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Werner N, Werten S, Hoppen J, Palm GJ, Göttfert M, Hinrichs W. The induction mechanism of the flavonoid-responsive regulator FrrA. FEBS J 2022; 289:507-518. [PMID: 34314575 DOI: 10.1111/febs.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation-promoting genetic programme in the presence of host-produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid-responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR-like fold whose DNA-binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C-H contacts to the π-system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA-binding domain and the absence of structural change upon ligand binding are corroborated by small-angle X-ray scattering (SAXS) experiments in solution. Together with a model of the promoter-bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA-binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.
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Affiliation(s)
- Nadine Werner
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Sebastiaan Werten
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Jens Hoppen
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Gottfried J Palm
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
| | - Michael Göttfert
- Institute of Genetics, Dresden University of Technology, Germany
| | - Winfried Hinrichs
- Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany
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2
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Piromyou P, Nguyen HP, Songwattana P, Boonchuen P, Teamtisong K, Tittabutr P, Boonkerd N, Alisha Tantasawat P, Göttfert M, Okazaki S, Teaumroong N. The Bradyrhizobium diazoefficiens type III effector NopE modulates the regulation of plant hormones towards nodulation in Vigna radiata. Sci Rep 2021; 11:16604. [PMID: 34400661 PMCID: PMC8367979 DOI: 10.1038/s41598-021-95925-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022] Open
Abstract
Host-specific legume-rhizobium symbiosis is strictly controlled by rhizobial type III effectors (T3Es) in some cases. Here, we demonstrated that the symbiosis of Vigna radiata (mung bean) with Bradyrhizobium diazoefficiens USDA110 is determined by NopE, and this symbiosis is highly dependent on host genotype. NopE specifically triggered incompatibility with V. radiata cv. KPS2, but it promoted nodulation in other varieties of V. radiata, including KPS1. Interestingly, NopE1 and its paralogue NopE2, which exhibits calcium-dependent autocleavage, yield similar results in modulating KPS1 nodulation. Furthermore, NopE is required for early infection and nodule organogenesis in compatible plants. Evolutionary analysis revealed that NopE is highly conserved among bradyrhizobia and plant-associated endophytic and pathogenic bacteria. Our findings suggest that V. radiata and B. diazoefficiens USDA110 may use NopE to optimize their symbiotic interactions by reducing phytohormone-mediated ETI-type (PmETI) responses via salicylic acid (SA) biosynthesis suppression.
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Affiliation(s)
- Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Hien P Nguyen
- Institute of Global Innovation Research (IGIR), Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8538, Japan.,Agricultural Research Service (ARS), The U.S. Department of Agriculture (USDA), Beltsville Agricultural Research Center (BARC), Beltsville, MD, 20705, USA
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Piyada Alisha Tantasawat
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Michael Göttfert
- Institut Für Genetik, Technische Universität Dresden, Helmholtzstrasse 10, 01062, Dresden, Germany
| | - Shin Okazaki
- Graduate School of Agriculture, TUAT, Fuchu, Tokyo, 183-8509, Japan.
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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3
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Bechtaoui N, Raklami A, Tahiri AI, Benidire L, El Alaoui A, Meddich A, Göttfert M, Oufdou K. Characterization of plant growth promoting rhizobacteria and their benefits on growth and phosphate nutrition of faba bean and wheat. Biol Open 2019; 8:bio043968. [PMID: 31278162 PMCID: PMC6679402 DOI: 10.1242/bio.043968] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/27/2019] [Indexed: 11/20/2022] Open
Abstract
In recent years, more attention has been paid to plant growth promoting (PGP) rhizobacteria use as a biofertilizer alternative to chemical fertilizers, which might cause damage to the environment. The main objective of this work was to evaluate the field application of PGP bacteria and rhizobial strains on the productivity of two food crops extensively used in Morocco; Vicia faba L. and Triticum durum L. A field experiment with four treatments was designed: (1) control without inoculation, (2) PGP bacteria alone (P), (3) rhizobia alone (R) and (4) a mixture of PGP-rhizobia (PR). Furthermore, the PGP strains were tested for their ability to solubilize complex mineral phosphorus and potassium and for their production of indole acetic acid and exopolysaccharides. The strains showed several plant growth promoting traits. Field inoculation by these rhizobacteria improved phosphorus uptake and the agronomic parameters of faba bean and wheat plants, such as biomass of shoots and roots, as well as the weight of bean pods and wheat spikes. The most pronounced effect was displayed by rhizobial strains or the combination of PGP-rhizobia. The rhizobacterial inoculation significantly stimulated the growth of both crops and could be used as potential biofertilizers to optimize growth and phosphorus retention capacity.
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Affiliation(s)
- Noura Bechtaoui
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Anas Raklami
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- Laboratory of Biotechnology and Plant Physiology, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Abdel-Ilah Tahiri
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- Laboratory of Biotechnology and Plant Physiology, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Loubna Benidire
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Abdelkhalek El Alaoui
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Abdelilah Meddich
- Laboratory of Biotechnology and Plant Physiology, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Michael Göttfert
- Technische Universität Dresden, Institut für Genetik, Helmholtzstr. 10, D-01069 Dresden Germany
| | - Khalid Oufdou
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
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Hoyer E, Knöppel J, Liebmann M, Steppert M, Raiwa M, Herczynski O, Hanspach E, Zehner S, Göttfert M, Tsushima S, Fahmy K, Oertel J. Calcium binding to a disordered domain of a type III-secreted protein from a coral pathogen promotes secondary structure formation and catalytic activity. Sci Rep 2019; 9:7115. [PMID: 31068617 PMCID: PMC6506597 DOI: 10.1038/s41598-019-42898-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/10/2019] [Indexed: 01/05/2023] Open
Abstract
Strains of the Gram-negative bacterium Vibrio coralliilyticus cause the bleaching of corals due to decomposition of symbiotic microalgae. The V. coralliilyticus strain ATCC BAA-450 (Vc450) encodes a type III secretion system (T3SS). The gene cluster also encodes a protein (locus tag VIC_001052) with sequence homology to the T3SS-secreted nodulation proteins NopE1 and NopE2 of Bradyrhizobium japonicum (USDA110). VIC_001052 has been shown to undergo auto-cleavage in the presence of Ca2+ similar to the NopE proteins. We have studied the hitherto unknown secondary structure, Ca2+-binding affinity and stoichiometry of the “metal ion-inducible autocleavage” (MIIA) domain of VIC_001052 which does not possess a classical Ca2+-binding motif. CD and fluorescence spectroscopy revealed that the MIIA domain is largely intrinsically disordered. Binding of Ca2+ and other di- and trivalent cations induced secondary structure and hydrophobic packing after partial neutralization of the highly negatively charged MIIA domain. Mass spectrometry and isothermal titration calorimetry showed two Ca2+-binding sites which promote structure formation with a total binding enthalpy of −110 kJ mol−1 at a low micromolar Kd. Putative binding motifs were identified by sequence similarity to EF-hand domains and their structure analyzed by molecular dynamics simulations. The stoichiometric Ca2+-dependent induction of structure correlated with catalytic activity and may provide a “host-sensing” mechanism that is shared among pathogens that use a T3SS for efficient secretion of disordered proteins.
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Affiliation(s)
- Elisabeth Hoyer
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany.,Ludwig-Maximilians-Universität München, Department of Biology I, Microbiology, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Julius Knöppel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Martina Liebmann
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Steppert
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Manuel Raiwa
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Olivia Herczynski
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Erik Hanspach
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Susanne Zehner
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Göttfert
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Satoru Tsushima
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Jana Oertel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany.
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5
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Piromyou P, Songwattana P, Teamtisong K, Tittabutr P, Boonkerd N, Tantasawat PA, Giraud E, Göttfert M, Teaumroong N. Mutualistic co-evolution of T3SSs during the establishment of symbiotic relationships between Vigna radiata and Bradyrhizobia. Microbiologyopen 2019; 8:e00781. [PMID: 30628192 PMCID: PMC6612562 DOI: 10.1002/mbo3.781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
This study supports the idea that the evolution of type III secretion system (T3SS) is one of the factors that controls Vigna radiata-bradyrhizobia symbiosis. Based on phylogenetic tree data and gene arrangements, it seems that the T3SSs of the Thai bradyrhizobial strains SUTN9-2, DOA1, and DOA9 and the Senegalese strain ORS3257 may share the same origin. Therefore, strains SUTN9-2, DOA1, DOA9, and ORS3257 may have evolved their T3SSs independently from other bradyrhizobia, depending on biological and/or geological events. For functional analyses, the rhcJ genes of ORS3257, SUTN9-2, DOA9, and USDA110 were disrupted. These mutations had cultivar-specific effects on nodulation properties. The T3SSs of ORS3257 and DOA9 showed negative effects on V. radiata nodulation, while the T3SS of SUTN9-2 showed no effect on V. radiata symbiosis. In the roots of V. radiata CN72, the expression levels of the PR1 gene after inoculation with ORS3257 and DOA9 were significantly higher than those after inoculation with ORS3257 ΩT3SS, DOA9 ΩT3SS, and SUTN9-2. The T3Es from ORS3257 and DOA9 could trigger PR1 expression, which ultimately leads to abort nodulation. In contrast, the T3E from SUTN9-2 reduced PR1 expression. It seems that the mutualistic relationship between SUTN9-2 and V. radiata may have led to the selection of the most well-adapted combination of T3SS and symbiotic bradyrhizobial genotype.
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Affiliation(s)
- Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological EquipmentSuranaree University of TechnologyNakhon RatchasimaThailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Piyada Alisha Tantasawat
- School of Crop Production Technology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Eric Giraud
- IRD, Laboratory of Tropical and Mediterranean SymbiosesUMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de BaillarguetMontpellierFrance
| | | | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
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6
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Nguyen HP, Ratu STN, Yasuda M, Göttfert M, Okazaki S. InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species. Front Microbiol 2018; 9:3155. [PMID: 30619219 PMCID: PMC6305347 DOI: 10.3389/fmicb.2018.03155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Bradyrhizobium elkanii USDA61 is incompatible with mung bean (Vigna radiata cv. KPS1) and soybean (Glycine max cv. BARC2) and unable to nodulate either plant. This incompatibility is due to the presence of a functional type III secretion system (T3SS) that translocates effector protein into host cells. We previously identified five genes in B. elkanii that are responsible for its incompatibility with KPS1 plants. Among them, a novel gene designated as innB exhibited some characteristics associated with the T3SS and was found to be responsible for the restriction of nodulation on KPS1. In the present study, we further characterized innB by analysis of gene expression, protein secretion, and symbiotic phenotypes. The innB gene was found to encode a hypothetical protein that is highly conserved among T3SS-harboring rhizobia. Similar to other rhizobial T3SS-associated genes, the expression of innB was dependent on plant flavonoids and a transcriptional regulator TtsI. The InnB protein was secreted via the T3SS and was not essential for secretion of other nodulation outer proteins. In addition, T3SS-dependent translocation of InnB into nodule cells was confirmed by an adenylate cyclase assay. According to inoculation tests using several Vigna species, InnB promoted nodulation of at least one V. mungo cultivar. These results indicate that innB encodes a novel type III effector controlling symbiosis with Vigna species.
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Affiliation(s)
- Hien P Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Safirah T N Ratu
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Michiko Yasuda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Michael Göttfert
- Institute of Genetics, Technische Universität Dresden, Dresden, Germany
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
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7
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Durán D, Imperial J, Palacios J, Ruiz-Argüeso T, Göttfert M, Zehner S, Rey L. Characterization of a novel MIIA domain-containing protein (MdcE) in Bradyrhizobium spp. FEMS Microbiol Lett 2018; 365:4769627. [PMID: 29281013 DOI: 10.1093/femsle/fnx276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/20/2017] [Indexed: 11/14/2022] Open
Abstract
Several genes coding for proteins with metal ion-inducible autocleavage (MIIA) domains were identified in type III secretion system tts gene clusters from draft genomes of recently isolated Bradyrhizobium spp. MIIA domains have been first described in the effectors NopE1 and NopE2 of Bradyrhizobium diazoefficiens USDA 110. All identified genes are preceded by tts box promoter motifs. The identified proteins contain one or two MIIA domains. A phylogenetic analysis of 35 MIIA domain sequences from 16 Bradyrhizobium strains revealed four groups. The protein from Bradyrhizobium sp. LmjC strain contains a single MIIA domain and was designated MdcE (MdcELmjC). It was expressed as a fusion to maltose-binding protein (MalE) in Escherichia coli and subsequently purified by affinity chromatography. Recombinant MalE-MdcELmjC-Strep protein exhibited autocleavage in the presence of Ca2+, Cu2+, Cd2+ and Mn2+, but not in the presence of Mg2+, Ni2+ or Co2+. Site-directed mutagenesis at the predicted cleavage site abolished autocleavage activity of MdcELmjC. An LmjC mdcE- mutant was impaired in the ability to nodulate Lupinus angustifolius and Macroptilium atropurpureum.
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Affiliation(s)
- David Durán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain and Departamento de Biotecnología y Biología Vegetal, ETSI Agrómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain and Departamento de Biotecnología y Biología Vegetal, ETSI Agrómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid.,Instituto de Ciencias Agrarias (ICA), Consejo Superior Investigaciones Científicas, Serrano 115, bis, 28006 Madrid, Spain
| | - José Palacios
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain and Departamento de Biotecnología y Biología Vegetal, ETSI Agrómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain and Departamento de Biotecnología y Biología Vegetal, ETSI Agrómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid
| | - Michael Göttfert
- Institute of Genetics, Technische Universität Dresden, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Susanne Zehner
- Institute of Genetics, Technische Universität Dresden, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain and Departamento de Biotecnología y Biología Vegetal, ETSI Agrómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid
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8
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Benidire L, Lahrouni M, Daoui K, Fatemi ZEA, Gomez Carmona R, Göttfert M, Oufdou K. Phenotypic and genetic diversity of Moroccan rhizobia isolated from Vicia faba and study of genes that are likely to be involved in their osmotolerance. Syst Appl Microbiol 2018; 41:51-61. [DOI: 10.1016/j.syapm.2017.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 01/28/2023]
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9
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Acosta-Jurado S, Alias-Villegas C, Navarro-Gómez P, Zehner S, Murdoch PDS, Rodríguez-Carvajal MA, Soto MJ, Ollero FJ, Ruiz-Sainz JE, Göttfert M, Vinardell JM. The Sinorhizobium fredii HH103 MucR1 Global Regulator Is Connected With the nod Regulon and Is Required for Efficient Symbiosis With Lotus burttii and Glycine max cv. Williams. Mol Plant Microbe Interact 2016; 29:700-712. [PMID: 27482821 DOI: 10.1094/mpmi-06-16-0116-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sinorhizobium fredii HH103 is a rhizobial strain showing a broad host range of nodulation. In addition to the induction of bacterial nodulation genes, transition from a free-living to a symbiotic state requires complex genetic expression changes with the participation of global regulators. We have analyzed the role of the zinc-finger transcriptional regulator MucR1 from S. fredii HH103 under both free-living conditions and symbiosis with two HH103 host plants, Glycine max and Lotus burttii. Inactivation of HH103 mucR1 led to a severe decrease in exopolysaccharide (EPS) biosynthesis but enhanced production of external cyclic glucans (CG). This mutant also showed increased cell aggregation capacity as well as a drastic reduction in nitrogen-fixation capacity with G. max and L. burttii. However, in these two legumes, the number of nodules induced by the mucR1 mutant was significantly increased and decreased, respectively, with respect to the wild-type strain, indicating that MucR1 can differently affect nodulation depending on the host plant. RNA-Seq analysis carried out in the absence and the presence of flavonoids showed that MucR1 controls the expression of hundreds of genes (including some related to EPS production and CG transport), some of them being related to the nod regulon.
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Affiliation(s)
- Sebastián Acosta-Jurado
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Cynthia Alias-Villegas
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Pilar Navarro-Gómez
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Susanne Zehner
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | | | - Miguel A Rodríguez-Carvajal
- 4 Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P. 41012, Sevilla, Spain, and
| | - María J Soto
- 5 Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Francisco-Javier Ollero
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - José E Ruiz-Sainz
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Michael Göttfert
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - José-María Vinardell
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
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Lahrouni M, Oufdou K, El Khalloufi F, Benidire L, Albert S, Göttfert M, Caviedes MA, Rodriguez-Llorente ID, Oudra B, Pajuelo E. Microcystin-tolerant Rhizobium protects plants and improves nitrogen assimilation in Vicia faba irrigated with microcystin-containing waters. Environ Sci Pollut Res Int 2016; 23:10037-10049. [PMID: 26865488 DOI: 10.1007/s11356-016-6223-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 02/01/2016] [Indexed: 06/05/2023]
Abstract
Irrigation of crops with microcystins (MCs)-containing waters-due to cyanobacterial blooms-affects plant productivity and could be a way for these potent toxins entering the food chain. This study was performed to establish whether MC-tolerant rhizobia could benefit growth, nodulation, and nitrogen metabolism of faba bean plants irrigated with MC-containing waters. For that, three different rhizobial strains-with different sensitivity toward MCs-were used: RhOF96 (most MC-sensitive strain), RhOF125 (most MC-tolerant strain), or Vicz1.1 (reference strain). As a control, plants grown without rhizobia and fertilized by NH4NO3 were included in the study. MC exposure decreased roots (30-37 %) and shoots (up to 15 %) dry weights in un-inoculated plants, whereas inoculation with rhizobia protects plants toward the toxic effects of MCs. Nodulation and nitrogen content were significantly impaired by MCs, with the exception of plants inoculated with the most tolerant strain RhOF125. In order to deep into the effect of inoculation on nitrogen metabolism, the nitrogen assimilatory enzymes (glutamine synthetase (GS) and glutamate synthase (GOGAT)) were investigated: Fertilized plants showed decreased levels (15-30 %) of these enzymes, both in shoots and roots. By contrast, inoculated plants retained the levels of these enzymes in shoots and roots, as well as the levels of NADH-GOGAT activity in nodules. We conclude that the microcystin-tolerant Rhizobium protects faba bean plants and improves nitrogen assimilation when grown in the presence of MCs.
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Affiliation(s)
- Majida Lahrouni
- Laboratory of Biology and Biotechnology of Microorganisms, Environmental Microbiology and Toxicology Unit, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- Technische Universität Dresden, Institut für Genetik, Helmholtzstr. 10, D-01069, Dresden, Germany
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Khalid Oufdou
- Laboratory of Biology and Biotechnology of Microorganisms, Environmental Microbiology and Toxicology Unit, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Fatima El Khalloufi
- Laboratory of Biology and Biotechnology of Microorganisms, Environmental Microbiology and Toxicology Unit, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- University Hassan 1st. Polydisciplinary Faculty of Khouribga, BP. 145, 25000, Khouribga, Morocco
| | - Loubna Benidire
- Laboratory of Biology and Biotechnology of Microorganisms, Environmental Microbiology and Toxicology Unit, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Susann Albert
- Technische Universität Dresden, Institut für Genetik, Helmholtzstr. 10, D-01069, Dresden, Germany
| | - Michael Göttfert
- Technische Universität Dresden, Institut für Genetik, Helmholtzstr. 10, D-01069, Dresden, Germany
| | - Miguel A Caviedes
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Ignacio D Rodriguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González, 2, 41012, Sevilla, Spain
| | - Brahim Oudra
- Laboratory of Biology and Biotechnology of Microorganisms, Environmental Microbiology and Toxicology Unit, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/ Profesor García González, 2, 41012, Sevilla, Spain.
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Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S. The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean. Mol Plant Microbe Interact 2015; 28:811-24. [PMID: 25675256 DOI: 10.1094/mpmi-12-14-0397-fi] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sinorhizobium fredii HH103 is a fast-growing rhizobial strain infecting a broad range of legumes including both American and Asiatic soybeans. In this work, we present the sequencing and annotation of the HH103 genome (7.25 Mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. Comparative genomic analyses of S. fredii HH103 with strains USDA257 and NGR234 showed that the core genome of these three strains contains 4,212 genes (61.7% of the HH103 genes). Synteny plot analysis revealed that the much larger chromosome of USDA257 (6.48 Mb) is colinear to the HH103 (4.3 Mb) and NGR324 chromosomes (3.9 Mb). An additional region of the USDA257 chromosome of about 2 Mb displays similarity to plasmid pSfHH103e. Remarkable differences exist between HH103 and NGR234 concerning nod genes, flavonoid effect on surface polysaccharide production, and quorum-sensing systems. Furthermore a number of protein secretion systems have been found. Two genes coding for putative type III-secreted effectors not previously described in S. fredii, nopI and gunA, have been located on the HH103 genome. These differences could be important to understand the different symbiotic behavior of S. fredii strains HH103, USDA257, and NGR234 with soybean.
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Affiliation(s)
- José-María Vinardell
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Sebastián Acosta-Jurado
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Susanne Zehner
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Michael Göttfert
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Anke Becker
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Irene Baena
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Jochem Blom
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Juan Carlos Crespo-Rivas
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Alexander Goesmann
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Elizaveta Krol
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Matthew McIntosh
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Isabel Margaret
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Francisco Pérez-Montaño
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Susanne Schneiker-Bekel
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Javier Serranía
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Rafael Szczepanowski
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Ana-María Buendía
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Javier Lloret
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Ildefonso Bonilla
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Alfred Pühler
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - José-Enrique Ruiz-Sainz
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Stefan Weidner
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
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12
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Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M. The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR). Mol Plant Microbe Interact 2014; 27:379-387. [PMID: 24224534 DOI: 10.1094/mpmi-09-13-0282-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The divergently oriented Sinorhizobium meliloti emrAB (SMc03168 and SMc03167) and emrR (SMc03169) genes are predicted to encode an efflux system of the major facilitator superfamily and a TetR-like transcriptional regulator, respectively. The transcription of the emrA gene was found to be inducible by flavonoids, including luteolin and apigenin, which are known inducers of the nodulation genes in S. meliloti. Interestingly, quercetin, which does not induce nodulation genes, was also a potent inducer of emrA, indicating that NodD is not directly involved in regulation of emrA. The likely regulator of emrAB is EmrR, which binds to palindrome-like sequences in the intergenic region. Several modifications of the palindromes, including an increase of the spacing between the two half sites, prevented binding of EmrR. Binding was also impaired by the presence of luteolin. Mutations in emrA had no obvious effect on symbiosis. This was in contrast to the emrR mutant, which exhibited a symbiotic deficiency with Medicago sativa. Conserved binding sites for TetR-like regulators within the intergenic regions between the emrAB and emrR genes were identified in many symbiotic and pathogenic members of the order Rhizobiales.
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13
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Schirrmeister J, Zocher S, Flor L, Göttfert M, Zehner S. The domain of unknown function DUF1521 exhibits metal ion-inducible autocleavage activity - a novel example from a putative effector protein ofVibrio coralliilyticusATCC BAA-450. FEMS Microbiol Lett 2013; 343:177-82. [DOI: 10.1111/1574-6968.12145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/21/2013] [Accepted: 03/28/2013] [Indexed: 01/13/2023] Open
Affiliation(s)
| | - Sara Zocher
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Liane Flor
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Michael Göttfert
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Susanne Zehner
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
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14
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Wenzel M, Lang K, Günther T, Bhandari A, Weiss A, Lulchev P, Szentgyörgyi E, Kranzusch B, Göttfert M. Characterization of the flavonoid-responsive regulator FrrA and its binding sites. J Bacteriol 2012; 194:2363-70. [PMID: 22389485 PMCID: PMC3347051 DOI: 10.1128/jb.06567-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/23/2012] [Indexed: 11/20/2022] Open
Abstract
Previous microarray analyses revealed that in Bradyrhizobium japonicum, about 100 genes are induced by genistein, an isoflavonoid secreted by soybean. This includes the three genes freC, freA, and freB (systematic designations bll4319, bll4320, and bll4321), which are likely to form a genistein-, daidzein-, and coumestrol-inducible operon and to encode a multidrug efflux system. Upstream of freCAB and in the opposite orientation, FrrA (systematic designation Blr4322), which has similarity to TetR-type regulators, is encoded. A deletion of frrA leads to increased expression of freB in the absence of an inducer. We identified the correct translational start codon of frrA and showed that the gene is inducible by genistein and daidzein. The protein, which was heterologously expressed and purified from Escherichia coli, binds to two palindrome-like DNA elements (operator A and operator B), which are located in the intergenic region between freC and frrA. The replacement of several nucleotides or the insertion of additional spacer nucleotides prevented binding. Binding of FrrA was also affected by the addition of genistein. By mapping the transcription start sites, we found that operator A covers the transcriptional start site of freC and operator B is probably located between the -35 regions of the two divergently oriented genes. Operator A seems to be conserved in a few similar gene constellations in other proteobacteria. Our data indicate that in B. japonicum, besides NodD1 (the LysR family) and NodVW (a two-component response regulator), a third regulator type (a TetR family member) which responds to the plant signal molecules genistein and daidzein exists.
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Affiliation(s)
- Mandy Wenzel
- Institute of Genetics, Dresden University of Technology, Dresden, Germany
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15
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Weidner S, Becker A, Bonilla I, Jaenicke S, Lloret J, Margaret I, Pühler A, Ruiz-Sainz JE, Schneiker-Bekel S, Szczepanowski R, Vinardell JM, Zehner S, Göttfert M. Genome sequence of the soybean symbiont Sinorhizobium fredii HH103. J Bacteriol 2012; 194:1617-8. [PMID: 22374952 PMCID: PMC3294874 DOI: 10.1128/jb.06729-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 01/04/2012] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium fredii HH103 is a fast-growing rhizobial strain that is able to nodulate legumes that develop determinate nodules, e.g., soybean, and legumes that form nodules of the indeterminate type. Here we present the genome of HH103, which consists of one chromosome and five plasmids with a total size of 7.22 Mb.
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Affiliation(s)
- Stefan Weidner
- Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | - Anke Becker
- Fakultät für Biologie, Institut für Biologie III, Universität Freiburg, Freiburg, Germany
| | - Ildefonso Bonilla
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Javier Lloret
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Isabel Margaret
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - Alfred Pühler
- Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | | | | | | | | | - Susanne Zehner
- Institut für Genetik, Technische Universität Dresden, Dresden, Germany
| | - Michael Göttfert
- Institut für Genetik, Technische Universität Dresden, Dresden, Germany
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16
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Margaret I, Becker A, Blom J, Bonilla I, Goesmann A, Göttfert M, Lloret J, Mittard-Runte V, Rückert C, Ruiz-Sainz JE, Vinardell JM, Weidner S. Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. J Biotechnol 2011; 155:11-9. [PMID: 21458507 DOI: 10.1016/j.jbiotec.2011.03.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 03/11/2011] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
Abstract
Glycine max (soybean) plants can be nodulated by fast-growing rhizobial strains of the genus Sinorhizobium as well as by slow-growing strains clustered in the genus Bradyrhizobium. Fast-growing rhizobia strains with different soybean cultivar specificities have been isolated from Chinese soils and from other geographical regions. Most of these strains have been clustered into the species Sinorhizobium fredii. The S. fredii strain HH103 was isolated from soils of Hubei province, Central China and was first described in 1985. This strain is capable to nodulate American and Asiatic soybean cultivars and many other different legumes and is so far the best studied fast-growing soybean-nodulating strain. Additionally to the chromosome S. fredii HH103 carries five indigenous plasmids. The largest plasmid (pSfrHH103e) harbours genes for the production of diverse surface polysaccharides, such as exopolysaccharides (EPS), lipopolysaccharides (LPS), and capsular polysaccharides (KPS). The second largest plasmid (pSfrHH103d) is a typical symbiotic plasmid (pSym), carrying nodulation and nitrogen fixation genes. The present mini review focuses on symbiotic properties of S. fredii HH103, in particular on nodulation and surface polysaccharides aspects. The model strain S. fredii HH103 was chosen for genomic sequencing, which is currently in progress. First analyses of the draft genome sequence revealed an extensive synteny between the chromosomes of S. fredii HH103 and Rhizobium sp. NGR234.
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Affiliation(s)
- Isabel Margaret
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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Okazaki S, Okabe S, Higashi M, Shimoda Y, Sato S, Tabata S, Hashiguchi M, Akashi R, Göttfert M, Saeki K. Identification and functional analysis of type III effector proteins in Mesorhizobium loti. Mol Plant Microbe Interact 2010; 23:223-34. [PMID: 20064065 DOI: 10.1094/mpmi-23-2-0223] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, possesses a cluster of genes (tts) that encode a type III secretion system (T3SS). In the presence of heterologous nodD from Rhizobium leguminosarum and a flavonoid naringenin, we observed elevated expression of the tts genes and secretion of several proteins into the culture medium. Inoculation experiments with wild-type and T3SS mutant strains revealed that the presence of the T3SS affected nodulation at a species level within the Lotus genus either positively (L. corniculatus subsp. frondosus and L. filicaulis) or negatively (L. halophilus and two other species). By inoculating L. halophilus with mutants of various type III effector candidate genes, we identified open reading frame mlr6361 as a major determinant of the nodulation restriction observed for L. halophilus. The predicted gene product of mlr6361 is a protein of 3,056 amino acids containing 15 repetitions of a sequence motif of 40 to 45 residues and a shikimate kinase-like domain at its carboxyl terminus. Homologues with similar repeat sequences are present in the hypersensitive-response and pathogenicity regions of several plant pathogens, including strains of Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas species. These results suggest that L. halophilus recognizes Mlr6361 as potentially pathogen derived and subsequently halts the infection process.
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Affiliation(s)
- Shin Okazaki
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
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Wenzel M, Friedrich L, Göttfert M, Zehner S. The type III-secreted protein NopE1 affects symbiosis and exhibits a calcium-dependent autocleavage activity. Mol Plant Microbe Interact 2010; 23:124-9. [PMID: 19958145 DOI: 10.1094/mpmi-23-1-0124] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The type III-secreted proteins NopE1 and NopE2 of Bradyrhizobium japonicum contain a repeated domain of unknown function (DUF1521), which is present in a few uncharacterized proteins. A nopE1/nopE2 double mutant strain exhibited higher nodulation efficiency on Vigna radiata KPS2 than the wild type or single nopE1 or nopE2 mutants. This indicates that both proteins are effectors that functionally overlap. To test translocation into the plant cell compartment during symbiosis, NopE1 and NopE2 were fused with adenylate cyclase (cya) as reporter. A fusion with the full-length proteins or N-terminal peptides resulted in increased cAMP levels in nodules, indicating translocation. Purified NopE1 exhibited self-cleavage in the presence of Ca(2+). Two identical cleavage sites (GD'PHVD) were identified inside the DUF1521 domains. The C-terminal cleavage site was analyzed by alanine scanning. Protein variants in which aspartate or proline next to the cleavage sites was substituted displayed no cleavage. A noncleavable protein was obtained by exchange of the aspartate residues preceding both cleavage sites. Complementation analysis with the noncleavable NopE1 variant did not restore wild-type phenotype on Vigna radiata KPS2, indicating a physiological role of NopE1 cleavage in effector function.
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Affiliation(s)
- Mandy Wenzel
- Institute of Genetics, Dresden University of Technology, Helmholtzstrasse 10, D-01062 Dresden, Germany
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Okazaki S, Zehner S, Hempel J, Lang K, Göttfert M. Genetic organization and functional analysis of the type III secretion system of Bradyrhizobium elkanii. FEMS Microbiol Lett 2009; 295:88-95. [PMID: 19473255 DOI: 10.1111/j.1574-6968.2009.01593.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Cloning and sequencing of a 47.1-kb chromosomal DNA region revealed the presence of a type III secretion system (T3SS) in Bradyrhizobium elkanii USDA61. The identified genes are likely to encode the transcriptional activator TtsI, core components of the secretion apparatus and secreted proteins. Several ORFs within the cluster are not conserved in other rhizobia. Nine tts box motifs, a promoter element of TtsI-regulated genes, were found; six of them upstream of annotated genes. For functional analyses, the rhcC2 and rhcJ genes were disrupted. These mutations had a cultivar-specific effect on nodulation. Vigna radiata cv. KPS1 developed nodules if infected with the mutant strains but not with the wild type. In contrast, V. radiata cv. CN36 was nodulated by all strains. Nodulation of rj(1) soybean depended on the T3SS. A comparison of the protein patterns from supernatants of the wild type and rhcJ mutant by two-dimensional gel electrophoresis revealed proteins that are secreted only in the wild-type background. These results show that B. elkanii encodes a functional T3SS that is involved in the interaction with host legumes.
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Affiliation(s)
- Shin Okazaki
- Institute of Genetics, Dresden University of Technology, Dresden, Germany
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Hempel J, Zehner S, Göttfert M, Patschkowski T. Analysis of the secretome of the soybean symbiont Bradyrhizobium japonicum. J Biotechnol 2008; 140:51-8. [PMID: 19095018 DOI: 10.1016/j.jbiotec.2008.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 10/20/2008] [Accepted: 11/20/2008] [Indexed: 11/29/2022]
Abstract
Proteins from the supernatant of Bradyrhizobium japonicum were separated by two-dimensional gel electrophoresis and stained with Coomassie. This revealed more than 100 protein spots. Sixty-eight proteins were identified by mass spectrometry. Thirty-five are predicted to contain an N-terminal signal peptide characteristic for proteins transported by the general secretory pathway. Most of these appear to be substrate-binding proteins of the ABC transporter family. Ten proteins were categorized as unclassified conserved or hypothetical. None of the proteins has similarity to proteins transported by a type I secretion system or to autotransporters. Three of the proteins might be located in the outer membrane. The addition of genistein led to changes in the spot pattern of three flagellar proteins and resulted in the identification of the nodulation outer protein Pgl. Moreover, the application of shot-gun mass spectrometry resulted in the first-time identification of NopB, NopH and NopT, which were present only after genistein induction. Replacing genistein with daidzein or coumestrol reduced the amount of the type III-secreted protein GunA2.
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Affiliation(s)
- Jana Hempel
- Institut für Genetik, Technische Universität Dresden, Dresden, Germany
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21
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Zehner S, Schober G, Wenzel M, Lang K, Göttfert M. Expression of the Bradyrhizobium japonicum type III secretion system in legume nodules and analysis of the associated tts box promoter. Mol Plant Microbe Interact 2008; 21:1087-93. [PMID: 18616405 DOI: 10.1094/mpmi-21-8-1087] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In Bradyrhizobium japonicum, as in some other rhizobia, symbiotic efficiency is influenced by a type III secretion system (T3SS). Most genes encoding the transport machinery and secreted proteins are preceded by a conserved 30-bp motif, the type-three secretion (tts) box. In this study, we found that regions downstream of 34 tts boxes are transcribed. For nopB, nopL, and gunA2, the transcriptional start sites were found to be 12, 11, and 10 bp downstream of their tts boxes, respectively. The deletion of this motif or modification of two or more conserved residues strongly reduced expression of nopB. This indicates that the tts box is an essential promoter element. Data obtained with lacZ reporter gene fusions of five genes preceded by a tts box (gunA2, nopB, rhcV, nopL, and blr1806) revealed that they are expressed in 4-week-old nodules of Macroptilium atropurpureum. These data suggest that the T3SS is active in mature nitrogen-fixing nodules. The two-component response regulator TtsI is required for the expression of rhcV, nopL, and blr1806 in bacteroids. Staining of inoculated roots showed that nopB is also expressed in early infection stages.
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Affiliation(s)
- Susanne Zehner
- Institute of Genetics, Dresden University of Technology, Helmholtzstrasse 10, Dresden, Germany.
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22
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Abstract
An initializing step in the rhizobia-legume symbiosis is the secretion of flavonoids by plants that leads to the expression of nodulation genes in rhizobia. Here we report the genome-wide transcriptional response of Bradyrhizobium japonicum to genistein, an isoflavone secreted by soybean. About 100 genes were induced in the wild type. This included all nod box-associated genes, the flagellar cluster and several genes that are likely to be involved in transport processes. To elucidate the role of known regulators, we analysed mutant strains. This revealed that the two-component response regulator NodW is essential for induction of almost all genistein-inducible genes, with the exception of 8 genes. The phenotype of the nodW mutant could be partially suppressed by overexpression of NwsB, which is also a two-component response regulator. These data indicate that genistein has a much broader function than mere induction of nod genes.
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Affiliation(s)
- Kathrin Lang
- Institute of Genetics, Dresden University of Technology, Helmholtzstrasse 10, 01069, Dresden, Germany
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23
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Ludwig F, Medger A, Börnick H, Opitz M, Lang K, Göttfert M, Röske I. Identification and expression analyses of putative sesquiterpene synthase genes in Phormidium sp. and prevalence of geoA-like genes in a drinking water reservoir. Appl Environ Microbiol 2007; 73:6988-93. [PMID: 17827321 PMCID: PMC2074963 DOI: 10.1128/aem.01197-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The occurrence of taste and odor problems in drinking water supplies is a widespread phenomenon. From a Saxonian water reservoir we isolated a cyanobacterial species which was classified as Phormidium sp. Under laboratory conditions it produced an earthy-musty smell due to the synthesis of geosmin. The only genes shown to be involved in geosmin biosynthesis are cyc2 and geoA of Streptomyces. Based on the alignment of Cyc2 with a putative sesquiterpene synthase of Nostoc punctiforme, a degenerate primer pair was designed. By PCR, we could amplify two similar genes in Phormidium sp., which we named geoA1 and geoA2. Their expression was studied by reverse transcription-PCR. This revealed that both genes are expressed at 20 degrees C and a light-dark cycle of 12 h. Expression was not detectable at the end of a 24-h dark period. To analyze the prevalence of geoA1 and geoA2 in samples from the phytobenthos, we generated PCR fragments with the same degenerate primer pair. Fifty-five different sequences that might represent geoA variants were obtained. The GC content ranged from 42% to 67%, suggesting that taxonomically very different bacteria might contain such genes.
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Affiliation(s)
- Frank Ludwig
- Institute of Microbiology, Dresden University of Technology, 01062 Dresden, Germany
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24
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Kanbe M, Yagasaki J, Zehner S, Göttfert M, Aizawa SI. Characterization of two sets of subpolar flagella in Bradyrhizobium japonicum. J Bacteriol 2007; 189:1083-9. [PMID: 17098908 PMCID: PMC1797282 DOI: 10.1128/jb.01405-06] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2006] [Accepted: 10/30/2006] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium japonicum is one of the soil bacteria that form nodules on soybean roots. The cell has two sets of flagellar systems, one thick flagellum and a few thin flagella, uniquely growing at subpolar positions. The thick flagellum appears to be semicoiled in morphology, and the thin flagella were in a tight-curly form as observed by dark-field microscopy. Flagellin genes were identified from the amino acid sequence of each flagellin. Flagellar genes for the thick flagellum are scattered into several clusters on the genome, while those genes for the thin flagellum are compactly organized in one cluster. Both types of flagella are powered by proton-driven motors. The swimming propulsion is supplied mainly by the thick flagellum. B. japonicum flagellar systems resemble the polar-lateral flagellar systems of Vibrio species but differ in several aspects.
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Affiliation(s)
- Masaomi Kanbe
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727-0023, Japan
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25
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Süss C, Hempel J, Zehner S, Krause A, Patschkowski T, Göttfert M. Identification of genistein-inducible and type III-secreted proteins of Bradyrhizobium japonicum. J Biotechnol 2006; 126:69-77. [PMID: 16707185 DOI: 10.1016/j.jbiotec.2006.03.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 02/07/2006] [Accepted: 03/29/2006] [Indexed: 10/24/2022]
Abstract
Flagellin is the bulk protein secreted by Bradyrhizobium japonicum. For easier identification of minor protein fractions, the flagellin genes bll6865 and bll6866 were deleted. Extracellular proteins of the corresponding mutant were purified and separated by 2D gel electrophoresis. Several of the protein spots were detectable only after addition of genistein to the growth medium-genistein is an isoflavone secreted by soybean that activates the expression of genes encoding a type III secretion system. These secreted proteins were not present in supernatants of mutants in which conserved genes of the type III secretion system or the regulatory gene ttsI, which is essential for activation of the type III secretion system, are deleted. Out of 22 genistein-inducible protein spots 8 different proteins could be identified by mass spectrometry. One of the proteins, Blr1752, has similarity to NopP of Rhizobium sp. strain NGR234 that is known to be secreted. Another protein is Blr1656 (GunA2) that was shown previously to have endoglucanase activity. Three proteins have similarity to subunits of the flagellar apparatus. Some proteins appeared in several separate spots indicating posttranslational modification. A conserved tts box motif was found in the putative promoter region of six genes encoding secreted proteins.
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Affiliation(s)
- Christin Süss
- Institut für Genetik, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
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26
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Pühler A, Arlat M, Becker A, Göttfert M, Morrissey JP, O'Gara F. What can bacterial genome research teach us about bacteria-plant interactions? Curr Opin Plant Biol 2004; 7:137-147. [PMID: 15003213 DOI: 10.1016/j.pbi.2004.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biological research is changing dramatically. Genomic and post-genomic research is responsible for the accumulation of enormous datasets, which allow the formation of holistic views of the organisms under investigation. In the field of microbiology, bacteria represent ideal candidates for this new development. It is relatively easy to sequence the genomes of bacteria, to analyse their transcriptomes and to collect information at the proteomic level. Genome research on symbiotic, pathogenic and associative bacteria is providing important information on bacteria-plant interactions, especially on type-III secretion systems (TTSS) and their role in the interaction of bacteria with plants.
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Affiliation(s)
- Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, 33594 Bielefeld, Germany.
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27
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Abstract
A cluster of genes coding for putative plant cell-wall degrading enzymes (i.e., genes for two endoglucanases [gunA and gunA2], one pectinmethylesterase [pme], and one polygalacturonase [pgl]) was identified by sequence similarities in the symbiotic region of the Bradyrhizobium japonicum chromosome. In addition, a systematic screen of the region revealed several genes potentially transcribed by the sigma(54)-RNA polymerase and activated by the transcriptional regulator NifA (i.e., genes for proteins with similarity to outer membrane proteins [id117 and id525] and a citrate carrier [id331 or citA] and one open reading frame without similarity to known proteins [id747]). Expression studies using transcriptional lacZ fusions showed that gunA2 and pgl were strongly induced by the isoflavone genistein in a NodW-dependent manner, suggesting a role of the gene products in early events of the nodulation process; by contrast, gunA and pme expression was very weak in the conditions tested. The gunA2 gene product was purified and was shown to have cellulase activity. beta-Galactosidase activity expressed from transcriptional lacZ fusions to id117, id525, and id747 in the wild type and in nifA and rpoN mutant backgrounds confirmed that their transcription was dependent on NifA and sigma(54). Despite the presence of a -24/-12-type promoter and a NifA binding site upstream of citA, no regulation could be demonstrated in this case. Null mutations introduced in gunA, gunA2, pgl, pme, citA, id117, id525, and id747 did not impair the symbiosis with the host plants.
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28
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Krause A, Doerfel A, Göttfert M. Mutational and transcriptional analysis of the type III secretion system of Bradyrhizobium japonicum. Mol Plant Microbe Interact 2002; 15:1228-35. [PMID: 12481995 DOI: 10.1094/mpmi.2002.15.12.1228] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sequencing the symbiotic region of Bradyrhizobium japonicum revealed a gene cluster (tts) encoding a type III secretion system (TTSS) that is similar to those found in Mesorhizobium loti MAFF303099 and Rhizobium strain NGR234. In addition to genes that are likely to encode structural core components of the TTSS, the cluster contains several open reading frames that are found exclusively in rhizobia or that are specific to B. japonicum. Depending on the host, mutations within this cluster affected nodulation capacity to different extents. One of the genes likely encodes a transcriptional activator (TtsI) of the two-component regulatory family. Upstream of ttsI, a nod box promoter was identified. Expression of ttsI could be induced by genistein. This induction depended on the transcriptional activator protein NodW as well as the nodD1nodD2nolA gene region. TtsI was found to be involved in transcriptional regulation of the tts gene cluster. Sequence comparison revealed a conserved tts box element within putative promoter regions of several genes. Here, we propose a model of the regulatory cascade leading to the induction of the tts gene cluster.
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Affiliation(s)
- Andrea Krause
- Institut für Genetik, Technische Universität Dresden, Mommsenstrasse 13, 01062 Dresden, Germany.
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29
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Mesa S, Göttfert M, Bedmar EJ. The nir, nor, and nos denitrification genes are dispersed over the Bradyrhizobium japonicum chromosome. Arch Microbiol 2001; 176:136-42. [PMID: 11479713 DOI: 10.1007/s002030100305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2000] [Accepted: 05/07/2001] [Indexed: 10/27/2022]
Abstract
Cleavage of genomic DNA from Bradyrhizobium japonicum strain 3I1b110 by the restriction enzymes PmeI, PacI, and SwaI has been used together with pulsed-field gel electrophoresis and Southern hybridization to locate the nirK, norCBQD, and nosRZDFYLX denitrification genes on the chromosomal map of B. japonicum strain 110spc4. Mutant strains GRK13, GRC131, and GRZ25 were obtained by insertion of plasmid pUC4-KIXX-aphII-PSP, which carries recognition sites for the enzymes PacI, PmeI and SwaI, into the B. japonicum 3I1b110 nirK, norC and nosZ genes, respectively. Restriction of strain 3I1b110 genomic DNA with PacI, PmeI and SwaI yielded three, five and nine fragments, respectively. Pulsed-field gel electrophoresis of restricted mutant DNAs resulted in an altered fragment pattern that allowed determination of the position of the selected genes. Complementary mapping data were obtained by hybridization using digoxigenin-labeled B. japonicum 3I1b110 nirK, norBQD and nosZD as gene probes. The nirK, norCBQD and nosRZDFYLX genes were located close to the groEL(2), cycH and cycVWX genes, respectively, on the strain 110spc4 genetic map. In contrast to other denitrifiers, B. japonicum 3I1b110 denitrification genes were dispersed over the entire chromosome.
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Affiliation(s)
- S Mesa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, PO Box 419, 18080 Granada, Spain
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30
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Fischer HM, Velasco L, Delgado MJ, Bedmar EJ, Schären S, Zingg D, Göttfert M, Hennecke H. One of two hemN genes in Bradyrhizobium japonicum is functional during anaerobic growth and in symbiosis. J Bacteriol 2001; 183:1300-11. [PMID: 11157943 PMCID: PMC95004 DOI: 10.1128/jb.183.4.1300-1311.2001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we screened the symbiotic gene region of the Bradyrhizobium japonicum chromosome for new NifA-dependent genes by competitive DNA-RNA hybridization (A. Nienaber, A. Huber, M. Göttfert, H. Hennecke, and H. M. Fischer, J. Bacteriol. 182:1472-1480, 2000). Here we report more details on one of the genes identified, a hemN-like gene (now called hemN(1)) whose product exhibits significant similarity to oxygen-independent coproporphyrinogen III dehydrogenases involved in heme biosynthesis in facultatively anaerobic bacteria. In the course of these studies, we discovered that B. japonicum possesses a second hemN-like gene (hemN(2)), which was then cloned by using hemN(1) as a probe. The hemN(2) gene maps outside of the symbiotic gene region; it is located 1.5 kb upstream of nirK, the gene for a Cu-containing nitrite reductase. The two deduced HemN proteins are similar in size (445 and 450 amino acids for HemN(1) and HemN(2), respectively) and share 53% identical (68% similar) amino acids. Expression of both hemN genes was monitored with the help of chromosomally integrated translational lacZ fusions. No significant expression of either gene was detected in aerobically grown cells, whereas both genes were strongly induced (> or = 20-fold) under microaerobic or anaerobic conditions. Induction was in both cases dependent on the transcriptional activator protein FixK(2). In addition, maximal anaerobic hemN(1) expression was partially dependent on NifA, which explains why this gene had been identified by the competitive DNA-RNA hybridization approach. Strains were constructed carrying null mutations either in individual hemN genes or simultaneously in both genes. All mutants showed normal growth in rich medium under aerobic conditions. Unlike the hemN(1) mutant, strains lacking a functional hemN(2) gene were unable to grow anaerobically under nitrate-respiring conditions and largely failed to fix nitrogen in symbiosis with the soybean host plant. Moreover, these mutants lacked several c-type cytochromes which are normally detectable by heme staining of proteins from anaerobically grown wild-type cells. Taken together, our results revealed that B. japonicum hemN(2), but not hemN(1), encodes a protein that is functional under the conditions tested, and this conclusion was further corroborated by the successful complementation of a Salmonella enterica serovar Typhimurium hemF hemN mutant with hemN(2) only.
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Affiliation(s)
- H M Fischer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule, CH-8092 Zürich, Switzerland.
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31
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Göttfert M, Röthlisberger S, Kündig C, Beck C, Marty R, Hennecke H. Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol 2001; 183:1405-12. [PMID: 11157954 PMCID: PMC95015 DOI: 10.1128/jb.183.4.1405-1412.2001] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physical and genetic map of the Bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. Because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. Therefore, we determined the nucleotide sequence of a 410-kb region. The overall G+C nucleotide content was 59.1%. Using a minimum gene length of 150 nucleotides, 388 open reading frames (ORFs) were selected as coding regions. Thirty-five percent of the predicted proteins showed similarity to proteins of rhizobia. Sixteen percent were similar only to proteins of other bacteria. No database match was found for 29%. Repetitive DNA sequence-derived ORFs accounted for the rest. The sequenced region contained all nitrogen fixation genes and, apart from nodM, all nodulation genes that were known to exist in B. japonicum. We found several genes that seem to encode transport systems for ferric citrate, molybdate, or carbon sources. Some of them are preceded by -24/-12 promoter elements. A number of putative outer membrane proteins and cell wall-modifying enzymes as well as a type III secretion system might be involved in the interaction with the host.
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Affiliation(s)
- M Göttfert
- Institut für Genetik, Technische Universität Dresden, D-01062 Dresden, Germany.
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32
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Nienaber A, Huber A, Göttfert M, Hennecke H, Fischer HM. Three new NifA-regulated genes in the Bradyrhizobium japonicum symbiotic gene region discovered by competitive DNA-RNA hybridization. J Bacteriol 2000; 182:1472-80. [PMID: 10692350 PMCID: PMC94442 DOI: 10.1128/jb.182.6.1472-1480.2000] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The so-called symbiotic region of the Bradyrhizobium japonicum chromosome (C. Kündig, H. Hennecke, and M. Göttfert, J. Bacteriol. 175:613-622, 1993) was screened for the presence of genes controlled by the nitrogen fixation regulatory protein NifA. Southern blots of restriction enzyme-digested cosmids that represent an ordered, overlapping library of the symbiotic region were competitively hybridized with in vitro-labeled RNA from anaerobically grown wild-type cells and an excess of RNA isolated either from anaerobically grown nifA and rpoN mutant cells or from aerobically grown wild-type cells. In addition to the previously characterized nif and fix gene clusters, we identified three new NifA-regulated genes that were named nrgA, nrgB, and nrgC (nrg stands for NifA-regulated gene). The latter two probably form an operon, nrgBC. The proteins encoded by nrgC and nrgA exhibited amino acid sequence similarity to bacterial hydroxylases and N-acetyltransferases, respectively. The product of nrgB showed no significant similarity to any protein with a database entry. Primer extension experiments and expression studies with translational lacZ fusions revealed the presence of a functional -24/-12-type promoter upstream of nrgA and nrgBC and proved the NifA- and RpoN (sigma(54))-dependent transcription of the respective genes. Null mutations introduced into nrgA and nrgBC resulted in mutant strains that exhibited wild-type-like symbiotic properties, including nitrogen fixation, when tested on soybean, cowpea, or mung bean host plants. Thus, the discovery of nrgA and nrgBC further emphasizes the previously suggested role of NifA as an activator of anaerobically induced genes other than the classical nitrogen fixation genes.
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Affiliation(s)
- A Nienaber
- Institut für Mikrobiologie, Eidgenössische Hochschule, CH-8092 Zürich, Switzerland
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33
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Hahn M, Neef U, Struck C, Göttfert M, Mendgen K. A putative amino acid transporter is specifically expressed in haustoria of the rust fungus Uromyces fabae. Mol Plant Microbe Interact 1997; 10:438-45. [PMID: 9150593 DOI: 10.1094/mpmi.1997.10.4.438] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A cDNA library constructed from haustoria of the rust fungus Uromyces fabae was screened for clones that are differentially expressed in haustoria. One family of cDNAs (in planta-induced gene 2 [PIG2] was isolated and found to encode a protein with high homologies to fungal amino acid transporters. A cDNA clone containing the complete coding region of PIG2 and the corresponding genomic clone were isolated and sequenced, revealing the presence of 17 introns in the PIG2 gene. Expression of PIG2 mRNA appeared to be restricted to haustoria. With antibodies raised against synthetic peptides, the PIG2-encoded protein was found in membranes fractions of isolated haustoria but not of germinated rust spores. With immunofluorescence microscopy, the putative amino acid transporter was localized to plasma membranes of the haustorial bodies, but not detected in the haustorial neck, haustorial mother cells, or intercellular fungal hyphae growing within infected leaf tissue. These data present for the first time molecular evidence that the rust haustorium plays a special role in the uptake of nutrients from an infected host cell.
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Affiliation(s)
- M Hahn
- Fakultät für Biologie, Universität Konstanz, Germany
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34
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Abstract
By using a PCR approach, the Bradyrhizobium japonicum sigA gene, which encodes the primary RNA polymerase sigma factor, sigma80, was cloned and its nucleotide sequence was established. The deduced protein is highly homologous to the SigA protein of Rhizobium meliloti (72% amino acid sequence identity) but less so to RpoD of Escherichia coli (51% identity). Well conserved is the C-terminal end of the protein, which is probably involved in promoter recognition and binding of the RNA polymerase core enzyme. A remarkable feature of the primary sequence is an alanine- and proline-rich segment of 24 amino acids between conserved regions 1 and 2, which might function as an interdomain linker. We purified the B. japonicum RNA polymerase holoenzyme. One of the subunits had an apparent molecular mass of 90 kDa and corresponded to the sigA gene product, as judged by N-terminal amino acid sequencing. The purified RNA polymerase was used in an in vitro transcription system to determine the transcription start sites of the rrn and groESL4 operons. They were identical to those previously identified in vivo. The rrn promoter was cloned upstream of a rho-independent terminator, yielding a transcript of about 240 bases. This served as a suitable template to analyze promoter activity. Then mutant derivatives of the rrn promoter were constructed and tested in in vitro transcription experiments. Several base pairs essential for promoter activity were thus identified. The results suggest that the well-characterized -35/-10 promoter class is predominantly used in B. japonicum for the expression of "housekeeping" genes.
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Affiliation(s)
- C Beck
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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35
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Abstract
Bradyrhizobium japonicum contains only a single rRNA (rrn) gene region, despite its comparatively large genome size of 8,700 kb. The nucleotide sequence revealed an organization of rRNA and tRNA genes that is frequently found in bacteria: 5'-rrs (16S rRNA)-ileT (tRNA(Ile))-alaT (tRNA(Ala))-rrl (23S rRNA)-rrf (5S rRNA)-3'. The 5' end of the primary transcript, one of the 16S rRNA processing sites, and the 5' end of the mature 16S rRNA were determined by primer extension. DNA hybridization experiments showed that the slowly growing Bradyrhizobium strains generally have only a single copy of the 16S rRNA gene, whereas the faster-growing Rhizobium species contain three rrs copies.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Ribosomal/genetics
- Gene Dosage
- Gene Expression
- Genes, Bacterial/genetics
- Genome, Bacterial
- Molecular Sequence Data
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/genetics
- Restriction Mapping
- Rhizobiaceae/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- C Kündig
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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36
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Grob P, Michel P, Hennecke H, Göttfert M. A novel response-regulator is able to suppress the nodulation defect of a Bradyrhizobium japonicum nodW mutant. Mol Gen Genet 1993; 241:531-41. [PMID: 8264528 DOI: 10.1007/bf00279895] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The two-component regulatory system Nod-VW of Bradyrhizobium japonicum is essential for the nodulation of the legume host plants Vigna radiata, V. unguiculata and Macroptilium atropurpureum. The NodV protein shares homology with the sensor-kinases, whereas the NodW protein is a member of the response-regulator class. We report here the identification of a new B. japonicum DNA region that is able to suppress the phenotypic defect of a nodW mutant, provided that this region is expressed from a foreign promoter. The minimal complementing region, which itself is not essential for nodulation in a nodW+ background, consists of one gene designated nwsB (nodW-suppressor). The deduced amino acid sequence of the nwsB gene product shows a high degree of homology to NodW. The nws B gene is preceded by a long open reading frame, nwsA, whose putative product appears to be a sensor-kinase. Downstream of nwsB, an open reading frame encoding a second putative response-regulator was identified. Interspecies hybridization revealed the presence of nwsAB-like DNA also in other Bradyrhizobium strains. Using nwsB'-'lacZ fusions, the nwsB gene was found to be expressed rather weakly in B. japonicum. This low level of expression is obviously not sufficient to compensate for a nodW- defect, whereas strong overexpression of nwsB is a condition that leads to suppression of the nodW- mutation.
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Affiliation(s)
- P Grob
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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37
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Abstract
We describe a compilation of 79 known genes of Bradyrhizobium japonicum 110, 63 of which were placed on a correlated physical and genetic map of the chromosome. Genomic DNA was restricted with enzymes PacI, PmeI, and SwaI, which yielded two, five, and nine fragments, respectively. Linkage of some of the fragments was established by performing Southern blot hybridization experiments. For probes we used isolated, labelled fragments that were produced either by PmeI or by SwaI. Genes were mapped on individual restriction fragments by performing gene-directed mutagenesis. The principle of this method was to introduce recognition sites for all three restriction enzymes mentioned above into or very near the desired gene loci. Pulsed-field gel electrophoresis of restricted mutant DNA then resulted in an altered fragment pattern compared with wild-type DNA. This allowed us to identify overlapping fragments and to determine the exact position of any selected gene locus. The technique was limited only by the accuracy of the fragment size estimates. After linkage of all of the restriction fragments we concluded that the B. japonicum genome consists of a single, circular chromosome that is approximately 8,700 kb long. Genes directly concerned with nodulation and symbiotic nitrogen fixation are clustered in a chromosomal section that is about 380 kb long.
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Affiliation(s)
- C Kündig
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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38
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Abstract
This review focuses on the functions of nodulation (nod) genes in the interaction between rhizobia and legumes. The nod genes are the key bacterial determinants of the signal exchange between the two symbiotic partners. The product of the nodD gene is a transcriptional activator protein that functions as receptor for a flavonoid plant compound. This signaling induces the expression of a set of nod genes that produces several related Nod factors, substituted lipooligosaccharides. The Nod factors are then excreted and serve as signals sent from the bacterium to the plant. The plant responds with the development of a root nodule. The plant-derived flavonoid, as well as the rhizobial signal, must have distinct chemical structures which guarantee that only matching partners are brought together.
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule Zürich, Switzerland
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Göttfert M, Holzhäuser D, Bäni D, Hennecke H. Structural and functional analysis of two different nodD genes in Bradyrhizobium japonicum USDA110. Mol Plant Microbe Interact 1992; 5:257-65. [PMID: 1421512 DOI: 10.1094/mpmi-5-257] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Bradyrhizobium japonicum has two closely linked homologs of the nodulation regulatory gene, nodD; these homologs are located upstream of and in divergent orientation to the nodYABCSUIJ gene cluster. We report here the nucleotide sequence and mutational analyses of both nodD copies. The predicted NodD1 and NodD2 proteins shared 62% identical amino acid residues at corresponding positions and exhibited different degrees of homology with NodD proteins of other Bradyrhizobium, Azorhizobium, and Rhizobium strains. Induction of the nodYABCSUIJ operon, as measured by expression of a translational nodC'-'lacZ fusion, required the nodD1 gene, but not nodD2. A B. japonicum mutant deleted for both nodD copies (strain delta 1267) still showed residual nodulation activity; however, nodulation of soybean was significantly delayed, and nodulation of mung bean and siratro resulted in strongly reduced nodule numbers. Fully efficient nodulation of mung bean and siratro by strain delta 1267 was restored by genetic complementation with the nodD1 gene, but not with nodD2. We conclude from these data that nodD1 is the critical gene that contributes to maximal nodulation efficiency, whereas the nodD2 gene does not play any obvious role in nodulation of the host plants tested.
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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40
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Abstract
To date, the sequences of 45 Bradyrhizobium japonicum genes are known. This provides sufficient information to determine their codon usage and G + C content. Surprisingly, B. japonicum nodulation and NifA-regulated genes were found to have a less biased codon usage and a lower G + C content than genes not belonging to these two groups. Thus, the coding regions of nodulation genes and NifA-regulated genes could hardly be identified in codon preference plots whereas this was not difficult with other genes. The codon frequency table of the highly biased genes was used in a codon preference plot to analyze the RSRj alpha 9 sequence which is an insertion sequence (IS)-like element. The plot helped identify a new open reading frame (ORF355) that escaped previous detection because of two sequencing errors. These were now corrected. The deduced gene product of ORF355 in RSRj alpha 9 showed extensive similarity to a putative protein encoded by an ORF in the T-DNA of Agrobacterium rhizogenes. The DNA sequences bordering both ORFs showed inverted repeats and potential target site duplications which supported the assumption that they were IS-like elements.
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Affiliation(s)
- T M Ramseier
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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41
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Göttfert M, Hitz S, Hennecke H. Identification of nodS and nodU, two inducible genes inserted between the Bradyrhizobium japonicum nodYABC and nodIJ genes. Mol Plant Microbe Interact 1990; 3:308-316. [PMID: 2134855 DOI: 10.1094/mpmi-3-308] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The so-called common nodulation (nod) gene cluster of Bradyrhizobium japonicum is characterized by a unique composition of genes that are arranged in the following order: nodY, nodA, nodB, nodC, nodS, nodU, nodI, nodJ. As reported here, the identification of the two new genes nodS and nodU resulted from the DNA sequencing of a 4.5-kilobase nodC-downstream region covering nodS, nodU, nodI, and nodJ. The predicted NodS, NodU, NodI, and NodJ proteins had the following respective amino acid (aa) lengths and molecular weights (Mr): 209 aa, Mr 23,405; 569 aa, Mr 62,068; 306 aa, Mr 34,127; and 262 aa, Mr 28,194. The 3' end of nodC overlapped the 5' end of nodS by 71 nucleotides. Using translational fusions of lacZ to nodC, nodS, and nodU, the expression of these genes was shown to be inducible by the isoflavone daidzein and depended on transcription from a DNA region farther upstream. These data and the adjacent location of all genes suggested the existence of a nodYABCSUIJ operon. The nodI and nodJ gene products shared about 70% sequence similarity with the corresponding Rhizobium leguminosarum bv. viciae proteins; NodI belongs to the family of ATP-binding proteins that are constituents of bacterial binding protein-dependent transport systems. By interspecies hybridization, DNA regions homologous to nodSU were detected in other strains of Bradyrhizobium. Likewise, nodS- and nodU-like genes were identified in Rhizobium sp. strain NGR234 (A. Lewin, E. Cervantes, W. Chee-Hoong, and W. J. Broughton, Molecular Plant-Microbe Interactions 3:317-326, 1990) in which nodS confers host specificity for Leucaena leucocephala.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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42
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Göttfert M, Grob P, Hennecke H. Proposed regulatory pathway encoded by the nodV and nodW genes, determinants of host specificity in Bradyrhizobium japonicum. Proc Natl Acad Sci U S A 1990; 87:2680-4. [PMID: 2320582 PMCID: PMC53754 DOI: 10.1073/pnas.87.7.2680] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bradyrhizobium japonicum is the root nodule endosymbiont of soybean (Glycine max), mung bean (Vigna radiata), cowpea (Vigna unguiculata), and Siratro (Macroptilium atropurpureum). We report the characteristics of a nodulation-gene region of B. japonicum that contributes only marginally to the bacterium's ability to nodulate soybean but is essential for the nodulation of the three alternative hosts. This DNA region consists of two open reading frames designated nodV and nodW. The predicted amino acid sequences of the NodV and NodW proteins suggest that they are members of the family of two-component regulatory systems, which supports the hypothesis that NodV responds to an environmental stimulus and, after signal transduction, NodW may be required to positively regulate the transcription of one or several unknown genes involved in the nodulation process. It seems likely that all host plants produce the necessary signal, whereas host specificity may be brought about by the product(s) of the gene(s) activated by NodW.
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zurich, Switzerland
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Göttfert M, Lamb JW, Gasser R, Semenza J, Hennecke H. Mutational analysis of the Bradyrhizobium japonicum common nod genes and further nod box-linked genomic DNA regions. Mol Gen Genet 1989; 215:407-15. [PMID: 2710106 DOI: 10.1007/bf00427037] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
By insertional and deletional marker replacement mutagenesis the common nod region of Bradyrhizobium japonicum was examined for the presence of additional, essential nodulation genes. An open reading frame located in the 800 bp large intergenic region between nodD1 and nodA did not appear to be essential for nodulation of soybean. Furthermore, a strain with a deletion of the nodI- and nodJ-like genes downstream of nodC had a Nod+ phenotype. A mutant with a 1.7 kb deletion immediately downstream of nodD1 considerably delayed the onset of nodulation. This region carried a second copy of nodD (nodD2). A nodD1-nodD2 double mutant had a similar phenotype to the nodD2 mutant. Using a 22-mer oligonucleotide probe partially identical to the nod box sequence, a total of six hybridizing regions were identified in B. japonicum genomic DNA and isolated from a cosmid library. Sequencing of the hybridizing regions revealed that at least three of them represented true nod box sequences whereas the others showed considerable deviations from the consensus sequence. One of the three nod box sequences was the one known to be associated with nodA, whereas the other two were located 60 to 70 kb away from nif cluster I. A deletion of one of these two sequences plus adjacent DNA material (mutant delta 308) led to a reduced nodulation on Vigna radiata but not on soybean. Thus, this region is probably involved in the determination of host specificity.
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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44
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Göttfert M, Horvath B, Kondorosi E, Putnoky P, Rodriguez-Quiñones F, Kondorosi A. At least two nodD genes are necessary for efficient nodulation of alfalfa by Rhizobium meliloti. J Mol Biol 1986; 191:411-20. [PMID: 3820290 DOI: 10.1016/0022-2836(86)90136-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A Rhizobium meliloti DNA region (nodD1) involved in the regulation of other early nodulation genes has been delimited by directed Tn5 mutagenesis and its nucleotide sequence has been determined. The sequence data indicate a large open reading frame with opposite polarity to nodA, -B and -C, coding for a protein of 308 (or 311) amino acid residues. Tn5 insertion within the gene caused a delay in nodulation of Medicago sativa from four to seven days. Hybridization of nodD1 to total DNA of Rhizobium meliloti revealed two additional nodD sequences (nodD2 and nodD3) and both were localized on the megaplasmid pRme41b in the vicinity of the other nod genes. Genetic and DNA hybridization data, combined with nucleotide sequencing showed that nodD2 is a functional gene, while requirement of nodD3 for efficient nodulation of M. sativa could not be detected under our experimental conditions. The nodD2 gene product consists of 310 amino acid residues and shares 86.4% homology with the nodD1 protein. Single nodD2 mutants had the same nodulation phenotype as the nodD1 mutants, while a double nodD1-nodD2 mutant exhibited a more severe delay in nodulation. These results indicate that at least two functional copies of the regulatory gene nodD are necessary for the optimal expression of nodulation genes in R. meliloti.
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45
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Nguyen ND, Göttfert M, Singh M, Klingmüller W. Nif-hybrids of Enterobacter cloacae: Selection for nif-gene integration with nif-plasmids containing the Mu transposon. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00392188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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