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Li X, Li Z. What determines symbiotic nitrogen fixation efficiency in rhizobium: recent insights into Rhizobium leguminosarum. Arch Microbiol 2023; 205:300. [PMID: 37542687 DOI: 10.1007/s00203-023-03640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
| | - Zhangqun Li
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China
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Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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Pedron R, Luchi E, Albiac MA, Di Cagno R, Catorci D, Esposito A, Bianconi I, Losa D, Cristofolini M, Guella G, Jousson O. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870580 DOI: 10.1099/ijsem.0.005131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 3P27G6T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6T clustered together with Mesorhizobium australicum WSM2073T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6T (=DSM 110654T=CECT 30067T). Strain 3P27G6T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Elena Luchi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Marta Acin Albiac
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Daniele Catorci
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy.,Department of Physics, University of Trento, 38123 Trento, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Irene Bianconi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Davide Losa
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, 38123 Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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Boivin S, Mahé F, Debellé F, Pervent M, Tancelin M, Tauzin M, Wielbo J, Mazurier S, Young P, Lepetit M. Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae. FRONTIERS IN PLANT SCIENCE 2021; 12:719987. [PMID: 34567032 PMCID: PMC8457355 DOI: 10.3389/fpls.2021.719987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
Abstract
Legumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv. A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum, Vicia faba, and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frederic Mahé
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frédéric Debellé
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, University of Toulouse, Castanet-Tolosan, France
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Mathilde Tancelin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Sylvie Mazurier
- Agroecology, AgroSup Dijon, INRAE, University Burgundy Franche-Comté, Dijon, France
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Institut Sophia Agrobiotech, INRAE, CNRS, Côte d’Azur University, Sophia-Antipolis, France
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Boivin S, Ait Lahmidi N, Sherlock D, Bonhomme M, Dijon D, Heulin‐Gotty K, Le‐Queré A, Pervent M, Tauzin M, Carlsson G, Jensen E, Journet E, Lopez‐Bellido R, Seidenglanz M, Marinkovic J, Colella S, Brunel B, Young P, Lepetit M. Host-specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae. THE NEW PHYTOLOGIST 2020; 226:555-568. [PMID: 31873949 PMCID: PMC7687279 DOI: 10.1111/nph.16392] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/09/2019] [Indexed: 05/07/2023]
Abstract
Fabeae legumes such as pea and faba bean form symbiotic nodules with a large diversity of soil Rhizobium leguminosarum symbiovar viciae (Rlv) bacteria. However, bacteria competitive to form root nodules (CFN) are generally not the most efficient to fix dinitrogen, resulting in a decrease in legume crop yields. Here, we investigate differential selection by host plants on the diversity of Rlv. A large collection of Rlv was collected by nodule trapping with pea and faba bean from soils at five European sites. Representative genomes were sequenced. In parallel, diversity and abundance of Rlv were estimated directly in these soils using metabarcoding. The CFN of isolates was measured with both legume hosts. Pea/faba bean CFN were associated to Rlv genomic regions. Variations of bacterial pea and/or faba bean CFN explained the differential abundance of Rlv genotypes in pea and faba bean nodules. No evidence was found for genetic association between CFN and variations in the core genome, but variations in specific regions of the nod locus, as well as in other plasmid loci, were associated with differences in CFN. These findings shed light on the genetic control of CFN in Rlv and emphasise the importance of host plants in controlling Rhizobium diversity.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Nassima Ait Lahmidi
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | | | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPSUniversité de Toulouse31326Castanet‐TolosanFrance
| | - Doriane Dijon
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Karine Heulin‐Gotty
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Antoine Le‐Queré
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Georg Carlsson
- Department of Biosystems and TechnologySwedish University of Agricultural SciencesSE‐230 53AlnarpSweden
| | - Erik Jensen
- Department of Biosystems and TechnologySwedish University of Agricultural SciencesSE‐230 53AlnarpSweden
| | - Etienne‐Pascal Journet
- AGroécologie, Innovation et teRritoires (AGIR) INRAEENSAT31326Castanet‐TolosanFrance
- Laboratoire des Interactions Plantes MicrorganismesUniversité de Toulouse, INRAE, CNRS31326Castanet‐TolosanFrance
| | - Raphael Lopez‐Bellido
- Departamento de Ciencias y Recursos Agrícolas y ForestalesUniversity of Córdoba14071CórdobaSpain
| | | | | | - Stefano Colella
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Brigitte Brunel
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
| | - Peter Young
- Department of BiologyUniversity of YorkYorkYO10 5DDUK
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) INRAE, IRD, CIRADUniversity of MontpellierMontpellier SupAgro34398Montpellier cedex 5France
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Safronova V, Belimov A, Sazanova A, Chirak E, Kuznetsova I, Andronov E, Pinaev A, Tsyganova A, Seliverstova E, Kitaeva A, Tsyganov V, Tikhonovich I. Two Broad Host Range Rhizobial Strains Isolated From Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants. Front Microbiol 2019; 10:514. [PMID: 30930885 PMCID: PMC6428766 DOI: 10.3389/fmicb.2019.00514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 02/28/2019] [Indexed: 11/23/2022] Open
Abstract
Two bacterial strains Ach-343 and Opo-235 were isolated, respectively from nodules of Miocene-Pliocene relict legumes Astragalus chorinensis Bunge and Oxytropis popoviana Peschkova originated from Buryatia (Baikal Lake region, Russia). For identification of these strains the sequencing of 16S rRNA (rrs) gene was used. Strain Opo-235 belonged to the species Mesorhizobium japonicum, while the strain Ach-343 was identified as M. kowhaii (100 and 99.9% rrs similarity with the type strains MAFF 303099T and ICMP 19512T, respectively). Symbiotic genes of these strains as well as some genes that promote plant growth (acdS, gibberellin- and auxin-synthesis related genes) were searched throughout the whole genome sequences. The sets of plant growth-promoting genes found were almost identical in both strains, whereas the sets of symbiotic genes were different and complemented each other with several nod, nif, and fix genes. Effects of mono- and co-inoculation of Astragalus sericeocanus, Oxytropis caespitosa, Glycyrrhiza uralensis, Medicago sativa, and Trifolium pratense plants with the strains M. kowhaii Ach-343 and M. japonicum Opo-235 expressing fluorescent proteins mCherry (red) and EGFP (green) were studied in the gnotobiotic plant nodulation assay. It was shown that both strains had a wide range of host specificity, including species of different legume genera from two tribes (Galegeae and Trifolieae). The effects of co-microsymbionts on plants depended on the plant species and varied from decrease, no effect, to increase in the number of nodules, nitrogen-fixing activity and plant biomass. One of the reasons for this phenomenon may be the discovered complementarity in co-microsymbionts of symbiotic genes responsible for the specific modification of Nod-factors and nitrogenase activity. Localization and co-localization of the strains in nodules was confirmed by the confocal microscopy. Analysis of histological and ultrastructural organization of A. chorinensis and O. popoviana root nodules was performed. It can be concluded that the strains M. kowhaii Ach-343 and M. japonicum Opo-235 demonstrate lack of high symbiotic specificity that is characteristic for primitive legume-rhizobia systems. Further study of the root nodule bacteria having complementary sets of symbiotic genes will contribute to clarify the evolutionary paths of legume-rhizobia relationships and the mechanisms of effective integration between partners.
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Affiliation(s)
- Vera Safronova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Andrey Belimov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Anna Sazanova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Elizaveta Chirak
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Irina Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Evgeny Andronov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexander Pinaev
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Elena Seliverstova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Anna Kitaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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Chitin Prevalence and Function in Bacteria, Fungi and Protists. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:19-59. [DOI: 10.1007/978-981-13-7318-3_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Cai J, Zhang LY, Liu W, Tian Y, Xiong JS, Wang YH, Li RJ, Li HM, Wen J, Mysore KS, Boller T, Xie ZP, Staehelin C. Role of the Nod Factor Hydrolase MtNFH1 in Regulating Nod Factor Levels during Rhizobial Infection and in Mature Nodules of Medicago truncatula. THE PLANT CELL 2018; 30:397-414. [PMID: 29367305 PMCID: PMC5868697 DOI: 10.1105/tpc.17.00420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/17/2017] [Accepted: 01/22/2018] [Indexed: 05/22/2023]
Abstract
Establishment of symbiosis between legumes and nitrogen-fixing rhizobia depends on bacterial Nod factors (NFs) that trigger symbiosis-related NF signaling in host plants. NFs are modified oligosaccharides of chitin with a fatty acid moiety. NFs can be cleaved and inactivated by host enzymes, such as MtNFH1 (MEDICAGO TRUNCATULA NOD FACTOR HYDROLASE1). In contrast to related chitinases, MtNFH1 hydrolyzes neither chitin nor chitin fragments, indicating a high cleavage preference for NFs. Here, we provide evidence for a role of MtNFH1 in the symbiosis with Sinorhizobium meliloti Upon rhizobial inoculation, MtNFH1 accumulated at the curled tip of root hairs, in the so-called infection chamber. Mutant analysis revealed that lack of MtNFH1 delayed rhizobial root hair infection, suggesting that excess amounts of NFs negatively affect the initiation of infection threads. MtNFH1 deficiency resulted in nodule hypertrophy and abnormal nodule branching of young nodules. Nodule branching was also stimulated in plants expressing MtNFH1 driven by a tandem CaMV 35S promoter and plants inoculated by a NF-overproducing S. meliloti strain. We suggest that fine-tuning of NF levels by MtNFH1 is necessary for optimal root hair infection as well as for NF-regulated growth of mature nodules.
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Affiliation(s)
- Jie Cai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Lan-Yue Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Wei Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Ye Tian
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Jin-Song Xiong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Yi-Han Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Ru-Jie Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Hao-Ming Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
| | - Jiangqi Wen
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Thomas Boller
- Botanisches Institut der Universität Basel, Zurich-Basel Plant Science Center, 4056 Basel, Switzerland
| | - Zhi-Ping Xie
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
- Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, East Campus, Guangzhou 510006, China
- Shenzhen Research and Development Center of State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Baoan, Shenzhen 518057, China
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Liu YH, Jiao YS, Liu LX, Wang D, Tian CF, Wang ET, Wang L, Chen WX, Wu SY, Guo BL, Guan ZG, Poinsot V, Chen WF. Nonspecific Symbiosis Between Sophora flavescens and Different Rhizobia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:224-232. [PMID: 29173048 DOI: 10.1094/mpmi-05-17-0117-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We explored the genetic basis of the promiscuous symbiosis of Sophora flavescens with diverse rhizobia. To determine the impact of Nod factors (NFs) on the symbiosis of S. flavescens, nodulation-related gene mutants of representative rhizobial strains were generated. Strains with mutations in common nodulation genes (nodC, nodM, and nodE) failed to nodulate S. flavescens, indicating that the promiscuous nodulation of this plant is strictly dependent on the basic NF structure. Mutations of the NF decoration genes nodH, nodS, nodZ, and noeI did not affect the nodulation of S. flavescens, but these mutations affected the nitrogen-fixation efficiency of nodules. Wild-type Bradyrhizobium diazoefficiens USDA110 cannot nodulate S. flavescens, but we obtained 14 Tn5 mutants of B. diazoefficiens that nodulated S. flavescens. This suggested that the mutations had disrupted a negative regulator that prevents nodulation of S. flavescens, leading to nonspecific nodulation. For Ensifer fredii CCBAU 45436 mutants, the minimal NF structure was sufficient for nodulation of soybean and S. flavescens. In summary, the mechanism of promiscuous symbiosis of S. flavescens with rhizobia might be related to its nonspecific recognition of NF structures, and the host specificity of rhizobia may also be controlled by currently unknown nodulation-related genes.
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Affiliation(s)
- Yuan Hui Liu
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Yin Shan Jiao
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Li Xue Liu
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Dan Wang
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Chang Fu Tian
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Lei Wang
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Wen Xin Chen
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Shang Ying Wu
- 3 Changzhi County Agriculture Committee, Changzhi County Welcome West Street. No. 6, Shanxi Province 046000, China
| | - Bao Lin Guo
- 4 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Zha Gen Guan
- 5 Shanxi Zhendong Pharmaceutical Co., Ltd. Changzhi, Shanxi Province 047100, China
| | - Véréna Poinsot
- 6 Laboratoire des IMRCP, UMR5623 Université Paul Sabatier, Toulouse, France
| | - Wen Feng Chen
- 1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
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Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti. J Bacteriol 2018; 200:JB.00501-17. [PMID: 29158240 DOI: 10.1128/jb.00501-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
Sinorhizobium meliloti is a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn5-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene, emmD, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn5-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation in rpoA corresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.IMPORTANCE The alphaproteobacterium Sinorhizobium meliloti converts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation of S. meliloti from a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, the S. meliloti cell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterized S. meliloti mutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.
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Sablok G, Rosselli R, Seeman T, van Velzen R, Polone E, Giacomini A, La Porta N, Geurts R, Muresu R, Squartini A. Draft Genome Sequence of the Nitrogen-Fixing Rhizobium sullae Type Strain IS123 T Focusing on the Key Genes for Symbiosis with its Host Hedysarum coronarium L. Front Microbiol 2017; 8:1348. [PMID: 28798728 PMCID: PMC5526965 DOI: 10.3389/fmicb.2017.01348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/03/2017] [Indexed: 11/24/2022] Open
Abstract
The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli) and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments.
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Riccardo Rosselli
- Division de Microbiología, Universidad Miguel HernandezSan Juan de Alicante, Spain
| | - Torsten Seeman
- Victorian Bioinformatics Consortium, Monash UniversityMelbourne, VIC, Australia
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Elisa Polone
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Alessio Giacomini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaLegnaro, Italy
| | - Nicola La Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy.,MOUNTFOR Project Centre, European Forest InstituteSan Michele all'Adige, Italy
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen UniversityWageningen, Netherlands
| | - Rosella Muresu
- Institute of Animal Production Systems in Mediterranean Environments-National Research CouncilSassari, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaLegnaro, Italy
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Romero-Jiménez L, Rodríguez-Carbonell D, Gallegos MT, Sanjuán J, Pérez-Mendoza D. Mini-Tn7 vectors for stable expression of diguanylate cyclase PleD* in Gram-negative bacteria. BMC Microbiol 2015; 15:190. [PMID: 26415513 PMCID: PMC4587759 DOI: 10.1186/s12866-015-0521-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
Background The cyclic diguanylate (c-di-GMP) is currently considered an ubiquitous second messenger in bacteria that influences a wide range of cellular processes. One of the methodological approaches to unravel c-di-GMP regulatory networks involves raising the c-di-GMP intracellular levels, e.g. by expressing a diguanylate cyclase (DGC), to provoke phenotypic changes. Results We have constructed mini-Tn7 delivery vectors for the integration and stable expression of the pleD* gene encoding a highly active DGC, which can be used to artificially increase the intracellular levels of c-di-GMP in Gram negative bacteria. The functionality of these new vectors has been validated in several plant-interacting α- and γ-proteobacteria. Similarly to vector plasmid-borne pleD*, the genome-borne mini-Tn7pleD* constructs provide significant increases in intracellular c-di-GMP, provoking expected phenotypic changes such as enhanced polysaccharide production, biofilm formation and reduced motility. However, the mini-Tn7pleD* constructs resulted far more stable in the absence of antibiotics than the plasmid-based pleD* constructs. Furthermore, we have also implemented an inducible system to modulate pleD* expression and intracellular c-di-GMP rises “on demand”. Conclusions mini-Tn7pleD* constructs are very stable and are maintained during bacterial free-living growth as well as during interaction with eukaryotic hosts, in the absence of selective pressure. This high stability ensures experimental homogeneity in time and space with regard to enhancing c-di-GMP intracellular levels in bacteria of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0521-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lorena Romero-Jiménez
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - David Rodríguez-Carbonell
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - María Trinidad Gallegos
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - Juan Sanjuán
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - Daniel Pérez-Mendoza
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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13
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Ormeño-Orrillo E, Menna P, Almeida LGP, Ollero FJ, Nicolás MF, Pains Rodrigues E, Shigueyoshi Nakatani A, Silva Batista JS, Oliveira Chueire LM, Souza RC, Ribeiro Vasconcelos AT, Megías M, Hungria M, Martínez-Romero E. Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.). BMC Genomics 2012; 13:735. [PMID: 23270491 PMCID: PMC3557214 DOI: 10.1186/1471-2164-13-735] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/15/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown. RESULTS Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins. CONCLUSIONS Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.
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Affiliation(s)
- Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pâmela Menna
- Embrapa Soja, C. P. 231, Londrina, Paraná, 86001-970, Brazil
| | - Luiz Gonzaga P Almeida
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | - Marisa Fabiana Nicolás
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | | | | | | | - Rangel Celso Souza
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | - Manuel Megías
- Universidad de Sevilla, Apdo Postal 874, Sevilla, 41080, Spain
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Involvement of the smeAB multidrug efflux pump in resistance to plant antimicrobials and contribution to nodulation competitiveness in Sinorhizobium meliloti. Appl Environ Microbiol 2011; 77:2855-62. [PMID: 21398477 DOI: 10.1128/aem.02858-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The contributions of multicomponent-type multidrug efflux pumps to antimicrobial resistance and nodulation ability in Sinorhizobium meliloti were comprehensively analyzed. Computational searches identified genes in the S. meliloti strain 1021 genome encoding 1 pump from the ATP-binding cassette family, 3 pumps from the major facilitator superfamily, and 10 pumps from the resistance-nodulation-cell division family, and subsequently, these genes were deleted either individually or simultaneously. Antimicrobial susceptibility tests demonstrated that deletion of the smeAB pump genes resulted in increased susceptibility to a range of antibiotics, dyes, detergents, and plant-derived compounds and, further, that specific deletion of the smeCD or smeEF genes in a ΔsmeAB background caused a further increase in susceptibility to certain antibiotics. Competitive nodulation experiments revealed that the smeAB mutant was defective in competing with the wild-type strain for nodulation. The introduction of a plasmid carrying smeAB into the smeAB mutant restored antimicrobial resistance and nodulation competitiveness. These findings suggest that the SmeAB pump, which is a major multidrug efflux system of S. meliloti, plays an important role in nodulation competitiveness by mediating resistance toward antimicrobial compounds produced by the host plant.
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15
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Carvalho FM, Souza RC, Barcellos FG, Hungria M, Vasconcelos ATR. Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol 2010; 10:37. [PMID: 20144182 PMCID: PMC2907836 DOI: 10.1186/1471-2180-10-37] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 02/08/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis. RESULTS Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes. CONCLUSIONS The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.
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Affiliation(s)
- Fabíola M Carvalho
- Laboratório Nacional de Computação Científica, Laboratório de Bioinformática, Av Getúlio Vargas 333, 25651-075 Petrópolis, Rio de Janeiro, Brazil
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A comparative proteomic analysis of Gluconacetobacter diazotrophicus PAL5 at exponential and stationary phases of cultures in the presence of high and low levels of inorganic nitrogen compound. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1578-89. [PMID: 18662807 DOI: 10.1016/j.bbapap.2008.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 06/07/2008] [Accepted: 06/23/2008] [Indexed: 11/23/2022]
Abstract
A proteomic view of G. diazotrophicus PAL5 at the exponential (E) and stationary phases (S) of cultures in the presence of low (L) and high levels (H) of combined nitrogen is presented. The proteomes analyzed on 2D-gels showed 131 proteins (42E+32S+29H+28L) differentially expressed by G. diazotrophicus, from which 46 were identified by combining mass spectrometry and bioinformatics tools. Proteins related to cofactor, energy and DNA metabolisms and cytoplasmic pH homeostasis were differentially expressed in E growth phase, under L and H conditions, in line with the high metabolic rate of the cells and the low pH of the media. Proteins most abundant in S-phase cells were stress associated and transporters plus transferases in agreement with the general phenomenon that binding protein-dependent systems are induced under nutrient limitation as part of hunger response. Cells grown in L condition produced nitrogen-fixation accessory proteins with roles in biosynthesis and stabilization of the nitrogenase complex plus proteins for protection of the nitrogenases from O(2)-induced inactivation. Proteins of the cell wall biogenesis apparatus were also expressed under nitrogen limitation and might function in the reshaping of the nitrogen-fixing G. diazotrophicus cells previously described. Genes whose protein products were detected in our analysis were mapped onto the chromosome and, based on the tendency of functionally related bacterial genes to cluster, we identified genes of particular pathways that could be organized in operons and are co-regulated. These results showed the great potential of proteomics to describe events in G. diazotrophicus cells by looking at proteins expressed under distinct growth conditions.
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17
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Dillon SC, Bateman A. The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. BMC Bioinformatics 2004; 5:109. [PMID: 15307895 PMCID: PMC516016 DOI: 10.1186/1471-2105-5-109] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 08/12/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Hotdog fold was initially identified in the structure of Escherichia coli FabA and subsequently in 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS. Since that time structural determinations have shown a number of other apparently unrelated proteins also share the Hotdog fold. RESULTS Using sequence analysis we unify a large superfamily of HotDog domains. Membership includes numerous prokaryotic, archaeal and eukaryotic proteins involved in several related, but distinct, catalytic activities, from metabolic roles such as thioester hydrolysis in fatty acid metabolism, to degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. The superfamily also includes FapR, a non-catalytic bacterial homologue that is involved in transcriptional regulation of fatty acid biosynthesis. We have defined 17 subfamilies, with some characterisation. Operon analysis has revealed numerous HotDog domain-containing proteins to be fusion proteins, where two genes, once separate but adjacent open-reading frames, have been fused into one open-reading frame to give a protein with two functional domains. Finally we have generated a Hidden Markov Model library from our analysis, which can be used as a tool for predicting the occurrence of HotDog domains in any protein sequence. CONCLUSIONS The HotDog domain is both an ancient and ubiquitous motif, with members found in the three branches of life.
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Affiliation(s)
- Shane C Dillon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Alex Bateman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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18
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López-Lara IM, Geiger O. The nodulation protein NodG shows the enzymatic activity of an 3-oxoacyl-acyl carrier protein reductase. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:349-357. [PMID: 11277432 DOI: 10.1094/mpmi.2001.14.3.349] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The acyl carrier protein NodF is required for the synthesis of unusual polyunsaturated fatty acids that confer specificity to lipochitin oligosaccharide nodulation (Nod) factors of Rhizobium leguminosarum. In this study, homogeneous NodF protein was used as a ligand to identify proteins of R. leguminosarum that specifically interact with NodF and presumably are involved in the biosynthesis or transfer of the unusual fatty acids. The N-terminal amino acid sequence of a 29-kDa protein that interacts strongly with NodF revealed high similarity to NodG of Rhizobium sp. N33 and to NodG of Sinorhizobium meliloti We cloned and sequenced the gene coding for the NodG-like protein of R. leguminosarum and found it to be the product of the constitutively expressed gene fabG. FabG is the 3-oxoacyl-acyl carrier protein reductase that catalyzes the first reduction step in each cycle of fatty acid elongation. FabG of R. leguminosarum and NodG of Rhizobium sp. N33 were expressed in Escherichia coli. In both cases, the purified protein showed 3-oxoacyl-acyl carrier protein reductase activity in vitro. Therefore, NodG has the same biochemical function as FabG, and the high degree of similarity at the protein and DNA level suggest that nodG is a duplication of the housekeeping genefabG.
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Affiliation(s)
- I M López-Lara
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Morelos, CP.
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López JC, Grasso DH, Frugier F, Crespi MD, Aguilar OM. Early symbiotic responses induced by Sinorhizobium meliloti iIvC mutants in alfalfa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:55-62. [PMID: 11194871 DOI: 10.1094/mpmi.2001.14.1.55] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A mutation in the ilvC gene of Sinorhizobium meliloti 1021 determines a symbiotically defective phenotype. ilvC mutants obtained from different S. meliloti wild-type strains are able to induce root hair deformation on alfalfa roots and show variable activation of the common nodulation genes nodABC. All of these mutants are noninfective. The presence of extra copies of nodD3-syrM in an IlvC- background does not promote nod expression but allows the detection of low levels of Nod factor production. The sulphation of the Nod factor metabolites, however, is not affected. Furthermore, IlvC- strains induce a specific pattern of starch accumulation on alfalfa roots as well as of early nodulin expression. Hence, the pleiotropic action of the ilvC gene in S. meliloti may reveal novel complexities involved in the symbiotic interaction.
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Affiliation(s)
- J C López
- Instituto de Bioquímica y Biologia Molecular, Universidad Nacional de La Plata, Facultad de Ciencias Exactas, Argentina
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20
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Schultze M, Kondorosi A. The role of Nod signal structures in the determination of host specificity in the Rhizobium-legume symbiosis. World J Microbiol Biotechnol 1996; 12:137-49. [DOI: 10.1007/bf00364678] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.
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Affiliation(s)
- S G Pueppke
- Department of Plant Pathology, University of Missouri, Columbia, MO 65211, USA
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22
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Schultze M, Staehelin C, Röhrig H, John M, Schmidt J, Kondorosi E, Schell J, Kondorosi A. In vitro sulfotransferase activity of Rhizobium meliloti NodH protein: lipochitooligosaccharide nodulation signals are sulfated after synthesis of the core structure. Proc Natl Acad Sci U S A 1995; 92:2706-9. [PMID: 7708710 PMCID: PMC42287 DOI: 10.1073/pnas.92.7.2706] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Rhizobium common nod gene products NodABC are involved in the synthesis of the core lipochitooligosaccharide (Nod factor) structure, whereas the products of the host-specific nod genes are necessary for diverse structural modifications, which vary in different Rhizobium species. The sulfate group attached to the Rhizobium meliloti Nod signal is necessary for activity on the host plant alfalfa, while its absence renders the Nod factor active on the non-host plant vetch. This substituent is therefore a major determinant of host specificity. The exact biosynthetic pathway of Nod factors has not been fully elucidated. In particular, it is not known why some chemical modifications are introduced with high fidelity whereas others are inaccurate, giving rise to a family of different Nod factor structures produced by a single Rhizobium strain. Using protein extracts and partially purified recombinant NodH protein obtained from Escherichia coli expressing the R. meliloti nodH gene, we demonstrate here NodH-dependent in vitro sulfotransferase activity. Kinetic analyses with Nod factors, chitooligosaccharides, and their deacetylated derivatives revealed that Nod factors are the preferred substrate for the sulfate transfer. Moreover, the tetrameric Nod factor, NodRm-IV, was a better substrate than the trimer, NodRm-III, or the pentamer, NodRm-V. These data suggest that the core lipochitooligosaccharide structure must be synthesized prior to its host-specific modification with a sulfate group. Since in R. meliloti tetrameric Nod factors are the most abundant and the most active ones, high affinity of NodH for the appropriate tetrameric substrate guarantees its modification and thus contributes to the fidelity of host-specific behavior.
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Affiliation(s)
- M Schultze
- Institut des Sciences Végétales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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Abstract
Rhizobium, Bradyrhizobium, and Azorhizobium species are able to elicit the formation of unique structures, called nodules, on the roots or stems of the leguminous host. In these nodules, the rhizobia convert atmospheric N2 into ammonia for the plant. To establish this symbiosis, signals are produced early in the interaction between plant and rhizobia and they elicit discrete responses by the two symbiotic partners. First, transcription of the bacterial nodulation (nod) genes is under control of the NodD regulatory protein, which is activated by specific plant signals, flavonoids, present in the root exudates. In return, the nod-encoded enzymes are involved in the synthesis and excretion of specific lipooligosaccharides, which are able to trigger on the host plant the organogenic program leading to the formation of nodules. An overview of the organization, regulation, and function of the nod genes and their participation in the determination of the host specificity is presented.
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Affiliation(s)
- P van Rhijn
- F.A. Janssens Laboratory of Genetics, KU Leuven, Heverlee, Belgium
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Cren M, Kondorosi A, Kondorosi E. NolR controls expression of the Rhizobium meliloti nodulation genes involved in the core Nod factor synthesis. Mol Microbiol 1995; 15:733-47. [PMID: 7783644 DOI: 10.1111/j.1365-2958.1995.tb02381.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The synthesis of Rhizobium meliloti Nod signal molecules, encoded by the nod gene products, is finely regulated. A negative control of plasmid-borne nod gene expression is provided by the NolR repressor encoded by the chromosomal nolR gene. NolR was previously shown to downregulate the expression of the activator nodD1 gene and the common nodABC operon by binding to an overlapping region of the two promoters adjacent to the n1 nod-box (Kondorosi et al., 1989). We demonstrate here that NolR also controls the expression of two additional genes, nodD2 and nodM, but does not directly regulate the expression of the host-specific nod genes located downstream of the n2, n3 and n5 nod-boxes. Thus, the nod genes are differentially regulated by NolR and only those providing common nodulation functions, by determining the synthesis of the core Nod factor structure, are subjected to this negative regulation. Furthermore, NolR has a strong negative effect on the production of Nod metabolites, the level of which may serve as a fine-tuning mechanism for optimal nodulation, specific to host-plant genotypes. In addition, it elicits preferential synthesis of Nod factors carrying unsaturated C16 fatty acids. Expression of nolR was high both in the free-living bacterium and in the bacteroid and it was downregulated by its own product and by the nod gene inducer luteolin.
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Affiliation(s)
- M Cren
- Institut des Sciences Végétales, CNRS, 91198 Gif-sur-Yvette, France
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Bauer P, Crespi MD, Szécsi J, Allison LA, Schultze M, Ratet P, Kondorosi E, Kondorosi A. Alfalfa Enod12 genes are differentially regulated during nodule development by Nod factors and Rhizobium invasion. PLANT PHYSIOLOGY 1994; 105:585-92. [PMID: 8066132 PMCID: PMC159397 DOI: 10.1104/pp.105.2.585] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MsEnod12A and MsEnod12B are two early nodulin genes from alfalfa (Medicago sativa). Differential expression of these genes was demonstrated using a reverse transcription-polymerase chain reaction approach. MsEnod12A RNA was detected only in nodules and not in other plant tissues. In contrast, MsEnod12B transcripts were found in nodules and also at low levels in roots, flowers, stems, and leaves. MsEnod12B expression was enhanced in the root early after inoculation with the microsymbiont Rhizobium meliloti and after treatment with purified Nod factors, whereas MsEnod12A induction was detected only when developing nodules were visible. In situ hybridization showed that in nodules, MsEnod12 expression occurred in the infection zone. In empty Fix- nodules the MsEnod12A transcript level was much reduced, and in spontaneous nodules it was not detectable. These data indicate that MsEnod12B expression in roots is related to the action of Nod factors, whereas MsEnod12A expression is associated with the invasion process in nodules. Therefore, alfalfa possesses different mechanisms regulating MsEnod12A and MsEnod12B expression.
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Affiliation(s)
- P Bauer
- Institut des Sciences Végétales, Centre National de la Recherche Scientifique, Gif sur Yvette, France
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Kondorosi E, Schultze M, Kondorosi A. Host Specific Signal Molecules Involved in Symbiotic Root Nodule Organogenesis. BIOTECHNOL BIOTEC EQ 1994. [DOI: 10.1080/13102818.1994.10818789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Cell and Molecular Biology of Rhizobium-Plant. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s0074-7696(08)62252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Affiliation(s)
- S R Long
- Department of Biological Sciences, Stanford University, California 94305-5020
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The Function of the Rhizobial NodABC and NodFEL Operons in the Biosynthesis of Lipo-Oligosaccharides. NEW HORIZONS IN NITROGEN FIXATION 1993. [DOI: 10.1007/978-94-017-2416-6_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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