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Han F, Li H, Lyu E, Zhang Q, Gai H, Xu Y, Bai X, He X, Khan AQ, Li X, Xie F, Li F, Fang X, Wei M. Soybean-mediated suppression of BjaI/BjaR 1 quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation. Appl Environ Microbiol 2024; 90:e0137423. [PMID: 38251894 PMCID: PMC10880635 DOI: 10.1128/aem.01374-23] [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: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR1 QS system in Bradyrhizobium diazoefficiens USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR1 showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR1 systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR1 exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR1 QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by B. diazoefficiens.IMPORTANCEThe present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes' role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.
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Affiliation(s)
- Fang Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Huiquan Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ermeng Lyu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qianqian Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haoyu Gai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yunfang Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xuemei Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xueqian He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Abdul Qadir Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fengmin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Min Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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Darwish DBE, Ali M, Abdelkawy AM, Zayed M, Alatawy M, Nagah A. Constitutive overexpression of GsIMaT2 gene from wild soybean enhances rhizobia interaction and increase nodulation in soybean (Glycine max). BMC PLANT BIOLOGY 2022; 22:431. [PMID: 36076165 PMCID: PMC9461152 DOI: 10.1186/s12870-022-03811-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Since the root nodules formation is regulated by specific and complex interactions of legume and rhizobial genes, there are still too many questions to be answered about the role of the genes involved in the regulation of the nodulation signaling pathway. RESULTS The genetic and biological roles of the isoflavone-7-O-beta-glucoside 6″-O-malonyltransferase gene GsIMaT2 from wild soybean (Glycine soja) in the regulation of nodule and root growth in soybean (Glycine max) were examined in this work. The effect of overexpressing GsIMaT2 from G. soja on the soybean nodulation signaling system and strigolactone production was investigated. We discovered that the GsIMaT2 increased nodule numbers, fresh nodule weight, root weight, and root length by boosting strigolactone formation. Furthermore, we examined the isoflavone concentration of transgenic G. max hairy roots 10 and 20 days after rhizobial inoculation. Malonyldaidzin, malonylgenistin, daidzein, and glycitein levels were considerably higher in GsMaT2-OE hairy roots after 10- and 20-days of Bradyrhizobium japonicum infection compared to the control. These findings suggest that isoflavones and their biosynthetic genes play unique functions in the nodulation signaling system in G. max. CONCLUSIONS Finally, our results indicate the potential effects of the GsIMaT2 gene on soybean root growth and nodulation. This study provides novel insights for understanding the epistatic relationship between isoflavones, root development, and nodulation in soybean. HIGHLIGHTS * Cloning and Characterization of 7-O-beta-glucoside 6″-O-malonyltransferase (GsIMaT2) gene from wild soybean (G. soja). * The role of GsIMaT2 gene in the regulation of root nodule development. *Overexpression of GsMaT2 gene increases the accumulation of isoflavonoid in transgenic soybean hairy roots. * This gene could be used for metabolic engineering of useful isoflavonoid production.
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Affiliation(s)
- Doaa Bahaa Eldin Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35511 Egypt
- Department of Biology, College of Science, Tabuk University, Tabuk, 74191 Saudi Arabia
| | - Mohammed Ali
- Department of Genetic Resources, Desert Research Center, Egyptian Deserts Gene Bank, North Sinai Research Station, 1 Mathaf El-Matarya St., El-Matareya, Cairo, 11753 Egypt
| | - Aisha M. Abdelkawy
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt
| | - Muhammad Zayed
- Botany and Microbiology Department, Faculty of Science, Menoufia University, Menoufia, Shebin El-Kom, 32511 Egypt
| | - Marfat Alatawy
- Department of Biology, College of Science, Tabuk University, Tabuk, 74191 Saudi Arabia
| | - Aziza Nagah
- Botany and Microbiology Department, Faculty of Science, Banha University, Qalyubia Governorate, Benha, 13518 Egypt
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Ali M, Miao L, Soudy FA, Darwish DBE, Alrdahe SS, Alshehri D, Benedito VA, Tadege M, Wang X, Zhao J. Overexpression of Terpenoid Biosynthesis Genes Modifies Root Growth and Nodulation in Soybean (Glycine max). Cells 2022; 11:cells11172622. [PMID: 36078031 PMCID: PMC9454526 DOI: 10.3390/cells11172622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Root nodule formation in many leguminous plants is known to be affected by endogen ous and exogenous factors that affect formation, development, and longevity of nodules in roots. Therefore, it is important to understand the role of the genes which are involved in the regulation of the nodulation signaling pathway. This study aimed to investigate the effect of terpenoids and terpene biosynthesis genes on root nodule formation in Glycine max. The study aimed to clarify not only the impact of over-expressing five terpene synthesis genes isolated from G. max and Salvia guaranitica on soybean nodulation signaling pathway, but also on the strigolactones pathway. The obtained results revealed that the over expression of GmFDPS, GmGGPPS, SgGPS, SgFPPS, and SgLINS genes enhanced the root nodule numbers, fresh weight of nodules, root, and root length. Moreover, the terpene content in the transgenic G. max hairy roots was estimated. The results explored that the monoterpenes, sesquiterpenes and diterpenes were significantly increased in transgenic soybean hairy roots in comparison with the control. Our results indicate the potential effects of terpenoids and terpene synthesis genes on soybean root growth and nodulation. The study provides novel insights for understanding the epistatic relationship between terpenoids, root development, and nodulation in soybean.
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Affiliation(s)
- Mohammed Ali
- Egyptian Deserts Gene Bank, North Sinai Research Station, Desert Research Center, Department of Genetic Resources, Cairo 11753, Egypt
| | - Long Miao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fathia A. Soudy
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Moshtohor, Toukh 13736, Egypt
| | - Doaa Bahaa Eldin Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Salma Saleh Alrdahe
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Dikhnah Alshehri
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Vagner A. Benedito
- Plant and Soil Sciences Division, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV 26506, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (X.W.); (J.Z.); Tel.: +86-186-7404-7685 (J.Z.)
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (X.W.); (J.Z.); Tel.: +86-186-7404-7685 (J.Z.)
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Ferreira EGC, Gomes DF, Delai CV, Barreiros MAB, Grange L, Rodrigues EP, Henning LMM, Barcellos FG, Hungria M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiol 2022; 22:122. [PMID: 35513812 PMCID: PMC9069715 DOI: 10.1186/s12866-022-02527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. RESULTS A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. CONCLUSIONS All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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Affiliation(s)
- Everton Geraldo Capote Ferreira
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
| | | | - Caroline Vanzzo Delai
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | | | - Luciana Grange
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | - Elisete Pains Rodrigues
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | | | - Fernando Gomes Barcellos
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | - Mariangela Hungria
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
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Identification of an Exopolysaccharide Biosynthesis Gene in Bradyrhizobium diazoefficiens USDA110. Microorganisms 2021; 9:microorganisms9122490. [PMID: 34946092 PMCID: PMC8707904 DOI: 10.3390/microorganisms9122490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/27/2023] Open
Abstract
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of Tn5 insertion mutants grown on agar plates led to the identification of a mutant with a transposon insertion site in the blr2358 gene. This gene is predicted to encode a phosphor-glycosyltransferase that transfers a phosphosugar onto a polyprenol phosphate substrate. The disruption of the blr2358 gene resulted in defective EPS synthesis. Accordingly, the blr2358 mutant showed a reduced capacity to induce nodules and stimulate the growth of soybean plants. Glycosyltransferase genes related to blr2358 were found to be well conserved and widely distributed among strains of the Bradyrhizobium genus. In conclusion, our study resulted in identification of a gene involved in EPS biosynthesis and highlights the importance of EPS in the symbiotic interaction between USDA110 and soybeans.
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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. FRONTIERS IN PLANT SCIENCE 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Han F, He X, Chen W, Gai H, Bai X, He Y, Takeshima K, Ohwada T, Wei M, Xie F. Involvement of a Novel TetR-Like Regulator (BdtR) of Bradyrhizobium diazoefficiens in the Efflux of Isoflavonoid Genistein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1411-1423. [PMID: 32924759 DOI: 10.1094/mpmi-08-20-0243-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A wide variety of leguminous plant-released (iso)flavonoids, such as genistein, are potential inducers of the nodulation (nod) genes of endosymbiotic rhizobia for the production of Nod factors, which are vital signaling molecules for triggering the symbiotic process. However, these (iso)flavonoids are generally thought to be toxic to the bacterial partner to varying degrees. Here, a novel TetR-like regulator gene of the soybean symbiont Bradyrhizobium diazoefficiens USDA110, bdtR (systematic designation blr7023), was characterized. It was found to be rapidly and preferentially induced by genistein, and its mutation resulted in significantly increased expression of the neighboring bll7019-bll7021 genes, encoding a multidrug resistance efflux pump system, in the absence of this isoflavonoid. Then, the transcriptional start site of BdtR was determined, and it was revealed that BdtR acted as a transcriptional repressor of the above efflux system through the binding of an AT-rich operator, which could be completely prevented by genistein. In addition, the ΔbdtR deletion mutant strain showed higher accumulation of extracellular genistein and became less susceptible to the isoflavonoid. In contrast, the inactivation of BdtR led to the significantly decreased induction of a nodulation gene (nodY) independent of the expression of nodD1 and nodW and to much weaker nodulation competitiveness. Taken together, the results show that BdtR plays an early sensing role in maintaining the intracellular homeostasis of genistein, helping to alleviate its toxic effect on this bacterium by negatively regulating neighboring genes encoding an efflux pump system while being essentially required for nodule occupancy competitiveness.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Fang Han
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Xueqian He
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Wenwen Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Haoyu Gai
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Xuemei Bai
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Yongxing He
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Keisuke Takeshima
- Department of Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Takuji Ohwada
- Department of Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Min Wei
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, School of Life Sciences, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730000, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Barros-Carvalho GA, Hungria M, Lopes FM, Van Sluys MA. Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation. FEMS Microbiol Lett 2019; 366:fnz046. [PMID: 30860585 DOI: 10.1093/femsle/fnz046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/15/2019] [Indexed: 11/14/2022] Open
Abstract
Bradyrhizobium diazoefficiens CPAC 7 and Bradyrhizobium japonicum CPAC 15 are broadly used in commercial inoculants in Brazil, contributing to most of the nitrogen required by the soybean crop. These strains differ in their symbiotic properties: CPAC 7 is more efficient in fixing nitrogen, whereas CPAC 15 is more competitive. Comparative genomics revealed many transposases close to genes associated with symbiosis in the symbiotic island of these strains. Given the importance that insertion sequences (IS) elements have to bacterial genomes, we focused on identifying the local impact of these elements in the genomes of these and other related Bradyrhizobium strains to further understand their phenotypic differences. Analyses were performed using bioinformatics approaches. We found IS elements disrupting and inserted at regulatory regions of genes involved in symbiosis. Further comparative analyses with 21 Bradyrhizobium genomes revealed insertional polymorphism with distinguishing patterns between B. diazoefficiens and B. japonicum lineages. Finally, 13 of these potentially impacted genes are differentially expressed under symbiotic conditions in B. diazoefficiens USDA 110. Thus, IS elements are associated with the diversity of Bradyrhizobium, possibly by providing mechanisms for natural variation of symbiotic effectiveness.
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Affiliation(s)
- Gesiele Almeida Barros-Carvalho
- GaTE Lab; Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, 277 Matão Street, 05508-090, São Paulo, SP, Brazil
- Instituto de Matemática e Estatística, Universidade de São Paulo, 1010 Matão Street, 05508-090, São Paulo, SP, Brazil
| | | | - Fabrício Martins Lopes
- Universidade Tecnológica Federal do Paraná, 1640 Alberto Carazzai Avenue, 86300-000, Cornélio Procópio, Pr, Brazil
| | - Marie-Anne Van Sluys
- GaTE Lab; Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, 277 Matão Street, 05508-090, São Paulo, SP, Brazil
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Strodtman KN, Frank S, Stevenson S, Thelen JJ, Emerich DW. Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules. Int J Mol Sci 2018; 19:E3947. [PMID: 30544819 PMCID: PMC6320959 DOI: 10.3390/ijms19123947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
The form and physiology of Bradyrhizobium diazoefficiens after the decline of symbiotic nitrogen fixation has been characterized. Proteomic analyses showed that post-symbiotic B. diazoefficiens underwent metabolic remodeling as well-defined groups of proteins declined, increased or remained unchanged from 56 to 119 days after planting, suggesting a transition to a hemibiotrophic-like lifestyle. Enzymatic analysis showed distinct patterns in both the cytoplasm and the periplasm. Similar to the bacteroid, the post-symbiotic bacteria rely on a non-citric acid cycle supply of succinate and, although viable, they did not demonstrate the ability to grow within the senescent nodule.
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Affiliation(s)
- Kent N Strodtman
- Department of Science, Columbia College, Columbia, MO 65216, USA.
| | - Sooyoung Frank
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | | | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - David W Emerich
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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10
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Yuan S, Li R, Chen S, Chen H, Zhang C, Chen L, Hao Q, Shan Z, Yang Z, Qiu D, Zhang X, Zhou X. RNA-Seq Analysis of Differential Gene Expression Responding to Different Rhizobium Strains in Soybean (Glycine max) Roots. FRONTIERS IN PLANT SCIENCE 2016; 7:721. [PMID: 27303417 PMCID: PMC4885319 DOI: 10.3389/fpls.2016.00721] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 05/25/2023]
Abstract
The root nodule symbiosis (RNS) between legume plants and rhizobia is the most efficient and productive source of nitrogen fixation, and has critical importance in agriculture and mesology. Soybean (Glycine max), one of the most important legume crops in the world, establishes a nitrogen-fixing symbiosis with different types of rhizobia, and the efficiency of symbiotic nitrogen fixation in soybean greatly depends on the symbiotic host-specificity. Although, it has been reported that rhizobia use surface polysaccharides, secretion proteins of the type-three secretion systems and nod factors to modulate host range, the host control of nodulation specificity remains poorly understood. In this report, the soybean roots of two symbiotic systems (Bradyrhizobium japonicum strain 113-2-soybean and Sinorhizobium fredii USDA205-soybean)with notable different nodulation phenotypes and the control were studied at five different post-inoculation time points (0.5, 7-24 h, 5, 16, and 21 day) by RNA-seq (Quantification). The results of qPCR analysis of 11 randomly-selected genes agreed with transcriptional profile data for 136 out of 165 (82.42%) data points and quality assessment showed that the sequencing library is of quality and reliable. Three comparisons (control vs. 113-2, control vs. USDA205 and USDA205 vs. 113-2) were made and the differentially expressed genes (DEGs) between them were analyzed. The number of DEGs at 16 days post-inoculation (dpi) was the highest in the three comparisons, and most of the DEGs in USDA205 vs. 113-2 were found at 16 dpi and 21 dpi. 44 go function terms in USDA205 vs. 113-2 were analyzed to evaluate the potential functions of the DEGs, and 10 important KEGG pathway enrichment terms were analyzed in the three comparisons. Some important genes induced in response to different strains (113-2 and USDA205) were identified and analyzed, and these genes primarily encoded soybean resistance proteins, NF-related proteins, nodulins and immunity defense proteins, as well as proteins involving flavonoids/flavone/flavonol biosynthesis and plant-pathogen interaction. Besides, 189 candidate genes are largely expressed in roots and\or nodules. The DEGs uncovered in this study provides molecular candidates for better understanding the mechanisms of symbiotic host-specificity and explaining the different symbiotic effects between soybean roots inoculated with different strains (113-2 and USDA205).
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Rong Li
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Shuilian Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Haifeng Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Limiao Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Qingnan Hao
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Zhihui Shan
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Zhonglu Yang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Dezhen Qiu
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
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11
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Shiro S, Kuranaga C, Yamamoto A, Sameshima-Saito R, Saeki Y. Temperature-Dependent Expression of NodC and Community Structure of Soybean-Nodulating Bradyrhizobia. Microbes Environ 2016; 31:27-32. [PMID: 26877137 PMCID: PMC4791112 DOI: 10.1264/jsme2.me15114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
In order to assess the physiological responses of bradyrhizobia and competition for the nodulation of soybean at different temperatures, we investigated the expression of the nodC gene at 20, 25, and 30°C and the abilities of bacteria to nodulate soybean in microcosms at day/night cultivation temperatures of 23/18°C, 28/23°C, and 33/28°C for 16/8 h. We tested five Bradyrhizobium USDA strains: B. diazoefficiens USDA 110(T) and 122, B. japonicum USDA 123, and B. elkanii USDA 31 and 76(T). The expression of nodC was up-regulated by increasing culture temperatures in USDA 110(T), 122, 31, and 76(T), but was down-regulated in USDA 123. The proportions of USDA 110(T) and 122 within the community were the greatest at 28/23°C. The population of USDA 31 increased, whereas that of USDA 123 decreased with increasing cultivation temperatures. On the other hand, infection by USDA 76(T) was not detected, and low numbers of USDA 76(T) nodules confirmed its poor nodulation ability. These results indicate that the competitiveness of and infection by USDA 110(T), 122, 123, and 31 for soybean nodulation depend on cultivation temperatures, and suggest that the temperature dependence of nodC expression affects the bradyrhizobial community structure.
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Affiliation(s)
- Sokichi Shiro
- Faculty of Life and Environmental Science, Shimane University1060 Nishikawatsu, Matsue, Shimane 690–8504Japan
| | - Chika Kuranaga
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University836 Otani, Suruga-ku, Shizuoka, Shizuoka 422–8529Japan
| | - Yuichi Saeki
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
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12
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Gomes DF, da Silva Batista JS, Rolla AAP, da Silva LP, Bloch C, Galli-Terasawa LV, Hungria M. Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis. BMC Genomics 2014; 15:643. [PMID: 25086822 PMCID: PMC4287336 DOI: 10.1186/1471-2164-15-643] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/25/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Strain CPAC 7 (=SEMIA 5080) was recently reclassified into the new species Bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [Glycine max (L.) Merr.] in Brazil and other South American countries. Although the efficiency of B. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available. RESULTS We provided a two-dimensional proteomic reference map of CPAC 7 obtained under free-living conditions, with the successful identification of 115 spots, representing 95 different proteins. The results highlighted the expression of molecular determinants potentially related to symbiosis establishment (e.g. inositol monophosphatase, IMPase), fixation of atmospheric nitrogen (N2) (e.g. NifH) and defenses against stresses (e.g. chaperones). By using bioinformatic tools, it was possible to attribute probable functions to ten hypothetical proteins. For another ten proteins classified as "NO related COG" group, we analyzed by RT-qPCR the relative expression of their coding-genes in response to the nodulation-gene inducer genistein. Six of these genes were up-regulated, including blr0227, which may be related to polyhydroxybutyrate (PHB) biosynthesis and competitiveness for nodulation. CONCLUSIONS The proteomic map contributed to the identification of several proteins of B. diazoefficiens under free-living conditions and our approach-combining bioinformatics and gene-expression assays-resulted in new information about unknown genes that might play important roles in the establishment of the symbiosis with soybean.
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Affiliation(s)
| | | | | | | | | | | | - Mariangela Hungria
- Embrapa Soja, Embrapa Soja, C,P, 231, 86001-970 Londrina, Paraná, Brazil.
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Takeshima K, Hidaka T, Wei M, Yokoyama T, Minamisawa K, Mitsui H, Itakura M, Kaneko T, Tabata S, Saeki K, Oomori H, Tajima S, Uchiumi T, Abe M, Tokuji Y, Ohwada T. Involvement of a novel genistein-inducible multidrug efflux pump of Bradyrhizobium japonicum early in the interaction with Glycine max (L.) Merr. Microbes Environ 2013; 28:414-21. [PMID: 24225224 PMCID: PMC4070704 DOI: 10.1264/jsme2.me13057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/20/2013] [Indexed: 11/12/2022] Open
Abstract
The early molecular dialogue between soybean and the bacterium Bradyrhizobium japonicum is crucial for triggering their symbiotic interaction. Here we found a single large genomic locus that is widely separated from the symbiosis island and was conspicuously induced within minutes after the addition of genistein. This locus (named BjG30) contains genes for the multidrug efflux pump, TetR family transcriptional regulator, and polyhydroxybutyrate (PHB) metabolism. The induction of BjG30 by genistein was competitively inhibited by daidzein, although both genistein and daidzein are soybean-derived inducers of nodulation (nod) genes. Such a differential expression pattern is also observed in some legume-derived flavonoids, which structurally differ in the hydroxy/deoxy group at the 5-position. In addition, not only did the induction start far in advance of nodW and nodD1 after the addition of genistein, but the levels showed distinct concentration dependence, indicating that the induction pattern of BjG30 is completely different from that of nod genes. The deletion of genes encoding either the multidrug efflux pump or PHB metabolism, especially the former, resulted in defective nodulation performance and nitrogen-fixing capability. Taken together, these results indicate that BjG30, and especially its multidrug efflux pump, may play a key role in the early stage of symbiosis by balancing the dual functions of genistein as both a nod gene inducer and toxicant.
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Affiliation(s)
- Keisuke Takeshima
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Tatsuo Hidaka
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Min Wei
- School of Life Science, Lanzhou University, 222 Tianshui South Rd, Gansu, Lanzhou, 730000, China
| | - Tadashi Yokoyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3–8–1, Harumi-cho, Fuchu, Tokyo, 183–8538, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Takakazu Kaneko
- Faculty of Engineering, Kyoto Sangyo University, Kitaku, Kyoto, 603–8555, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2–6–7, Kazusa-kamatari, Kisarazu, Chiba, 292–0818, Japan
| | - Kazuhiko Saeki
- Department of Biological Science, Faculty of Science, Nara Women’s University, Kitauoyanishi-machi, Nara, 630–8506, Japan
| | - Hirofumi Oomori
- Graduate School of Science, Osaka University, 1–1, Machikaneyama, Toyonaka, 560–0043, Osaka, Japan
| | - Shigeyuki Tajima
- Department of Life Science, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761–0795, Japan
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Mikiko Abe
- Graduate School of Science and Engineering, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Yoshihiko Tokuji
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
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14
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Moscatiello R, Baldan B, Squartini A, Mariani P, Navazio L. Oligogalacturonides: novel signaling molecules in Rhizobium-legume communications. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1387-1395. [PMID: 22835276 DOI: 10.1094/mpmi-03-12-0066-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Oligogalacturonides are pectic fragments of the plant cell wall, whose signaling role has been described thus far during plant development and plant-pathogen interactions. In the present work, we evaluated the potential involvement of oligogalacturonides in the molecular communications between legumes and rhizobia during the establishment of nitrogen-fixing symbiosis. Oligogalacturonides with a degree of polymerization of 10 to 15 were found to trigger a rapid intracellular production of reactive oxygen species in Rhizobium leguminosarum bv. viciae 3841. Accumulation of H(2)O(2), detected by both 2',7'-dichlorodihydrofluorescein diacetate-based fluorescence and electron-dense deposits of cerium perhydroxides, was transient and did not affect bacterial cell viability, due to the prompt activation of the katG gene encoding a catalase. Calcium measurements carried out in R. leguminosarum transformed with the bioluminescent Ca(2+) reporter aequorin demonstrated the induction of a rapid and remarkable intracellular Ca(2+) increase in response to oligogalacturonides. When applied jointly with naringenin, oligogalacturonides effectively inhibited flavonoid-induced nod gene expression, indicating an antagonistic interplay between oligogalacturonides and inducing flavonoids in the early stages of plant root colonization. The above data suggest a novel role for oligogalacturonides as signaling molecules released in the rhizosphere in the initial rhizobium-legume interaction.
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15
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Salavati A, Bushehri AAS, Taleei A, Hiraga S, Komatsu S. A comparative proteomic analysis of the early response to compatible symbiotic bacteria in the roots of a supernodulating soybean variety. J Proteomics 2012; 75:819-32. [PMID: 22005398 DOI: 10.1016/j.jprot.2011.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/04/2011] [Accepted: 09/26/2011] [Indexed: 02/03/2023]
Abstract
To reveal the processes involved in the early stages of symbiosis between soybean plants and root nodule bacteria, we conducted a proteomic analysis of the response to bacterial inoculation in the roots of supernodulating (En-b0-1) and non-nodulating (En1282) varieties, and their parental normal-nodulating variety (Enrei). A total of 56 proteins were identified from 48 differentially expressed protein spots in normal-nodulating variety after bacterial inoculation. Among 56 proteins, metabolism- and energy production-related proteins were upregulated in supernodulating and downregulated in non-nodulating varieties compared to normal-nodulating variety. The supernodulating and non-nodulating varieties responded oppositely to bacterial inoculation with respect to the expression of 11 proteins. Seven proteins of these proteins was downregulated in supernodulating varieties compared to non-nodulating variety, but expression of proteasome subunit alpha type 6, gamma glutamyl hydrolase, glucan endo-1,3-beta glucosidase, and nodulin 35 was upregulated. The expression of seven proteins mirrored the degree of nodule formation. At the transcript level, expression of stem 31kDa glycoprotein, leucine aminopeptidase, phosphoglucomutase, and peroxidase was downregulated in the supernodulating variety compared to the non-nodulating variety, and their expression in the normal-nodulating variety was intermediate. These results suggest that suppression of the autoregulatory mechanism in the supernodulating variety might be due to negative regulation of defense and signal transduction-related processes.
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Affiliation(s)
- Afshin Salavati
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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16
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Abstract
To allow rhizobial infection of legume roots, plant cell walls must be locally degraded for plant-made infection threads (ITs) to be formed. Here we identify a Lotus japonicus nodulation pectate lyase gene (LjNPL), which is induced in roots and root hairs by rhizobial nodulation (Nod) factors via activation of the nodulation signaling pathway and the NIN transcription factor. Two Ljnpl mutants produced uninfected nodules and most infections arrested as infection foci in root hairs or roots. The few partially infected nodules that did form contained large abnormal infections. The purified LjNPL protein had pectate lyase activity, demonstrating that this activity is required for rhizobia to penetrate the cell wall and initiate formation of plant-made infection threads. Therefore, we conclude that legume-determined degradation of plant cell walls is required for root infection during initiation of the symbiotic interaction between rhizobia and legumes.
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17
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da Silva Batista JS, Hungria M. Proteomics reveals differential expression of proteins related to a variety of metabolic pathways by genistein-induced Bradyrhizobium japonicum strains. J Proteomics 2011; 75:1211-9. [PMID: 22119543 DOI: 10.1016/j.jprot.2011.10.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 10/28/2011] [Accepted: 10/31/2011] [Indexed: 11/19/2022]
Abstract
The rhizobia-legume symbiosis requires a coordinated molecular interaction between the symbionts, initiated by seed and root exudation of several compounds, mainly flavonoids, that trigger the expression of nodulation genes in the bacteria. Since the role of flavonoids seems to be broader than the induction of nodulation genes, we aimed at characterizing genistein-induced proteins of Bradyrhizobium japonicum CPAC 15 (=SEMIA 5079), used in commercial soybean inoculants in Brazil, and of two genetically related strains grown in vitro. Whole-cell proteins were extracted both from induced (1 μM genistein) and from non-induced cultures of the three strains, and separated by two-dimensional electrophoresis. Spot profiles were compared between the two conditions and selected spots were excised and identified by mass spectrometry. Forty-seven proteins were significantly induced by genistein, including several hypothetical proteins, the cytoplasmic flagellar component FliG, periplasmic ABC transporters, a protein related to biosynthesis of exopolysaccharides (ExoN), and proteins involved in redox-state maintenance. Noteworthy was the induction of the PhyR-σ(EcfG) regulon, recently demonstrated to be involved in the symbiotic efficiency of, and general stress response in B. japonicum. Our results confirm that the role of flavonoids, such as genistein, can go far beyond the expression of nodulation-related proteins in B. japonicum.
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18
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Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. Genes (Basel) 2011; 2:763-87. [PMID: 24710291 PMCID: PMC3927601 DOI: 10.3390/genes2040763] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/03/2022] Open
Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
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Affiliation(s)
- Takakazu Kaneko
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Hiroko Maita
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Nobukazu Uchiike
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
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Kucho KI, Hay AE, Normand P. The determinants of the actinorhizal symbiosis. Microbes Environ 2011; 25:241-52. [PMID: 21576879 DOI: 10.1264/jsme2.me10143] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The actinorhizal symbiosis is a major contributor to the global nitrogen budget, playing a dominant role in ecological successions following disturbances. The mechanisms involved are still poorly known but there emerges the vision that on the plant side, the kinases that transmit the symbiotic signal are conserved with those involved in the transmission of the Rhizobium Nod signal in legumes. However, on the microbial side, complementation with Frankia DNA of Rhizobium nod mutants failed to permit identification of symbiotic genes. Furthermore, analysis of three Frankia genomes failed to permit identification of canonical nod genes and revealed symbiosis-associated genes such as nif, hup, suf and shc to be spread around the genomes. The present review explores some recently published approaches aimed at identifying bacterial symbiotic determinants.
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Affiliation(s)
- Ken-Ichi Kucho
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima UniversityKorimoto1–21–35, Kagoshima 890–0065, Japan
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20
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da Silva Batista JS, Torres AR, Hungria M. Towards a two-dimensional proteomic reference map of Bradyrhizobium japonicum
CPAC 15: Spotlighting “hypothetical proteins”. Proteomics 2010; 10:3176-89. [DOI: 10.1002/pmic.201000092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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21
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Wei M, Takeshima K, Yokoyama T, Minamisawa K, Mitsui H, Itakura M, Kaneko T, Tabata S, Saeki K, Omori H, Tajima S, Uchiumi T, Abe M, Ishii S, Ohwada T. Temperature-dependent expression of type III secretion system genes and its regulation in Bradyrhizobium japonicum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:628-637. [PMID: 20367471 DOI: 10.1094/mpmi-23-5-0628] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The genome-wide expression profiles of Bradyrhizobium japonicum in response to soybean (Glycine max (L.) Merr.) seed extract (SSE) and genistein were monitored with time at a low temperature (15 degrees C). A comparison with the expression profiles of the B. japonicum genome previously captured at the common growth temperature (30 degrees C) revealed that the expression of SSE preferentially induced genomic loci, including a large gene cluster encoding the type III secretion system (T3SS), were considerably delayed at 15 degrees C, whereas most nodulation (nod) gene loci, including nodD1 and nodW, were rapidly and strongly induced by both SSE and genistein. Induction of the T3SS genes was progressively activated upon the elevation of temperature to 30 degrees C and positively responded to culture population density. In addition, genes nolA and nodD2 were dramatically induced by SSE, concomitantly with the expression of T3SS genes. However, the deletion mutation of nodD2 but not nolA led to elimination of the T3SS genes expression. These results indicate that the expression of the T3SS gene cluster is tightly regulated with integration of environmental cues such as temperature and that NodD2 may be involved in its efficient induction in B. japonicum.
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Affiliation(s)
- Min Wei
- Department of Food Sciences, Obihiro University of Agiculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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Oliveira LR, Marcelino FC, Barcellos FG, Rodrigues EP, Megías M, Hungria M. The nodC, nodG, and glgX genes of Rhizobium tropici strain PRF 81. Funct Integr Genomics 2009; 10:425-31. [DOI: 10.1007/s10142-009-0151-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 11/15/2009] [Accepted: 11/15/2009] [Indexed: 10/20/2022]
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Sánchez C, Iannino F, Deakin WJ, Ugalde RA, Lepek VC. Characterization of the Mesorhizobium loti MAFF303099 type-three protein secretion system. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:519-28. [PMID: 19348570 DOI: 10.1094/mpmi-22-5-0519] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Type III secretion systems (T3SS) have been found in several species of rhizobia. Proteins (termed effectors) secreted by this system are involved in host-range determination and influence nodulation efficiency. Mesorhizobium loti MAFF303099 possesses a functional T3SS in its symbiotic island whose expression is induced by flavonoids. As in other rhizobia, conserved cis-elements (tts box) were found in the promoter regions of genes or operons encoding T3SS components. Using a bioinformatics approach, we searched for other tts-box-controlled genes, and confirmed this transcriptional regulation for some of them using lacZ fusions to the predicted promoter regions. Translational fusions to a reporter peptide were created to demonstrate T3SS-mediated secretion of two new MAFF303099 effectors. Finally, we showed that mutation of the M. loti MAFF303099 T3SS affects its competitiveness on Lotus glaber and investigated, at the molecular level, responses of the model legume L. japonicus to the T3SS.
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Affiliation(s)
- Cintia Sánchez
- Instituto de Investigaciones Biotecnológicas, INTECH, Universidad Nacional de General San Martín, CONICET, Buenos Aires, Argentina
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Itakura M, Saeki K, Omori H, Yokoyama T, Kaneko T, Tabata S, Ohwada T, Tajima S, Uchiumi T, Honnma K, Fujita K, Iwata H, Saeki Y, Hara Y, Ikeda S, Eda S, Mitsui H, Minamisawa K. Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. THE ISME JOURNAL 2009; 3:326-39. [PMID: 18971963 DOI: 10.1038/ismej.2008.88] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G+C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.
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Affiliation(s)
- Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
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