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Prieto A, Bernabeu M, Aznar S, Ruiz-Cruz S, Bravo A, Queiroz MH, Juárez A. Evolution of Bacterial Global Modulators: Role of a Novel H-NS Paralogue in the Enteroaggregative Escherichia coli Strain 042. mSystems 2018; 3:e00220-17. [PMID: 29577085 PMCID: PMC5861252 DOI: 10.1128/msystems.00220-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/14/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial genomes sometimes contain genes that code for homologues of global regulators, the function of which is unclear. In members of the family Enterobacteriaceae, cells express the global regulator H-NS and its paralogue StpA. In Escherichia coli, out of providing a molecular backup for H-NS, the role of StpA is poorly characterized. The enteroaggregative E. coli strain 042 carries, in addition to the hns and stpA genes, a third gene encoding an hns paralogue (hns2). We present in this paper information about its biological function. Transcriptomic analysis has shown that the H-NS2 protein targets a subset of the genes targeted by H-NS. Genes targeted by H-NS2 correspond mainly with horizontally transferred (HGT) genes and are also targeted by the Hha protein, a fine-tuner of H-NS activity. Compared with H-NS, H-NS2 expression levels are lower. In addition, H-NS2 expression exhibits specific features: it is sensitive to the growth temperature and to the nature of the culture medium. This novel H-NS paralogue is widespread within the Enterobacteriaceae. IMPORTANCE Global regulators such as H-NS play key relevant roles enabling bacterial cells to adapt to a changing environment. H-NS modulates both core and horizontally transferred (HGT) genes, but the mechanism by which H-NS can differentially regulate these genes remains to be elucidated. There are several instances of bacterial cells carrying genes that encode homologues of the global regulators. The question is what the roles of these proteins are. We noticed that the enteroaggregative E. coli strain 042 carries a new hitherto uncharacterized copy of the hns gene. We decided to investigate why this pathogenic E. coli strain requires an extra H-NS paralogue, termed H-NS2. In our work, we show that H-NS2 displays specific expression and regulatory properties. H-NS2 targets a subset of H-NS-specific genes and may help to differentially modulate core and HGT genes by the H-NS cellular pool.
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Affiliation(s)
- A. Prieto
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - M. Bernabeu
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - S. Aznar
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - S. Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - A. Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - M. H. Queiroz
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A. Juárez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
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Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res 2018; 46:3400-3411. [PMID: 29474582 PMCID: PMC5909445 DOI: 10.1093/nar/gky118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rajvardhan M Kapshikar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
| | - Jillella Mallikarjun
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
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Wade JT, Grainger DC. Waking the neighbours: disruption of H-NS repression by overlapping transcription. Mol Microbiol 2018; 108:221-225. [PMID: 29473964 DOI: 10.1111/mmi.13939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2018] [Indexed: 11/30/2022]
Abstract
The histone-like nucleoid structuring (H-NS) protein and its analogues bind large stretches of horizontally acquired AT-rich DNA in a broad range of bacterial species. Binding by H-NS silences the promoters within such DNA that would otherwise deplete the cellular pool of RNA polymerase. Selective de-repression can occur when sequence-specific DNA-binding proteins locally disrupt H-NS function; this mechanism is important for the regulation of many virulence genes. In this issue of Molecular Microbiology, Rangarajan and Schnetz show that when transcription from a neighbouring region invades an H-NS-bound locus, it can disrupt local H-NS repression. Moreover, they show that de-repression occurs in a dose-dependent manner, and they demonstrate a natural example of this in Escherichia coli. This finding has important implications for H-NS function and its impact on genome evolution.
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Affiliation(s)
- Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - David C Grainger
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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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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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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Mordaka PM, Heap JT. Stringency of Synthetic Promoter Sequences in Clostridium Revealed and Circumvented by Tuning Promoter Library Mutation Rates. ACS Synth Biol 2018; 7:672-681. [PMID: 29320851 DOI: 10.1021/acssynbio.7b00398] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Collections of characterized promoters of different strengths are key resources for synthetic biology, but are not well established for many important organisms, including industrially relevant Clostridium spp. When generating promoters, reporter constructs are used to measure expression, but classical fluorescent reporter proteins are oxygen-dependent and hence inactive in anaerobic bacteria like Clostridium. We directly compared oxygen-independent reporters of different types in Clostridium acetobutylicum and found that glucuronidase (GusA) from E. coli performed best. Using GusA, a library of synthetic promoters was first generated by a typical approach entailing complete randomization of a constitutive thiolase gene promoter (Pthl) except for the consensus -35 and -10 elements. In each synthetic promoter, the chance of each degenerate position matching Pthl was 25%. Surprisingly, none of the tested synthetic promoters from this library were functional in C. acetobutylicum, even though they functioned as expected in E. coli. Next, instead of complete randomization, we specified lower promoter mutation rates using oligonucleotide primers synthesized using custom mixtures of nucleotides. Using these primers, two promoter libraries were constructed in which the chance of each degenerate position matching Pthl was 79% or 58%, instead of 25% as before. Synthetic promoters from these "stringent" libraries functioned well in C. acetobutylicum, covering a wide range of strengths. The promoters functioned similarly in the distantly related species Clostridium sporogenes, and allowed predictable metabolic engineering of C. acetobutylicum for acetoin production. Besides generating the desired promoters and demonstrating their useful properties, this work indicates an unexpected "stringency" of promoter sequences in Clostridium, not reported previously.
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Affiliation(s)
- Paweł M. Mordaka
- Imperial College Centre for
Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - John T. Heap
- Imperial College Centre for
Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Escudero JA, Nivina A, Cambray G, López-Igual R, Loot C, Mazel D. Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation. Biotechnol Bioeng 2018; 115:184-191. [DOI: 10.1002/bit.26450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Jose A. Escudero
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
- Departamento de Sanidad Animal; Facultad de Veterinaria; Universidad Complutense de Madrid; Madrid Spain
- VISAVET Health Surveillance Centre; Universidad Complutense Madrid; Madrid Spain
| | - Aleksandra Nivina
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
- Université Paris Descartes; Sorbonne Paris Cité; Paris France
| | | | - Rocío López-Igual
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
| | - Celine Loot
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
| | - Didier Mazel
- Institut Pasteur; Unité de Plasticité du Génome Bactérien; Département Génomes et Génétique; Paris France
- CNRS; UMR3525; Paris France
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58
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Abstract
Most RNA polymerases can initiate transcription from diverse DNA template sequences with relatively few outright sequence restraints. Recent reports have demonstrated that failure to subdue the promiscuity of RNA polymerase in vivo can severely impede cell function. This phenomenon appears common to all cell types with undesirable effects ranging from growth inhibition in prokaryotes to cancer in higher organisms. Here we discuss similarities and differences in strategies employed by cells to minimise spurious transcription across life's domains.
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Affiliation(s)
- Joseph T Wade
- a Wadsworth Center , New York State Department of Health , Albany , NY , USA.,b Department of Biomedical Sciences , School of Public Health, University at Albany, SUNY , Albany , NY , USA
| | - David C Grainger
- c Institute of Microbiology and Infection, School of Biosciences, University of Birmingham , Edgbaston, Birmingham , UK
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