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Fuentes-Romero F, Mercogliano M, De Chiara S, Alias-Villegas C, Navarro-Gómez P, Acosta-Jurado S, Silipo A, Medina C, Rodríguez-Carvajal MÁ, Dardanelli MS, Ruiz-Sainz JE, López-Baena FJ, Molinaro A, Vinardell JM, Di Lorenzo F. Exopolysaccharide is detrimental for the symbiotic performance of Sinorhizobium fredii HH103 mutants with a truncated lipopolysaccharide core. Biochem J 2024; 481:1621-1637. [PMID: 39450641 DOI: 10.1042/bcj20240599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/22/2024] [Accepted: 10/24/2024] [Indexed: 10/26/2024]
Abstract
The nitrogen-fixing rhizobia-legume symbiosis relies on a complex interchange of molecular signals between the two partners during the whole interaction. On the bacterial side, different surface polysaccharides, such as lipopolysaccharide (LPS) and exopolysaccharide (EPS), might play important roles for the success of the interaction. In a previous work we studied two Sinorhizobium fredii HH103 mutants affected in the rkpK and lpsL genes, which are responsible for the production of glucuronic acid and galacturonic acid, respectively. Both mutants produced an altered LPS, and the rkpK mutant, in addition, lacked EPS. These mutants were differently affected in symbiosis with Glycine max and Vigna unguiculata, with the lpsL mutant showing a stronger impairment than the rkpK mutant. In the present work we have further investigated the LPS structure and the symbiotic abilities of the HH103 lpsL and rkpK mutants. We demonstrate that both strains produce the same LPS, with a truncated core oligosaccharide devoid of uronic acids. We show that the symbiotic performance of the lpsL mutant with Macroptilium atropurpureum and Glycyrrhiza uralensis is worse than that of the rkpK mutant. Introduction of an exoA mutation (which avoids EPS production) in HH103 lpsL improved its symbiotic performance with G. max, M. atropurpureum, and G. uralensis to the level exhibited by HH103 rkpK, suggesting that the presence of EPS might hide the truncated LPS produced by the former mutant.
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Affiliation(s)
| | - Marcello Mercogliano
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Stefania De Chiara
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | | | - Pilar Navarro-Gómez
- Department of Microbiology, Faculty of Biology, University of Seville, Sevilla, Spain
| | | | - Alba Silipo
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | - Carlos Medina
- Department of Microbiology, Faculty of Biology, University of Seville, Sevilla, Spain
| | | | - Marta S Dardanelli
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto-INBIAS, CONICET, Córdoba, Argentina
| | | | | | - Antonio Molinaro
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | - José-María Vinardell
- Department of Microbiology, Faculty of Biology, University of Seville, Sevilla, Spain
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
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2
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Matte LM, Genal AV, Landolt EF, Danka ES. T6SS in plant pathogens: unique mechanisms in complex hosts. Infect Immun 2024; 92:e0050023. [PMID: 39166846 PMCID: PMC11385963 DOI: 10.1128/iai.00500-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
Type VI secretion systems (T6SSs) are complex molecular machines that allow bacteria to deliver toxic effector proteins to neighboring bacterial and eukaryotic cells. Although initial work focused on the T6SS as a virulence mechanism of human pathogens, the field shifted to examine the use of T6SSs for interbacterial competition in various environments, including in the plant rhizosphere. Genes encoding the T6SS are estimated to be found in a quarter of all Gram-negative bacteria and are especially highly represented in Proteobacteria, a group which includes the most important bacterial phytopathogens. Many of these pathogens encode multiple distinct T6SS gene clusters which can include the core components of the apparatus as well as effector proteins. The T6SS is deployed by pathogens at multiple points as they colonize their hosts and establish an infection. In this review, we describe what is known about the use of T6SS by phytopathogens against plant hosts and non-plant organisms, keeping in mind that the structure of plants requires unique mechanisms of attack that are distinct from the mechanisms used for interbacterial interactions and against animal hosts. While the interactions of specific effectors (such as phospholipases, endonucleases, peptidases, and amidases) with targets have been well described in the context of interbacterial competition and in some eukaryotic interactions, this review highlights the need for future studies to assess the activity of phytobacterial T6SS effectors against plant cells.
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Affiliation(s)
- Lexie M Matte
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Abigail V Genal
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Emily F Landolt
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Elizabeth S Danka
- Biology Discipline, Division of Natural and Social Sciences, St. Norbert College, De Pere, Wisconsin, USA
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3
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Zadegan SB, Kim W, Abbas HMK, Kim S, Krishnan HB, Hewezi T. Differential symbiotic compatibilities between rhizobium strains and cultivated and wild soybeans revealed by anatomical and transcriptome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1435632. [PMID: 39290740 PMCID: PMC11405202 DOI: 10.3389/fpls.2024.1435632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024]
Abstract
Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome that differentiate between functional or non-functional nodules remain largely unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA110 Bradyrhizobium sp. strain LVM105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA110 and LVM105 strains effectively nodulate G. soja but only USDA110 can form symbiotic relationships with Williams 82. LVM105 formed pseudonodules on Williams 82 that consist of a central nodule-like mass that are devoid of any rhizobia. RNA-seq data revealed that USDA110 and LVM105 induce distinct transcriptome programing in functional mature nodules formed on G. soja roots, where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans.
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Affiliation(s)
- Sobhan Bahrami Zadegan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - Wonseok Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | | | - Sunhyung Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MO, United States
- Plant Genetics Research, The United States Department of Agriculture (USDA) Agricultural Research Service, Columbia, MO, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
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4
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Ni H, Hou X, Tian S, Liu C, Zhang G, Peng Y, Chen L, Wang J, Chen Q, Xin D. Insights into the Early Steps of the Symbiotic Interaction between Soybean ( Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17084-17098. [PMID: 39013023 PMCID: PMC11299180 DOI: 10.1021/acs.jafc.4c02312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/18/2024]
Abstract
Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.
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Affiliation(s)
| | | | - Siyi Tian
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Chunyan Liu
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Guoqing Zhang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Yang Peng
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Lin Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Jinhui Wang
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Qingshan Chen
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
| | - Dawei Xin
- Key Laboratory of Soybean
Biology of the Chinese Ministry of Education, Key Laboratory of Soybean
Biology and Breeding, Genetics of Chinese Agriculture Ministry, College
of Agriculture, Northeast Agricultural University, Harbin 150036, China
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Wangthaisong P, Piromyou P, Songwattana P, Phimphong T, Songsaeng A, Pruksametanan N, Boonchuen P, Wongdee J, Teamtaisong K, Boonkerd N, Sato S, Tittabutr P, Teaumroong N. CopG 1, a Novel Transcriptional Regulator Affecting Symbiosis in Bradyrhizobium sp. SUTN9-2. BIOLOGY 2024; 13:415. [PMID: 38927295 PMCID: PMC11201211 DOI: 10.3390/biology13060415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
The symbiotic interaction between leguminous and Bradyrhizobium sp. SUTN9-2 mainly relies on the nodulation process through Nod factors (NFs), while the type IV secretion system (T4SS) acts as an alternative pathway in this symbiosis. Two copies of T4SS (T4SS1 and T4SS2) are located on the chromosome of SUTN9-2. ΔT4SS1 reduces both nodule number and nitrogenase activity in all SUTN9-2 nodulating legumes. The functions of three selected genes (copG1, traG1, and virD21) within the region of T4SS1 were examined. We generated deleted mutants and tested them in Vigna radiata cv. SUT4. ΔtraG1 and ΔvirD21 exhibited lower invasion efficiency at the early stages of root infection but could be recently restored. In contrast, ΔcopG1 completely hindered nodule organogenesis and nitrogenase activity in all tested legumes. ΔcopG1 showed low expression of the nodulation gene and ttsI but exhibited high expression levels of the T4SS genes, traG1 and trbE1. The secreted proteins from ΔT4SS1 were down-regulated compared to the wild-type. Although ΔcopG1 secreted several proteins after flavonoid induction, T3SS (nopP and nopX) and the C4-dicarboxylate transporter (dct) were not detected. These results confirm the crucial role of the copG1 gene as a novel key regulator in the symbiotic relationship between SUTN9-2 and legumes.
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Affiliation(s)
- Praneet Wangthaisong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Pongdet Piromyou
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Pongpan Songwattana
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Tarnee Phimphong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Apisit Songsaeng
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Natcha Pruksametanan
- 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
| | - Jenjira Wongdee
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kamonluck Teamtaisong
- The Center for Scientific and Technological Equipment, 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
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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6
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Li Y, Perez-Gil J, Lois LM, Varejão N, Reverter D. Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150). Commun Biol 2024; 7:644. [PMID: 38802699 PMCID: PMC11130253 DOI: 10.1038/s42003-024-06344-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
The post-translational modification of proteins by ubiquitin-like modifiers (UbLs), such as SUMO, ubiquitin, and Nedd8, regulates a vast array of cellular processes. Dedicated UbL deconjugating proteases families reverse these modifications. During bacterial infection, effector proteins, including deconjugating proteases, are released to disrupt host cell defenses and promote bacterial survival. NopD, an effector protein from rhizobia involved in legume nodule symbiosis, exhibits deSUMOylation activity and, unexpectedly, also deubiquitination and deNeddylation activities. Here, we present two crystal structures of Bradyrhizobium (sp. XS1150) NopD complexed with either Arabidopsis SUMO2 or ubiquitin at 1.50 Å and 1.94 Å resolution, respectively. Despite their low sequence similarity, SUMO and ubiquitin bind to a similar NopD interface, employing a unique loop insertion in the NopD sequence. In vitro binding and activity assays reveal specific residues that distinguish between deubiquitination and deSUMOylation. These unique multifaceted deconjugating activities against SUMO, ubiquitin, and Nedd8 exemplify an optimized bacterial protease that disrupts distinct UbL post-translational modifications during host cell infection.
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Affiliation(s)
- Ying Li
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Qingdao University, 266071, Qingdao, China
| | - Jordi Perez-Gil
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- ARC Centre of Excellence in Synthetic Biology and Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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7
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Semenova MG, Petina AN, Fedorova EE. Autophagy and Symbiosis: Membranes, ER, and Speculations. Int J Mol Sci 2024; 25:2918. [PMID: 38474164 DOI: 10.3390/ijms25052918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The interaction of plants and soil bacteria rhizobia leads to the formation of root nodule symbiosis. The intracellular form of rhizobia, the symbiosomes, are able to perform the nitrogen fixation by converting atmospheric dinitrogen into ammonia, which is available for plants. The symbiosis involves the resource sharing between two partners, but this exchange does not include equivalence, which can lead to resource scarcity and stress responses of one of the partners. In this review, we analyze the possible involvement of the autophagy pathway in the process of the maintenance of the nitrogen-fixing bacteria intracellular colony and the changes in the endomembrane system of the host cell. According to in silico expression analysis, ATG genes of all groups were expressed in the root nodule, and the expression was developmental zone dependent. The analysis of expression of genes involved in the response to carbon or nitrogen deficiency has shown a suboptimal access to sugars and nitrogen in the nodule tissue. The upregulation of several ER stress genes was also detected. Hence, the root nodule cells are under heavy bacterial infection, carbon deprivation, and insufficient nitrogen supply, making nodule cells prone to autophagy. We speculate that the membrane formation around the intracellular rhizobia may be quite similar to the phagophore formation, and the induction of autophagy and ER stress are essential to the success of this process.
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Affiliation(s)
- Maria G Semenova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Alekandra N Petina
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Elena E Fedorova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
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8
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Fedorova EE, Pueyo JJ. Microbial Colonization of the Host Plant: Cellular and Molecular Mechanisms of Symbiosis. Int J Mol Sci 2024; 25:639. [PMID: 38203809 PMCID: PMC10779097 DOI: 10.3390/ijms25010639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Nitrogen is an essential element for all plants, animals, and microorganisms in the Earth's biosphere [...].
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Affiliation(s)
- Elena E. Fedorova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
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Fuentes-Romero F, Alías-Villegas C, Navarro-Gómez P, Acosta-Jurado S, Bernabéu-Roda LM, Cuéllar V, Soto MJ, Vinardell JM. Methods for Studying Swimming and Surface Motilities in Rhizobia. Methods Mol Biol 2024; 2751:205-217. [PMID: 38265718 DOI: 10.1007/978-1-0716-3617-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Rhizobia are soil proteobacteria able to establish a nitrogen-fixing interaction with legumes. In this interaction, rhizobia must colonize legume roots, infect them, and become hosted inside new organs formed by the plants and called nodules. Rhizobial motility, not being essential for symbiosis, might affect the degree of success of the interaction with legumes. Because of this, the study of rhizobial motility (either swimming or surface motility) might be of interest for research teams working on rhizobial symbiotic performance. In this chapter, we describe the protocols we use in our laboratories for studying the different types of motilities exhibited by Sinorhizobium fredii and Sinorhizobium meliloti, as well as for analyzing the presence of flagella in these bacteria. All these protocols might be used (or adapted) for studying bacterial motility in rhizobia.
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Affiliation(s)
| | - Cynthia Alías-Villegas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Consejo Superior de Investigaciones Científicas and Junta de Andalucía, Seville, Spain
| | - Pilar Navarro-Gómez
- Department of Microbiology, Faculty of Biology, University of Seville, Seville, Spain
| | - Sebastián Acosta-Jurado
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, Consejo Superior de Investigaciones Científicas and Junta de Andalucía, Seville, Spain
| | - Lydia M Bernabéu-Roda
- Department ofBiotechnology and EnvironmentalProtection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Virginia Cuéllar
- Department ofBiotechnology and EnvironmentalProtection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María J Soto
- Department ofBiotechnology and EnvironmentalProtection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José M Vinardell
- Department of Microbiology, Faculty of Biology, University of Seville, Seville, Spain.
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10
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Navarro-Gómez P, Fuentes-Romero F, Pérez-Montaño F, Jiménez-Guerrero I, Alías-Villegas C, Ayala-García P, Almozara A, Medina C, Ollero FJ, Rodríguez-Carvajal MÁ, Ruiz-Sainz JE, López-Baena FJ, Vinardell JM, Acosta-Jurado S. A complex regulatory network governs the expression of symbiotic genes in Sinorhizobium fredii HH103. FRONTIERS IN PLANT SCIENCE 2023; 14:1322435. [PMID: 38186594 PMCID: PMC10771577 DOI: 10.3389/fpls.2023.1322435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
Introduction The establishment of the rhizobium-legume nitrogen-fixing symbiosis relies on the interchange of molecular signals between the two symbionts. We have previously studied by RNA-seq the effect of the symbiotic regulators NodD1, SyrM, and TtsI on the expression of the symbiotic genes (the nod regulon) of Sinorhizobium fredii HH103 upon treatment with the isoflavone genistein. In this work we have further investigated this regulatory network by incorporating new RNA-seq data of HH103 mutants in two other regulatory genes, nodD2 and nolR. Both genes code for global regulators with a predominant repressor effect on the nod regulon, although NodD2 acts as an activator of a small number of HH103 symbiotic genes. Methods By combining RNA-seq data, qPCR experiments, and b-galactosidase assays of HH103 mutants harbouring a lacZ gene inserted into a regulatory gene, we have analysed the regulatory relations between the nodD1, nodD2, nolR, syrM, and ttsI genes, confirming previous data and discovering previously unknown relations. Results and discussion Previously we showed that HH103 mutants in the nodD2, nolR, syrM, or ttsI genes gain effective nodulation with Lotus japonicus, a model legume, although with different symbiotic performances. Here we show that the combinations of mutations in these genes led, in most cases, to a decrease in symbiotic effectiveness, although all of them retained the ability to induce the formation of nitrogen-fixing nodules. In fact, the nodD2, nolR, and syrM single and double mutants share a set of Nod factors, either overproduced by them or not generated by the wild-type strain, that might be responsible for gaining effective nodulation with L. japonicus.
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Affiliation(s)
- Pilar Navarro-Gómez
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
| | | | | | | | - Cynthia Alías-Villegas
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
| | | | - Andrés Almozara
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Carlos Medina
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | | | | | | | | | | | - Sebastián Acosta-Jurado
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
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Yao D, Zhou J, Zhang A, Wang J, Liu Y, Wang L, Pi W, Li Z, Yue W, Cai J, Liu H, Hao W, Qu X. Advances in CRISPR/Cas9-based research related to soybean [ Glycine max (Linn.) Merr] molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1247707. [PMID: 37711287 PMCID: PMC10499359 DOI: 10.3389/fpls.2023.1247707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Soybean [Glycine max (Linn.) Merr] is a source of plant-based proteins and an essential oilseed crop and industrial raw material. The increase in the demand for soybeans due to societal changes has coincided with the increase in the breeding of soybean varieties with enhanced traits. Earlier gene editing technologies involved zinc finger nucleases and transcription activator-like effector nucleases, but the third-generation gene editing technology uses clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The rapid development of CRISPR/Cas9 technology has made it one of the most effective, straightforward, affordable, and user-friendly technologies for targeted gene editing. This review summarizes the application of CRISPR/Cas9 technology in soybean molecular breeding. More specifically, it provides an overview of the genes that have been targeted, the type of editing that occurs, the mechanism of action, and the efficiency of gene editing. Furthermore, suggestions for enhancing and accelerating the molecular breeding of novel soybean varieties with ideal traits (e.g., high yield, high quality, and durable disease resistance) are included.
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Affiliation(s)
- Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Junming Zhou
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Aijing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yixuan Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Lixue Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zihao Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenjun Yue
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jinliang Cai
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyuan Hao
- Jilin Provincial Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiangchun Qu
- Institute of Crop Resources, Jilin Provincial Academy of Agricultural Sciences, Gongzhuling, Jilin, China
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Jiménez-Guerrero I, López-Baena FJ, Medina C. Multitask Approach to Localize Rhizobial Type Three Secretion System Effector Proteins Inside Eukaryotic Cells. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112133. [PMID: 37299112 DOI: 10.3390/plants12112133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Rhizobia can establish mutually beneficial interactions with legume plants by colonizing their roots to induce the formation of a specialized structure known as a nodule, inside of which the bacteria are able to fix atmospheric nitrogen. It is well established that the compatibility of such interactions is mainly determined by the bacterial recognition of flavonoids secreted by the plants, which in response to these flavonoids trigger the synthesis of the bacterial Nod factors that drive the nodulation process. Additionally, other bacterial signals are involved in the recognition and the efficiency of this interaction, such as extracellular polysaccharides or some secreted proteins. Some rhizobial strains inject proteins through the type III secretion system to the cytosol of legume root cells during the nodulation process. Such proteins, called type III-secreted effectors (T3E), exert their function in the host cell and are involved, among other tasks, in the attenuation of host defense responses to facilitate the infection, contributing to the specificity of the process. One of the main challenges of studying rhizobial T3E is the inherent difficulty in localizing them in vivo in the different subcellular compartments within their host cells, since in addition to their low concentration under physiological conditions, it is not always known when or where they are being produced and secreted. In this paper, we use a well-known rhizobial T3E, named NopL, to illustrate by a multitask approach where it localizes in heterologous hosts models, such as tobacco plant leaf cells, and also for the first time in transfected and/or Salmonella-infected animal cells. The consistency of our results serves as an example to study the location inside eukaryotic cells of effectors in distinct hosts with different handling techniques that can be used in almost every research laboratory.
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Affiliation(s)
- Irene Jiménez-Guerrero
- Departamento de Microbiología, Universidad de Sevilla, Avenida de Reina Mercedes, 6, 41012 Sevilla, Spain
| | | | - Carlos Medina
- Departamento de Microbiología, Universidad de Sevilla, Avenida de Reina Mercedes, 6, 41012 Sevilla, Spain
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De Sousa BFS, Domingo-Serrano L, Salinero-Lanzarote A, Palacios JM, Rey L. The T6SS-Dependent Effector Re78 of Rhizobium etli Mim1 Benefits Bacterial Competition. BIOLOGY 2023; 12:678. [PMID: 37237492 PMCID: PMC10215855 DOI: 10.3390/biology12050678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
The genes of the type VI secretion system (T6SS) from Rhizobium etli Mim1 (ReMim1) that contain possible effectors can be divided into three modules. The mutants in them indicated that they are not required for effective nodulation with beans. To analyze T6SS expression, a putative promoter region between the tssA and tssH genes was fused in both orientations to a reporter gene. Both fusions are expressed more in free living than in symbiosis. When the module-specific genes were studied using RT-qPCR, a low expression was observed in free living and in symbiosis, which was clearly lower than the structural genes. The secretion of Re78 protein from the T6SS gene cluster was dependent on the presence of an active T6SS. Furthermore, the expression of Re78 and Re79 proteins in E. coli without the ReMim1 nanosyringe revealed that these proteins behave as a toxic effector/immunity protein pair (E/I). The harmful action of Re78, whose mechanism is still unknown, would take place in the periplasmic space of the target cell. The deletion of this ReMim1 E/I pair resulted in reduced competitiveness for bean nodule occupancy and in lower survival in the presence of the wild-type strain.
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Affiliation(s)
- Bruna Fernanda Silva De Sousa
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - Lucía Domingo-Serrano
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - Alvaro Salinero-Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - José Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Safronova V, Sazanova A, Belimov A, Guro P, Kuznetsova I, Karlov D, Chirak E, Yuzikhin O, Verkhozina A, Afonin A, Tikhonovich I. Synergy between Rhizobial Co-Microsymbionts Leads to an Increase in the Efficiency of Plant-Microbe Interactions. Microorganisms 2023; 11:1206. [PMID: 37317180 DOI: 10.3390/microorganisms11051206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 06/16/2023] Open
Abstract
Combined inoculation of legumes with rhizobia and plant growth-promoting rhizobacteria or endophytes is a known technique for increasing the efficiency of nitrogen-fixing symbiosis and plant productivity. The aim of this work was to expand knowledge about the synergistic effects between commercial rhizobia of pasture legumes and root nodule bacteria of relict legume species. Pot experiments were performed on common vetch (Vicia sativa L.) and red clover (Trifolium pratense L.) co-inoculated with the participation of the corresponding commercial rhizobial strains (R. leguminosarum bv. viciae RCAM0626 and R. leguminosarum bv. trifolii RCAM1365) and seven strains isolated from nodules of relict legumes inhabiting the Baikal Lake region and the Altai Republic: Oxytropis popoviana, Astragalus chorinensis, O. tragacanthoides and Vicia costata. The inoculation of plants with combinations of strains (commercial strain plus the isolate from relict legume) had a different effect on symbiosis depending on the plant species: the increase in the number of nodules was mainly observed on vetch, whereas increased acetylene reduction activity was evident on clover. It was shown that the relict isolates differ significantly in the set of genes related to different genetic systems that affect plant-microbe interactions. At the same time, they had additional genes that are involved in the formation of symbiosis and determine its effectiveness, but are absent in the used commercial strains: symbiotic genes fix, nif, nod, noe and nol, as well as genes associated with the hormonal status of the plant and the processes of symbiogenesis (acdRS, genes for gibberellins and auxins biosynthesis, genes of T3SS, T4SS and T6SS secretion systems). It can be expected that the accumulation of knowledge about microbial synergy on the example of the joint use of commercial and relict rhizobia will allow in the future the development of methods for the targeted selection of co-microsymbionts to increase the efficiency of agricultural legume-rhizobia systems.
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Affiliation(s)
- Vera Safronova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Anna Sazanova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Andrey Belimov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Polina Guro
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Irina Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Denis Karlov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Elizaveta Chirak
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Oleg Yuzikhin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Alla Verkhozina
- Siberian Institute of Plant Physiology and Biochemistry (SIPPB), P.O. Box 1243, 664033 Irkutsk, Russia
| | - Alexey Afonin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 St. Petersburg, Russia
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Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
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Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
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Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System. Int J Mol Sci 2023; 24:ijms24032800. [PMID: 36769110 PMCID: PMC9917363 DOI: 10.3390/ijms24032800] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.
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Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction. Genes (Basel) 2023; 14:genes14020274. [PMID: 36833201 PMCID: PMC9957244 DOI: 10.3390/genes14020274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.
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Non-Ionic Osmotic Stress Induces the Biosynthesis of Nodulation Factors and Affects Other Symbiotic Traits in Sinorhizobium fredii HH103. BIOLOGY 2023; 12:biology12020148. [PMID: 36829427 PMCID: PMC9952627 DOI: 10.3390/biology12020148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
(1) Background: Some rhizobia, such as Rhizobium tropici CIAT 899, activate nodulation genes when grown under osmotic stress. This work aims to determine whether this phenomenon also takes place in Sinorhizobium fredii HH103. (2) Methods: HH103 was grown with and without 400 mM mannitol. β-galactosidase assays, nodulation factor extraction, purification and identification by mass spectrometry, transcriptomics by RNA sequencing, motility assays, analysis of acyl-homoserine lactones, and indole acetic acid quantification were performed. (3) Results: Non-ionic osmotic stress induced the production of nodulation factors. Forty-two different factors were detected, compared to 14 found in the absence of mannitol. Transcriptomics indicated that hundreds of genes were either activated or repressed upon non-ionic osmotic stress. The presence of 400 mM mannitol induced the production of indole acetic acid and acyl homoserine lactones, abolished swimming, and promoted surface motility. (4) Conclusions: In this work, we show that non-ionic stress in S. fredii HH103, caused by growth in the presence of 400 mM mannitol, provokes notable changes not only in gene expression but also in various bacterial traits, including the production of nodulation factors and other symbiotic signals.
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Soto MJ, Staehelin C, Gourion B, Cárdenas L, Vinardell JM. Editorial: Early signaling in the rhizobium-legume symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:1056830. [PMID: 36340408 PMCID: PMC9627477 DOI: 10.3389/fpls.2022.1056830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Affiliation(s)
- María J. Soto
- Genetics of Phytobacterial Infections, Estación Experimental del Zaidín, Department of Biotechnology and Environmental Protection, CSIC, Granada, Spain
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Benjamin Gourion
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Luis Cárdenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Mexico
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