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Xie Y, Liu W, Shao X, Zhang W, Deng X. Signal transduction schemes in Pseudomonas syringae. Comput Struct Biotechnol J 2020; 18:3415-3424. [PMID: 33294136 PMCID: PMC7691447 DOI: 10.1016/j.csbj.2020.10.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 11/11/2022] Open
Abstract
To cope with their continually fluctuating surroundings, pathovars of the unicellular phytopathogen Pseudomonas syringae have developed rapid and sophisticated signalling networks to sense extracellular stimuli, which allow them to adjust their cellular composition to survive and cause diseases in host plants. Comparative genomic analyses of P. syringae strains have identified various genes that encode several classes of signalling proteins, although how this bacterium directly perceives these environmental cues remains elusive. Recent work has revealed new mechanisms of a cluster of bacterial signal transduction systems that mainly include two-component systems (such as RhpRS, GacAS, CvsRS and AauRS), extracytoplasmic function sigma factors (such as HrpL and AlgU), nucleotide-based secondary messengers, methyl-accepting chemotaxis sensor proteins and several other intracellular surveillance systems. In this review, we compile a list of the signal transduction mechanisms that P. syringae uses to monitor and respond in a timely manner to intracellular and external conditions. Further understanding of these surveillance processes will provide new perspectives from which to combat P. syringae infections.
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Affiliation(s)
- Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region
| | - Wenbao Liu
- College of Agricultural Sciences and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China
| | - Xiaolong Shao
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region
| | - Weihua Zhang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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Butcher BG, Bao Z, Wilson J, Stodghill P, Swingle B, Filiatrault M, Schneider D, Cartinhour S. The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response. PLoS One 2017; 12:e0180340. [PMID: 28700608 PMCID: PMC5507510 DOI: 10.1371/journal.pone.0180340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/14/2017] [Indexed: 01/14/2023] Open
Abstract
The bacterial plant pathogen Pseudomonas syringae adapts to changes in the environment by modifying its gene expression profile. In many cases, the response is mediated by the activation of extracytoplasmic function (ECF) sigma factors that direct RNA polymerase to transcribe specific sets of genes. In this study we focus on PSPTO_1043, one of ten ECF sigma factors in P. syringae pv. tomato DC3000 (DC3000). PSPTO_1043, together with PSPTO_1042, encode an RpoERsp/ChrR-like sigma/anti-sigma factor pair. Although this gene pair is unique to the P. syringae group among the pseudomonads, homologous genes can be found in photosynthetic genera such as Rhodospirillum, Thalassospira, Phaeospirillum and Parvibaculum. Using ChIP-Seq, we detected 137 putative PSPTO_1043 binding sites and identified a likely promoter motif. We characterized 13 promoter candidates, six of which regulate genes that appear to be found only in P. syringae. PSPTO_1043 responds to the presence of singlet oxygen (1O2) and tert-butyl hydroperoxide (tBOOH) and several of the genes regulated by PSPTO_1043 appear to be involved in response to oxidative stress.
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Affiliation(s)
- Bronwyn G. Butcher
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - Zhongmeng Bao
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - Janet Wilson
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
| | - Paul Stodghill
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
- * E-mail:
| | - Bryan Swingle
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
| | - Melanie Filiatrault
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
| | - David Schneider
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
| | - Samuel Cartinhour
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, United States of America
- Robert W. Holley Center, USDA-ARS, 583 Tower Road, Ithaca, NY 14853, United States of America
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AlgU Controls Expression of Virulence Genes in Pseudomonas syringae pv. tomato DC3000. J Bacteriol 2016; 198:2330-44. [PMID: 27325679 DOI: 10.1128/jb.00276-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/14/2016] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Plant-pathogenic bacteria are able to integrate information about their environment and adjust gene expression to provide adaptive functions. AlgU, an extracytoplasmic function (ECF) sigma factor encoded by Pseudomonas syringae, controls expression of genes for alginate biosynthesis and genes involved with resisting osmotic and oxidative stress. AlgU is active while these bacteria are associated with plants, where its presence supports bacterial growth and disease symptoms. We found that AlgU is an important virulence factor for P. syringae pv. tomato DC3000 but that alginate production is dispensable for disease in host plants. This implies that AlgU regulates additional genes that facilitate bacterial pathogenesis. We used transcriptome sequencing (RNA-seq) to characterize the AlgU regulon and chromatin immunoprecipitation sequencing (ChIP-seq) to identify AlgU-regulated promoters associated with genes directly controlled by this sigma factor. We found that in addition to genes involved with alginate and osmotic and oxidative stress responses, AlgU regulates genes with known virulence functions, including components of the Hrp type III secretion system, virulence effectors, and the hrpL and hrpRS transcription regulators. These data suggest that P. syringae pv. tomato DC3000 has adapted to use signals that activate AlgU to induce expression of important virulence functions that facilitate survival and disease in plants. IMPORTANCE Plant immune systems produce antimicrobial and bacteriostatic conditions in response to bacterial infection. Plant-pathogenic bacteria are adapted to suppress and/or tolerate these conditions; however, the mechanisms controlling these bacterial systems are largely uncharacterized. The work presented here provides a mechanistic explanation for how P. syringae pv. tomato DC3000 coordinates expression of multiple genetic systems, including those dedicated to pathogenicity, in response to environmental conditions. This work demonstrates the scope of AlgU regulation in P. syringae pv. tomato DC3000 and characterizes the promoter sequence regulated by AlgU in these bacteria.
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Chatnaparat T, Li Z, Korban SS, Zhao Y. The Stringent Response Mediated by (p)ppGpp Is Required for Virulence of Pseudomonas syringae pv. tomato and Its Survival on Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:776-789. [PMID: 25675257 DOI: 10.1094/mpmi-11-14-0378-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The hypersensitive response and pathogenicity (hrp) type III secretion system (T3SS) is a key pathogenicity factor in Pseudomonas syringae pv. tomato DC3000 (DC3000). In this study, the role of the second messenger (p)ppGpp on virulence and survival of DC3000 was investigated. Results have demonstrated that (p)ppGpp-deficient mutant (ppGpp(0)) of DC3000 exhibited lower levels of expression of the T3SS and genes of other virulence traits, such as coronatine toxin. The ppGpp(0) mutant of DC3000 was greatly impaired in causing disease and in growth in planta. Furthermore, (p)ppGpp was required for swarming motility, pyoverdine production, the oxidative stress response, as well as γ-amino butyric acid utilization. Screening of amino acids, major signals in activation of ppGpp biosynthesis, revealed that promoter activities of the avrPto gene could be either activated or suppressed by various amino acids in a ppGpp-dependent or -independent manner. Moreover, the ppGpp(0) mutant exhibited increased cell size and decreased survival on plant surfaces. Altogether, these findings indicate that ppGpp acts as an internal signal that regulates the T3SS as well as other virulence factors in pseudomonads and suggest that bacterial pathogens utilize intracellular messengers to sense environmental and nutritional signals for rapid, precise, and reversible control of their pathogenesis and survival.
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Affiliation(s)
- Tiyakhon Chatnaparat
- 1 Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Zhong Li
- 2 Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at-Urbana-Champaign
| | - Schuyler S Korban
- 3 Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign
- 4 Department of Biology, University of Massachusetts Boston, Boston, MA 02125, U.S.A
| | - Youfu Zhao
- 1 Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
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Chatnaparat T, Li Z, Korban SS, Zhao Y. The bacterial alarmone (p)ppGpp is required for virulence and controls cell size and survival of Pseudomonas syringae on plants. Environ Microbiol 2015; 17:4253-70. [PMID: 25626964 DOI: 10.1111/1462-2920.12744] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/29/2014] [Accepted: 12/06/2014] [Indexed: 11/29/2022]
Abstract
The stringent response, mediated by second messenger (p)ppGpp, results in swift and massive transcriptional reprogramming under nutrient limited conditions. In this study, the role of (p)ppGpp on virulence of Pseudomonas syringae pv. syringae B728a (PssB728a) was investigated. The virulence of the relA/spoT (ppGpp(0) ) double mutant was completely impaired on bean, and bacterial growth was significantly reduced, suggesting that (p)ppGpp is required for full virulence of P. syringae. Expression of T3SS and other virulence genes was reduced in ppGpp(0) mutants. In addition, ppGpp deficiency resulted in loss of swarming motility, reduction of pyoverdine production, increased sensitivity to oxidative stress and antibiotic tolerance, as well as reduced ability to utilize γ-amino butyric acid. Increased levels of ppGpp resulted in reduced cell size of PssB728a when grown in a minimal medium and on plant surfaces, while most ppGpp(0) mutant cells were not viable on plant surfaces 24 h after spray inoculation, suggesting that ppGpp-mediated stringent response temporarily limits cell growth, and might control cell survival on plants by limiting their growth. These results demonstrated that ppGpp-mediated stringent response plays a central role in P. syringae virulence and survival and indicated that ppGpp serves as a global signal for regulating various virulence traits in PssB728a.
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Affiliation(s)
- Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhong Li
- Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Llamas MA, Imperi F, Visca P, Lamont IL. Cell-surface signaling inPseudomonas: stress responses, iron transport, and pathogenicity. FEMS Microbiol Rev 2014; 38:569-97. [DOI: 10.1111/1574-6976.12078] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/20/2014] [Accepted: 05/27/2014] [Indexed: 01/06/2023] Open
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Thakur PB, Vaughn-Diaz VL, Greenwald JW, Gross DC. Characterization of five ECF sigma factors in the genome of Pseudomonas syringae pv. syringae B728a. PLoS One 2013; 8:e58846. [PMID: 23516563 PMCID: PMC3597554 DOI: 10.1371/journal.pone.0058846] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. syringae B728a, a bacterial pathogen of bean, utilizes large surface populations and extracellular signaling to initiate a fundamental change from an epiphytic to a pathogenic lifestyle. Extracytoplasmic function (ECF) sigma (σ) factors serve as important regulatory factors in responding to various environmental signals. Bioinformatic analysis of the B728a genome revealed 10 ECF sigma factors. This study analyzed deletion mutants of five previously uncharacterized ECF sigma factor genes in B728a, including three FecI-type ECF sigma factors (ECF5, ECF6, and ECF7) and two ECF sigma factors placed in groups ECF11 and ECF18. Transcriptional profiling by qRT-PCR analysis of ECF sigma factor mutants was used to measure expression of their associated anti-sigma and outer membrane receptor proteins, and expression of genes associated with production of extracellular polysaccharides, fimbriae, glycine betaine and syringomycin. Notably, the B728aΔecf7 mutant displayed reduced swarming and had decreased expression of CupC fimbrial genes. Growth and pathogenicity assays, using a susceptible bean host, revealed that none of the tested sigma factor genes are required for in planta growth and lesion formation.
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Affiliation(s)
- Poulami Basu Thakur
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Vanessa L. Vaughn-Diaz
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Jessica W. Greenwald
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Dennis C. Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- * E-mail: .
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Mitter B, Petric A, Shin MW, Chain PSG, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A. Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. FRONTIERS IN PLANT SCIENCE 2013; 4:120. [PMID: 23641251 PMCID: PMC3639386 DOI: 10.3389/fpls.2013.00120] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/16/2013] [Indexed: 05/20/2023]
Abstract
Burkholderia phytofirmans PsJN is a naturally occurring plant-associated bacterial endophyte that effectively colonizes a wide range of plants and stimulates their growth and vitality. Here we analyze whole genomes, of PsJN and of eight other endophytic bacteria. This study illustrates that a wide spectrum of endophytic life styles exists. Although we postulate the existence of typical endophytic traits, no unique gene cluster could be exclusively linked to the endophytic lifestyle. Furthermore, our study revealed a high genetic diversity among bacterial endophytes as reflected in their genotypic and phenotypic features. B. phytofirmans PsJN is in many aspects outstanding among the selected endophytes. It has the biggest genome consisting of two chromosomes and one plasmid, well-equipped with genes for the degradation of complex organic compounds and detoxification, e.g., 24 glutathione-S-transferase (GST) genes. Furthermore, strain PsJN has a high number of cell surface signaling and secretion systems and harbors the 3-OH-PAME quorum-sensing system that coordinates the switch of free-living to the symbiotic lifestyle in the plant-pathogen R. solanacearum. The ability of B. phytofirmans PsJN to successfully colonize such a wide variety of plant species might be based on its large genome harboring a broad range of physiological functions.
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Affiliation(s)
- Birgit Mitter
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
- *Correspondence: Birgit Mitter, Bioresources Unit, Austrian Institute of Technology Gmbh, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria. e-mail:
| | - Alexandra Petric
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
| | - Maria W. Shin
- Department of Energy, Joint Genome InstituteWalnut Creek, CA, USA
| | | | | | | | - Jerzy Nowak
- Department of Agriculture and Life Sciences, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
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Regulons of three Pseudomonas syringae pv. tomato DC3000 iron starvation sigma factors. Appl Environ Microbiol 2012; 79:725-7. [PMID: 23124242 DOI: 10.1128/aem.02801-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 contains genes for 15 sigma factors. The majority are members of the extracytoplasmic function class of sigma factors, including five that belong to the iron starvation subgroup. In this study, we identified the genes controlled by three iron starvation sigma factors. Their regulons are composed of a small number of genes likely to be involved in iron uptake.
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An extracytoplasmic function sigma factor-mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. J Bacteriol 2011; 193:5775-83. [PMID: 21840980 DOI: 10.1128/jb.05114-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The diversity of regulatory systems encoded by bacteria provides an indication of the variety of stresses and interactions that these organisms encounter in nature. We have been investigating how the plant pathogen Pseudomonas syringae pv. tomato DC3000 responds to iron limitation and have focused on the iron starvation (IS) sigma factors to identify regulon members and to explore the mechanistic details of genetic control for this class of regulators. In the study described in this report, we used chromatin immunoprecipitation paired with high-throughput sequencing (ChIP-Seq) to screen the genome for locations associated with binding of the P. syringae IS sigma factor PSPTO_1203. We used multiple methods to demonstrate differential regulation of two genes identified in the ChIP-Seq screen and characterize the promoter elements that facilitate PSPTO_1203-dependent regulation. The genes regulated by PSPTO_1203 encode a TonB-dependent transducer (PSPTO_1206) and a cytoplasmic membrane protein (PSPTO_2145), which is located in the P. syringae pyoverdine cluster. Additionally, we identified siderophores that induce the activity of PSPTO_1203 and used this information to investigate the functional components of the signal transduction cascade.
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Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. J Bacteriol 2011; 193:4598-611. [PMID: 21784947 DOI: 10.1128/jb.00340-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant pathogen Pseudomonas syringae pv. tomato DC3000 (DC3000) is found in a wide variety of environments and must monitor and respond to various environmental signals such as the availability of iron, an essential element for bacterial growth. An important regulator of iron homeostasis is Fur (ferric uptake regulator), and here we present the first study of the Fur regulon in DC3000. Using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq), 312 chromosomal regions were highly enriched by coimmunoprecipitation with a C-terminally tagged Fur protein. Integration of these data with previous microarray and global transcriptome analyses allowed us to expand the putative DC3000 Fur regulon to include genes both repressed and activated in the presence of bioavailable iron. Using nonradioactive DNase I footprinting, we confirmed Fur binding in 41 regions, including upstream of 11 iron-repressed genes and the iron-activated genes encoding two bacterioferritins (PSPTO_0653 and PSPTO_4160), a ParA protein (PSPTO_0855), and a two-component system (TCS) (PSPTO_3382 to PSPTO_3380).
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Pérez-Rueda E, Janga SC, Martínez-Antonio A. Scaling relationship in the gene content of transcriptional machinery in bacteria. MOLECULAR BIOSYSTEMS 2009; 5:1494-501. [DOI: 10.1039/b907384a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Swingle B, Thete D, Moll M, Myers CR, Schneider DJ, Cartinhour S. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads. Mol Microbiol 2008; 68:871-89. [PMID: 18363796 DOI: 10.1111/j.1365-2958.2008.06209.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria that survive under variable conditions possess an assortment of genetic regulators to meet these challenges. The group IV or extracytoplasmic function (ECF) sigma factors regulate gene expression in response to specific environmental signals by altering the promoter specificity of RNA polymerase. We have undertaken a study of PvdS, a group IV sigma factor encoded by Pseudomonas syringae pv. tomato DC3000 (DC3000), a plant pathogen that is likely to encounter variations in nutrient availability as well as plant host defences. The gene encoding PvdS was previously identified by sequence similarity to the Pseudomonas aeruginosa orthologue, which directs transcription of genes encoding the biosynthesis of pyoverdine, a siderophore involved in iron acquisition, and is responsible for the characteristic fluorescence of the pseudomonads. We identified 15 promoters regulated by PvdS in DC3000 and characterized the promoter motif using computational analysis. Mutagenesis of conserved nucleotides within the motif interfered with promoter function and the degree of the effect was different depending on which region of the motif was mutated. Hidden Markov models constructed from alignments of sequence motifs extracted from DC3000 and PAO1 were used to query genomes of DC3000 and other fluorescent pseudomonads for similar motifs. We conclude that the role of PvdS as a regulator of pyoverdine synthesis is conserved among the fluorescent pseudomonads, but the promoters recognized by PvdS orthologues may differ subtly from species to species.
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Affiliation(s)
- Bryan Swingle
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.
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14
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Abstract
In Pseudomonas aeruginosa, as in most bacterial species, the expression of genes is tightly controlled by a repertoire of transcriptional regulators, particularly the so-called sigma (sigma) factors. The basic understanding of these proteins in bacteria has initially been described in Escherichia coli where seven sigma factors are involved in core RNA polymerase interactions and promoter recognition. Now, 7 years have passed since the completion of the first genome sequence of the opportunistic pathogen P. aeruginosa. Information from the genome of P. aeruginosa PAO1 identified 550 transcriptional regulators and 24 putative sigma factors. Of the 24 sigma, 19 were of extracytoplasmic function (ECF). Here, basic knowledge of sigma and ECF proteins was reviewed with particular emphasis on their role in P. aeruginosa global gene regulation. Summarized data are obtained from in silico analysis of P. aeruginosasigma and ECF including rpoD (sigma(70)), RpoH (sigma(32)), RpoF (FliA or sigma(28)), RpoS (sigma(S) or sigma(38)), RpoN (NtrA, sigma(54) or sigma(N)), ECF including AlgU (RpoE or sigma(22)), PvdS, SigX and a collection of uncharacterized sigma ECF, some of which are implicated in iron transport. Coupled to systems biology, identification and functional genomics analysis of P. aeruginosasigma and ECF are expected to provide new means to prevent infection, new targets for antimicrobial therapy, as well as new insights into the infection process.
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Affiliation(s)
- Eric Potvin
- Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculté de Médecine, Pavillon Charles-Eugène Marchand, Université Laval, Sainte-Foy, Quebec, Canada
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15
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Lavín JL, Kiil K, Resano O, Ussery DW, Oguiza JA. Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae. BMC Genomics 2007; 8:397. [PMID: 17971244 PMCID: PMC2222644 DOI: 10.1186/1471-2164-8-397] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 10/31/2007] [Indexed: 11/26/2022] Open
Abstract
Background Pseudomonas syringae is a widespread bacterial plant pathogen, and strains of P. syringae may be assigned to different pathovars based on host specificity among different plant species. The genomes of P. syringae pv. syringae (Psy) B728a, pv. tomato (Pto) DC3000 and pv. phaseolicola (Pph) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR). P. syringae requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions. Results Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes of Psy B728a, Pto DC3000 and Pph 1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed important differences in TCS proteins among the three P. syringae pathovars. Conclusion In this article we present a thorough analysis of the identification and distribution of TCS proteins among the sequenced genomes of P. syringae. We have identified differences in TCS proteins among the three P. syringae pathovars that may contribute to their diverse host ranges and association with plant hosts. The identification and analysis of the repertoire of TCS proteins in the genomes of P. syringae pathovars constitute a basis for future functional genomic studies of the signal transduction pathways in this important bacterial phytopathogen.
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Affiliation(s)
- José L Lavín
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain.
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Tralau T, Vuilleumier S, Thibault C, Campbell BJ, Hart CA, Kertesz MA. Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa. J Bacteriol 2007; 189:6743-50. [PMID: 17675390 PMCID: PMC2045191 DOI: 10.1128/jb.00889-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a number of infections in humans, but is best known for its association with cystic fibrosis. It is able to use a wide range of sulfur compounds as sources of sulfur for growth. Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as the sulfur source led not only to a sulfate starvation response but also to induction of genes involved with type III secretion systems.
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Affiliation(s)
- Tewes Tralau
- Faculty of Life Sciences, University of Manchester, Michael Smith Bldg., Oxford Rd., Manchester M13 9PT, England
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