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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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Puccio S, Grillo G, Licciulli F, Severgnini M, Liuni S, Bicciato S, De Bellis G, Ferrari F, Peano C. WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes. Nucleic Acids Res 2019; 45:W109-W115. [PMID: 28460063 PMCID: PMC5570229 DOI: 10.1093/nar/gkx329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it
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Affiliation(s)
- Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Giorgio Grillo
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Flavio Licciulli
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Sabino Liuni
- Institute of Biomedical Technologies, National Research Council, 70126, Bari, Italy
| | - Silvio Bicciato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, 20139, Milan, Italy.,Institute of Molecular Genetics, National Research Council, 27100, Pavia, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Segrate, 20090, Milan, Italy
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El Sayyed H, Le Chat L, Lebailly E, Vickridge E, Pages C, Cornet F, Cosentino Lagomarsino M, Espéli O. Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome. PLoS Genet 2016; 12:e1006025. [PMID: 27171414 PMCID: PMC4865107 DOI: 10.1371/journal.pgen.1006025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/11/2016] [Indexed: 11/27/2022] Open
Abstract
Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle. DNA topoisomerases are ubiquitous enzymes that solve the topological problems associated with replication, transcription and recombination. Type II Topoisomerases play a major role in the management of newly replicated DNA. They contribute to the condensation and segregation of chromosomes to the future daughter cells and are essential for the optimal transmission of genetic information. In most bacteria, including the model organism Escherichia coli, these tasks are performed by two enzymes, DNA gyrase and DNA Topoisomerase IV (Topo IV). The distribution of the roles between these enzymes during the cell cycle is not yet completely understood. In the present study we use genomic and molecular biology methods to decipher the regulation of Topo IV during the cell cycle. Here we present data that strongly suggest the interaction of Topo IV with the chromosome is controlled by DNA replication and chromatin factors responsible for its loading to specific regions of the chromosome. In addition, our observations reveal, that by sharing several key factors, the DNA management processes ensuring accuracy of the late steps of chromosome segregation are all interconnected.
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Affiliation(s)
- Hafez El Sayyed
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, UMR-CNRS 7241, Paris, France
- Université Paris–Saclay, Gif-sur-Yvette, France
| | - Ludovic Le Chat
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, UMR-CNRS 7241, Paris, France
| | - Elise Lebailly
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CNRS-Université Toulouse III, Toulouse, France
| | - Elise Vickridge
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, UMR-CNRS 7241, Paris, France
- Université Paris–Saclay, Gif-sur-Yvette, France
| | - Carine Pages
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CNRS-Université Toulouse III, Toulouse, France
| | - Francois Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CNRS-Université Toulouse III, Toulouse, France
| | | | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, UMR-CNRS 7241, Paris, France
- * E-mail:
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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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Srinivasan R, Scolari VF, Lagomarsino MC, Seshasayee ASN. The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli. Nucleic Acids Res 2014; 43:295-308. [PMID: 25429971 PMCID: PMC4288151 DOI: 10.1093/nar/gku1229] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gene expression state of exponentially growing Escherichia coli cells is manifested by high expression of essential and growth-associated genes and low levels of stress-related and horizontally acquired genes. An important player in maintaining this homeostasis is the H-NS-StpA gene silencing system. A Δhns-stpA deletion mutant results in high expression of otherwise-silent horizontally acquired genes, many located in the terminus-half of the chromosome, and an indirect downregulation of many highly expressed genes. The Δhns-stpA double mutant displays slow growth. Using laboratory evolution we address the evolutionary strategies that E. coli would adopt to redress this gene expression imbalance. We show that two global gene regulatory mutations-(i) point mutations inactivating the stress-responsive sigma factor RpoS or σ38 and (ii) an amplification of ∼40% of the chromosome centred around the origin of replication-converge in partially reversing the global gene expression imbalance caused by Δhns-stpA. Transcriptome data of these mutants further show a three-way link amongst the global gene regulatory networks of H-NS and σ38, as well as chromosome architecture. Increasing gene expression around the terminus of replication results in a decrease in the expression of genes around the origin and vice versa; this appears to be a persistent phenomenon observed as an association across ∼300 publicly-available gene expression data sets for E. coli. These global suppressor effects are transient and rapidly give way to more specific mutations, whose roles in reversing the growth defect of H-NS mutations remain to be understood.
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Affiliation(s)
- Rajalakshmi Srinivasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India Manipal University, Manipal 576104, India
| | - Vittore Ferdinando Scolari
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India Manipal University, Manipal 576104, India Genomic Physics Group, UMR 7238 CNRS Microorganism Genomics, UPMC, Paris, France
| | - Marco Cosentino Lagomarsino
- Genomic Physics Group, UMR 7238 CNRS Microorganism Genomics, UPMC, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, 15 Rue de l'École de Médecine Paris, France CNRS, UMR 7238, Paris, France
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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Chandraprakash D, Seshasayee ASN. Inhibition of factor-dependent transcription termination in Escherichia coli might relieve xenogene silencing by abrogating H-NS-DNA interactions in vivo. J Biosci 2014; 39:53-61. [PMID: 24499790 DOI: 10.1007/s12038-014-9413-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many horizontally acquired genes (xenogenes) in the bacterium Escherichia coli are maintained in a silent transcriptional state by the nucleoid-associated transcription regulatory protein H-NS. Recent evidence has shown that antibiotic-mediated inhibition of the transcription terminator protein Rho leads to de-repression of horizontally acquired genes, akin to a deletion of hns. The mechanism behind this similarity in outcomes between the perturbations of two distinct processes remains unclear. Using ChIP-seq of H-NS in wild-type cells, in addition to that in cells treated with bicyclomycin--a specific inhibitor of Rho, we show that bicyclomycin treatment leads to a decrease in binding signal for H-NS to the E. coli chromosome. Rho inhibition leads to RNA polymerase readthrough, which in principle could displace H-NS from the DNA, thus leading to transcriptional derepression of H-NS-silenced genes. Other possible mediators of the effect of Rho on H-NS are discussed. A possible positive feedback between Rho and H-NS might help reinforce xenogene silencing.
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Affiliation(s)
- Deepti Chandraprakash
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560 065, India
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Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization. Nat Commun 2013; 4:3003. [DOI: 10.1038/ncomms3003] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/09/2013] [Indexed: 11/08/2022] Open
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Srinivasan R, Chandraprakash D, Krishnamurthi R, Singh P, Scolari VF, Krishna S, Seshasayee ASN. Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12. MOLECULAR BIOSYSTEMS 2013; 9:2021-33. [PMID: 23661089 DOI: 10.1039/c3mb70035f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
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Affiliation(s)
- Rajalakshmi Srinivasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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Zarei M, Sclavi B, Cosentino Lagomarsino M. Gene silencing and large-scale domain structure of the E. coli genome. MOLECULAR BIOSYSTEMS 2013; 9:758-67. [DOI: 10.1039/c3mb25364c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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