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Liebrenz K, Gómez C, Brambilla S, Frare R, Stritzler M, Maguire V, Ruiz O, Soldini D, Pascuan C, Soto G, Ayub N. Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization. MICROBIAL ECOLOGY 2022; 84:1133-1140. [PMID: 34782938 DOI: 10.1007/s00248-021-01925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.
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Affiliation(s)
- Karen Liebrenz
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Romina Frare
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Vanina Maguire
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Oscar Ruiz
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Diego Soldini
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
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Wülser J, Ernst C, Vetsch D, Emmenegger B, Michel A, Lutz S, Ahrens CH, Vorholt JA, Ledermann R, Fischer HM. Salt- and Osmo-Responsive Sensor Histidine Kinases Activate the Bradyrhizobium diazoefficiens General Stress Response to Initiate Functional Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:604-615. [PMID: 35322688 DOI: 10.1094/mpmi-02-22-0051-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The general stress response (GSR) enables bacteria to sense and overcome a variety of environmental stresses. In alphaproteobacteria, stress-perceiving histidine kinases of the HWE and HisKA_2 families trigger a signaling cascade that leads to phosphorylation of the response regulator PhyR and, consequently, to activation of the GSR σ factor σEcfG. In the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens, PhyR and σEcfG are crucial for tolerance against a variety of stresses under free-living conditions and also for efficient infection of its symbiotic host soybean. However, the molecular players involved in stress perception and activation of the GSR remained largely unknown. In this work, we first showed that a mutant variant of PhyR where the conserved phosphorylatable aspartate residue D194 was replaced by alanine (PhyRD194A) failed to complement the ΔphyR mutant in symbiosis, confirming that PhyR acts as a response regulator. To identify the PhyR-activating kinases in the nitrogen-fixing symbiont, we constructed in-frame deletion mutants lacking single, distinct combinations, or all of the 11 predicted HWE and HisKA_2 kinases, which we named HRXXN histidine kinases HhkA through HhkK. Phenotypic analysis of the mutants and complemented derivatives identified two functionally redundant kinases, HhkA and HhkE, that are required for nodulation competitiveness and during initiation of symbiosis. Using σEcfG-activity reporter strains, we further showed that both HhkA and HhkE activate the GSR in free-living cells exposed to salt and hyperosmotic stress. In conclusion, our data suggest that HhkA and HhkE trigger GSR activation in response to osmotically stressful conditions which B. diazoefficiens encounters during soybean host infection.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Janine Wülser
- Institute of Microbiology, ETH Zurich, CH-8093 Zürich, Switzerland
| | - Chantal Ernst
- Institute of Microbiology, ETH Zurich, CH-8093 Zürich, Switzerland
| | - Dominik Vetsch
- Institute of Microbiology, ETH Zurich, CH-8093 Zürich, Switzerland
| | | | - Anja Michel
- Institute of Microbiology, ETH Zurich, CH-8093 Zürich, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, ETH Zurich, CH-8093 Zürich, Switzerland
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3
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de Dios R, Santero E, Reyes-Ramírez F. The functional differences between paralogous regulators define the control of the General Stress Response in Sphingopyxis granuli TFA. Environ Microbiol 2022; 24:1918-1931. [PMID: 35049124 PMCID: PMC9303464 DOI: 10.1111/1462-2920.15907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 11/30/2022]
Abstract
Sphingopyxis granuli TFA is a contaminant degrading alphaproteobacterium that responds to adverse conditions by inducing the general stress response (GSR), an adaptive response that controls the transcription of a variety of genes to overcome adverse conditions. The core GSR regulators (the response regulator PhyR, the anti‐σ factor NepR and the σ factor EcfG) are duplicated in TFA, being PhyR1 and PhyR2, NepR1 and NepR2 and EcfG1 and EcfG2. Based on multiple genetic, phenotypical and biochemical evidences including in vitro transcription assays, we have assigned distinct functional features to each paralogue and assessed their contribution to the GSR regulation, dictating its timing and the intensity. We show that different stress signals are differentially integrated into the GSR by PhyR1 and PhyR2, therefore producing different levels of GSR activation. We demonstrate in vitro that both NepR1 and NepR2 bind EcfG1 and EcfG2, although NepR1 produces a more stable interaction than NepR2. Conversely, NepR2 interacts with phosphorylated PhyR1 and PhyR2 more efficiently than NepR1. We propose an integrative model where NepR2 would play a dual negative role: it would directly inhibit the σ factors upon activation of the GSR and it would modulate the GSR activity indirectly by titrating the PhyR regulators.
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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 and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide
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Abstract
This article comments on: Tian L, Liu L, Xu S, Deng R, Wu P, Jiang H, Wu G, Chen Y. 2022. A d-pinitol transporter, LjPLT11, regulates plant growth and nodule development in Lotus japonicus. Journal of Experimental Botany 73, 351–365.
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Affiliation(s)
- Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Raphael Ledermann
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Tookmanian EM, Belin BJ, Sáenz JP, Newman DK. The role of hopanoids in fortifying rhizobia against a changing climate. Environ Microbiol 2021; 23:2906-2918. [PMID: 33989442 DOI: 10.1111/1462-2920.15594] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.
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Affiliation(s)
- Elise M Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Brittany J Belin
- Department of Embryology, The Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - James P Sáenz
- B CUBE Center for Molecular Bioengineering, Tatzberg 41, Technische Universität Dresden, Dresden, 01307, Germany
| | - Dianne K Newman
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
- Division of Geology & Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems 2021; 6:6/3/e01237-20. [PMID: 33975972 PMCID: PMC8125078 DOI: 10.1128/msystems.01237-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions varies from nonfixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont, but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy, and increased membrane permeability, leading to a loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics, and transcriptomics along with cytological analyses were used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establishes a poorly efficient symbiosis with A. afraspera despite the full activation of the bacterial symbiotic program. We found molecular signatures of high levels of stress in A. afraspera bacteroids, whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not coevolve with such a host. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Some, but not all, legume plants optimize their return on investment in the symbiosis by imposing on their microsymbionts a terminal differentiation program that increases their symbiotic efficiency but imposes a high level of stress and drastically reduces their viability. We combined multi-omics with physiological analyses to show that the symbiotic couple formed by Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera, in which the host and symbiont did not evolve together, is functional but displays a low symbiotic efficiency associated with a disconnection of terminal bacteroid differentiation features.
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7
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Pérez-Giménez J, Iturralde ET, Torres Tejerizo G, Quelas JI, Krol E, Borassi C, Becker A, Estevez JM, Lodeiro AR. A Stringent-Response-Defective Bradyrhizobium diazoefficiens Strain Does Not Activate the Type 3 Secretion System, Elicits an Early Plant Defense Response, and Circumvents NH 4NO 3-Induced Inhibition of Nodulation. Appl Environ Microbiol 2021; 87:e02989-20. [PMID: 33608284 PMCID: PMC8091029 DOI: 10.1128/aem.02989-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
When subjected to nutritional stress, bacteria modify their amino acid metabolism and cell division activities by means of the stringent response, which is controlled by the Rsh protein in alphaproteobacteria. An important group of alphaproteobacteria are the rhizobia, which fix atmospheric N2 in symbiosis with legume plants. Although nutritional stress is common for rhizobia while infecting legume roots, the stringent response has scarcely been studied in this group of soil bacteria. In this report, we obtained a mutant with a kanamycin resistance insertion in the rsh gene of Bradyrhizobium diazoefficiens, the N2-fixing symbiont of soybean. This mutant was defective for type 3 secretion system induction, plant defense suppression at early root infection, and nodulation competition. Furthermore, the mutant produced smaller nodules, although with normal morphology, which led to lower plant biomass production. Soybean (Glycine max) genes GmRIC1 and GmRIC2, involved in autoregulation of nodulation, were upregulated in plants inoculated with the mutant under the N-free condition. In addition, when plants were inoculated in the presence of 10 mM NH4NO3, the mutant produced nodules containing bacteroids, and GmRIC1 and GmRIC2 were downregulated. The rsh mutant released more auxin to the culture supernatant than the wild type, which might in part explain its symbiotic behavior in the presence of combined N. These results indicate that the B. diazoefficiens stringent response integrates into the plant defense suppression and regulation of nodulation circuits in soybean, perhaps mediated by the type 3 secretion system.IMPORTANCE The symbiotic N2 fixation carried out between prokaryotic rhizobia and legume plants performs a substantial contribution to the N cycle in the biosphere. This symbiotic association is initiated when rhizobia infect and penetrate the root hairs, which is followed by the growth and development of root nodules, within which the infective rhizobia are established and protected. Thus, the nodule environment allows the expression and function of the enzyme complex that catalyzes N2 fixation. However, during early infection, the rhizobia find a harsh environment while penetrating the root hairs. To cope with this nuisance, the rhizobia mount a stress response known as the stringent response. In turn, the plant regulates nodulation in response to the presence of alternative sources of combined N in the surrounding medium. Control of these processes is crucial for a successful symbiosis, and here we show how the rhizobial stringent response may modulate plant defense suppression and the networks of regulation of nodulation.
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Affiliation(s)
- Julieta Pérez-Giménez
- IBBM, Facultad de Ciencias Exactas, CCT-La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Esteban T Iturralde
- IBBM, Facultad de Ciencias Exactas, CCT-La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- IBBM, Facultad de Ciencias Exactas, CCT-La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan Ignacio Quelas
- IBBM, Facultad de Ciencias Exactas, CCT-La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Cecilia Borassi
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - José M Estevez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aníbal R Lodeiro
- IBBM, Facultad de Ciencias Exactas, CCT-La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- Laboratorio de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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Ledermann R, Emmenegger B, Couzigou JM, Zamboni N, Kiefer P, Vorholt JA, Fischer HM. Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection. mBio 2021; 12:e00390-21. [PMID: 33785618 PMCID: PMC8092242 DOI: 10.1128/mbio.00390-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/24/2023] Open
Abstract
When engaging in symbiosis with legume hosts, rhizobia are confronted with environmental changes, including nutrient availability and stress exposure. Genetic circuits allow responding to these environmental stimuli to optimize physiological adaptations during the switch from the free-living to the symbiotic life style. A pivotal regulatory system of the nitrogen-fixing soybean endosymbiont Bradyrhizobium diazoefficiens for efficient symbiosis is the general stress response (GSR), which relies on the alternative sigma factor σEcfG However, the GSR-controlled process required for symbiosis has not been identified. Here, we demonstrate that biosynthesis of trehalose is under GSR control, and mutants lacking the respective biosynthetic genes otsA and/or otsB phenocopy GSR-deficient mutants under symbiotic and selected free-living stress conditions. The role of trehalose as a cytoplasmic chemical chaperone and stress protectant can be functionally replaced in an otsA or otsB mutant by introducing heterologous genetic pathways for biosynthesis of the chemically unrelated compatible solutes glycine betaine and (hydroxy)ectoine. Alternatively, uptake of exogenously provided trehalose also restores efficient symbiosis and tolerance to hyperosmotic and hyperionic stress of otsA mutants. Hence, elevated cytoplasmic trehalose levels resulting from GSR-controlled biosynthesis are crucial for B. diazoefficiens cells to overcome adverse conditions during early stages of host infection and ensure synchronization with root nodule development.IMPORTANCE The Bradyrhizobium-soybean symbiosis is of great agricultural significance and serves as a model system for fundamental research in bacterium-plant interactions. While detailed molecular insight is available about mutual recognition and early nodule organogenesis, our understanding of the host-imposed conditions and the physiology of infecting rhizobia during the transition from a free-living state in the rhizosphere to endosymbiotic bacteroids is currently limited. In this study, we show that the requirement of the rhizobial general stress response (GSR) during host infection is attributable to GSR-controlled biosynthesis of trehalose. Specifically, trehalose is crucial for an efficient symbiosis by acting as a chemical chaperone to protect rhizobia from osmostress during host infection.
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Affiliation(s)
| | | | | | - Nicola Zamboni
- ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Patrick Kiefer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
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Abstract
Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs which host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate global reprogramming of physiological processes and rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and more recently computational modelling. Here we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth-arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.
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Acosta-Jurado S, Alias-Villegas C, Navarro-Gómez P, Almozara A, Rodríguez-Carvajal MA, Medina C, Vinardell JM. Sinorhizobium fredii HH103 syrM inactivation affects the expression of a large number of genes, impairs nodulation with soybean and extends the host-range to Lotus japonicus. Environ Microbiol 2020; 22:1104-1124. [PMID: 31845498 DOI: 10.1111/1462-2920.14897] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022]
Abstract
Sinorhizobium fredii HH103 RifR is a broad host-range rhizobial strain able to nodulate with soybean and Lotus burttii, but it is ineffective with L. japonicus. Here, we study the role of the HH103 RifR SyrM protein in the regulation of gene expression and its relevance in symbiosis with those three legumes. RNAseq analyses show that HH103 SyrM is an important transcriptional regulator not only in the presence of inducer flavonoids but also in its absence. Lack of SyrM increases Nod factors production and decreases genistein-mediated repression of exopolysaccharide production in HH103. In symbiosis, mutation of syrM partially impaired interaction with soybean but improves effectiveness with L. burttii and extends the host-rage to L. japonicus Gifu. In addition, HH103 syrM mutants enter in both Lotus species by infection threads, whereas HH103 uses the more primitive intercellular infection to enter into L. burttii roots These symbiotic phenotypes were previously observed in two other HH103 mutants affected in symbiotic regulators, nodD2 and nolR, revealing that in S. fredii HH103 numerous transcriptional regulators finely modulate symbiotic gene expression.
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Affiliation(s)
- Sebastián Acosta-Jurado
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
| | - Cynthia Alias-Villegas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
| | - Pilar Navarro-Gómez
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
| | - Andrés Almozara
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
| | - Miguel A Rodríguez-Carvajal
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P. 41012, Sevilla, Spain
| | - Carlos Medina
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
| | - José-María Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P, 41012, Sevilla, Spain
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11
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Benezech C, Doudement M, Gourion B. Legumes tolerance to rhizobia is not always observed and not always deserved. Cell Microbiol 2019; 22:e13124. [DOI: 10.1111/cmi.13124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Claire Benezech
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
| | - Maëva Doudement
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
| | - Benjamin Gourion
- LIPM, Université de Toulouse, INRA, CNRS Castanet‐Tolosan France
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Belin BJ, Tookmanian EM, de Anda J, Wong GCL, Newman DK. Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1415-1428. [PMID: 31170026 PMCID: PMC7583662 DOI: 10.1094/mpmi-04-19-0111-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here, we demonstrate that the nitrogen-fixation defect conferred by extended hopanoid loss can be fully explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen-fixation levels. Using a single-nodule tracking approach to quantify A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and the presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
| | - Elise M. Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology
| | - Jaime de Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, and California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, U.S.A
| | - Gerard C. L. Wong
- Division of Geological & Planetary Sciences, California Institute of Technology
| | - Dianne K. Newman
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
- Division of Geological & Planetary Sciences, California Institute of Technology
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From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant. J Bacteriol 2019; 201:JB.00191-19. [PMID: 31182497 DOI: 10.1128/jb.00191-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.
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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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Wippel K, Long SR. Symbiotic Performance of Sinorhizobium meliloti Lacking ppGpp Depends on the Medicago Host Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:717-728. [PMID: 30576265 DOI: 10.1094/mpmi-11-18-0306-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Host specificity in the root-nodule symbiosis between legumes and rhizobia is crucial for the establishment of a successful interaction and ammonia provision to the plant. The specificity is mediated by plant-bacterial signal exchange during early stages of interaction. We observed that a Sinorhizobium meliloti mutant ∆relA, which is deficient in initiating the bacterial stringent response, fails to nodulate Medicago sativa (alfalfa) but successfully infects Medicago truncatula. We used biochemical, histological, transcriptomic, and imaging approaches to compare the behavior of the S. meliloti ∆relA mutant and wild type (WT) on the two plant hosts. ∆relA performed almost WT-like on M. truncatula, except for reduced nitrogen-fixation capacity and a disorganized positioning of bacteroids within nodule cells. In contrast, ∆relA showed impaired root colonization on alfalfa and failed to infect nodule primordia. Global transcriptome analyses of ∆relA cells treated with the alfalfa flavonoid luteolin and of mature nodules induced by the mutant on M. truncatula revealed normal nod gene expression but overexpression of exopolysaccharide biosynthesis genes and a slight suppression of plant defense-like reactions. Many RelA-dependent transcripts overlap with the hypo-osmolarity-related FeuP regulon or are characteristic of stress responses. Based on our findings, we suggest that RelA is not essential until the late stages of symbiosis with M. truncatula, in which it may be involved in processes that optimize nitrogen fixation.
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Affiliation(s)
- Kathrin Wippel
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Sharon R Long
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
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Cherni AE, Perret X. Deletion of rRNA Operons of Sinorhizobium fredii Strain NGR234 and Impact on Symbiosis With Legumes. Front Microbiol 2019; 10:154. [PMID: 30814981 PMCID: PMC6381291 DOI: 10.3389/fmicb.2019.00154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/22/2019] [Indexed: 01/08/2023] Open
Abstract
During their lifecycle, from free-living soil bacteria to endosymbiotic nitrogen-fixing bacteroids of legumes, rhizobia must colonize, and cope with environments where nutrient concentrations and compositions vary greatly. Bacterial colonization of legume rhizospheres and of root surfaces is subject to a fierce competition for plant exudates. By contrast root nodules offer to rhizobia sheltered nutrient-rich environments within which the cells that successfully propagated via infection threads can rapidly multiply. To explore the effects on symbiosis of a slower rhizobia growth and metabolism, we deleted one or two copies of the three functional rRNA operons of the promiscuous Sinorhizobium fredii strain NGR234 and examined the impact of these mutations on free-living and symbiotic lifestyles. Strains with two functional rRNA operons (NGRΔrRNA1 and NGRΔrRNA3) grew almost as rapidly as NGR234, and NGRΔrRNA1 was as proficient as the parent strain on all of the five legume species tested. By contrast, the NGRΔrRNA1,3 double mutant, which carried a single rRNA operon and grew significantly slower than NGR234, had a reduced symbiotic proficiency on Cajanus cajan, Macroptilium atropurpureum, Tephrosia vogelii, and Vigna unguiculata. In addition, while NGRΔrRNA1 and NGR234 equally competed for nodulation of V. unguiculata, strain NGRΔrRNA1,3 was clearly outcompeted by wild-type. Surprisingly, on Leucaena leucocephala, NGRΔrRNA1,3 was the most proficient strain and competed equally NGR234 for nodule occupation. Together, these results indicate that for strains with otherwise identical repertoires of symbiotic genes, a faster growth on roots and/or inside plant tissues may contribute to secure access to nodules of some hosts. By contrast, other legumes such as L. leucocephala appear as less selective and capable of providing symbiotic environments susceptible to accommodate strains with a broader spectrum of competences.
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Affiliation(s)
- Ala Eddine Cherni
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
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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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Abstract
Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress. Bacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF σs) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti carries genes for 11 ECF-like σs (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entire S. meliloti cohort of ECF σs. We discovered new targets for individual σs, confirmed others by overexpressing individual ECF σs, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF σ gene and its demonstrated or putative anti-σ gene and also a strain in which all 11 ECF σ and anti-σ genes were deleted. This all-ECF σ deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF σs were required for symbiosis on the host plants Medicago sativa and Medicago truncatula: the strain deleted for all ECF σ and anti-σ genes was symbiotically normal. IMPORTANCE Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.
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