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Klepa MS, diCenzo GC, Hungria M. Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions. Microbiol Spectr 2024; 12:e0026024. [PMID: 38842312 PMCID: PMC11218460 DOI: 10.1128/spectrum.00260-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024] Open
Abstract
Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.
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Affiliation(s)
- Milena Serenato Klepa
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
- CNPq, Brasília, Brazil
| | | | - Mariangela Hungria
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
- CNPq, Brasília, Brazil
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Long X, Wang X, Mao D, Wu W, Luo Y. A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0351122. [PMID: 36445133 PMCID: PMC9769523 DOI: 10.1128/spectrum.03511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.
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Affiliation(s)
- Xiang Long
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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Mandon K, Nazaret F, Farajzadeh D, Alloing G, Frendo P. Redox Regulation in Diazotrophic Bacteria in Interaction with Plants. Antioxidants (Basel) 2021; 10:antiox10060880. [PMID: 34070926 PMCID: PMC8226930 DOI: 10.3390/antiox10060880] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/23/2022] Open
Abstract
Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance nutrient acquisition. Nitrogen-fixing bacteria, either as endophytes or as endosymbionts, specifically improve the growth and development of plants by supplying them with nitrogen, a key macro-element. Survival and proliferation of these bacteria require their adaptation to the rhizosphere and host plant, which are particular ecological environments. This adaptation highly depends on bacteria response to the Reactive Oxygen Species (ROS), associated to abiotic stresses or produced by host plants, which determine the outcome of the plant-bacteria interaction. This paper reviews the different antioxidant defense mechanisms identified in diazotrophic bacteria, focusing on their involvement in coping with the changing conditions encountered during interaction with plant partners.
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Affiliation(s)
- Karine Mandon
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Fanny Nazaret
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Davoud Farajzadeh
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz 5375171379, Iran;
- Center for International Scientific Studies and Collaboration (CISSC), Ministry of Science, Research and Technology, Tehran 158757788, Iran
| | - Geneviève Alloing
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Pierre Frendo
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
- Correspondence:
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Si M, Chen C, Zhong J, Li X, Liu Y, Su T, Yang G. MsrR is a thiol-based oxidation-sensing regulator of the XRE family that modulates C. glutamicum oxidative stress resistance. Microb Cell Fact 2020; 19:189. [PMID: 33008408 PMCID: PMC7532634 DOI: 10.1186/s12934-020-01444-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/25/2020] [Indexed: 11/10/2022] Open
Abstract
Background Corynebacterium glutamicum thrives under oxidative stress caused by the inevitably extreme environment during fermentation as it harbors antioxidative stress genes. Antioxidant genes are controlled by pathway-specific sensors that act in response to growth conditions. Although many families of oxidation-sensing regulators in C. glutamicum have been well described, members of the xenobiotic-response element (XRE) family, involved in oxidative stress, remain elusive. Results In this study, we report a novel redox-sensitive member of the XER family, MsrR (multiple stress resistance regulator). MsrR is encoded as part of the msrR-3-mst (3-mercaptopyruvate sulfurtransferase) operon; msrR-3-mst is divergent from multidrug efflux protein MFS. MsrR was demonstrated to bind to the intergenic region between msrR-3-mst and mfs. This binding was prevented by an MsrR oxidation-mediated increase in MsrR dimerization. MsrR was shown to use Cys62 oxidation to sense oxidative stress, resulting in its dissociation from the promoter. Elevated expression of msrR-3-mst and mfs was observed under stress. Furthermore, a ΔmsrR mutant strain displayed significantly enhanced growth, while the growth of strains lacking either 3-mst or mfs was significantly inhibited under stress. Conclusion This report is the first to demonstrate the critical role of MsrR-3-MST-MFS in bacterial stress resistance.
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Affiliation(s)
- Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Can Chen
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China
| | - Jingyi Zhong
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xiaona Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Yang Liu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Tao Su
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Ge Yang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
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Narra HP, Sahni A, Alsing J, Schroeder CLC, Golovko G, Nia AM, Fofanov Y, Khanipov K, Sahni SK. Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells. BMC Genomics 2020; 21:665. [PMID: 32977742 PMCID: PMC7519539 DOI: 10.1186/s12864-020-07077-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts, resulting in disease manifestations attributed primarily to endothelial damage or dysfunction. Although rickettsiae are known to undergo evolution through genomic reduction, the mechanisms by which these pathogens regulate their transcriptome to ensure survival in tick vectors and maintenance by transovarial/transstadial transmission, in contrast to their ability to cause debilitating infections in human hosts remain unknown. In this study, we compare the expression profiles of rickettsial sRNAome/transcriptome and determine the transcriptional start sites (TSSs) of R. conorii transcripts during in vitro infection of human and tick host cells. RESULTS We performed deep sequencing on total RNA from Amblyomma americanum AAE2 cells and human microvascular endothelial cells (HMECs) infected with R. conorii. Strand-specific RNA sequencing of R. conorii transcripts revealed the expression 32 small RNAs (Rc_sR's), which were preferentially expressed above the limit of detection during tick cell infection, and confirmed the expression of Rc_sR61, sR71, and sR74 by quantitative RT-PCR. Intriguingly, a total of 305 and 132 R. conorii coding genes were differentially upregulated (> 2-fold) in AAE2 cells and HMECs, respectively. Further, enrichment for primary transcripts by treatment with Terminator 5'-Phosphate-dependent Exonuclease resulted in the identification of 3903 and 2555 transcription start sites (TSSs), including 214 and 181 primary TSSs in R. conorii during the infection to tick and human host cells, respectively. Seventy-five coding genes exhibited different TSSs depending on the host environment. Finally, we also observed differential expression of 6S RNA during host-pathogen and vector-pathogen interactions in vitro, implicating an important role for this noncoding RNA in the regulation of rickettsial transcriptome depending on the supportive host niche. CONCLUSIONS In sum, the findings of this study authenticate the presence of novel Rc_sR's in R. conorii, reveal the first evidence for differential expression of coding transcripts and utilization of alternate transcriptional start sites depending on the host niche, and implicate a role for 6S RNA in the regulation of coding transcriptome during tripartite host-pathogen-vector interactions.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jessica Alsing
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna M Nia
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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de Dios R, Rivas-Marin E, Santero E, Reyes-Ramírez F. Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA. Sci Rep 2020; 10:5177. [PMID: 32198475 PMCID: PMC7083833 DOI: 10.1038/s41598-020-62101-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/20/2020] [Indexed: 12/15/2022] Open
Abstract
Under ever-changing environmental conditions, the General Stress Response (GSR) represents a lifesaver for bacteria in order to withstand hostile situations. In α-proteobacteria, the EcfG-type extracytoplasmic function (ECF) σ factors are the key activators of this response at the transcriptional level. In this work, we address the hierarchical function of the ECF σ factor paralogs EcfG1 and EcfG2 in triggering the GSR in Sphingopyxis granuli TFA and describe the role of EcfG2 as global switch of this response. In addition, we define a GSR regulon for TFA and use in vitro transcription analysis to study the relative contribution of each EcfG paralog to the expression of selected genes. We show that the features of each promoter ultimately dictate this contribution, though EcfG2 always produced more transcripts than EcfG1 regardless of the promoter. These first steps in the characterisation of the GSR in TFA suggest a tight regulation to orchestrate an adequate protective response in order to survive in conditions otherwise lethal.
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Affiliation(s)
- Rubén de Dios
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía. Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.
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Gottschlich L, Geiser P, Bortfeld-Miller M, Field CM, Vorholt JA. Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses. Sci Rep 2019; 9:9404. [PMID: 31253827 PMCID: PMC6599016 DOI: 10.1038/s41598-019-45788-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/12/2019] [Indexed: 01/31/2023] Open
Abstract
The general stress response (GSR) represents an important trait to survive in the environment by leading to multiple stress resistance. In alphaproteobacteria, the GSR is under the transcriptional control of the alternative sigma factor EcfG. Here we performed transcriptome analyses to investigate the genes controlled by EcfG of Sphingomonas melonis Fr1 and the plasticity of this regulation under stress conditions. We found that EcfG regulates genes for proteins that are typically associated with stress responses. Moreover, EcfG controls regulatory proteins, which likely fine-tune the GSR. Among these, we identified a novel negative GSR feedback regulator, termed NepR2, on the basis of gene reporter assays, phenotypic analyses, and biochemical assays. Transcriptional profiling of signaling components upstream of EcfG under complex stress conditions showed an overall congruence with EcfG-regulated genes. Interestingly however, we found that the GSR is transcriptionally linked to the regulation of motility and biofilm formation via the single domain response regulator SdrG and GSR-activating histidine kinases. Altogether, our findings indicate that the GSR in S. melonis Fr1 underlies a complex regulation to optimize resource allocation and resilience in stressful and changing environments.
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Affiliation(s)
- Lisa Gottschlich
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Petra Geiser
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Christopher M Field
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland.
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Fiebig A, Varesio LM, Alejandro Navarreto X, Crosson S. Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light. Mol Microbiol 2019; 112:442-460. [PMID: 31125464 DOI: 10.1111/mmi.14310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 01/23/2023]
Abstract
Extracytoplasmic function (ECF) sigma factors are environmentally responsive transcriptional regulators. In Alphaproteobacteria, σEcfG activates general stress response (GSR) transcription and protects cells from multiple stressors. A phosphorylation-dependent protein partner switching mechanism, involving HWE/HisKA_2-family histidine kinases, underlies σEcfG activation. The identity of these sensor kinases and the signals that regulate them remain largely uncharacterized. We have developed the aerobic anoxygenic photoheterotroph (AAP), Erythrobacter litoralis DSM 8509, as a comparative genetic model to investigate GSR. Using this system, we sought to define the role of visible light and a photosensory HWE kinase, LovK, in regulation of GSR transcription. We identified three HWE kinase genes that collectively control GSR: gsrK and lovK are activators, while gsrP is a repressor. In wild-type cells, GSR transcription is activated in the dark and nearly off in the light, and the opposing activities of gsrK and gsrP are sufficient to modulate GSR transcription in response to illumination. In the absence of gsrK and gsrP, lovK alone is sufficient to activate GSR transcription. lovK is a more robust activator in the dark, and light-dependent regulation by LovK requires that its N-terminal LOV domain be photochemically active. Our studies establish a role for visible light and an ensemble of HWE kinases in light-dependent regulation of GSR transcription in E. litoralis.
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Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Lydia M Varesio
- The Committee on Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Sean Crosson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,The Committee on Microbiology, The University of Chicago, Chicago, IL, 60637, USA
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Sańko-Sawczenko I, Łotocka B, Mielecki J, Rekosz-Burlaga H, Czarnocka W. Transcriptomic Changes in Medicago truncatula and Lotus japonicus Root Nodules during Drought Stress. Int J Mol Sci 2019; 20:E1204. [PMID: 30857310 PMCID: PMC6429210 DOI: 10.3390/ijms20051204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Abstract
Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research, we focused on plants from the Fabaceae family, which has a unique ability for the establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We have presented the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results proved a decrease in the efficiency of nitrogen fixation, as well as extensive changes in plant and bacterial transcriptomes, shortly after watering cessation. We showed for the first time that not only symbiotic plant components but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrated that both M. truncatula and L. japonicus root nodules were susceptible to water deprivation, they indicated significant differences in plant and bacterial response to drought between the tested species, which might be related to the various types of root nodules formed by these species.
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Affiliation(s)
- Izabela Sańko-Sawczenko
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Barbara Łotocka
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Jakub Mielecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Hanna Rekosz-Burlaga
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Weronika Czarnocka
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Hu Y, Hu Q, Wei R, Li R, Zhao D, Ge M, Yao Q, Yu X. The XRE Family Transcriptional Regulator SrtR in Streptococcus suis Is Involved in Oxidant Tolerance and Virulence. Front Cell Infect Microbiol 2019; 8:452. [PMID: 30687648 PMCID: PMC6335249 DOI: 10.3389/fcimb.2018.00452] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen that harbors anti-oxidative stress genes, which have been reported to be associated with virulence. Serial passage has been widely used to obtain phenotypic variant strains to investigate the functions of important genes. In the present study, S. suis serotype 9 strain DN13 was serially passaged in mice 30 times. The virulence of a single colony from passage 10 (SS9-P10) was found to increase by at least 140-fold as indicated by LD50 values, and the increased virulence was stable for single colonies from passage 20 (SS0-P20) and 30 (SS0-P30). Compared to the parental strain, the mouse-adapted strains were more tolerant to oxidative and high temperature stress. Genome-wide analysis of nucleotide variations found that reverse mutations occurred in seven genes, as indicated by BLAST analysis. Three of the reverse mutation genes or their homologs in other bacteria were reported to be virulence-associated, including ideSsuis in S. suis, a homolog of malR of Streptococcus pneumoniae, and a homolog of the prepilin peptidase-encoding gene in Legionella pneumophila. However, these genes were not involved in the stress response. Another gene, srtR (stress response transcriptional regulator), encoding an XRE family transcriptional regulator, which had an internal stop in the parental strain, was functionally restored in the adapted strains. Further analysis of DN13 and SS9-P10-background srtR-knock-out and complementing strains supported the contribution of this gene to stress tolerance in vitro and virulence in mice. srtR and its homologs are widely distributed in Gram-positive bacteria including several important human pathogens such as Enterococcus faecium and Clostridioides difficile, indicating similar functions in these bacteria. Taken together, our study identified the first member of the XRE family of transcriptional regulators that is involved in stress tolerance and virulence. It also provides insight into the mechanism of enhanced virulence after serial passage in experimental animals.
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Affiliation(s)
- Yuli Hu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Qian Hu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Rong Wei
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Runcheng Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Dun Zhao
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Meng Ge
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Qing Yao
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Xinglong Yu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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12
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Ledermann R, Bartsch I, Müller B, Wülser J, Fischer HM. A Functional General Stress Response of Bradyrhizobium diazoefficiens Is Required for Early Stages of Host Plant Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:537-547. [PMID: 29278144 DOI: 10.1094/mpmi-11-17-0284-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phylogenetically diverse bacteria respond to various stress conditions by mounting a general stress response (GSR) resulting in the induction of protection or damage repair functions. In α-proteobacteria, the GSR is induced by a regulatory cascade consisting of the extracytoplasmic function (ECF) σ factor σEcfG, its anti-σ factor NepR, and the anti-anti-σ factor PhyR. We have reported previously that σEcfG and PhyR of Bradyrhizobium diazoefficiens (formerly named Bradyrhizobium japonicum), the nitrogen-fixing root nodule symbiont of soybean and related legumes, are required for efficient symbiosis; however, the precise role of the GSR remained undefined. Here, we analyze the symbiotic defects of a B. diazoefficiens mutant lacking σEcfG by comparing distinct infection stages of enzymatically or fluorescently tagged wild-type and mutant bacteria. Although root colonization and root hair curling were indistinguishable, the mutant was not competitive, and showed delayed development of emerging nodules and only a few infection threads. Consequently, many of the mutant-induced nodules were aborted, empty, or partially colonized. Congruent with these results, we found that σEcfG was active in bacteria present in root-hair-entrapped microcolonies and infection threads but not in root-associated bacteria and nitrogen-fixing bacteroids. We conclude that GSR-controlled functions are crucial for synchronization of infection thread formation, colonization, and nodule development.
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Affiliation(s)
- Raphael Ledermann
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Ilka Bartsch
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Barbara Müller
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Janine Wülser
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Hans-Martin Fischer
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
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Bouillet S, Arabet D, Jourlin-Castelli C, Méjean V, Iobbi-Nivol C. Regulation of σ factors by conserved partner switches controlled by divergent signalling systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:127-139. [PMID: 29393573 DOI: 10.1111/1758-2229.12620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
Partner-Switching Systems (PSS) are widespread regulatory systems, each comprising a kinase-anti-σ, a phosphorylatable anti-σ antagonist and a phosphatase module. The anti-σ domain quickly sequesters or delivers the target σ factor according to the phosphorylation state of the anti-σ antagonist induced by environmental signals. The PSS components are proteins alone or merged to other domains probably to adapt to the input signals. PSS are involved in major cellular processes including stress response, sporulation, biofilm formation and pathogenesis. Surprisingly, the target σ factors are often unknown and the sensing modules acting upstream from the PSS diverge according to the bacterial species. Indeed, they belong to either two-component systems or complex pathways as the stressosome or Chemosensory Systems (CS). Based on a phylogenetic analysis, we propose that the sensing module in Gram-negative bacteria is often a CS.
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Affiliation(s)
- Sophie Bouillet
- Aix-Marseille University, CNRS, BIP UMR7281, 13402 Marseille, France
| | - Dallel Arabet
- Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | | | - Vincent Méjean
- Aix-Marseille University, CNRS, BIP UMR7281, 13402 Marseille, France
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da-Silva JR, Alexandre A, Brígido C, Oliveira S. Can stress response genes be used to improve the symbiotic performance of rhizobia? AIMS Microbiol 2017; 3:365-382. [PMID: 31294167 PMCID: PMC6604987 DOI: 10.3934/microbiol.2017.3.365] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/16/2017] [Indexed: 12/31/2022] Open
Abstract
Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.
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Affiliation(s)
- José Rodrigo da-Silva
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal
| | - Ana Alexandre
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal
| | - Clarisse Brígido
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal
| | - Solange Oliveira
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal
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15
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Kimura Y, Tanaka C, Sasaki K, Sasaki M. High concentrations of intracellular Ap4A and/or Ap5A in developing Myxococcus xanthus cells inhibit sporulation. MICROBIOLOGY-SGM 2017; 163:86-93. [PMID: 27902428 DOI: 10.1099/mic.0.000403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Diadenosine polyphosphates (ApnA) are thought to act as signalling molecules regulating stress responses and biofilm formation in prokaryotes. However, ApnA function in Myxococcus xanthus remains unknown. Here, we investigated the role of ApnA in M. xanthus, using the wild-type and ApnA hydrolase (apaH) mutant strains exposed to various stress conditions. In both wild-type and apaH mutant cells cultured on starvation medium (CF agar), the levels of intracellular diadenosine tetraphosphate (Ap4A) and pentaphosphate (Ap5A) increased several fold during the first 16 h of development and decreased gradually thereafter. The levels of Ap4A and Ap5A in the apaH mutant were about 5- and 11-fold higher than those in the wild-type strain at 16 h, respectively. ApnA hydrolase activity of the wild-type strain increased 1.5-fold during the first 8 h of development, and it then gradually decreased. The apaH mutant formed spores 1-2 days after the wild-type strain did, and the yield of viable spores was 5.5 % of that in the wild-type strain 5 days after inoculation onto CF agar. These results suggest the possibility that high intracellular levels of Ap4A and/or Ap5A may inhibit M. xanthus sporulation at the early stage of development and that the bacteria reduce intracellular Ap4A and Ap5A accumulation through ApnA hydrolase activity.
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Affiliation(s)
- Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Chihiro Tanaka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Katsuho Sasaki
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Masashi Sasaki
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
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16
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Reyes-Pérez A, Vargas MDC, Hernández M, Aguirre-von-Wobeser E, Pérez-Rueda E, Encarnacion S. Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42. Arch Microbiol 2016; 198:847-60. [PMID: 27226009 DOI: 10.1007/s00203-016-1241-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 12/19/2022]
Abstract
Organisms belonging to the genus Rhizobium colonize leguminous plant roots and establish a mutually beneficial symbiosis. Biofilms are structured ecosystems in which microbes are embedded in a matrix of extracellular polymeric substances, and their development is a multistep process. The biofilm formation processes of R. etli CFN42 were analyzed at an early (24-h incubation) and mature stage (72 h), comparing cells in the biofilm with cells remaining in the planktonic stage. A genome-wide microarray analysis identified 498 differentially regulated genes, implying that expression of ~8.3 % of the total R. etli gene content was altered during biofilm formation. In biofilms-attached cells, genes encoding proteins with diverse functions were overexpressed including genes involved in membrane synthesis, transport and chemotaxis, repression of flagellin synthesis, as well as surface components (particularly exopolysaccharides and lipopolysaccharides), in combination with the presence of activators or stimulators of N-acyl-homoserine lactone synthesis This suggests that R. etli is able to sense surrounding environmental conditions and accordingly regulate the transition from planktonic and biofilm growth. In contrast, planktonic cells differentially expressed genes associated with transport, motility (flagellar and twitching) and inhibition of exopolysaccharide synthesis. To our knowledge, this is the first report of nodulation and nitrogen assimilation-related genes being involved in biofilm formation in R. etli. These results contribute to the understanding of the physiological changes involved in biofilm formation by bacteria.
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Affiliation(s)
- Agustín Reyes-Pérez
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico.,Facultad de Ciencias, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Apartado Postal 70-153, C.P. 0415, Cuernavaca, D.F., Mexico.,Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos, 62209, Mexico
| | - María Del Carmen Vargas
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Magdalena Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Eneas Aguirre-von-Wobeser
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A. C. Coatepec 351, El Haya, Xalapa, Veracruz, Mexico
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad s/n, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Sergio Encarnacion
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico.
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17
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López-Leal G, Cevallos MA, Castillo-Ramírez S. Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation. Front Microbiol 2016; 7:581. [PMID: 27199915 PMCID: PMC4843759 DOI: 10.3389/fmicb.2016.00581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/08/2016] [Indexed: 01/11/2023] Open
Abstract
Sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. However, their molecular evolution, especially for the alternative sigma factors, is poorly understood. Here, we analyze the evolutionary forces that have shaped the rpoH sigma factors within the alphaproteobacteria. We found that an ancient duplication gave rise to two major groups of rpoH sigma factors and that after this event horizontal gene transfer (HGT) occurred in rpoH1 group. We also noted that purifying selection has differentially affected distinct parts of the gene; singularly, the gene segment that encodes the region 4.2, which interacts with the −35 motif of the RpoH-dependent genes, has been under relaxed purifying selection. Furthermore, these two major groups are clearly differentiated from one another regarding their promoter selectivity, as rpoH1 is under the transcriptional control of σ70 and σ32, whereas rpoH2 is under the transcriptional control of σ24. Our results suggest a scenario in which HGT, gene loss, variable purifying selection and clear promoter specialization occurred after the ancestral duplication event. More generally, our study offers insights into the molecular evolution of alternative sigma factors and highlights the importance of analyzing not only the coding regions but also the promoter regions.
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Affiliation(s)
- Gamaliel López-Leal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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18
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Abstract
The Alphaproteobacteria uniquely integrate features of two-component signal transduction and alternative σ factor regulation to control transcription of genes that ensure growth and survival across a range of stress conditions. Research over the past decade has led to the discovery of the key molecular players of this general stress response (GSR) system, including the sigma factor σ(EcfG), its anti-σ factor NepR, and the anti-anti-σ factor PhyR. The central molecular event of GSR activation entails aspartyl phosphorylation of PhyR, which promotes its binding to NepR and thereby releases σ(EcfG) to associate with RNAP and direct transcription. Recent studies are providing a new understanding of complex, multilayered sensory networks that activate and repress this central protein partner switch. This review synthesizes our structural and functional understanding of the core GSR regulatory proteins and highlights emerging data that are defining the systems that regulate GSR transcription in a variety of species.
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Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - Jonathan Willett
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
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19
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Thaweethawakorn A, Parks D, So JS, Chang WS. Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum. J Microbiol 2015; 53:526-34. [PMID: 26224455 DOI: 10.1007/s12275-015-5308-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/17/2015] [Accepted: 07/21/2015] [Indexed: 12/11/2022]
Abstract
As a nitrogen-fixing bacterium, Bradyrhizobium japonicum can establish a symbiotic relationship with the soybean plant (Glycine max). To be a successful symbiont, B. japonicum must deal with plant defense responses, such as an oxidative burst. Our previous functional genomics study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (107.8-fold induction) under oxidative stress. Little is known about the underlying mechanisms of how CarQ responds to oxidative stress. In this study, a carQ knock-out mutant was constructed using site-specific mutagenesis to identify the role of carQ in the oxidative response of B. japonicum. The carQ mutant showed a longer generation time than the wild type and exhibited significantly decreased survival at 10 mM H(2)O(2) for 10 min of exposure. Surprisingly, there was no significant difference in expression of oxidative stress-responsive genes such as katG and sod between the wild type and carQ mutant. The mutant also showed a significant increase in susceptibility to H(2)O(2) compared to the wild type in the zone inhibition assay. Nodulation phenotypes of the carQ mutant were distinguishable compared to those of the wild type, including lower numbers of nodules, decreased nodule dry weight, decreased plant dry weight, and a lower nitrogen fixation capability. Moreover, desiccation of mutant cells also resulted in significantly lower percent of survival in both early (after 4 h) and late (after 24 h) desiccation periods. Taken together, this information will provide an insight into the role of the ECF sigma factor in B. japonicum to deal with a plant-derived oxidative burst.
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20
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The general stress response in Alphaproteobacteria. Trends Microbiol 2015; 23:164-71. [DOI: 10.1016/j.tim.2014.12.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022]
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Gourley CR, Petersen E, Harms J, Splitter G. Decreased in vivo virulence and altered gene expression by a Brucella melitensis light-sensing histidine kinase mutant. Pathog Dis 2015; 73:1-8. [PMID: 25132657 DOI: 10.1111/2049-632x.12209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Brucella species utilize diverse virulence factors. Previously, Brucella abortus light-sensing histidine kinase was identified as important for cellular infection. Here, we demonstrate that a Brucella melitensis LOV-HK (BM-LOV-HK) mutant strain has strikingly different gene expression than wild type. General stress response genes including the alternative sigma factor rpoE1 and its anti-anti-sigma factor phyR were downregulated, while flagellar, quorum sensing (QS), and type IV secretion system genes were upregulated in the ΔBM-LOV-HK strain vs. wild type. Contextually, expression results agree with other studies of transcriptional regulators involving ΔrpoE1, ΔphyR, ΔvjbR, and ΔblxR (ΔbabR) Brucella strains. Additionally, deletion of BM-LOV-HK decreases virulence in mice. During C57BL/6 mouse infection, the ΔBM-LOV-HK strain had 2 logs less CFUs in the spleen 3 days postinfection, but similar levels 6 days post infection compared to wild type. Infection of IRF-1(-/-) mice more specifically define ΔBM-LOV-HK strain attenuation with fewer bacteria in spleens and significantly increased survival of mutant vs. wild-type infected IRF-1(-/-) mice. Upregulation of flagella, QS, and VirB genes, along with downregulation of rpoE1 and related sigma factor, rpoH2 (BMEI0280) suggest that BM-LOV-HK modulates both QS and general stress response regulatory components to control Brucella gene expression on a global level.
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Affiliation(s)
- Christopher R Gourley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Erik Petersen
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Jerome Harms
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Gary Splitter
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
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22
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Yu X, Zhang C, Yang L, Zhao L, Lin C, Liu Z, Mao Z. CrdR function in a curdlan-producing Agrobacterium sp. ATCC31749 strain. BMC Microbiol 2015; 15:25. [PMID: 25880528 PMCID: PMC4327974 DOI: 10.1186/s12866-015-0356-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/20/2015] [Indexed: 12/17/2022] Open
Abstract
Background Agrobacterium sp. ATCC31749 is an efficient curdlan producer at low pH and under nitrogen starvation. The helix-turn-helix transcriptional regulatory protein (crdR) essential for curdlan production has been analyzed, but whether crdR directly acts to cause expression of the curdlan biosynthesis operon (crdASC) is uncertain. To elucidate the molecular function of crdR in curdlan biosynthesis, we constructed a crdR knockout mutant along with pBQcrdR and pBQNcrdR vectors with crdR expression driven by a T5 promoter and crdR native promoter, respectively. Also, we constructed a pAG with the green fluorescent protein (GFP) gene driven by a curdlan biosynthetic operon promoter (crdP) to measure the effects of crdR expression on curdlan biosynthesis. Results Compared with wild-type (WT) strain biomass production, the biomass of the crdR knockout mutant was not significantly different in either exponential or stationary phases of growth. Mutant cells were non-capsulated and planktonic and produced significantly less curdlan. WT cells were curdlan-capsulated and aggregated in the stationery phase. pBQcrdR transformed to the WT strain had a 38% greater curdlan yield and pBQcrdR and pBQNcrdR transformed to the crdR mutant strain recovered 18% and 105% curdlan titers of the WT ATCC31749 strain, respectively. Consistent with its function of promoting curdlan biosynthesis, curdlan biosynthetic operon promoter (crdP) controlled GFP expression caused the transgenic strain to have higher GFP relative fluorescence in the WT strain, and no color change was observed with low GFP relative fluorescence in the crdR mutant strain as evidenced by fluorescent microscopy and spectrometric assay. q-RT-PCR revealed that crdR expression in the stationary phase was greater than in the exponential phase, and crdR overexpression in the WT strain increased crdA, crdS, and crdC expression. We also confirmed that purified crdR protein can specifically bind to the crd operon promoter region, and we inferred that crdR directly acts to cause expression of the curdlan biosynthesis operon (crdASC). Conclusions CrdR is a positive transcriptional regulator of the crd operon for promoting curdlan biosynthesis in ATCC31749. The potential binding region of crdR is located within the −98 bp fragment upstream from the crdA start codon Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0356-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoqin Yu
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Chao Zhang
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Liping Yang
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Lamei Zhao
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Chun Lin
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Zhengjie Liu
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China.
| | - Zichao Mao
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China. .,National and Local Joint Engineering Research Center for Screening and Application of Microbial Strains, Kunming, China.
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Complex two-component signaling regulates the general stress response in Alphaproteobacteria. Proc Natl Acad Sci U S A 2014; 111:E5196-204. [PMID: 25404331 DOI: 10.1073/pnas.1410095111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The general stress response (GSR) in Alphaproteobacteria was recently shown to be controlled by a partner-switching mechanism that is triggered by phosphorylation of the response regulator PhyR. Activation of PhyR ultimately results in release of the alternative extracytoplasmic function sigma factor σ(EcfG), which redirects transcription toward the GSR. Little is known about the signal transduction pathway(s) controlling PhyR phosphorylation. Here, we identified the single-domain response regulator (SDRR) SdrG and seven histidine kinases, PakA to PakG, belonging to the HWE/HisKA2 family as positive modulators of the GSR in Sphingomonas melonis Fr1. Phenotypic analyses, epistasis experiments, and in vitro phosphorylation assays indicate that Paks directly phosphorylate PhyR and SdrG, and that SdrG acts upstream of or in concert with PhyR, modulating its activity in a nonlinear pathway. Furthermore, we found that additional SDRRs negatively affect the GSR in a way that strictly requires PhyR and SdrG. Finally, analysis of GSR activation by thermal, osmotic, and oxidative stress indicates that Paks display different degrees of redundancy and that a specific kinase can sense multiple stresses, suggesting that the GSR senses a particular condition as a combination of, rather than individual, molecular cues. This study thus establishes the alphaproteobacterial GSR as a complex and interlinked network of two-component systems, in which multiple histidine kinases converge to PhyR, the phosphorylation of which is, in addition, subject to regulation by several SDRRs. Our finding that most HWE/HisKA2 kinases contribute to the GSR in S. melonis Fr1 opens the possibility that this notion might also be true for other Alphaproteobacteria.
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López-Leal G, Tabche ML, Castillo-Ramírez S, Mendoza-Vargas A, Ramírez-Romero MA, Dávila G. RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock. BMC Genomics 2014; 15:770. [PMID: 25201548 PMCID: PMC4167512 DOI: 10.1186/1471-2164-15-770] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/03/2014] [Indexed: 12/23/2022] Open
Abstract
Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-770) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos C,P 62210, México.
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Perez-Cenci M, Salerno GL. Functional characterization of Synechococcus amylosucrase and fructokinase encoding genes discovers two novel actors on the stage of cyanobacterial sucrose metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:95-102. [PMID: 24908510 DOI: 10.1016/j.plantsci.2014.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 06/03/2023]
Abstract
Plants and most cyanobacteria metabolize sucrose (Suc) with a similar set of enzymes. In Synechococcus sp. PCC 7002, a marine cyanobacterium strain, genes involved in Suc synthesis (spsA and sppA) have been characterized; however, its breakdown was still unknown. Indeed, neither invertase nor sucrose synthase genes, usually found in plants and cyanobacteria, were found in that Synechococcus genome. In the present study, we functionally characterized the amsA gene that codes for an amylosucrase (AMS), a glycoside-hydrolase family 13 enzyme described in bacteria, which may catabolyze Suc in Synechococcus. Additionally, we identified and characterized the frkA gene that codes for a fructokinase (FRK), enzyme that yields fructose-6P, one of the substrates for Suc synthesis. Interestingly, we demonstrate that spsA, sppA, frkA and amsA are grouped in a transcriptional unit that were named Suc cluster, whose expression is increased in response to a salt treatment. This is the first report on the characterization of an AMS and FRK in an oxygenic photosynthetic microorganism, which could be associated with Suc metabolism.
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Affiliation(s)
- Macarena Perez-Cenci
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
| | - Graciela L Salerno
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina.
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A putative bifunctional histidine kinase/phosphatase of the HWE family exerts positive and negative control on the Sinorhizobium meliloti general stress response. J Bacteriol 2014; 196:2526-35. [PMID: 24794560 DOI: 10.1128/jb.01623-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The EcfG-type sigma factor RpoE2 is the regulator of the general stress response in Sinorhizobium meliloti. RpoE2 activity is negatively regulated by two NepR-type anti-sigma factors (RsiA1/A2), themselves under the control of two anti-anti-sigma factors (RsiB1/B2) belonging to the PhyR family of response regulators. The current model of RpoE2 activation suggests that in response to stress, RsiB1/B2 are activated by phosphorylation of an aspartate residue in their receiver domain. Once activated, RsiB1/B2 become able to interact with the anti-sigma factors and release RpoE2, which can then associate with the RNA polymerase to transcribe its target genes. The purpose of this work was to identify and characterize proteins involved in controlling the phosphorylation status of RsiB1/B2. Using in vivo approaches, we show that the putative histidine kinase encoded by the rsiC gene (SMc01507), located downstream from rpoE2, is able to both positively and negatively regulate the general stress response. In addition, our data suggest that the negative action of RsiC results from inhibition of RsiB1/B2 phosphorylation. From these observations, we propose that RsiC is a bifunctional histidine kinase/phosphatase responsible for RsiB1/B2 phosphorylation or dephosphorylation in the presence or absence of stress, respectively. Two proteins were previously proposed to control PhyR phosphorylation in Caulobacter crescentus and Sphingomonas sp. strain FR1. However, these proteins contain a Pfam:HisKA_2 domain of dimerization and histidine phosphotransfer, whereas S. meliloti RsiC harbors a Pfam:HWE_HK domain instead. Therefore, this is the first report of an HWE_HK-containing protein controlling the general stress response in Alphaproteobacteria.
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Gupta N, Gupta A, Kumar S, Mishra R, Singh C, Tripathi AK. Cross-talk between cognate and noncognate RpoE sigma factors and Zn(2+)-binding anti-sigma factors regulates photooxidative stress response in Azospirillum brasilense. Antioxid Redox Signal 2014; 20:42-59. [PMID: 23725220 DOI: 10.1089/ars.2013.5314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS Azospirillum brasilense harbors two redox-sensitive Zinc-binding anti-sigma (ZAS) factors (ChrR1 and ChrR2), which negatively regulate the activity of their cognate extra-cytoplasmic function (ECF) σ factors (RpoE1 and RpoE2) by occluding their binding to the core enzyme. Both pairs of RpoE-ChrR control responses to photooxidative stress. The aim of this study was to investigate whether the two RpoE-ChrR pairs cross-talk while responding to the stress. RESULTS In silico analysis showed a high sequence similarity between ChrR1 and ChrR2 proteins, but differences in redox sensitivity. Using in silico and in vitro methods of protein-protein interaction, we have shown that both ChrR1 and ChrR2 proteins physically bind to their noncognate RpoE proteins. Restoration of the phenotypes of chrR1::Tn5 and chrR2::Km mutants related to carotenoid biosynthesis and photooxidative stress tolerance by expressing chrR1 or chrR2 provided in vivo evidence for the cross-talk. In addition, up- or down-regulation of several identical proteins by expressing chrR1 or chrR2 in the chrR1::Tn5 mutant provided another in vivo evidence for the cross-talk. INNOVATION Although multiple redox-sensitive ZAS anti-σ factors occur in some Gram-positive bacteria, no cross-talk is reported among them. We report here, for the first time, that the two ZAS anti-σ factors of A. brasilense also interact with their noncognate σ factors and affect gene expression. CONCLUSION The two redox-sensitive ZAS anti-σ factors in A. brasilense may interact with their cognate as well as noncognate ECF σ factors to play an important role in redox homeostasis by facilitating recovery from the oxidative stress.
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Affiliation(s)
- Namrata Gupta
- Faculty of Science, School of Biotechnology, Banaras Hindu University , Varanasi, India
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Ramírez M, Guillén G, Fuentes SI, Iñiguez LP, Aparicio-Fabre R, Zamorano-Sánchez D, Encarnación-Guevara S, Panzeri D, Castiglioni B, Cremonesi P, Strozzi F, Stella A, Girard L, Sparvoli F, Hernández G. Transcript profiling of common bean nodules subjected to oxidative stress. PHYSIOLOGIA PLANTARUM 2013; 149:389-407. [PMID: 23432573 DOI: 10.1111/ppl.12040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 06/01/2023]
Abstract
Several environmental stresses generate high amounts of reactive oxygen species (ROS) in plant cells, resulting in oxidative stress. Symbiotic nitrogen fixation (SNF) in the legume-rhizobia symbiosis is sensitive to damage from oxidative stress. Active nodules of the common bean (Phaseolus vulgaris) exposed to the herbicide paraquat (1,1'-dimethyl-4,4'-bipyridinium dichloride hydrate), which stimulates ROS accumulation, exhibited reduced nitrogenase activity and ureide content. We analyzed the global gene response of nodules subjected to oxidative stress using the Bean Custom Array 90K, which includes probes from 30,000 expressed sequence tags (ESTs). A total of 4280 ESTs were differentially expressed in stressed bean nodules; of these, 2218 were repressed. Based on Gene Ontology analysis, these genes were grouped into 42 different biological process categories. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic pathways related to carbon/nitrogen metabolism, which is crucial for nodule function. Quantitative reverse transcription (qRT)-PCR analysis of transcription factor (TF) gene expression showed that 67 TF genes were differentially expressed in nodules exposed to oxidative stress. Putative cis-elements recognized by highly responsive TF were detected in promoter regions of oxidative stress regulated genes. The expression of oxidative stress responsive genes and of genes important for SNF in bacteroids analyzed in stressed nodules revealed that these conditions elicited a transcriptional response.
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Affiliation(s)
- Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Cuernavaca, Mor. 62209, Mexico
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Jans A, Vercruysse M, Gao S, Engelen K, Lambrichts I, Fauvart M, Michiels J. Canonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli. Microbiologyopen 2013; 2:976-87. [PMID: 24311555 PMCID: PMC3892343 DOI: 10.1002/mbo3.137] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/16/2013] [Accepted: 09/23/2013] [Indexed: 01/14/2023] Open
Abstract
A core component of the α-proteobacterial general stress response (GSR) is the extracytoplasmic function (ECF) sigma factor EcfG, exclusively present in this taxonomic class. Half of the completed α-proteobacterial genome sequences contain two or more copies of genes encoding σEcfG-like sigma factors, with the primary copy typically located adjacent to genes coding for a cognate anti-sigma factor (NepR) and two-component response regulator (PhyR). So far, the widespread occurrence of additional, non-canonical σEcfG copies has not satisfactorily been explained. This study explores the hierarchical relation between Rhizobium etli σEcfG1 and σEcfG2, canonical and non-canonical σEcfG proteins, respectively. Contrary to reports in other species, we find that σEcfG1 and σEcfG2 act in parallel, as nodes of a complex regulatory network, rather than in series, as elements of a linear regulatory cascade. We demonstrate that both sigma factors control unique yet also shared target genes, corroborating phenotypic evidence. σEcfG1 drives expression of rpoH2, explaining the increased heat sensitivity of an ecfG1 mutant, while katG is under control of σEcfG2, accounting for reduced oxidative stress resistance of an ecfG2 mutant. We also identify non-coding RNA genes as novel σEcfG targets. We propose a modified model for GSR regulation in R. etli, in which σEcfG1 and σEcfG2 function largely independently. Based on a phylogenetic analysis and considering the prevalence of α-proteobacterial genomes with multiple σEcfG copies, this model may also be applicable to numerous other species.
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Affiliation(s)
- Ann Jans
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, B-3001, Belgium
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Gupta N, Kumar S, Mishra MN, Tripathi AK. A constitutively expressed pair of rpoE2–chrR2 in Azospirillum brasilense Sp7 is required for survival under antibiotic and oxidative stress. Microbiology (Reading) 2013; 159:205-218. [DOI: 10.1099/mic.0.061937-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Namrata Gupta
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221005, India
| | - Santosh Kumar
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221005, India
| | - Mukti Nath Mishra
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221005, India
| | - Anil Kumar Tripathi
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221005, India
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Masloboeva N, Reutimann L, Stiefel P, Follador R, Leimer N, Hennecke H, Mesa S, Fischer HM. Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum. PLoS One 2012; 7:e43421. [PMID: 22916258 PMCID: PMC3420878 DOI: 10.1371/journal.pone.0043421] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022] Open
Abstract
Extracytoplasmic function (ECF) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. The genome of Bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ECF σ factors belonging to nine different ECF σ factor families. The genes for two of them, ecfQ (bll1028) and ecfF (blr3038), are highly induced in response to the reactive oxygen species hydrogen peroxide (H2O2) and singlet oxygen (1O2). The ecfF gene is followed by the predicted anti-σ factor gene osrA (blr3039). Mutants lacking EcfQ, EcfF plus OsrA, OsrA alone, or both σ factors plus OsrA were phenotypically characterized. While the symbiotic properties of all mutants were indistinguishable from the wild type, they showed increased sensitivity to singlet oxygen under free-living conditions. Possible target genes of EcfQ and EcfF were determined by microarray analyses, and candidate genes were compared with the H2O2-responsive regulon. These experiments disclosed that the two σ factors control rather small and, for the most part, distinct sets of genes, with about half of the genes representing 13% of the members of H2O2-responsive regulon. To get more insight into transcriptional regulation of both σ factors, the 5′ ends of ecfQ and ecfF mRNA were determined. The presence of conserved sequence motifs in the promoter region of ecfQ and genes encoding EcfQ-like σ factors in related α-proteobacteria suggests regulation via a yet unknown transcription factor. By contrast, we have evidence that ecfF is autoregulated by transcription from an EcfF-dependent consensus promoter, and its product is negatively regulated via protein-protein interaction with OsrA. Conserved cysteine residues 129 and 179 of OsrA are required for normal function of OsrA. Cysteine 179 is essential for release of EcfF from an EcfF-OsrA complex upon H2O2 stress while cysteine 129 is possibly needed for EcfF-OsrA interaction.
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Affiliation(s)
| | | | | | | | - Nadja Leimer
- ETH, Institute of Microbiology, Zurich, Switzerland
| | | | - Socorro Mesa
- ETH, Institute of Microbiology, Zurich, Switzerland
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Role of Sphingomonas sp. strain Fr1 PhyR-NepR-σEcfG cascade in general stress response and identification of a negative regulator of PhyR. J Bacteriol 2011; 193:6629-38. [PMID: 21949070 DOI: 10.1128/jb.06006-11] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The general stress response in Alphaproteobacteria was recently described to depend on the alternative sigma factor σ(EcfG), whose activity is regulated by its anti-sigma factor NepR. The response regulator PhyR, in turn, regulates NepR activity in a partner-switching mechanism according to which phosphorylation of PhyR triggers sequestration of NepR by the sigma factor-like effector domain of PhyR. Although genes encoding predicted histidine kinases can often be found associated with phyR, little is known about their role in modulation of PhyR phosphorylation status. We demonstrate here that the PhyR-NepR-σ(EcfG) cascade is important for multiple stress resistance and competitiveness in the phyllosphere in a naturally abundant plant epiphyte, Sphingomonas sp. strain Fr1, and provide evidence that the partner switching mechanism is conserved. We furthermore identify a gene, designated phyP, encoding a predicted histidine kinase at the phyR locus as essential. Genetic epistasis experiments suggest that PhyP acts upstream of PhyR, keeping PhyR in an unphosphorylated, inactive state in nonstress conditions, strictly depending on the predicted phosphorylatable site of PhyP, His-341. In vitro experiments show that Escherichia coli inner membrane fractions containing PhyP disrupt the PhyR-P/NepR complex. Together with the fact that PhyP lacks an obvious ATPase domain, these results are in agreement with PhyP functioning as a phosphatase of PhyR, rather than a kinase.
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Appels R, Adelson DL, Moolhuijzen P, Webster H, Barrero R, Bellgard M. Genome studies at the PAG 2011 conference. Funct Integr Genomics 2011; 11:1-11. [PMID: 21360134 DOI: 10.1007/s10142-011-0215-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 01/15/2023]
Abstract
The contents of the plenary lectures presented at the Plant and Animal Genome (PAG) meeting in January 2011 are summarized in order to provide some insights into the advances in plant, animal and microbe genome studies as they impact on our understanding of complex biological systems. The areas of biology covered include the dynamics of genome change, biological recognition processes and the new processes that underpin investment in science. This overview does not attempt to summarize the diversity of activities that are covered during the PAG through workshops, posters and the suppliers of cutting-edge technologies, but reviews major advances in specific research areas.
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Affiliation(s)
- R Appels
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, WA, Australia.
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Vercruysse M, Fauvart M, Jans A, Beullens S, Braeken K, Cloots L, Engelen K, Marchal K, Michiels J. Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli. Genome Biol 2011; 12:R17. [PMID: 21324192 PMCID: PMC3188799 DOI: 10.1186/gb-2011-12-2-r17] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/01/2011] [Accepted: 02/16/2011] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The alarmone (p)ppGpp mediates a global reprogramming of gene expression upon nutrient limitation and other stresses to cope with these unfavorable conditions. Synthesis of (p)ppGpp is, in most bacteria, controlled by RelA/SpoT (Rsh) proteins. The role of (p)ppGpp has been characterized primarily in Escherichia coli and several Gram-positive bacteria. Here, we report the first in-depth analysis of the (p)ppGpp-regulon in an α-proteobacterium using a high-resolution tiling array to better understand the pleiotropic stress phenotype of a relA/rsh mutant. RESULTS We compared gene expression of the Rhizobium etli wild type and rsh (previously rel) mutant during exponential and stationary phase, identifying numerous (p)ppGpp targets, including small non-coding RNAs. The majority of the 834 (p)ppGpp-dependent genes were detected during stationary phase. Unexpectedly, 223 genes were expressed (p)ppGpp-dependently during early exponential phase, indicating the hitherto unrecognized importance of (p)ppGpp during active growth. Furthermore, we identified two (p)ppGpp-dependent key regulators for survival during heat and oxidative stress and one regulator putatively involved in metabolic adaptation, namely extracytoplasmic function sigma factor EcfG2/PF00052, transcription factor CH00371, and serine protein kinase PrkA. CONCLUSIONS The regulatory role of (p)ppGpp in R. etli stress adaptation is far-reaching in redirecting gene expression during all growth phases. Genome-wide transcriptome analysis of a strain deficient in a global regulator, and exhibiting a pleiotropic phenotype, enables the identification of more specific regulators that control genes associated with a subset of stress phenotypes. This work is an important step toward a full understanding of the regulatory network underlying stress responses in α-proteobacteria.
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Affiliation(s)
- Maarten Vercruysse
- Centre of Microbial and Plant Genetics, Katholiek Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Ferooz J, Lemaire J, Delory M, De Bolle X, Letesson JJ. RpoE1, an extracytoplasmic function sigma factor, is a repressor of the flagellar system in Brucella melitensis. MICROBIOLOGY-SGM 2011; 157:1263-1268. [PMID: 21273248 DOI: 10.1099/mic.0.044875-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome of Brucella melitensis contains genes coding for the sigma factors RpoD, RpoN, RpoH1, RpoH2, RpoE1 and RpoE2. Previously published data show that B. melitensis is flagellated and that an rpoE1 mutant overexpresses the flagellar protein FlgE. In this study, we demonstrate that mutation of rpoE1 causes an overexpression of the flagellar genes fliF, flgE, fliC, flaF and flbT, correlating with the production of a longer filament and thereby demonstrating that RpoE1 acts as a flagellar repressor. Moreover, mutation of rpoE1 increases the promoter activity of the flagellar master regulator ftcR, suggesting that RpoE1 acts upstream of ftcR. Together, these data show that RpoE1 represses the flagellar synthesis and filament length in B. melitensis.
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Affiliation(s)
- Jonathan Ferooz
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Julien Lemaire
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Marie Delory
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Xavier De Bolle
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
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Abstract
In addition to stress-specific responses, most bacteria can mount a general stress response (GSR), which protects the cells against a wide range of unspecific stress conditions. The best-understood examples of GSR are the σ(B)-cascade of Bacillus subtilis and the RpoS response in Escherichia coli. While the latter is conserved in many other proteobacteria of the ß-, γ- and δ-clades, RpoS homologues are absent in α-proteobacteria and their GSR has long been a mystery. Recent publications finally unraveled the core of the GSR in this proteobacterial class, which is mediated by EcfG-like σ-factors. EcfG activity is controlled by NepR-like anti-σ factors and PhyR-like proteins that act as anti-anti-σ factors. These unusual hybrid proteins contain an N-terminal EcfG-like domain that acts as a docking interface for NepR, and a C-terminal receiver domain typical for bacterial response regulators. Upon phosphorylation, PhyR titrates NepR away from EcfG, thereby releasing the σ-factor to recruit RNA polymerase and initiate transcription of its target genes. In this issue of Molecular Microbiology, Herrou et al. describe the function and three-dimensional structure of PhyR from Caulobacter crescentus. This structure is key to understanding the mechanism of the reversible, phosphorylation-dependent partner switching module that orchestrates the GSR in α-proteobacteria.
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Affiliation(s)
- Anna Staroń
- Department Biology I, Microbiology, Ludwig-Maximilians-University, Munich, Germany
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Cumino AC, Perez-Cenci M, Giarrocco LE, Salerno GL. The proteins involved in sucrose synthesis in the marine cyanobacteriumSynechococcussp. PCC 7002 are encoded by two genes transcribed from a gene cluster. FEBS Lett 2010; 584:4655-60. [DOI: 10.1016/j.febslet.2010.10.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 10/12/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
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Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by two PhyR-type two-component response regulators. J Bacteriol 2010; 192:2255-65. [PMID: 20154128 DOI: 10.1128/jb.01666-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RpoE2 is an extracytoplasmic function (ECF) sigma factor involved in the general stress response of Sinorhizobium meliloti, the nitrogen-fixing symbiont of the legume plant alfalfa. RpoE2 orthologues are widely found among alphaproteobacteria, where they play various roles in stress resistance and/or host colonization. In this paper, we report a genetic and biochemical investigation of the mechanisms of signal transduction leading to S. meliloti RpoE2 activation in response to stress. We showed that RpoE2 activity is negatively controlled by two paralogous anti-sigma factors, RsiA1 (SMc01505) and RsiA2 (SMc04884), and that RpoE2 activation by stress requires two redundant paralogous PhyR-type response regulators, RsiB1 (SMc01504) and RsiB2 (SMc00794). RsiB1 and RsiB2 do not act at the level of rpoE2 transcription but instead interact with the anti-sigma factors, and we therefore propose that they act as anti-anti-sigma factors to relieve RpoE2 inhibition in response to stress. This model closely resembles a recently proposed model of activation of RpoE2-like sigma factors in Methylobacterium extorquens and Bradyrhizobium japonicum, but the existence of two pairs of anti- and anti-anti-sigma factors in S. meliloti adds an unexpected level of complexity, which may allow the regulatory system to integrate multiple stimuli.
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Staroń A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T. The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Mol Microbiol 2009; 74:557-81. [PMID: 19737356 DOI: 10.1111/j.1365-2958.2009.06870.x] [Citation(s) in RCA: 335] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial for survival. After one- and two-component systems, extracytoplasmic function (ECF) sigma factors - the largest group of alternative sigma factors - represent the third fundamental mechanism of bacterial signal transduction, with about six such regulators on average per bacterial genome. Together with their cognate anti-sigma factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF sigma factor protein family identified more than 40 distinct major groups of ECF sigma factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-sigma factors, genomic context conservation, and potential target promoter motifs. Moreover, this phylogenetic analysis revealed unique features indicating novel mechanisms of ECF-mediated signal transduction. This classification, together with the web tool ECFfinder and the information stored in the Microbial Signal Transduction (MiST) database, provides a comprehensive resource for the analysis of ECF sigma factor-dependent gene regulation.
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Affiliation(s)
- Anna Staroń
- KIT Research Group 11-1, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Gourion B, Sulser S, Frunzke J, Francez-Charlot A, Stiefel P, Pessi G, Vorholt JA, Fischer HM. The PhyR-sigma(EcfG) signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum. Mol Microbiol 2009; 73:291-305. [PMID: 19555458 DOI: 10.1111/j.1365-2958.2009.06769.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PhyR is an unusual type of response regulator consisting of a receiver domain and an extracytoplasmic function (ECF) sigma factor-like domain. It was recently described as a master regulator of general stress response in Methylobacterium extorquens. Orthologues of this regulator are present in essentially all free-living Alphaproteobacteria. In most of them, phyR is genetically closely linked to a gene encoding an ECF sigma factor. Here, we investigate the role of these two regulators in the soybean symbiont Bradyrhizobium japonicum USDA110. Using deletion mutants and phenotypic assays, we showed that PhyR and the ECF sigma factor sigma(EcfG) are involved in heat shock and desiccation resistance upon carbon starvation. Both mutants had symbiotic defects on the plant hosts Glycine max (soybean) and Vigna radiata (mungbean). They induced fewer nodules than the wild type and these nodules were smaller, less pigmented, and their specific nitrogenase activity was drastically reduced 2 or 3 weeks after inoculation. Four weeks after infection, soybean nodule development caught up to a large extent whereas most mungbean nodules remained defective even 5 weeks after infection. Remarkably, both mutants triggered aberrant nodules on the different host plants with ectopically emerging roots. Microarray analysis revealed that PhyR and sigma(EcfG) control congruent regulons suggesting both regulators are part of the same signalling cascade. This finding was further substantiated by in vitro protein-protein interaction studies which are in line with a partner-switching mechanism controlling gene regulation triggered by phosphorylation of PhyR. The large number of genes of unknown function present in the PhyR/sigma(EcfG) regulon and the conspicuous symbiotic phenotype suggest that these regulators are involved in the Bradyrhizobium-legume interaction via yet undisclosed mechanisms.
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