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Yu X, Meng C, Tan X, Su Y, Cao Z, Hwang TS, Li L. RsmA3 modulates RpoS through the RetS-Gac-Rsm signaling pathway in response to H 2 O 2 stress in the phytopathogen Pseudomonas syringae. Environ Microbiol 2022; 24:4755-4770. [PMID: 35837862 DOI: 10.1111/1462-2920.16132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/27/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signaling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H2 O2 and ultimately affecting pathogenicity to the host plant. Following increased H2 O2 by external addition or endogenous induction by menadione, the resistance of the mutant strain ΔretS to H2 O2 is significantly enhanced due to rapid increases in the transcription of Rsm-related non-coding small RNAs (nc sRNAs), a sigma factor RpoS, and H2 O2 -detoxifying enzymes. Moreover, the ΔretS mutant is significantly less pathogenic in cucumber leaves. Seven Rsm-related nc sRNAs (namely, rsmZ, rsmY, and rsmX1-5 ) show functional redundancy in the RetS-Gac-Rsm signaling pathway. External addition of H2 O2 stimulates increases in the transcription of both rsmY and rsmZ. Thus, we propose a regulatory model of the RetS-Gac-Rsm signaling pathway in P. syringae MB03 for the regulation of H2 O2 tolerance and phytopathogenicity in the host plant.
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Affiliation(s)
- Xun Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Cui Meng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Xiaocheng Tan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Yuwei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Zhiping Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Tzann-Shun Hwang
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
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2
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López-Pliego L, González-Acocal V, García-González DL, Reyes-Nicolau JI, Sánchez-Cuapio Z, Meneses-Carbajal AS, Fuentes-Ramírez LE, Castañeda M. HrgS (Avin 34990), a novel histidine-kinase related to GacS, regulates alginate synthesis in Azotobacter vinelandii. FEMS Microbiol Lett 2022; 369:6546211. [PMID: 35266527 DOI: 10.1093/femsle/fnac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/31/2022] [Accepted: 03/08/2022] [Indexed: 11/14/2022] Open
Abstract
Azotobacter vinelandii is a soil bacterium that produces alginates, a family of polymers of biotechnological interest. In A. vinelandii, alginate production is controlled by the two-component system GacS/GacA. GacS/GacA, in turn, regulates the Rsm post-transcriptional regulatory system establishing a cascade that regulates alginate biosynthesis by controlling the expression of the algD biosynthetic gene. In Pseudomonas aeruginosa, GacS/GacA is influenced by other histidine-kinases constituting a multicomponent signal transduction system. In this study, we explore the presence of GacS-related histidine-kinases in A. vinelandii and discover a novel histidine-kinase (Avin_34990, renamed HrgS). This histidin-kinase acts as a negative regulator of alginate synthesis by controlling the transcription of the sRNAs belonging to the Rsm post-transcriptional regulatory system, for which a functional GacS is required.
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Affiliation(s)
- Liliana López-Pliego
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Verónica González-Acocal
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Diana Laura García-González
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Jimena Itzel Reyes-Nicolau
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Zaira Sánchez-Cuapio
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Alan Shared Meneses-Carbajal
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Luis Ernesto Fuentes-Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Miguel Castañeda
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
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3
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Monteagudo-Cascales E, Santero E, Canosa I. The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions. Genes (Basel) 2022; 13:genes13020375. [PMID: 35205417 PMCID: PMC8871633 DOI: 10.3390/genes13020375] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.
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Affiliation(s)
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
| | - Inés Canosa
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
- Correspondence: ; Tel.: +34-954349052
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4
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Ferreiro MD, Behrmann LV, Corral A, Nogales J, Gallegos MT. Exploring the expression and functionality of the rsm sRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biol 2021; 18:1818-1833. [PMID: 33406981 PMCID: PMC8583166 DOI: 10.1080/15476286.2020.1871217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/08/2020] [Accepted: 12/29/2020] [Indexed: 12/18/2022] Open
Abstract
The Gac-rsm pathway is a global regulatory network that governs mayor lifestyle and metabolic changes in gamma-proteobacteria. In a previous study, we uncovered the role of CsrA proteins promoting growth and repressing motility, alginate production and virulence in the model phytopathogen Pseudomonas syringae pv. tomato (Pto) DC3000. Here, we focus on the expression and regulation of the rsm regulatory sRNAs, since Pto DC3000 exceptionally has seven variants (rsmX1-5, rsmY and rsmZ). The presented results offer further insights into the functioning of the complex Gac-rsm pathway and the interplay among its components. Overall, rsm expressions reach maximum levels at high cell densities, are unaffected by surface detection, and require GacA for full expression. The rsm levels of expression and GacA-dependence are determined by the sequences found in their -35/-10 promoter regions and GacA binding boxes, respectively. rsmX5 stands out for being the only rsm in Pto DC3000 whose high expression does not require GacA, constituting the main component of the total rsm pool in a gacA mutant. The deletion of rsmY and rsmZ had minor effects on Pto DC3000 motility and virulence phenotypes, indicating that rsmX1-5 can functionally replace them. On the other hand, rsmY or rsmZ overexpression in a gacA mutant did not revert its phenotype. Additionally, a negative feedback regulatory loop in which the CsrA3 protein promotes its own titration by increasing the levels of several rsm RNAs in a GacA-dependent manner has been disclosed as part of this work.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Lara Vanessa Behrmann
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Ana Corral
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Joaquina Nogales
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
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5
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O’Malley MR, Anderson JC. Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals. Microorganisms 2021; 9:microorganisms9061227. [PMID: 34198761 PMCID: PMC8228185 DOI: 10.3390/microorganisms9061227] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas syringae are Gram-negative, plant pathogenic bacteria that use a type III secretion system (T3SS) to disarm host immune responses and promote bacterial growth within plant tissues. Despite the critical role for type III secretion in promoting virulence, T3SS-encoding genes are not constitutively expressed by P. syringae and must instead be induced during infection. While it has been known for many years that culturing P. syringae in synthetic minimal media can induce the T3SS, relatively little is known about host signals that regulate the deployment of the T3SS during infection. The recent identification of specific plant-derived amino acids and organic acids that induce T3SS-inducing genes in P. syringae has provided new insights into host sensing mechanisms. This review summarizes current knowledge of the regulatory machinery governing T3SS deployment in P. syringae, including master regulators HrpRS and HrpL encoded within the T3SS pathogenicity island, and the environmental factors that modulate the abundance and/or activity of these key regulators. We highlight putative receptors and regulatory networks involved in linking the perception of host signals to the regulation of the core HrpRS–HrpL pathway. Positive and negative regulation of T3SS deployment is also discussed within the context of P. syringae infection, where contributions from distinct host signals and regulatory networks likely enable the fine-tuning of T3SS deployment within host tissues. Last, we propose future research directions necessary to construct a comprehensive model that (a) links the perception of host metabolite signals to T3SS deployment and (b) places these host–pathogen signaling events in the overall context of P. syringae infection.
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Ferreiro MD, Gallegos MT. Distinctive features of the Gac-Rsm pathway in plant-associated Pseudomonas. Environ Microbiol 2021; 23:5670-5689. [PMID: 33939255 DOI: 10.1111/1462-2920.15558] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 02/04/2023]
Abstract
Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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7
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Ormazábal A, Palma J, Pierdominici-Sottile G. Molecular Dynamics Simulations Unveil the Basis of the Sequential Binding of RsmE to the Noncoding RNA RsmZ. J Phys Chem B 2021; 125:3045-3056. [PMID: 33755488 DOI: 10.1021/acs.jpcb.0c09770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CsrA/RsmE are dimeric proteins that bind to targeted mRNAs repressing translation. This mechanism modulates several metabolic pathways and allows bacteria to efficiently adjust their responses to environmental changes. In turn, small RNAs (sRNA) such as CsrB or RsmZ, restore translation by sequestering CsrA/RsmE dimers. Thus, these molecules act in tandem as a gene-expression regulatory system. Recently, a combined NMR-EPR approach solved the structure of part of RsmZ of Pseudomonas fluorescens, attached to three RsmE dimers. The study demonstrated that RsmE assembles onto RsmZ following a specific sequential order. The reasons underlying this peculiar behavior are still unclear. Here, we present a molecular dynamics analysis that explores the conformational diversity of RsmZ and RsmZ-RsmE complexes. The results reveal a clear pattern regarding the exposure of the alternative GGA binding motifs of RsmZ. This pattern is tuned by the attachment of RsmE dimers. Altogether, the observations provide a simple and convincing explanation for the order observed in the sequestration of RsmE dimers. Typical structures for RsmZ and RsmZ-RsmE complexes have been identified. Their characteristics concerning the exposure of the GGA sequences are presented and their most significant interactions are described.
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Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
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Liu J, Yu M, Ge Y, Tian Y, Hu B, Zhao Y. The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:637595. [PMID: 33719314 PMCID: PMC7952654 DOI: 10.3389/fpls.2021.637595] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The post-transcriptional regulator RsmA globally controls gene expression in bacteria. Previous studies showed that RsmA2 and RsmA3 played critical roles in regulating type III secretion system (T3SS), motility, syringafactin, and alginate productions in Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000). In this study, we investigated global gene expression profiles of the wild-type PstDC3000, the rsmA3 mutant, and the rsmA2/A3 double mutant in the hrp-inducing minimum medium (HMM) and King's B (KB) medium. By comparing the rsmA2/A3 and rsmA3 mutants to PstDC3000, a total of 1358 and 1074 differentially expressed genes (DEGs) in HMM, and 870 and 1463 DEGs in KB were uncovered, respectively. When comparing the rsmA2/A3 mutant with the rsmA3 mutant, 277 and 741 DEGs in HMM and KB, respectively, were revealed. Transcriptomic analysis revealed that the rsmY, rsmZ, and rsmX1-5 non-coding small RNAs (ncsRNAs) were positively affected by RsmA2 and RsmA3, while RsmA3 positively regulates the expression of the rsmA2 gene and negatively regulates both rsmA1 and rsmA5 gene expression. Comparative transcriptomic analysis showed that RsmA2 and RsmA3 synergistically influenced the expression of genes involved in T3SS and alginate biosynthesis in HMM and chemotaxis in KB. RsmA2 and RsmA3 inversely affected genes involved in syringafactin production in HMM and ribosomal protein biosynthesis in KB. In addition, RsmA2 played a major role in influencing genes involved in sarcosine and thiamine biosynthesis in HMM and in mannitol and phosphate metabolism in KB. On the other hand, genes involved in fatty acid metabolism, cellulose biosynthesis, signal transduction, and stress responses were mainly impacted by RsmA3 in both HMM and KB; whereas RsmA3 played a major role in controlling genes involved in c-di-GMP, phosphate metabolism, chemotaxis, and capsular polysaccharide in HMM. Furthermore, regulation of syringafactin production and oxidative stress by RsmA2 and RsmA3 was experimentally verified. Our results suggested the potential interplay among the RsmA proteins, which exhibit distinct and overlapping roles in modulating virulence and survival in P. syringae under different nutritional conditions.
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Affiliation(s)
- Jun Liu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yixin Ge
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments. Microorganisms 2021; 9:microorganisms9020250. [PMID: 33530561 PMCID: PMC7911923 DOI: 10.3390/microorganisms9020250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.
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Sobrero PM, Valverde C. Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. Front Mol Biosci 2020; 7:127. [PMID: 32754614 PMCID: PMC7366521 DOI: 10.3389/fmolb.2020.00127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).
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Affiliation(s)
- Patricio Martín Sobrero
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
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11
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Zhang Y, Zhang B, Wu X, Zhang LQ. Characterization the role of GacA-dependent small RNAs and RsmA family proteins on 2,4-diacetylphloroglucinol production in Pseudomonas fluorescens 2P24. Microbiol Res 2019; 233:126391. [PMID: 31865097 DOI: 10.1016/j.micres.2019.126391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/26/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Pseudomonas fluorescens 2P24 is a plant-beneficial rhizobacteria that controls many root diseases caused by soil-borne pathogens, and the production of the antibiotic compound 2,4-diacetylphloroglucinol (2,4-DAPG) is essential for its biocontrol ability. In the present study, we investigated the regulatory mechanism acting on the production of 2,4-DAPG by the GacA-dependent small non-coding RNAs (sRNAs) and RsmA/E proteins in strain 2P24. Our results showed that the GacS-GacA system regulates the expression of the phlACBD locus, which is responsible for 2,4-DAPG production, by inducing the expression of rsmX, rsmX1, rsmY, and rsmZ. A novel GacA-regulated sRNA, RgsA, was found to negatively regulate 2,4-DAPG production. Activation of the phlACBD locus by the GacS-GacA system is mediated through RsmA and RsmE proteins (but not RsmI), which inhibit phlACBD translation by binding to the putative RsmA/E recognition element in the phlACBD leader. Taken together, our results suggested that in P. fluorescens 2P24, the GacS-GacA system controls the cellular 2,4-DAPG levels in the cell by fine-tuning the function of sRNAs in P. fluorescens.
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Affiliation(s)
- Yang Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Bo Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiaogang Wu
- College of Agriculture, Guangxi University, Nanning 530004, China.
| | - Li-Qun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
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12
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Study of the sRNA RsmY involved in the genetic regulation of the synthesis of alginate and alkyl resorcinols in Azotobacter vinelandii. Arch Microbiol 2019; 202:579-589. [DOI: 10.1007/s00203-019-01769-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022]
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Zhang B, Zhang Y, Liang F, Ma Y, Wu X. An Extract Produced by Bacillus sp. BR3 Influences the Function of the GacS/GacA Two-Component System in Pseudomonas syringae pv. tomato DC3000. Front Microbiol 2019; 10:2005. [PMID: 31572307 PMCID: PMC6749012 DOI: 10.3389/fmicb.2019.02005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/15/2019] [Indexed: 12/03/2022] Open
Abstract
The GacS/GacA two-component system is essential for virulence in many plant pathogenic bacteria, and thus represents a promising anti-virulence target. In the present study, we isolated and screened rhizobacteria that were capable of inhibiting the expression of the gacS gene in the phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pto) DC3000. One candidate inhibitor bacterium, BR3 was obtained and identified as a Bacillus sp. strain based on 16s rRNA gene sequence analysis. Besides the gacS gene, the GacA-dependent small RNA genes rsmZ and rsmY were repressed transcriptionally when DC3000 was treated with an extract from strain BR3. Importantly, the extract also influenced bacterial motility, the expression of type three secretion system effector AvrPto, and the plant hypersensitive response triggered by strain DC3000. The results suggested that the extract from strain BR3 might offer an alternative method to control bacterial diseases in plants by targeting the GacS/GacA system.
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Affiliation(s)
- Bo Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Fei Liang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yinan Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xiaogang Wu
- College of Agriculture, Guangxi University, Nanning, China
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Ge Y, Lee JH, Liu J, Yang H, Tian Y, Hu B, Zhao Y. Homologues of the RNA binding protein RsmA in Pseudomonas syringae pv. tomato DC3000 exhibit distinct binding affinities with non-coding small RNAs and have distinct roles in virulence. MOLECULAR PLANT PATHOLOGY 2019; 20:1217-1236. [PMID: 31218814 PMCID: PMC6715622 DOI: 10.1111/mpp.12823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudomonas syringae pv. tomato DC3000 (PstDC3000) contains five RsmA protein homologues. In this study, four were functionally characterized, with a focus on RsmA2, RsmA3 and RsmA4. RNA electrophoretic mobility shift assays demonstrated that RsmA1 and RsmA4 exhibited similar low binding affinities to non-coding small RNAs (ncsRNAs), whereas RsmA2 and RsmA3 exhibited similar, but much higher, binding affinities to ncsRNAs. Our results showed that both RsmA2 and RsmA3 were required for disease symptom development and bacterial growth in planta by significantly affecting virulence gene expression. All four RsmA proteins, especially RsmA2 and RsmA3, influenced γ-amino butyric acid utilization and pyoverdine production to some degree, whereas RsmA2, RsmA3 and RsmA4 influenced protease activities. A single RsmA, RsmA3, played a dominant role in regulating motility. Furthermore, reverse transcription quantitative real-time PCR and western blot results showed that RsmA proteins, especially RsmA2 and RsmA3, regulated target genes and possibly other RsmA proteins at both transcriptional and translational levels. These results indicate that RsmA proteins in PstDC3000 exhibit distinct binding affinities to ncsRNAs and have distinct roles in virulence. Our results also suggest that RsmA proteins in PstDC3000 interact with each other, where RsmA2 and RsmA3 play a major role in regulating various functions in a complex manner.
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Affiliation(s)
- Yixin Ge
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and PestsNanjing Agricultural UniversityNanjing210095P. R. China
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Jae Hoon Lee
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Jun Liu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and PestsNanjing Agricultural UniversityNanjing210095P. R. China
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Ho‐wen Yang
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and PestsNanjing Agricultural UniversityNanjing210095P. R. China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and PestsNanjing Agricultural UniversityNanjing210095P. R. China
| | - Youfu Zhao
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
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15
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Quorum-dependent expression of rsmX and rsmY, small non-coding RNAs, in Pseudomonas syringae. Microbiol Res 2019; 223-225:72-78. [DOI: 10.1016/j.micres.2019.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/19/2019] [Accepted: 04/11/2019] [Indexed: 01/01/2023]
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Farias GA, Olmedilla A, Gallegos MT. Visualization and characterization of Pseudomonas syringae pv. tomato DC3000 pellicles. Microb Biotechnol 2019; 12:688-702. [PMID: 30838765 PMCID: PMC6559019 DOI: 10.1111/1751-7915.13385] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/04/2019] [Accepted: 02/08/2019] [Indexed: 01/10/2023] Open
Abstract
Cellulose, whose production is controlled by c-di-GMP, is a commonly found exopolysaccharide in bacterial biofilms. Pseudomonas syringae pv. tomato (Pto) DC3000, a model organism for molecular studies of plant-pathogen interactions, carries the wssABCDEFGHI operon for the synthesis of acetylated cellulose. The high intracellular levels of the second messenger c-di-GMP induced by the overexpression of the heterologous diguanylate cyclase PleD stimulate cellulose production and enhance air-liquid biofilm (pellicle) formation. To characterize the mechanisms involved in Pto DC3000 pellicle formation, we studied this process using mutants lacking flagella, biosurfactant or different extracellular matrix components, and compared the pellicles produced in the absence and in the presence of PleD. We have discovered that neither alginate nor the biosurfactant syringafactin are needed for their formation, whereas cellulose and flagella are important but not essential. We have also observed that the high c-di-GMP levels conferred more cohesion to Pto cells within the pellicle and induced the formation of intracellular inclusion bodies and extracellular fibres and vesicles. Since the pellicles were very labile and this greatly hindered their handling and processing for microscopy, we have also developed new methods to collect and process them for scanning and transmission electron microscopy. These techniques open up new perspectives for the analysis of fragile biofilms in other bacterial strains.
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Affiliation(s)
- Gabriela A Farias
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain.,Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Adela Olmedilla
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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Abstract
Quorum sensing is a vital property of bacteria that enables community-wide coordination of collective behaviors. A key example of such a behavior is biofilm formation, in which groups of bacteria invest in synthesizing a protective, joint extracellular matrix. Quorum sensing involves the production, release, and subsequent detection of extracellular signaling molecules called autoinducers. The architecture of quorum-sensing signal transduction pathways is highly variable among different species of bacteria, but frequently involves posttranscriptional regulation carried out by small regulatory RNA molecules. This review illustrates the diverse roles small trans-acting regulatory RNAs can play, from constituting a network's core to auxiliary roles in adjusting the rate of autoinducer synthesis, mediating cross talk among different parts of a network, or integrating different regulatory inputs to trigger appropriate changes in gene expression. The emphasis is on describing how the study of small RNA-based regulation in quorum sensing and biofilm formation has uncovered new general properties or expanded our understanding of bacterial riboregulation.
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López-Pliego L, García-Ramírez L, Cruz-Gómez EA, Domínguez-Ojeda P, López-Pastrana A, Fuentes-Ramírez LE, Núñez C, Castañeda M. Transcriptional Study of the RsmZ-sRNAs and Their Relationship to the Biosynthesis of Alginate and Alkylresorcinols in Azotobacter vinelandii. Mol Biotechnol 2018; 60:670-680. [DOI: 10.1007/s12033-018-0102-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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19
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Ferreiro MD, Nogales J, Farias GA, Olmedilla A, Sanjuán J, Gallegos MT. Multiple CsrA Proteins Control Key Virulence Traits in Pseudomonas syringae pv. tomato DC3000. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:525-536. [PMID: 29261011 DOI: 10.1094/mpmi-09-17-0232-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The phytopathogenic bacterium Pseudomonas syringae pv. tomato DC3000 has a complex Gac-rsm global regulatory pathway that controls virulence, motility, production of secondary metabolites, carbon metabolism, and quorum sensing. However, despite the fact that components of this pathway are known, their physiological roles have not yet been established. Regarding the CsrA/RsmA type proteins, five paralogs, three of which are well conserved within the Pseudomonas genus (csrA1, csrA2, and csrA3), have been found in the DC3000 genome. To decipher their function, mutants lacking the three most conserved CsrA proteins have been constructed and their physiological outcomes examined. We show that they exert nonredundant functions and demonstrate that CsrA3 and, to a lesser extent, CsrA2 but not CsrA1 alter the expression of genes involved in a variety of pathways and systems important for motility, exopolysaccharide synthesis, growth, and virulence. Particularly, alginate synthesis, syringafactin production, and virulence are considerably de-repressed in a csrA3 mutant, whereas growth in planta is impaired. We propose that the linkage of growth and symptom development is under the control of CsrA3, which functions as a pivotal regulator of the DC3000 life cycle, repressing virulence traits and promoting cell division in response to environmental cues.
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Affiliation(s)
- María-Dolores Ferreiro
- 1 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain; and
| | - Joaquina Nogales
- 1 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain; and
| | - Gabriela A Farias
- 1 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain; and
- 2 Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Adela Olmedilla
- 2 Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Juan Sanjuán
- 1 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain; and
| | - María Trinidad Gallegos
- 1 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain; and
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20
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Sawada T, Eguchi M, Asaki S, Kashiwagi R, Shimomura K, Taguchi F, Matsui H, Yamamoto M, Noutoshi Y, Toyoda K, Ichinose Y. MexEF-OprN multidrug efflux pump transporter negatively controls N-acyl-homoserine lactone accumulation in pseudomonas syringae pv. Tabaci 6605. Mol Genet Genomics 2018; 293:907-917. [PMID: 29549432 DOI: 10.1007/s00438-018-1430-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/09/2018] [Indexed: 01/28/2023]
Abstract
Our previous studies revealed that flagellar-motility-defective mutants such as ∆fliC of Pseudomonas syringae pv. tabaci 6605 (Pta6605) have remarkably reduced production of N-acyl-homoserine lactones (AHL), quorum-sensing molecules. To investigate the reason of loss of AHL production in ∆fliC mutant, we carried out transposon mutagenesis. Among approximately 14,000 transconjugants, we found 11 AHL production-recovered (APR) strains. In these APR strains, a transposon was inserted into either mexE or mexF, genes encoding for the multidrug efflux pump transporter MexEF-OprN, and mexT, a gene encoding a putative transcriptional activator for mexEF-oprN. These results suggest that MexEF-OprN is a negative regulator of AHL production. To confirm the negative effect of MexEF-OprN on AHL production, loss- and gain-of-function experiments for mexEF-oprN were carried out. The ∆fliC∆mexF and ∆fliC∆mexT double mutant strains recovered AHL production, whereas the mexT overexpressing strain abolished AHL production, although the psyI, a gene encoding AHL synthase, is transcribed as wild type. Introduction of a mexF or mexT mutation into another flagellar-motility- and AHL production-defective mutant strain, ∆motCD, also recovered the ability to produce AHL. Furthermore, introduction of the mexF mutation into other AHL production-defective mutant strains such as ∆gacA and ∆aefR also recovered AHL production but not to the ∆psyI mutant. These results indicate that MexEF-OprN is a decisive negative determinant of AHL production and accumulation.
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Affiliation(s)
- Takahiro Sawada
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Miho Eguchi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Seiya Asaki
- Faculty of Agriculture, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Ryota Kashiwagi
- Faculty of Agriculture, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Kousuke Shimomura
- Faculty of Agriculture, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Fumiko Taguchi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan.
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21
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Ca 2+-Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000. J Bacteriol 2018; 200:JB.00538-17. [PMID: 29263098 DOI: 10.1128/jb.00538-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/12/2017] [Indexed: 11/20/2022] Open
Abstract
Two-component systems (TCSs) of bacteria regulate many different aspects of the bacterial life cycle, including pathogenesis. Most TCSs remain uncharacterized, with no information about the signal(s) or regulatory targets and/or role in bacterial pathogenesis. Here, we characterized a TCS in the plant-pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 composed of the histidine kinase CvsS and the response regulator CvsR. CvsSR is necessary for virulence of P. syringae pv. tomato DC3000, since ΔcvsS and ΔcvsR strains produced fewer symptoms than the wild type (WT) and demonstrated reduced growth on multiple hosts. We discovered that expression of cvsSR is induced by Ca2+ concentrations found in leaf apoplastic fluid. Thus, Ca2+ can be added to the list of signals that promote pathogenesis of P. syringae pv. tomato DC3000 during host colonization. Through chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) and global transcriptome analysis (RNA-seq), we discerned the CvsR regulon. CvsR directly activated expression of the type III secretion system regulators, hrpR and hrpS, that regulate P. syringae pv. tomato DC3000 virulence in a type III secretion system-dependent manner. CvsR also indirectly repressed transcription of the extracytoplasmic sigma factor algU and production of alginate. Phenotypic analysis determined that CvsSR inversely regulated biofilm formation, swarming motility, and cellulose production in a Ca2+-dependent manner. Overall, our results show that CvsSR is a key regulatory hub critical for interaction with host plants.IMPORTANCE Pathogenic bacteria must be able to react and respond to the surrounding environment, make use of available resources, and avert or counter host immune responses. Often, these abilities rely on two-component systems (TCSs) composed of interacting proteins that modulate gene expression. We identified a TCS in the plant-pathogenic bacterium Pseudomonas syringae that responds to the presence of calcium, which is an important signal during the plant defense response. We showed that when P. syringae is grown in the presence of calcium, this TCS regulates expression of factors contributing to disease. Overall, our results provide a better understanding of how bacterial pathogens respond to plant signals and control systems necessary for eliciting disease.
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Liu Y, Gokhale CS, Rainey PB, Zhang XX. Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25. Mol Microbiol 2017; 105:589-605. [PMID: 28557013 DOI: 10.1111/mmi.13720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
Abstract
The two-component system CbrAB is the principal regulator for cellular metabolic balance in Pseudomonas fluorescens SBW25 and is necessary for growth on many substrates including xylose. To understand the regulatory linkage between CbrAB and genes for xylose utilization (xut), we performed transposon mutagenesis of ΔcbrB to select for Xut+ suppressors. This led to identification of crc and hfq. Subsequent genetic and biochemical analysis showed that Crc and Hfq are key mediators of succinate-provoked carbon catabolite repression (CCR). Specifically, Crc/Hfq sequentially bind to mRNAs of both the transcriptional activator and structural genes involved in xylose catabolism. However, in the absence of succinate, repression is relieved through competitive binding by two ncRNAs, CrcY and CrcZ, whose expression is activated by CbrAB. These findings provoke a model for CCR in which it is assumed that crc and hfq are functionally complementary, whereas crcY and crcZ are genetically redundant. Inactivation of either crcY or crcZ produced no effects on bacterial fitness in laboratory media, however, results of mathematical modelling predict that the co-existence of crcY and crcZ requires separate functional identity. Finally, we provide empirical evidence that CCR is advantageous in nutrient-complex environments where preferred carbon sources are present at high concentrations but fluctuate in their availability.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand.,New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, 75231 Paris Cedex 05, France
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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23
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Butcher BG, Chakravarthy S, D'Amico K, Stoos KB, Filiatrault MJ. Disruption of the carA gene in Pseudomonas syringae results in reduced fitness and alters motility. BMC Microbiol 2016; 16:194. [PMID: 27558694 PMCID: PMC4997734 DOI: 10.1186/s12866-016-0819-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/19/2016] [Indexed: 02/05/2023] Open
Abstract
Background Pseudomonas syringae infects diverse plant species and is widely used in the study of effector function and the molecular basis of disease. Although the relationship between bacterial metabolism, nutrient acquisition and virulence has attracted increasing attention in bacterial pathology, there is limited knowledge regarding these studies in Pseudomonas syringae. The aim of this study was to investigate the function of the carA gene and the small RNA P32, and characterize the regulation of these transcripts. Results Disruption of the carA gene (ΔcarA) which encodes the predicted small chain of carbamoylphosphate synthetase, resulted in arginine and pyrimidine auxotrophy in Pseudomonas syringae pv. tomato DC3000. Complementation with the wild type carA gene was able to restore growth to wild-type levels in minimal medium. Deletion of the small RNA P32, which resides immediately upstream of carA, did not result in arginine or pyrimidine auxotrophy. The expression of carA was influenced by the concentrations of both arginine and uracil in the medium. When tested for pathogenicity, ΔcarA showed reduced fitness in tomato as well as Arabidopsis when compared to the wild-type strain. In contrast, mutation of the region encoding P32 had minimal effect in planta. ΔcarA also exhibited reduced motility and increased biofilm formation, whereas disruption of P32 had no impact on motility or biofilm formation. Conclusions Our data show that carA plays an important role in providing arginine and uracil for growth of the bacteria and also influences other factors that are potentially important for growth and survival during infection. Although we find that the small RNA P32 and carA are co-transcribed, P32 does not play a role in the phenotypes that carA is required for, such as motility, cell attachment, and virulence. Additionally, our data suggests that pyrimidines may be limited in the apoplastic space of the plant host tomato. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0819-z) contains supplementary material, which is available to authorized users.
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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, USA.,Present Address: Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Rd, Ithaca, NY, USA
| | - Suma Chakravarthy
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Katherine D'Amico
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA.,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
| | - Kari Brossard Stoos
- Department of Health Promotion and Physical Education, School of Health Sciences and Human Performance, Ithaca College, Ithaca, NY, USA
| | - Melanie J Filiatrault
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA. .,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA.
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RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions. BMC Microbiol 2016; 16:155. [PMID: 27430253 PMCID: PMC4950607 DOI: 10.1186/s12866-016-0771-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-sequencing (RNA-seq) to detect sRNAs differentially expressed in Pseudomonas aeruginosa biofilm versus planktonic state. RESULTS A computational algorithm was devised to detect and categorize sRNAs into 5 types: intergenic, intragenic, 5'-UTR, 3'-UTR, and antisense. Here we report a novel RsmY/RsmZ-type sRNA, termed RsmW, in P. aeruginosa up-transcribed in biofilm versus planktonic growth. RNA-Seq, 5'-RACE and Mfold predictions suggest RsmW has a secondary structure with 3 of 7 GGA motifs located on outer stem loops. Northern blot revealed two RsmW binding bands of 400 and 120 bases, suggesting RsmW is derived from the 3'-UTR of the upstream hypothetical gene, PA4570. RsmW expression is elevated in late stationary versus logarithmic growth phase in PB minimal media, at higher temperatures (37 °C versus 28 °C), and in both gacA and rhlR transposon mutants versus wild-type. RsmW specifically binds to RsmA protein in vitro and restores biofilm production and reduces swarming in an rsmY/rsmZ double mutant. PA4570 weakly resembles an RsmA/RsmN homolog having 49 % and 51 % similarity, and 16 % and 17 % identity to RsmA and RsmN amino acid sequences, respectively. PA4570 was unable to restore biofilm and swarming phenotypes in ΔrsmA deficient strains. CONCLUSION Collectively, our study reveals an interesting theme regarding another sRNA regulator of the Rsm system and further unravels the complexities regulating adaptive responses for Pseudomonas species.
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Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
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Harfouche L, Haichar FEZ, Achouak W. Small regulatory RNAs and the fine-tuning of plant–bacteria interactions. THE NEW PHYTOLOGIST 2015; 206:98-106. [PMID: 25866855 DOI: 10.1111/nph.13195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Small regulatory RNAs (sRNAs) play a key role in many physiological and adaptive responses in bacteria. Faced with rapidly changing environments, it is more advantageous for bacteria to use sRNA-mediated responses than regulation by protein transcriptional factors, as sRNAs act at the post-transcriptional level and require less energy and time for their synthesis and turnover. The use of RNA deep sequencing has provided hundreds of sRNA candidates in different bacterial species that interact with plants. Here, we review the most recent results for the involvement of bacterial sRNAs in beneficial as well as deleterious plant–bacteria interactions. We describe the current view for the role of sRNAs, which are suggested to improve competition for both niches and resources in plant-interacting bacteria. These sRNAs also help plant-associated bacteria individually adapt to the rapidly changing conditions to which they are exposed, during different stages of this interaction.
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Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. mBio 2014; 5:e01683-14. [PMID: 25182327 PMCID: PMC4173789 DOI: 10.1128/mbio.01683-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The plant pathogen Pseudomonas syringae pv. syringae B728a grows and survives on leaf surfaces and in the leaf apoplast of its host, bean (Phaseolus vulgaris). To understand the contribution of distinct regulators to B728a fitness and pathogenicity, we performed a transcriptome analysis of strain B728a and nine regulatory mutants recovered from the surfaces and interior of leaves and exposed to environmental stresses in culture. The quorum-sensing regulators AhlR and AefR influenced few genes in planta or in vitro. In contrast, GacS and a downstream regulator, SalA, formed a large regulatory network that included a branch that regulated diverse traits and was independent of plant-specific environmental signals and a plant signal-dependent branch that positively regulated secondary metabolite genes and negatively regulated the type III secretion system. SalA functioned as a central regulator of iron status based on its reciprocal regulation of pyoverdine and achromobactin genes and also sulfur uptake, suggesting a role in the iron-sulfur balance. RetS functioned almost exclusively to repress secondary metabolite genes when the cells were not on leaves. Among the sigma factors examined, AlgU influenced many more genes than RpoS, and most AlgU-regulated genes depended on RpoN. RpoN differentially impacted many AlgU- and GacS-activated genes in cells recovered from apoplastic versus epiphytic sites, suggesting differences in environmental signals or bacterial stress status in these two habitats. Collectively, our findings illustrate a central role for GacS, SalA, RpoN, and AlgU in global regulation in B728a in planta and a high level of plasticity in these regulators’ responses to distinct environmental signals. Leaves harbor abundant microorganisms, all of which must withstand challenges such as active plant defenses and a highly dynamic environment. Some of these microbes can influence plant health. Despite knowledge of individual regulators that affect the fitness or pathogenicity of foliar pathogens, our understanding of the relative importance of various global regulators to leaf colonization is limited. Pseudomonas syringae strain B728a is a plant pathogen and a good colonist of both the surfaces and interior of leaves. This study used global transcript profiles of strain B728a to investigate the complex regulatory network of putative quorum-sensing regulators, two-component regulators, and sigma factors in cells colonizing the leaf surface and leaf interior under stressful in vitro conditions. The results highlighted the value of evaluating these networks in planta due to the impact of leaf-specific environmental signals and suggested signal differences that may enable cells to differentiate surface versus interior leaf habitats.
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29
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Sievers S, Sternkopf Lillebæk EM, Jacobsen K, Lund A, Mollerup MS, Nielsen PK, Kallipolitis BH. A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. Nucleic Acids Res 2014; 42:9383-98. [PMID: 25034691 PMCID: PMC4132741 DOI: 10.1093/nar/gku630] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The multicopy sRNA LhrC of the intracellular pathogen Listeria monocytogenes has been shown to be induced under infection-relevant conditions, but its physiological role and mechanism of action is not understood. In an attempt to pinpoint the exact terms of LhrC expression, cell envelope stress could be defined as a specific inducer of LhrC. In this process, the two-component system LisRK was shown to be indispensable for expression of all five copies of LhrC. lapB mRNA, encoding a cell wall associated protein that was recently identified as an important virulence factor, was disclosed to be directly bound by LhrC leading to an impediment of its translation. Although LhrC binds to Hfq, it does not require the RNA chaperone for stability or lapB mRNA interaction. The mechanism of LhrC-lapB mRNA binding was shown to involve three redundant CU-rich sites and a structural rearrangement in the sRNA. This study represents an extensive depiction of a so far uncharacterized multicopy sRNA and reveals interesting new aspects concerning its regulation, virulence association and mechanism of target binding.
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Affiliation(s)
- Susanne Sievers
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Kirstine Jacobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anja Lund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria Storm Mollerup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Pia Kiil Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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30
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Park SH, Bao Z, Butcher BG, D'Amico K, Xu Y, Stodghill P, Schneider DJ, Cartinhour S, Filiatrault MJ. Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. MICROBIOLOGY-SGM 2014; 160:941-953. [PMID: 24600027 DOI: 10.1099/mic.0.076497-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacteria contain small non-coding RNAs (ncRNAs) that are typically responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they often regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae DC3000, spot 42 (now referred to as spf), was investigated. A putative RpoE binding site was identified upstream of spf in strain DC3000. RpoE is shown to regulate the expression of spf. Also, deletion of spf results in increased sensitivity to hydrogen peroxide compared with the wild-type strain, suggesting that spf plays a role in susceptibility to oxidative stress. Furthermore, expression of alg8 is shown to be influenced by spf, suggesting that this ncRNA plays a role in alginate biosynthesis. Structural and comparative genomic analyses show this ncRNA is well conserved among the pseudomonads. The findings provide new information on the regulation and role of this ncRNA in P. syringae.
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Affiliation(s)
- So Hae Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bronwyn G Butcher
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Katherine D'Amico
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yun Xu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Paul Stodghill
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - David J Schneider
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Samuel Cartinhour
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - M J Filiatrault
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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31
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Hay ID, Wang Y, Moradali MF, Rehman ZU, Rehm BHA. Genetics and regulation of bacterial alginate production. Environ Microbiol 2014; 16:2997-3011. [DOI: 10.1111/1462-2920.12389] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 12/18/2013] [Accepted: 12/22/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Iain D. Hay
- Institute of Fundamental Sciences; Massey University; Palmerston North 4442 New Zealand
| | - Yajie Wang
- Institute of Fundamental Sciences; Massey University; Palmerston North 4442 New Zealand
| | - Mohammed F. Moradali
- Institute of Fundamental Sciences; Massey University; Palmerston North 4442 New Zealand
| | - Zahid U. Rehman
- Institute of Fundamental Sciences; Massey University; Palmerston North 4442 New Zealand
| | - Bernd H. A. Rehm
- Institute of Fundamental Sciences; Massey University; Palmerston North 4442 New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology; Massey University; Palmerston North 4442 New Zealand
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32
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Vargas P, Farias GA, Nogales J, Prada H, Carvajal V, Barón M, Rivilla R, Martín M, Olmedilla A, Gallegos MT. Plant flavonoids target Pseudomonas syringae pv. tomato DC3000 flagella and type III secretion system. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:841-50. [PMID: 24249293 DOI: 10.1111/1758-2229.12086] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/10/2013] [Indexed: 05/23/2023]
Abstract
Flavonoids are among the most abundant plant secondary metabolites involved in plant protection against pathogens, but micro-organisms have developed resistance mechanisms to those compounds. We previously demonstrated that the MexAB-OprM efflux pump mediates resistance of Pseudomonas syringae pv. tomato (Pto) DC3000 to flavonoids, facilitating its survival and the colonization of the host. Here, we have shown that tomato plants respond to Pto infection producing flavonoids and other phenolic compounds. The effects of flavonoids on key traits of this model plant-pathogen bacterium have also been investigated observing that they reduce Pto swimming and swarming because of the loss of flagella, and also inhibited the expression and assembly of a functional type III secretion system. Those effects were more severe in a mutant lacking the MexAB-OprM pump. Our results suggest that flavonoids inhibit the function of the GacS/GacA two-component system, causing a depletion of rsmY RNA, therefore affecting the synthesis of two important virulence factors in Pto DC3000, flagella and the type III secretion system. These data provide new insights into the flavonoid role in the molecular dialog between host and pathogen.
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Affiliation(s)
- Paola Vargas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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Bobrovskyy M, Vanderpool CK. Regulation of bacterial metabolism by small RNAs using diverse mechanisms. Annu Rev Genet 2013; 47:209-32. [PMID: 24016191 DOI: 10.1146/annurev-genet-111212-133445] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria live in many dynamic environments with alternating cycles of feast or famine that have resulted in the evolution of mechanisms to quickly alter their metabolic capabilities. Such alterations often involve complex regulatory networks that modulate expression of genes involved in nutrient uptake and metabolism. A great number of protein regulators of metabolism have been characterized in depth. However, our ever-increasing understanding of the roles played by RNA regulators has revealed far greater complexity to regulation of metabolism in bacteria. Here, we review the mechanisms and functions of selected bacterial RNA regulators and discuss their importance in modulating nutrient uptake as well as primary and secondary metabolic pathways.
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Affiliation(s)
- Maksym Bobrovskyy
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
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34
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Filiatrault MJ, Stodghill PV, Wilson J, Butcher BG, Chen H, Myers CR, Cartinhour SW. CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000. RNA Biol 2013; 10:245-55. [PMID: 23353577 DOI: 10.4161/rna.23019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Small non-coding RNAs (ncRNAs) are important components of many regulatory pathways in bacteria and play key roles in regulating factors important for virulence. Carbon catabolite repression control is modulated by small RNAs (crcZ or crcZ and crcY) in Pseudomonas aeruginosa and Pseudomonas putida. In this study, we demonstrate that expression of crcZ and crcX (formerly designated psr1 and psr2, respectively) is dependent upon RpoN together with the two-component system CbrAB, and is influenced by the carbon source present in the medium in the model plant pathogen Pseudomonas syringae pv tomato DC3000. The distribution of the members of the Crc ncRNA family was also determined by screening available genomic sequences of the Pseudomonads. Interestingly, variable numbers of the Crc family members exist in Pseudomonas genomes. The ncRNAs are comprised of three main subfamilies, named CrcZ, CrcX and CrcY. Most importantly the CrcX subfamily appears to be unique to all P. syringae strains sequenced to date.
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Affiliation(s)
- Melanie J Filiatrault
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA.
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Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 2012; 41:D226-32. [PMID: 23125362 PMCID: PMC3531072 DOI: 10.1093/nar/gks1005] [Citation(s) in RCA: 594] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.
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Affiliation(s)
- Sarah W Burge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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36
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Kong HS, Roberts DP, Patterson CD, Kuehne SA, Heeb S, Lakshman DK, Lydon J. Effect of overexpressing rsmA from Pseudomonas aeruginosa on virulence of select phytotoxin-producing strains of P. syringae. PHYTOPATHOLOGY 2012; 102:575-587. [PMID: 22568815 DOI: 10.1094/phyto-09-11-0267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The GacS/GacA two-component system functions mechanistically in conjunction with global post-transcriptional regulators of the RsmA family to allow pseudomonads and other bacteria to adapt to changing environmental stimuli. Analysis of this Gac/Rsm signal transduction pathway in phytotoxin-producing pathovars of Pseudmonas syringae is incomplete, particularly with regard to rsmA. Our approach in studying it was to overexpress rsmA in P. syringae strains through introduction of pSK61, a plasmid constitutively expressing this gene. Disease and colonization of plant leaf tissue were consistently diminished in all P. syringae strains tested (pv. phaseolicola NPS3121, pv. syringae B728a, and BR2R) when harboring pSK61 relative to these isolates harboring the empty vector pME6031. Phaseolotoxin, syringomycin, and tabtoxin were not produced in any of these strains when transformed with pSK61. Production of protease and pyoverdin as well as swarming were also diminished in all of these strains when harboring pSK61. In contrast, alginate production, biofilm formation, and the hypersensitive response were diminished in some but not all of these isolates under the same growth conditions. These results indicate that rsmA is consistently important in the overarching phenotypes disease and endophtyic colonization but that its role varies with pathovar in certain underpinning phenotypes in the phytotoxin-producing strains of P. syringae.
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Affiliation(s)
- Hye Suk Kong
- Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20852, USA
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37
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Lindeberg M. Genome-enabled perspectives on the composition, evolution, and expression of virulence determinants in bacterial plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:111-132. [PMID: 22559066 DOI: 10.1146/annurev-phyto-081211-173022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
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Affiliation(s)
- Magdalen Lindeberg
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, USA.
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38
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Manzo J, Cocotl-Yañez M, Tzontecomani T, Martínez VM, Bustillos R, Velásquez C, Goiz Y, Solís Y, López L, Fuentes LE, Nuñez C, Segura D, Espín G, Castañeda M. Post-Transcriptional Regulation of the Alginate Biosynthetic Gene algD by the Gac/Rsm System in Azotobacter vinelandii. J Mol Microbiol Biotechnol 2012; 21:147-59. [DOI: 10.1159/000334244] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, Grills G, Schweitzer P, Wang W, Schneider DJ, Cartinhour SW. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One 2011; 6:e29335. [PMID: 22216251 PMCID: PMC3247240 DOI: 10.1371/journal.pone.0029335] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/25/2011] [Indexed: 12/28/2022] Open
Abstract
RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5'-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5'-ends obtained by this method were consistent with results obtained using global RNA-Seq and 5'RACE. As expected, many 5'-ends were positioned a short distance upstream of annotated genes. We also captured 5'-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 5'-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broad foundation for future investigations of regulation at the genomic and single gene levels.
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Affiliation(s)
- Melanie J Filiatrault
- lant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, USA.
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40
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Moreno R, Fonseca P, Rojo F. Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression. Mol Microbiol 2011; 83:24-40. [PMID: 22053874 DOI: 10.1111/j.1365-2958.2011.07912.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Crc protein is a translational repressor that recognizes a specific target at some mRNAs, controlling catabolite repression and co-ordinating carbon metabolism in pseudomonads. In Pseudomonas aeruginosa, the levels of free Crc protein are controlled by CrcZ, a sRNA that sequesters Crc, acting as an antagonist. We show that, in Pseudomonas putida, the levels of free Crc are controlled by CrcZ and by a novel 368 nt sRNA named CrcY. CrcZ and CrcY, which contain six potential targets for Crc, were able to bind Crc specifically in vitro. The levels of CrcZ and CrcY were low under conditions generating a strong catabolite repression, and increased strongly when catabolite repression was absent. Deletion of either crcZ or crcY had no effect on catabolite repression, but the simultaneous absence of both sRNAs led to constitutive catabolite repression that compromised growth on some carbon sources. Overproduction of CrcZ or CrcY significantly reduced repression. We propose that CrcZ and CrcY act in concert, sequestering and modulating the levels of free Crc according to metabolic conditions. The CbrA/CbrB two-component system activated crcZ transcription, but had little effect on crcY. CrcY was detected in P. putida, Pseudomonas fluorescens and Pseudomonas syringae, but not in P. aeruginosa.
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Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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