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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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2
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Boldogkői Z, Moldován N, Balázs Z, Snyder M, Tombácz D. Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research. Trends Microbiol 2019; 27:578-592. [DOI: 10.1016/j.tim.2019.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/21/2019] [Accepted: 01/30/2019] [Indexed: 12/16/2022]
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3
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Boldogkői Z, Tombácz D, Balázs Z. Interactions between the transcription and replication machineries regulate the RNA and DNA synthesis in the herpesviruses. Virus Genes 2019; 55:274-279. [PMID: 30767118 PMCID: PMC6536478 DOI: 10.1007/s11262-019-01643-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/24/2019] [Indexed: 12/04/2022]
Abstract
The temporal coordination of viral gene expression is imperative for the regulation of the herpesvirus replication cycle. While the main factors of this transcriptional coordination are known, the subtler control mechanisms of gene expression remain elusive. Recent long read sequencing-based approached have revealed an intricate meshwork of overlaps between the herpesvirus transcripts and the overlap of the replication origins with noncoding RNAs. It has been shown that the transcriptional apparatuses can physically interfere with one another while transcribing overlapping regions. We hypothesize that transcriptional interference regulates the global gene expression across the herpesvirus genome. Additionally, an overall decrease in transcriptional activity in individual viral genes has been observed following the onset of DNA replication. An overlap of the replication origins with specific transcripts has also been described in several herpesviruses. The genome-wide interactions between the transcriptional apparatuses and between the replication and transcriptional machineries suggest the existence of novel layers of genetic regulation.
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Affiliation(s)
- Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary.
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
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4
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Chromosomal organization of transcription: in a nutshell. Curr Genet 2017; 64:555-565. [PMID: 29184972 DOI: 10.1007/s00294-017-0785-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/25/2023]
Abstract
Early studies of transcriptional regulation focused on individual gene promoters defined specific transcription factors as central agents of genetic control. However, recent genome-wide data propelled a different view by linking spatially organized gene expression patterns to chromosomal dynamics. Therefore, the major problem in contemporary molecular genetics concerned with transcriptional gene regulation is to establish a unifying model that reconciles these two views. This problem, situated at the interface of polymer physics and network theory, requires development of an integrative methodology. In this review, we discuss recent achievements in classical model organism E. coli and provide some novel insights gained from studies of a bacterial plant pathogen, D. dadantii. We consider DNA topology and the basal transcription machinery as key actors of regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription. We argue that the spatial organization of genome plays a fundamental role in its own regulation.
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Gerganova V, Berger M, Zaldastanishvili E, Sobetzko P, Lafon C, Mourez M, Travers A, Muskhelishvili G. Chromosomal position shift of a regulatory gene alters the bacterial phenotype. Nucleic Acids Res 2015; 43:8215-26. [PMID: 26170236 PMCID: PMC4751926 DOI: 10.1093/nar/gkv709] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
Recent studies strongly suggest that in bacterial cells the order of genes along the chromosomal origin-to-terminus axis is determinative for regulation of the growth phase-dependent gene expression. The prediction from this observation is that positional displacement of pleiotropic genes will affect the genetic regulation and hence, the cellular phenotype. To test this prediction we inserted the origin-proximal dusB-fis operon encoding the global regulator FIS in the vicinity of replication terminus on both arms of the Escherichia coli chromosome. We found that the lower fis gene dosage in the strains with terminus-proximal dusB-fis operons was compensated by increased fis expression such that the intracellular concentration of FIS was homeostatically adjusted. Nevertheless, despite unchanged FIS levels the positional displacement of dusB-fis impaired the competitive growth fitness of cells and altered the state of the overarching network regulating DNA topology, as well as the cellular response to environmental stress, hazardous substances and antibiotics. Our finding that the chromosomal repositioning of a regulatory gene can determine the cellular phenotype unveils an important yet unexplored facet of the genetic control mechanisms and paves the way for novel approaches to manipulate bacterial physiology.
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Affiliation(s)
- Veneta Gerganova
- Jacobs University Bremen, School of Engineering and Science, Bremen, 28758, Germany
| | - Michael Berger
- Institut für Hygiene, Universitätsklinikum Münster, Münster, 48149, Germany
| | | | - Patrick Sobetzko
- Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Department of Chromosome Biology, Marburg, 35032, Germany
| | - Corinne Lafon
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Michael Mourez
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Gerganova V, Maurer S, Stoliar L, Japaridze A, Dietler G, Nasser W, Kutateladze T, Travers A, Muskhelishvili G. Upstream binding of idling RNA polymerase modulates transcription initiation from a nearby promoter. J Biol Chem 2015; 290:8095-109. [PMID: 25648898 DOI: 10.1074/jbc.m114.628131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial gene regulatory regions often demonstrate distinctly organized arrays of RNA polymerase binding sites of ill-defined function. Previously we observed a module of closely spaced polymerase binding sites upstream of the canonical promoter of the Escherichia coli fis operon. FIS is an abundant nucleoid-associated protein involved in adjusting the chromosomal DNA topology to changing cellular physiology. Here we show that simultaneous binding of the polymerase at the canonical fis promoter and an upstream transcriptionally inactive site stabilizes a RNAP oligomeric complex in vitro. We further show that modulation of the upstream binding of RNA polymerase affects the fis promoter activity both in vivo and in vitro. The effect of the upstream RNA polymerase binding on the fis promoter activity depends on the spatial arrangement of polymerase binding sites and DNA supercoiling. Our data suggest that a specific DNA geometry of the nucleoprotein complex stabilized on concomitant binding of RNA polymerase molecules at the fis promoter and the upstream region acts as a topological device regulating the fis transcription. We propose that transcriptionally inactive RNA polymerase molecules can act as accessory factors regulating the transcription initiation from a nearby promoter.
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Affiliation(s)
- Veneta Gerganova
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Sebastian Maurer
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Liubov Stoliar
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Aleksandre Japaridze
- the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland
| | - William Nasser
- the UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003, INSA-Lyon, Villeurbanne, F-69621, France
| | - Tamara Kutateladze
- the Ivane Beritashvili Centre of Experimental Biomedicine, Gotua str.14, Tbilisi, Georgia, and
| | - Andrew Travers
- the MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 QH, United Kingdom
| | - Georgi Muskhelishvili
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany,
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Cameron ADS, Kröger C, Quinn HJ, Scally IK, Daly AJ, Kary SC, Dorman CJ. Transmission of an oxygen availability signal at the Salmonella enterica serovar Typhimurium fis promoter. PLoS One 2013; 8:e84382. [PMID: 24358360 PMCID: PMC3865300 DOI: 10.1371/journal.pone.0084382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
The nucleoid-associated protein FIS is a global regulator of gene expression and chromosome structure in Escherichia coli and Salmonella enterica. Despite the importance of FIS for infection and intracellular invasion, very little is known about the regulation of S. enterica fis expression. Under standard laboratory growth conditions, fis is highly expressed during rapid growth but is then silenced as growth slows. However, if cells are cultured in non-aerated conditions, fis expression is sustained during stationary phase. This led us to test whether the redox-sensing transcription factors ArcA and FNR regulate S. enterica fis. Deletion of FNR had no detectable effect, whereas deletion of ArcA had the unexpected effect of further elevating fis expression in stationary phase. ArcA required RpoS for induction of fis expression, suggesting that ArcA indirectly affects fis expression. Other putative regulators were found to play diverse roles: FIS acted directly as an auto-repressor (as expected), whereas CRP had little direct effect on fis expression. Deleting regions of the fis promoter led to the discovery of a novel anaerobically-induced transcription start site (Pfis-2) upstream of the primary transcription start site (Pfis-1). Promoter truncation also revealed that the shortest functional fis promoter was incapable of sustained expression. Moreover, fis expression was observed to correlate directly with DNA supercoiling in non-aerated conditions. Thus, the full-length S. enterica fis promoter region may act as a topological switch that is sensitive to stress-induced duplex destabilisation and up-regulates expression in non-aerated conditions.
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Affiliation(s)
- Andrew D. S. Cameron
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Carsten Kröger
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Heather J. Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Isobel K. Scally
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Anne J. Daly
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Stefani C. Kary
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Charles J. Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- * E-mail:
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8
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Wang H, Liu B, Wang Q, Wang L. Genome-wide analysis of the salmonella Fis regulon and its regulatory mechanism on pathogenicity islands. PLoS One 2013; 8:e64688. [PMID: 23717649 PMCID: PMC3662779 DOI: 10.1371/journal.pone.0064688] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/17/2013] [Indexed: 11/19/2022] Open
Abstract
Fis, one of the most important nucleoid-associated proteins, functions as a global regulator of transcription in bacteria that has been comprehensively studied in Escherichia coli K12. Fis also influences the virulence of Salmonella enterica and pathogenic E. coli by regulating their virulence genes, however, the relevant mechanism is unclear. In this report, using combined RNA-seq and chromatin immunoprecipitation (ChIP)-seq technologies, we first identified 1646 Fis-regulated genes and 885 Fis-binding targets in the S. enterica serovar Typhimurium, and found a Fis regulon different from that in E. coli. Fis has been reported to contribute to the invasion ability of S. enterica. By using cell infection assays, we found it also enhances the intracellular replication ability of S. enterica within macrophage cell, which is of central importance for the pathogenesis of infections. Salmonella pathogenicity islands (SPI)-1 and SPI-2 are crucial for the invasion and survival of S. enterica in host cells. Using mutation and overexpression experiments, real-time PCR analysis, and electrophoretic mobility shift assays, we demonstrated that Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes: i) binds to SPI regulators in the gene body or in upstream regions; ii) binds to SPI genes directly to mediate transcriptional activation of themselves and downstream genes; iii) binds to gene encoding OmpR which affects SPI gene expression by controlling SPI regulators SsrA and HilD. Our results provide new insights into the impact of Fis on SPI genes and the pathogenicity of S. enterica.
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Affiliation(s)
- Hui Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Quan Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, P. R. China
- * E-mail:
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9
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Prigent-Combaret C, Zghidi-Abouzid O, Effantin G, Lejeune P, Reverchon S, Nasser W. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle-biofilms in the phytopathogenic bacterium Dickeya dadantii. Mol Microbiol 2012; 86:172-86. [PMID: 22925161 DOI: 10.1111/j.1365-2958.2012.08182.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.
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10
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Ouafa ZA, Reverchon S, Lautier T, Muskhelishvili G, Nasser W. The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii. Nucleic Acids Res 2012; 40:4306-19. [PMID: 22275524 PMCID: PMC3378864 DOI: 10.1093/nar/gks014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dickeya dadantii is a pathogen infecting a wide range of plant species. Soft rot, the visible symptom, is mainly due to the production of pectate lyases (Pels) that can destroy the plant cell walls. Previously we found that the pel gene expression is modulated by H-NS and FIS, two nucleoid-associated proteins (NAPs) modulating the DNA topology. Here, we show that relaxation of the DNA in growing D. dadantii cells decreases the expression of pel genes. Deletion of fis aggravates, whereas that of hns alleviates the negative impact of DNA relaxation on pel expression. We further show that H-NS and FIS directly bind the pelE promoter and that the response of D. dadantii pel genes to stresses that induce DNA relaxation is modulated, although to different extents, by H-NS and FIS. We infer that FIS acts as a repressor buffering the negative impact of DNA relaxation on pel gene transcription, whereas H-NS fine-tunes the response of virulence genes precluding their expression under suboptimal conditions of supercoiling. This novel dependence of H-NS effect on DNA topology expands our understanding of the role of NAPs in regulating the global bacterial gene expression and bacterial pathogenicity.
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Abstract
The Bacillus thuringiensis temperate phage GIL01 does not integrate into the host chromosome but exists stably as an independent linear replicon within the cell. Similar to that of the lambdoid prophages, the lytic cycle of GIL01 is induced as part of the cellular SOS response to DNA damage. However, no CI-like maintenance repressor has been detected in the phage genome, suggesting that GIL01 uses a novel mechanism to maintain lysogeny. To gain insights into the GIL01 regulatory circuit, we isolated and characterized a set of 17 clear plaque (cp) mutants that are unable to lysogenize. Two phage-encoded proteins, gp1 and gp7, are required for stable lysogen formation. Analysis of cp mutants also identified a 14-bp palindromic dinBox1 sequence within the P1-P2 promoter region that resembles the known LexA-binding site of Gram-positive bacteria. Mutations at conserved positions in dinBox1 result in a cp phenotype. Genomic analysis identified a total of three dinBox sites within GIL01 promoter regions. To investigate the possibility that the host LexA regulates GIL01, phage induction was measured in a host carrying a noncleavable lexA (Ind(-)) mutation. GIL01 formed stable lysogens in this host, but lytic growth could not be induced by treatment with mitomycin C. Also, mitomycin C induced β-galactosidase expression from GIL01-lacZ promoter fusions, and induction was similarly blocked in the lexA (Ind(-)) mutant host. These data support a model in which host LexA binds to dinBox sequences in GIL01, repressing phage gene expression during lysogeny and providing the switch necessary to enter lytic development.
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Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS. Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res 2010; 38:5893-908. [PMID: 20460466 PMCID: PMC2943607 DOI: 10.1093/nar/gkq281] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR–DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense–antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi.
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Affiliation(s)
- Suresh V Chinni
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
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Lautier T, Blot N, Muskhelishvili G, Nasser W. Integration of two essential virulence modulating signals at the Erwinia chrysanthemi pel gene promoters: a role for Fis in the growth-phase regulation. Mol Microbiol 2007; 66:1491-505. [PMID: 18028312 DOI: 10.1111/j.1365-2958.2007.06010.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Production of the essential virulence factors, called pectate lyases (Pels), in the phytopathogenic bacterium Erwinia chrysanthemi is controlled by a complex regulation system and responds to various stimuli, such as the presence of pectin or plant extracts, growth phase, temperature and iron concentration. The presence of pectin and growth phase are the most important signals identified. Eight regulators modulating the expression of the pel genes (encoding Pels) have been characterized. These regulators are organized in a network allowing a sequential functioning of the regulators during infection. Although many studies have been carried out, the mechanisms of control of Pel production by growth phase have not yet been elucidated. Here we report that a fis mutant of E. chrysanthemi showed a strong increase in transcription of the pel genes during exponential growth whereas induction of expression in the parental strain occurred at the end of exponential growth. This reveals that Fis acts to prevent an efficient transcription of pel genes at the beginning of exponential growth and also provides evidence of the involvement of Fis in the growth-phase regulation of the pel genes. By using in vitro DNA-protein interactions and transcription experiments, we find that Fis directly represses the pel gene expression at the transcription initiation step. In addition, we show that Fis acts in concert with KdgR, the main repressor responding to the presence of pectin compounds, to shut down the pel gene transcription. Finally, we find that active Fis is required for the efficient translocation of the Pels in growth medium. Together, these data indicate that Fis tightly controls the availability of Pels during pathogenesis by acting on both their production and their translocation in the external medium.
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Affiliation(s)
- Thomas Lautier
- Université de Lyon, F-69003, Université Lyon 1, F-69622; INSA-Lyon, Villeurbanne, F-69621, CNRS, UMR 5240, Unité Microbiologie Adaptation et Pathogénie, F-69622, France
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14
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Lautier T, Nasser W. The DNA nucleoid-associated protein Fis co-ordinates the expression of the main virulence genes in the phytopathogenic bacterium Erwinia chrysanthemi. Mol Microbiol 2007; 66:1474-90. [PMID: 18028311 DOI: 10.1111/j.1365-2958.2007.06012.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Erwinia chrysanthemi strain 3937 is a necrotrophic bacterial plant pathogen. Pectinolytic enzymes and, in particular, pectate lyases (Pels) play a key role in soft rot symptoms but the efficient colonization of plants by E. chrysanthemi requires additional factors. These factors include the harpin HrpN, the cellulase Cel5, proteases (Prts), flagellar proteins and the Sap system, involved in the detoxification of plant antimicrobial peptides. HrpN and flagellum are mostly involved in the early steps of infection whereas the degradative enzymes (Pels, Cel5, Prts) are mainly required in the advanced stages. Production of these virulence factors is tightly regulated by environmental conditions. This report shows that the nucleoid-associated protein Fis plays a pivotal role in the expression of the main virulence genes. Its production is regulated in a growth phase-dependent manner and is under negative autoregulation. An E. chrysanthemi fis mutant displays a reduced motility and expression of hrpN, prtC and the sap operon. In contrast, the expression of the cel5 gene is increased in this mutant. Furthermore, the induction of the Pel activity is delayed and increased during the stationary growth phase in the fis mutant. Most of these controls occur through a direct effect because purified Fis binds to the promoter regions of fis, hrpN, sapA, cel5 and fliC. Moreover, potassium permanganate footprinting and in vitro transcription assays have revealed that Fis prevents transcription initiation at the fis promoter and also transcript elongation from the cel5 promoter. Finally, the fis mutant has a decreased virulence. These results suggest a co-ordinated regulation by Fis of virulence factors involved in certain key steps of infection, early (asymptomatic) and advanced (symptomatic) phases.
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Affiliation(s)
- Thomas Lautier
- Université de Lyon, F-69003, France; Université Lyon 1, F-69622, France; INSA-Lyon, Villeurbanne, F-69621, France; CNRS, UMR 5240, Unité Microbiologie Adaptation et Pathogénie, F-69622, France
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15
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Pandey J, Koyutürk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. ACTA ACUST UNITED AC 2007; 23:i377-86. [PMID: 17646320 DOI: 10.1093/bioinformatics/btm203] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Standardized annotations of biomolecules in interaction networks (e.g. Gene Ontology) provide comprehensive understanding of the function of individual molecules. Extending such annotations to pathways is a critical component of functional characterization of cellular signaling at the systems level. RESULTS We propose a framework for projecting gene regulatory networks onto the space of functional attributes using multigraph models, with the objective of deriving statistically significant pathway annotations. We first demonstrate that annotations of pairwise interactions do not generalize to indirect relationships between processes. Motivated by this result, we formalize the problem of identifying statistically overrepresented pathways of functional attributes. We establish the hardness of this problem by demonstrating the non-monotonicity of common statistical significance measures. We propose a statistical model that emphasizes the modularity of a pathway, evaluating its significance based on the coupling of its building blocks. We complement the statistical model by an efficient algorithm and software, Narada, for computing significant pathways in large regulatory networks. Comprehensive results from our methods applied to the Escherichia coli transcription network demonstrate that our approach is effective in identifying known, as well as novel biological pathway annotations. AVAILABILITY Narada is implemented in Java and is available at http://www.cs.purdue.edu/homes/jpandey/narada/.
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Affiliation(s)
- Jayesh Pandey
- Department of Computer Science, Purdue University, USA.
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Berube PM, Samudrala R, Stahl DA. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol 2007; 189:3935-44. [PMID: 17384196 PMCID: PMC1913382 DOI: 10.1128/jb.01861-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 03/14/2007] [Indexed: 11/20/2022] Open
Abstract
The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal sigma(70) type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC(3) may modify the activity of the holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.
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Affiliation(s)
- Paul M Berube
- Department of Microbiology, University of Washington, Seattle, WA 98195-2700, USA
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Ropers D, de Jong H, Page M, Schneider D, Geiselmann J. Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 2006; 84:124-52. [PMID: 16325332 DOI: 10.1016/j.biosystems.2005.10.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Revised: 09/28/2005] [Accepted: 10/04/2005] [Indexed: 10/25/2022]
Abstract
In case of nutritional stress, like carbon starvation, Escherichia coli cells abandon their exponential-growth state to enter a more resistant, non-growth state called stationary phase. This growth-phase transition is controlled by a genetic regulatory network integrating various environmental signals. Although E. coli is a paradigm of the bacterial world, it is little understood how its response to carbon starvation conditions emerges from the interactions between the different components of the regulatory network. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift.
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Affiliation(s)
- Delphine Ropers
- Institut National de Recherche en Informatique et en Automatique (INRIA), Unité de recherche Rhône-Alpes, 655 Avenue de l 'Europe, Montbonnot, 38334 Saint Ismier Cedex, France.
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18
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Shearwin KE, Callen BP, Egan JB. Transcriptional interference--a crash course. Trends Genet 2005; 21:339-45. [PMID: 15922833 PMCID: PMC2941638 DOI: 10.1016/j.tig.2005.04.009] [Citation(s) in RCA: 416] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Revised: 03/09/2005] [Accepted: 04/12/2005] [Indexed: 12/13/2022]
Abstract
The term "transcriptional interference" (TI) is widely used but poorly defined in the literature. There are a variety of methods by which one can interfere with the process or the product of transcription but the term TI usually refers to the direct negative impact of one transcriptional activity on a second transcriptional activity in cis. Two recent studies, one examining Saccharomyces cerevisiae and the other Escherichia coli, clearly show TI at one promoter caused by the arrival of a transcribing complex initiating at a distant promoter. TI is potentially widespread throughout biology; therefore, it is timely to assess exactly its nature, significance and operative mechanisms. In this article, we will address the following questions: what is TI, how important and widespread is it, how does it work and where should we focus our future research efforts?
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Affiliation(s)
- Keith E Shearwin
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia 5005.
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19
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Rochman M, Blot N, Dyachenko M, Glaser G, Travers A, Muskhelishvili G. Buffering of stable RNA promoter activity against DNA relaxation requires a far upstream sequence. Mol Microbiol 2004; 53:143-52. [PMID: 15225310 DOI: 10.1111/j.1365-2958.2004.04126.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stable RNA promoters of Escherichia coli are exquisitely sensitive to variations in the superhelical density of DNA. Previously, we have shown that binding of the DNA architectural protein FIS at the upstream activating sequences (UASs) of stable RNA promoters prevents the transcription complexes from inactivation induced by changes in the supercoiling level of DNA. Here, we identify a strong FIS binding site 89 bp upstream of the previously described cluster of FIS binding sites located between positions -64 and -150 in the rrnA P1 UAS. Binding of FIS to this 'far upstream sequence' allows the recruitment of additional FIS molecules to the region. We demonstrate that, upon DNA relaxation, the maintenance of promoter activity requires, in addition to UAS, the presence of the far upstream sequence. The far upstream sequence shows no effect in the absence of an intact cluster. This requirement for the integrity of the region encompassing the far upstream sequence and the UAS cluster is correlated with the in vitro modulation of binding of FIS to UAS and interaction of RNA polymerase with the UP element and the region around the transcriptional start point. Our results suggest that, at the rrnA P1 promoter, the entire region comprising the UAS and the far upstream sequence is involved in the assembly of the transcription initiation complex. We propose that the extensive engagement of upstream DNA in this nucleoprotein complex locally compensates for the lack of torsional strain in relaxed DNA, thus increasing the resistance of the promoter to global DNA relaxation.
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Affiliation(s)
- Mark Rochman
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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20
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Owens RM, Pritchard G, Skipp P, Hodey M, Connell SR, Nierhaus KH, O'Connor CD. A dedicated translation factor controls the synthesis of the global regulator Fis. EMBO J 2004; 23:3375-85. [PMID: 15297874 PMCID: PMC514516 DOI: 10.1038/sj.emboj.7600343] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 07/05/2004] [Indexed: 11/09/2022] Open
Abstract
BipA is a highly conserved protein with global regulatory properties in Escherichia coli. We show here that it functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of elongation factor G and has a GTPase activity that is sensitive to high GDP:GTP ratios and stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. We propose a model in which BipA destabilizes unusually strong interactions between the 5' untranslated region of fis mRNA and the ribosome. Since BipA spans phylogenetic domains, transcript-selective translational control for the 'fast-track' expression of specific mRNAs may have wider significance.
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Affiliation(s)
- Róisín M Owens
- School of Biological Sciences, University of Southampton, Southampton, UK
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Gareth Pritchard
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Paul Skipp
- School of Biological Sciences, University of Southampton, Southampton, UK
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Michelle Hodey
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sean R Connell
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | - C David O'Connor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Centre for Proteomic Research, University of Southampton, Southampton, UK
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Mallik P, Pratt TS, Beach MB, Bradley MD, Undamatla J, Osuna R. Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli. J Bacteriol 2004; 186:122-35. [PMID: 14679232 PMCID: PMC303451 DOI: 10.1128/jb.186.1.122-135.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular concentration of the Escherichia coli factor for inversion stimulation (Fis), a global regulator of transcription and a facilitator of certain site-specific DNA recombination events, varies substantially in response to changes in the nutritional environment and growth phase. Under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. We show that both of these regulatory processes operate on the chromosomal fis genes of the enterobacteria Klebsiella pneumoniae, Serratia marcescens, Erwinia carotovora, and Proteus vulgaris, strongly suggesting that the physiological role of Fis is closely tied to its transcriptional regulation in response to the nutritional environment. These transcriptional regulatory processes were previously shown to involve a single promoter (fis P) preceding the fis operon in E. coli. Recent work challenged this notion by presenting evidence from primer extension assays which appeared to indicate that there are multiple promoters upstream of fis P that contribute significantly to the expression and regulation of fis in E. coli. Thus, a rigorous analysis of the fis promoter region was conducted to assess the contribution of such additional promoters. However, our data from primer extension analysis, S1 nuclease mapping, beta-galactosidase assays, and in vitro transcription analysis all indicate that fis P is the sole E. coli fis promoter in vivo and in vitro. We further show how certain conditions used in the primer extension reactions can generate artifacts resulting from secondary annealing events that are the likely source of incorrect assignment of additional fis promoters.
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Affiliation(s)
- Prabhat Mallik
- Department of Biological Sciences, University at Albany, SUNY, Albany, New York 12222, USA
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