Res 2019; 46:4592-4606. [PMID: 29648658 PMCID: PMC5961200 DOI: 10.1093/nar/gky257] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/28/2018] [Indexed: 12/16/2022] Open
Abstract
ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is lethal. However, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over 1000 genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets. Here, we show that indeed ParB binds specifically to hundreds of sites in the genome. ChIP-seq analysis revealed 420 ParB-associated regions in wild-type strain and around 1000 in a ParB-overproducing strain and in various parS mutants. The vast majority of the ParB-enriched loci contained a heptanucleotide motif corresponding to one arm of the parS palindrome. All previously postulated parSs, except parS5, interacted with ParB in vivo. Whereas the ParB binding to the four parS sites closest to oriC, parS1-4, is involved in chromosome segregation, its genome-wide interactions with hundreds of parS half-sites could affect chromosome topology, compaction and gene expression, thus allowing P. aeruginosa ParB to be classified as a nucleoid-associated protein.
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Affiliation(s)
- Adam Kawalek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aneta A Bartosik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krzysztof Glabski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Microbial Biochemistry, Pawinskiego 5a, 02-106 Warsaw, Poland
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15
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Yan Y, Leng F, Finzi L, Dunlap D. Protein-mediated looping of DNA under tension requires supercoiling. Nucleic Acids Res 2019; 46:2370-2379. [PMID: 29365152 PMCID: PMC5861448 DOI: 10.1093/nar/gky021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023] Open
Abstract
Protein-mediated DNA looping is ubiquitous in chromatin organization and gene regulation, but to what extent supercoiling or nucleoid associated proteins promote looping is poorly understood. Using the lac repressor (LacI), a paradigmatic loop-mediating protein, we measured LacI-induced looping as a function of either supercoiling or the concentration of the HU protein, an abundant nucleoid protein in Escherichia coli. Negative supercoiling to physiological levels with magnetic tweezers easily drove the looping probability from 0 to 100% in single DNA molecules under slight tension that likely exists in vivo. In contrast, even saturating (micromolar) concentrations of HU could not raise the looping probability above 30% in similarly stretched DNA or 80% in DNA without tension. Negative supercoiling is required to induce significant looping of DNA under any appreciable tension.
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Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
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16
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NapA (Rv0430), a Novel Nucleoid-Associated Protein that Regulates a Virulence Operon in Mycobacterium tuberculosis in a Supercoiling-Dependent Manner. J Mol Biol 2019; 431:1576-1591. [DOI: 10.1016/j.jmb.2019.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/17/2022]
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17
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Datta C, Jha RK, Ahmed W, Ganguly S, Ghosh S, Nagaraja V. Physical and functional interaction between nucleoid-associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation. Mol Microbiol 2019; 111:981-994. [PMID: 30633392 DOI: 10.1111/mmi.14202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
Abstract
Nucleoid-associated proteins (NAPs) in bacteria contribute to key activities such as DNA compaction, chromosome organization and regulation of gene expression. HU and Lsr2 are two principal NAPs in Mycobacterium tuberculosis (Mtb). HU is essential for Mtb survival and is one of the most abundant NAPs. It differs from other eubacterial HU proteins in having a long, flexible lysine- and arginine-rich carboxy-terminal domain. Lsr2 of Mtb is the functional analogue of the bacterial NAP commonly called H-NS. Lsr2 binds to and regulates expression of A/T-rich portions of the otherwise G/C-rich mycobacterial chromosome. Here, we demonstrate that HU and Lsr2 interact to form a complex. The interaction occurs primarily through the flexible carboxy-terminal domain of HU and the acidic amino-terminal domain of Lsr2. The resulting complex, upon binding to DNA, forms thick nucleoprotein rods, in contrast to the DNA bridging seen with Lsr2 and the DNA compaction seen with HU. Furthermore, transcription assays indicate that the HU-Lsr2 complex is a regulator of gene expression. This physical and functional interaction between two NAPs, which has not been reported previously, is likely to be important for DNA organization and gene expression in Mtb and perhaps other bacterial species.
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Affiliation(s)
- Chandreyee Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Sohini Ganguly
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, C.V. Raman Avenue, Bangalore, 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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18
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Guha S, Udupa S, Ahmed W, Nagaraja V. Rewired Downregulation of DNA Gyrase Impacts Cell Division, Expression of Topology Modulators, and Transcription in Mycobacterium smegmatis. J Mol Biol 2018; 430:4986-5001. [PMID: 30316784 DOI: 10.1016/j.jmb.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 09/22/2018] [Accepted: 10/02/2018] [Indexed: 10/28/2022]
Abstract
DNA gyrase, essential for DNA replication and transcription, has traditionally been studied in vivo by treatments that inhibit the enzyme activity. Due to its indispensable function, gyrA and gyrB deletions cannot be generated. The coumarin inhibitors of gyrase induce the supercoiling-sensitive gyrase promoter by a mechanism termed relaxation-stimulated transcription. Hence, to study the effect of sustained reduction in gyrase levels, a conditional-knockdown strain was generated in Mycobacterium smegmatis such that gyrase expression was controlled by a supercoiling non-responsive regulatory circuit. Decreasing intracellular gyrase protein levels beyond 50% affected cell growth. Reduced gyrase levels in the reprogrammed gyr operon caused chromosome relaxation, diffuse nucleoid structure, cell elongation, and altered gene expression. The key cell division protein, ftsZ, was severely reduced in the elongated cells, indicating a link between gyrase and cell division. Low levels of gyrase resulted in low compensatory expression of topoisomerase I and elevated expression of topology modulators hupB and lsr2. Altered supercoiling due to gyrase depletion caused corresponding changes in the RNA polymerase density on transcription units leading to their altered transcription. The enhanced susceptibility of the knockdown strain to anti-tubercular drugs suggests its utility for screening new molecules that may act synergistically with gyrase inhibitors.
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Affiliation(s)
- Sarmistha Guha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Shubha Udupa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
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19
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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20
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Liu G, Ma Q, Xu Y. Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome. Math Biosci 2018; 301:50-58. [PMID: 29625128 DOI: 10.1016/j.mbs.2018.03.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/22/2018] [Accepted: 03/28/2018] [Indexed: 11/26/2022]
Abstract
Nucleoid-associated proteins (NAPs) play important roles in both chromosome packaging and gene regulation in bacteria. The underlying mechanisms, however, remain elusive particularly for how NAPs contribute to chromosome packaging. We report here a characterization of the binding sites for several major NAPs in E. coli, namely HNS, IHF, Fis, Dps and a non-NAP protein, FNR, in terms of the physical properties of their binding DNA. Our study shows that (i) as compared with flanking regions, the binding sites for IHF, Fis and FNR tend to have high intrinsic curvature, while no characterized pattern of intrinsic curvature distribution around those of HNS and Dps; (ii) all the binding sites analyzed in this study except those of HNS are characterized by high structural flexibility; (iii) the intrinsic curvature and flexibility at the binding sites for Fis and IHF are found to be coupled with the sequence specificity required in their binding, while the physical properties of the binding regions for both Dps and FNR are independent of sequence specificity. Our data suggest that physical properties of DNA sequence may contribute to binding of NAPs and mediate genome packaging and transcriptional regulation of the downstream genes. Our results should be informative for prediction of NAPs binding sites and understanding of the bacterial chromosome packaging.
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Affiliation(s)
- Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA.
| | - Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA; Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakot State University, SD 57007, USA
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA; College of Computer Science and Technology, Jilin University, Changchun 130012, China.
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21
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Ferrándiz MJ, Carreño D, Ayora S, de la Campa AG. HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling. Front Microbiol 2018; 9:493. [PMID: 29662473 PMCID: PMC5890176 DOI: 10.3389/fmicb.2018.00493] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 01/11/2023] Open
Abstract
The histone-like protein HU is a conserved nucleoid-associated protein that is involved in the maintenance of the bacterial chromosome architecture. It is the only known nucleoid-associated protein in Streptococcus pneumoniae, but it has not been studied. The pneumococcal gene encoding this protein, hlp, is shown herein to be essential for cell viability. Its disruption was only possible either when it was duplicated in the chromosome and its expression induced from the P Zn promoter, or when hlp was cloned into a plasmid under the control of the inducible P mal promoter. In vitro assays indicated that pneumococcal HU shows a preference for binding to supercoiled DNA rather than to linear or nicked DNA. In vivo experiments in which the amount of HU was manipulated showed a relationship between the amount of HU and the level of DNA supercoiling. A twofold reduction in the amount of HU triggered a 21% increase in DNA relaxation in untreated cells. However, in cells treated with novobiocin, a drug that relaxes DNA by inhibiting DNA gyrase, a 35% increase in DNA relaxation was observed, instead of the expected 20% in cells with a constitutive HU amount. Conversely, a fourfold HU increase caused only 14% of DNA relaxation in the presence of novobiocin. Taken together, these results support an essential role for HU in the maintenance of DNA supercoiling in S. pneumoniae.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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22
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Rangarajan AA, Schnetz K. Interference of transcription across H-NS binding sites and repression by H-NS. Mol Microbiol 2018; 108:226-239. [PMID: 29424946 DOI: 10.1111/mmi.13926] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2018] [Indexed: 11/28/2022]
Abstract
Nucleoid-associated protein H-NS represses transcription by forming extended DNA-H-NS complexes. Repression by H-NS operates mostly at the level of transcription initiation. Less is known about how DNA-H-NS complexes interfere with transcription elongation. In vitro H-NS has been shown to enhance RNA polymerase pausing and to promote Rho-dependent termination, while in vivo inhibition of Rho resulted in a decrease of the genome occupancy by H-NS. Here we show that transcription directed across H-NS binding regions relieves H-NS (and H-NS/StpA) mediated repression of promoters in these regions. Further, we observed a correlation of transcription across the H-NS-bound region and de-repression. The data suggest that the transcribing RNA polymerase is able to remodel the H-NS complex and/or dislodge H-NS from the DNA and thus relieve repression. Such an interference of transcription and H-NS mediated repression may imply that poorly transcribed AT-rich loci are prone to be repressed by H-NS, while efficiently transcribed loci escape repression.
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Affiliation(s)
| | - Karin Schnetz
- Institute for Genetics, University of Cologne, Zuelpicher Str. 47a, Cologne, Germany
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23
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Ayala JC, Wang H, Benitez JA, Silva AJ. Molecular basis for the differential expression of the global regulator VieA in Vibrio cholerae biotypes directed by H-NS, LeuO and quorum sensing. Mol Microbiol 2017; 107:330-343. [PMID: 29152799 DOI: 10.1111/mmi.13884] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2017] [Indexed: 01/05/2023]
Abstract
VieA is a cyclic diguanylate phosphodiesterase that modulates biofilm development and motility in Vibrio cholerae O1 of the classical biotype. vieA is part of an operon encoding the VieSAB signal transduction pathway that is nearly silent in V. cholerae of the El Tor biotype. A DNA pull-down assay for proteins interacting with the vieSAB promoter identified the LysR-type regulator LeuO. We show that in classical biotype V. cholerae, LeuO cooperates with the nucleoid-associated protein H-NS to repress vieSAB transcription. LeuO and H-NS interacted with the vieSAB promoter of both biotypes with similar affinities and protected overlapping DNA sequences. H-NS was expressed at similar levels in both cholera biotypes. In contrast, El Tor biotype strains expressed negligible LeuO under identical conditions. In El Tor biotype vibrios, transcription of vieSAB is repressed by the quorum sensing regulator HapR, which is absent in classical biotype strains. Restoring HapR expression in classical biotype V. cholerae repressed vieSAB transcription by binding to its promoter. We propose that double locking of the vieSAB promoter by H-NS and HapR in the El Tor biotype prior to the cessation of exponential growth results in a more pronounced decline in VieA specific activity compared to the classical biotype.
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Affiliation(s)
- Julio C Ayala
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Hongxia Wang
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Jorge A Benitez
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Anisia J Silva
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
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24
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Pannier L, Merino E, Marchal K, Collado-Vides J. Effect of genomic distance on coexpression of coregulated genes in E. coli. PLoS One 2017; 12:e0174887. [PMID: 28419102 PMCID: PMC5395161 DOI: 10.1371/journal.pone.0174887] [Citation(s) in RCA: 14] [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: 12/13/2016] [Accepted: 03/16/2017] [Indexed: 12/26/2022] Open
Abstract
In prokaryotes, genomic distance is a feature that in addition to coregulation affects coexpression. Several observations, such as genomic clustering of highly coexpressed small regulons, support the idea that coexpression behavior of coregulated genes is affected by the distance between the coregulated genes. However, the specific contribution of distance in addition to coregulation in determining the degree of coexpression has not yet been studied systematically. In this work, we exploit the rich information in RegulonDB to study how the genomic distance between coregulated genes affects their degree of coexpression, measured by pairwise similarity of expression profiles obtained under a large number of conditions. We observed that, in general, coregulated genes display higher degrees of coexpression as they are more closely located on the genome. This contribution of genomic distance in determining the degree of coexpression was relatively small compared to the degree of coexpression that was determined by the tightness of the coregulation (degree of overlap of regulatory programs) but was shown to be evolutionary constrained. In addition, the distance effect was sufficient to guarantee coexpression of coregulated genes that are located at very short distances, irrespective of their tightness of coregulation. This is partly but definitely not always because the close distance is also the cause of the coregulation. In cases where it is not, we hypothesize that the effect of the distance on coexpression could be caused by the fact that coregulated genes closely located to each other are also relatively more equidistantly located from their common TF and therefore subject to more similar levels of TF molecules. The absolute genomic distance of the coregulated genes to their common TF-coding gene tends to be less important in determining the degree of coexpression. Our results pinpoint the importance of taking into account the combined effect of distance and coregulation when studying prokaryotic coexpression and transcriptional regulation.
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Affiliation(s)
- Lucia Pannier
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Kathleen Marchal
- Department of Microbial and Molecular Systems, KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Department of Information Technology, Ghent University, IMinds, Ghent, Belgium
- Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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25
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Japaridze A, Renevey S, Sobetzko P, Stoliar L, Nasser W, Dietler G, Muskhelishvili G. Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein. J Biol Chem 2017; 292:7607-7618. [PMID: 28316324 PMCID: PMC5418058 DOI: 10.1074/jbc.m117.780239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Indexed: 11/28/2022] Open
Abstract
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.
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Affiliation(s)
- Aleksandre Japaridze
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | - Sylvain Renevey
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | | | | | - William Nasser
- UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003 INSA Lyon, Villeurbanne F-69621, France, and
| | - Giovanni Dietler
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland,
| | - Georgi Muskhelishvili
- Jacobs University, D-28759 Bremen, Germany, .,Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159 Tbilisi, Republik of Georgia
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26
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27
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H-NS: an overarching regulator of the Vibrio cholerae life cycle. Res Microbiol 2016; 168:16-25. [PMID: 27492955 DOI: 10.1016/j.resmic.2016.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/22/2016] [Accepted: 07/24/2016] [Indexed: 12/22/2022]
Abstract
Vibrio cholerae has become a model organism for studies connecting virulence, pathogen evolution and infectious disease ecology. The coordinate expression of motility, virulence and biofilm enhances its pathogenicity, environmental fitness and fecal-oral transmission. The histone-like nucleoid structuring protein negatively regulates gene expression at multiple phases of the V. cholerae life cycle. Here we discuss: (i) the regulatory and structural implications of H-NS chromatin-binding in the two-chromosome cholera bacterium; (ii) the factors that counteract H-NS repression; and (iii) a model for the regulation of the V. cholerae life cycle that integrates H-NS repression, cyclic diguanylic acid signaling and the general stress response.
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Ghosh S, Padmanabhan B, Godbole AA, Tare P, Ahmed W, Vasu K, China A, Kumar R, Mitra A, Nagaraja V. Transcriptional regulation of topology modulators and transcription regulators of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2016; 475:257-63. [PMID: 27207833 DOI: 10.1016/j.bbrc.2016.05.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a formidable pathogen which has the ability to survive the hostile environment of the host by evading the host defense system. The re-configuration of its transcriptional and metabolic process allows the pathogen to confront the adverse environment within the host macrophages. The factors that assist the transcription and modulate the DNA topology would have to play a key role in the regulation of global gene expression of the organism. How transcription of these essential housekeeping genes alters in response to growth conditions and environmental stress has not been addressed together in a set of experimental conditions in Mtb. Now, we have mapped the transcription start sites (TSS) and promoters of several genes that play a central role in the regulation of DNA topology and transcription in Mtb. Using in vivo reporter assays, we validated the activity of the identified promoter elements in different growth conditions. The variation in transcript abundance of these essential genes was also analyzed in growth phase-dependent manner. These data provide the first glimpse into the specific adaptive changes in the expression of genes involved in transcription and DNA topology modulation in Mtb.
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Affiliation(s)
- Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Bhavna Padmanabhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rupesh Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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Sobetzko P. Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes. Nucleic Acids Res 2016; 44:1514-24. [PMID: 26783203 PMCID: PMC4770239 DOI: 10.1093/nar/gkw007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/03/2016] [Indexed: 11/14/2022] Open
Abstract
Over the recent decade, the central importance of DNA supercoiling in chromosome organization and global gene regulation of bacteria became more and more visible. With a regulon comprising more than 2000 genes in Escherichia coli, DNA supercoiling is among the most influential regulators of gene expression found in bacteria so far. However, the mechanism creating thousands of diverse temporal gene expression patterns coordinated by DNA supercoiling remains unclear. In this study we show that a specific chromosomal arrangement of genes modulates the local levels of DNA supercoiling at gene promoters via transcription-coupled DNA supercoiling (TCDS) in the model organism E. coli. Our findings provide a consistent explanation for the strong positive coupling of temporal gene expression patterns of neighboring genes. Using comparative genomics we are furthermore able to provide evidence that TCDS is a driving force for the evolution of chromosomal gene arrangement patterns in other Enterobacteriaceae. With the currently available data of promoter supercoiling sensitivity we prove that the same principle is applicable also for the evolutionary distant gram-positive pathogenic bacterium Streptococcus pneumoniae. Moreover, our findings are fully consistent with recent investigations concerning the regulatory impact of TCDS on gene pairs in eukaryots underpinning the broad applicability of our analysis.
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Affiliation(s)
- Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University Marburg, Hans-Meerwein-Strasse 6, Mehrzweckgebäude, D-35043 Marburg, Germany
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30
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A model for chromosome organization during the cell cycle in live E. coli. Sci Rep 2015; 5:17133. [PMID: 26597953 PMCID: PMC4657085 DOI: 10.1038/srep17133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/22/2015] [Indexed: 11/09/2022] Open
Abstract
Bacterial chromosomal DNA is a highly compact nucleoid. The organization of this nucleoid is poorly understood due to limitations in the methods used to monitor the complexities of DNA organization in live bacteria. Here, we report that circular plasmid DNA is auto-packaged into a uniform dual-toroidal-spool conformation in response to mechanical stress stemming from sharp bending and un-winding by atomic force microscopic analysis. The mechanism underlying this phenomenon was deduced with basic physical principles to explain the auto-packaging behaviour of circular DNA. Based on our observations and previous studies, we propose a dynamic model of how chromosomal DNA in E. coli may be organized during a cell division cycle. Next, we test the model by monitoring the development of HNS clusters in live E. coli during a cell cycle. The results were in close agreement with the model. Furthermore, the model accommodates a majority of the thus-far-discovered remarkable features of nucleoids in vivo.
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31
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Molecular scribes in the spotlight: Methods for illuminating Bacterial and Archaeal transcription. Methods 2015; 86:1-3. [PMID: 26192471 DOI: 10.1016/j.ymeth.2015.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Abstract
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.
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Scolari VF, Sclavi B, Cosentino Lagomarsino M. The nucleoid as a smart polymer. Front Microbiol 2015; 6:424. [PMID: 26005440 PMCID: PMC4424877 DOI: 10.3389/fmicb.2015.00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/21/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
- Vittore F Scolari
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France
| | - Bianca Sclavi
- Centre National de la Recherche Scientifique, LBPA, UMR 8113, ENS Cachan Cachan, France
| | - Marco Cosentino Lagomarsino
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France ; Centre National de la Recherche Scientifique, UMR 7238 Paris, France
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Transcriptional analysis of the MrpJ network: modulation of diverse virulence-associated genes and direct regulation of mrp fimbrial and flhDC flagellar operons in Proteus mirabilis. Infect Immun 2015; 83:2542-56. [PMID: 25847961 DOI: 10.1128/iai.02978-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/29/2015] [Indexed: 01/14/2023] Open
Abstract
The enteric bacterium Proteus mirabilis is associated with a significant number of catheter-associated urinary tract infections (UTIs). Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the mrp fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects an array of cellular processes beyond adherence and motility. Microarray analysis found that expression of mrpJ mimicking levels observed during UTIs leads to differential expression of 217 genes related to, among other functions, bacterial virulence, type VI secretion, and metabolism. We probed the molecular mechanism of transcriptional regulation by MrpJ using transcriptional reporters and chromatin immunoprecipitation (ChIP). Binding of MrpJ to two virulence-associated target gene promoters, the promoters of the flagellar master regulator flhDC and mrp itself, appears to be affected by the condensation state of the native chromosome, although both targets share a direct MrpJ binding site proximal to the transcriptional start. Furthermore, an mrpJ deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observed that mrpJ is widely conserved in a collection of recent clinical isolates. Altogether, these findings support a role of MrpJ as a global regulator of P. mirabilis virulence.
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Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli. G3-GENES GENOMES GENETICS 2015; 5:605-14. [PMID: 25701587 PMCID: PMC4390576 DOI: 10.1534/g3.114.016139] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins. Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal position on the efficiency of these global regulators. Here we show for the first time that genome position can affect transcription activity of a promoter regulated by the histone-like nucleoid-structuring protein (H-NS), a global regulator of bacterial transcription and genome organization. We have used as a local reporter of H-NS activity the level of expression of a fluorescent reporter protein under control of an H-NS−regulated promoter (Phns) at different sites along the genome. Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS. This modulation of gene expression moreover depends on the growth phase and the growth rate of the cells, reflecting the changes taking place in the relative abundance of different nucleoid proteins and the inherent heterogeneous organization of the nucleoid. Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene’s position during evolution.
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Muskhelishvili G, Travers A. Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome. J Mol Microbiol Biotechnol 2015; 24:332-43. [DOI: 10.1159/000368852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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The Intimin-Like Protein FdeC Is Regulated by H-NS and Temperature in Enterohemorrhagic Escherichia coli. Appl Environ Microbiol 2014; 80:7337-47. [PMID: 25239893 DOI: 10.1128/aem.02114-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/15/2014] [Indexed: 01/01/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a Shiga-toxigenic pathogen capable of inducing severe forms of enteritis (e.g., hemorrhagic colitis) and extraintestinal sequelae (e.g., hemolytic-uremic syndrome). The molecular basis of colonization of human and animal hosts by EHEC is not yet completely understood, and an improved understanding of EHEC mucosal adherence may lead to the development of interventions that could disrupt host colonization. FdeC, also referred to by its IHE3034 locus tag ECOK1_0290, is an intimin-like protein that was recently shown to contribute to kidney colonization in a mouse urinary tract infection model. The expression of FdeC is tightly regulated in vitro, and FdeC shows promise as a vaccine candidate against extraintestinal E. coli strains. In this study, we characterized the prevalence, regulation, and function of fdeC in EHEC. We showed that the fdeC gene is conserved in both O157 and non-O157 EHEC and encodes a protein that is expressed at the cell surface and promotes biofilm formation under continuous-flow conditions in a recombinant E. coli strain background. We also identified culture conditions under which FdeC is expressed and showed that minor alterations of these conditions, such as changes in temperature, can significantly alter the level of FdeC expression. Additionally, we demonstrated that the transcription of the fdeC gene is repressed by the global regulator H-NS. Taken together, our data suggest a role for FdeC in EHEC when it grows at temperatures above 37°C, a condition relevant to its specialized niche at the rectoanal junctions of cattle.
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Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila. J Bacteriol 2014; 196:4172-83. [PMID: 25225276 DOI: 10.1128/jb.02017-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Legionella pneumophila is an intracellular human pathogen that utilizes the Icm/Dot type IVB secretion system to translocate a large repertoire of effectors into host cells. For most of these effectors, there is no information regarding their regulation. Therefore, the aim of this study was to examine the involvement of the three L. pneumophila Fis homologs in the regulation of effector-encoding genes. Deletion mutants constructed in the genes encoding the three Fis regulators revealed that Fis1 (lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of L. pneumophila in Acanthamoeba castellanii. To identify pathogenesis-related genes directly regulated by Fis, we established a novel in vivo system which resulted in the discovery of numerous effector-encoding genes directly regulated by Fis. Further examination of these genes revealed that Fis1 and Fis3 repress the level of expression of effector-encoding genes during exponential phase. Three groups of effector-encoding genes were identified: (i) effectors regulated mainly by Fis1, (ii) effectors regulated mainly by Fis3, and (iii) effectors regulated by both Fis1 and Fis3. Examination of the upstream regulatory region of all of these effector-encoding genes revealed multiple putative Fis regulatory elements, and site-directed mutagenesis confirmed that a few of these sites constitute part of a repressor binding element. Furthermore, gel mobility shift assays demonstrated the direct relation between the Fis1 and Fis3 regulators and these regulatory elements. Collectively, our results demonstrate for the first time that two of the three L. pneumophila Fis regulators directly repress the expression of Icm/Dot effector-encoding genes.
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Duprey A, Reverchon S, Nasser W. Bacterial virulence and Fis: adapting regulatory networks to the host environment. Trends Microbiol 2013; 22:92-9. [PMID: 24370464 DOI: 10.1016/j.tim.2013.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/21/2013] [Accepted: 11/26/2013] [Indexed: 11/18/2022]
Abstract
Pathogenic bacteria have to cope with adverse conditions, such as the host environment and host defense reactions. To adapt quickly to environmental changes, pathogens have developed complex regulatory networks that ensure adequate expression of their virulence genes. Recent evidence suggests that Fis, an abundant nucleoid-associated protein transiently produced during early exponential growth, plays a major role in these networks in several pathogenic bacteria. This review focuses on two enterobacteria, Salmonella enterica and Dickeya dadantii, that inhabit distinct ecological niches to illustrate how Fis uses different strategies to coordinate virulence gene expression, depending on the bacterial lifestyle.
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Affiliation(s)
- Alexandre Duprey
- Université Lyon 1, F-69622 Villeurbanne, France; INSA de Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Sylvie Reverchon
- Université Lyon 1, F-69622 Villeurbanne, France; INSA de Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - William Nasser
- Université Lyon 1, F-69622 Villeurbanne, France; INSA de Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France.
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The Haemophilus ducreyi Fis protein is involved in controlling expression of the lspB-lspA2 operon and other virulence factors. Infect Immun 2013; 81:4160-70. [PMID: 23980107 DOI: 10.1128/iai.00714-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Expression of the lspB-lspA2 operon encoding a virulence-related two-partner secretion system in Haemophilus ducreyi 35000HP is directly regulated by the CpxRA regulatory system (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402-3411, 2009). In the present study, we show that this secretion system is also regulated by the small nucleoid-associated protein Fis. Inactivation of the H. ducreyi fis gene resulted in a reduction in expression of both the H. ducreyi LspB and LspA2 proteins. DNA microarray experiments showed that a H. ducreyi fis deletion mutant exhibited altered expression levels of genes encoding other important H. ducreyi virulence factors, including DsrA and Flp1, suggesting a possible global role for Fis in the control of virulence in this obligate human pathogen. While the H. ducreyi Fis protein has a high degree of sequence and structural similarity to the Fis proteins of other bacteria, its temporal pattern of expression was very different from that of enterobacterial Fis proteins. The use of a lacZ-based transcriptional reporter provided evidence which indicated that the H. ducreyi Fis homolog is a positive regulator of gyrB, a gene that is negatively regulated by Fis in enteric bacteria. Taken together, the Fis protein expression data and the observed regulatory effects of Fis in H. ducreyi suggest that this small DNA binding protein has a regulatory role in H. ducreyi which may differ in substantial ways from that of other Fis proteins.
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Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keleş S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 2013; 9:e1003565. [PMID: 23818864 PMCID: PMC3688515 DOI: 10.1371/journal.pgen.1003565] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/29/2013] [Indexed: 01/05/2023] Open
Abstract
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut. Regulation of gene expression by transcription factors (TFs) is key to adaptation to environmental changes. Our comprehensive, genome-scale analysis of a prototypical global TF, the anaerobic regulator FNR from Escherichia coli, leads to several novel and unanticipated insights into the influences on FNR binding genome-wide and the complex structure of bacterial regulons. We found that binding of NAPs restricts FNR binding at a subset of sites, suggesting that the bacterial genome is not freely accessible for FNR binding. Our finding that less than half of the predicted FNR binding sites were occupied in vivo further challenges the utility of using bioinformatic searches alone to predict regulon structure, reinforcing the need for experimental determination of TF binding. By correlating the occupancy data with transcriptomic data, we confirm that FNR serves as a global signal of anaerobiosis but expression of some operons in the FNR regulon require other regulators sensitive to alternative environmental stimuli. Thus, FNR binding and regulation appear to depend on both the nucleoprotein structure of the chromosome and on combinatorial binding of FNR with other regulators. Both of these phenomena are typical of TF binding in eukaryotes; our results establish that they are also features of bacterial TF binding.
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Affiliation(s)
- Kevin S. Myers
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Huihuang Yan
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dongjun Chung
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kun Liang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Frances Tran
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
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Abstract
The Topological Aspects of DNA Function and Protein Folding international meeting provided an interdisciplinary forum for biological scientists, physicists and mathematicians to discuss recent developments in the application of topology to the study of DNA and protein structure. It had 111 invited participants, 48 talks and 21 posters. The present article discusses the importance of topology and introduces the articles from the meeting's speakers.
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