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Matamoros MA, Romero LC, Tian T, Román Á, Duanmu D, Becana M. Persulfidation of plant and bacteroid proteins is involved in legume nodule development and senescence. J Exp Bot 2024; 75:3009-3025. [PMID: 37952184 PMCID: PMC11103110 DOI: 10.1093/jxb/erad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Legumes establish symbiosis with rhizobia, forming nitrogen-fixing nodules. The central role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in nodule biology has been clearly established. Recently, hydrogen sulfide (H2S) and other reactive sulfur species (RSS) have emerged as novel signaling molecules in animals and plants. A major mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification of proteins. To identify possible functions of H2S in nodule development and senescence, we used the tag-switch method to quantify changes in the persulfidation profile of common bean (Phaseolus vulgaris) nodules at different developmental stages. Proteomic analyses indicate that persulfidation plays a regulatory role in plant and bacteroid metabolism and senescence. The effect of a H2S donor on nodule functioning and on several proteins involved in ROS and RNS homeostasis was also investigated. Our results using recombinant proteins and nodulated plants support a crosstalk among H2S, ROS, and RNS, a protective function of persulfidation on redox-sensitive enzymes, and a beneficial effect of H2S on symbiotic nitrogen fixation. We conclude that the general decrease of persulfidation levels observed in plant proteins of aging nodules is one of the mechanisms that disrupt redox homeostasis leading to senescence.
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Affiliation(s)
- Manuel A Matamoros
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Sevilla, Spain
| | - Tao Tian
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ángela Román
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Manuel Becana
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
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Chen X, Hu X, Jiang J, Wang X. Functions and Mechanisms of Brassinosteroids in Regulating Crop Agronomic Traits. Plant Cell Physiol 2024:pcae044. [PMID: 38619133 DOI: 10.1093/pcp/pcae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Brassinosteroids (BRs) perform crucial functions controlling plant growth and developmental processes, encompassing many agronomic traits in crops. Studies of BR-related genes involved in agronomic traits have suggested that BRs could serve as a potential target for crop breeding. Given the pleiotropic effect of BRs, a systematic understanding of their functions and molecular mechanisms is conducive for application in crop improvement. Here, we summarize the functions and underlying mechanisms by which BRs regulate the several major crop agronomic traits, including plant architecture, grain size, as well as the specific trait of symbiotic nitrogen fixation in legume crops. For plant architecture, we discuss the roles of BRs in plant height, branching number, and leaf erectness and propose how progress in these fields may contribute to designing crops with optimal agronomic traits and improved grain yield by accurately modifying BR levels and signaling pathways.
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Affiliation(s)
- Xu Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Zhengzhou, Henan 450046, China
- College of Agriculture, Henan University, Zhengzhou, Henan 450046, China
| | - Xiaotong Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Zhengzhou, Henan 450046, China
- College of Agriculture, Henan University, Zhengzhou, Henan 450046, China
| | - Jianjun Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Zhengzhou, Henan 450046, China
- Sanya Institute of Henan University, Sanya, Hainan 572025, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Zhengzhou, Henan 450046, China
- Sanya Institute of Henan University, Sanya, Hainan 572025, China
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3
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Li X, Li Z, Wei Y, Chen Z, Xie S. Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii. Appl Environ Microbiol 2024; 90:e0185123. [PMID: 38426790 PMCID: PMC10952539 DOI: 10.1128/aem.01851-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Yajuan Wei
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zirui Chen
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Shijie Xie
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
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Ke X, Wang X. Energy sensors: emerging regulators of symbiotic nitrogen fixation. Trends Plant Sci 2024:S1360-1385(24)00027-X. [PMID: 38402014 DOI: 10.1016/j.tplants.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
Legume-rhizobium symbiotic nitrogen fixation is a highly energy-consuming process. Recent studies demonstrate that nodule-specific energy sensors play important roles in modulating nodule nitrogen fixation capacity. This opens a new field in the energy regulation of symbiotic nitrogen fixation that can provide insights into designing leguminous crops with efficient nitrogen fixation.
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Affiliation(s)
- Xiaolong Ke
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou 450046, China; Sanya Institute of Henan University, Sanya 572025, Hainan, China; The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou 450046, Henan, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou 450046, China; Sanya Institute of Henan University, Sanya 572025, Hainan, China; The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou 450046, Henan, China.
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Cai J, Longo A, Dickstein R. Expression and mutagenesis studies in the Medicago truncatula iron transporter MtVTL8 confirm its role in symbiotic nitrogen fixation and reveal amino acids essential for transport. Front Plant Sci 2024; 14:1306491. [PMID: 38239208 PMCID: PMC10794610 DOI: 10.3389/fpls.2023.1306491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024]
Abstract
The model legume Medicago truncatula establishes a symbiosis with soil bacteria (rhizobia) that carry out symbiotic nitrogen fixation (SNF) in plant root nodules. SNF requires the exchange of nutrients between the plant and rhizobia in the nodule that occurs across a plant-derived symbiosome membrane. One iron transporter, belonging to the Vacuolar iron Transporter-Like (VTL) family, MtVTL8, has been identified as essential for bacteria survival and therefore SNF. In this work we investigated the spatial expression of MtVTL8 in nodules and addressed whether it could be functionally interchangeable with a similar nodule-expressed iron transporter, MtVTL4. Using a structural model for MtVTL8 and the previously hypothesized mechanism for iron transport in a phylogenetically-related Vacuolar Iron Transporter (VIT), EgVIT1 with known crystal structure, we identified critical amino acids and obtained their mutants. Mutants were tested in planta for complementation of an SNF defective line and in an iron sensitive mutant yeast strain. An extended phylogenetic assessment of VTLs and VITs showed that amino acids critical for function are conserved differently in VTLs vs. VITs. Our studies showed that some amino acids are essential for iron transport leading us to suggest a model for MtVTL8 function, one that is different for other iron transporters (VITs) studied so far. This study extends the understanding of iron transport mechanisms in VTLs as well as those used in SNF.
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Zeng RE, Geng QH, Gao HK, Pan QQ, Chen TT, Chen Y, Zhang L. Mechanism of symbiotic nodulation between nitrogen and peanut. Yi Chuan 2023; 45:801-812. [PMID: 37731234 DOI: 10.16288/j.yczz.23-083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Nitrogen is critical for peanut growth and development, and symbiotic nodulation and nitrogen fixation is one of the main ways for peanut to obtain nitrogen. The influence of exogenous nitrogen on nodule nitrogen fixation involves complex regulatory mechanisms, revealing the regulatory mechanisms of nitrogen on nodule nitrogen fixation is of great significance for realizing the potential of biological nitrogen fixation. In this review, we summarize the mechanism of "Crack entry" in the formation of peanut root nodule, the mechanism of symbiotic nodulation and quantitative regulation of peanut, and the regulatory mechanism of nitrogen affecting peanut nodulation. At present, the molecular mechanism by which nitrogen affects the interaction between Bradyrhizobium and peanut, thereby regulating nodulation, is still unclear. Therefore, future research should focus on the signal exchange, nodule number regulation, and nutrient exchange mechanism of nitrogen effects on Bradyrhizobium and peanut, which would provide a theoretical basis for improving nodule nitrogen fixation efficiency and peanut yield, and reduce chemical nitrogen fertilizer application.
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Affiliation(s)
- Rui-Er Zeng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Qing-Hui Geng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Heng-Kuan Gao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Qing-Qing Pan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Ting-Ting Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Yong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
| | - Lei Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou 510642, China
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Long S, Su M, Chen X, Hu A, Yu F, Zou Q, Cheng G. Proteomic and Mutant Analysis of Hydrogenase Maturation Protein Gene hypE in Symbiotic Nitrogen Fixation of Mesorhizobium huakuii. Int J Mol Sci 2023; 24:12534. [PMID: 37628715 PMCID: PMC10454058 DOI: 10.3390/ijms241612534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Hydrogenases catalyze the simple yet important redox reaction between protons and electrons and H2, thus mediating symbiotic interactions. The contribution of hydrogenase to this symbiosis and anti-oxidative damage was investigated using the M. huakuii hypE (encoding hydrogenase maturation protein) mutant. The hypE mutant grew a little faster than its parental 7653R and displayed decreased antioxidative capacity under H2O2-induced oxidative damage. Real-time quantitative PCR showed that hypE gene expression is significantly up-regulated in all the detected stages of nodule development. Although the hypE mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 47% reduction in nitrogen fixation capacity. This phenotype was linked to the formation of smaller abnormal nodules containing disintegrating and prematurely senescent bacteroids. Proteomics analysis allowed a total of ninety differentially expressed proteins (fold change > 1.5 or <0.67, p < 0.05) to be identified. Of these proteins, 21 are related to stress response and virulence, 21 are involved in transporter activity, and 18 are involved in energy and nitrogen metabolism. Overall, the HypE protein is essential for symbiotic nitrogen fixation, playing independent roles in supplying energy and electrons, in bacterial detoxification, and in the control of bacteroid differentiation and senescence.
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Affiliation(s)
| | | | | | | | | | | | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
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de Vries S, Herrfurth C, Li FW, Feussner I, de Vries J. An ancient route towards salicylic acid and its implications for the perpetual Trichormus-Azolla symbiosis. Plant Cell Environ 2023. [PMID: 37394786 DOI: 10.1111/pce.14659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Despite its small size, the water fern Azolla is a giant among plant symbioses. Within each of its leaflets, a specialized leaf cavity is home to a population of nitrogen-fixing cyanobacteria (cyanobionts). Although a number of plant-cyanobiont symbioses exist, Azolla is unique in that its symbiosis is perpetual: the cyanobionts are inherited during sexual and vegetative propagation. What underpins the communication between the two partners? In angiosperms, the phytohormone salicylic acid (SA) is a well-known regulator of plant-microbe interactions. Using high-performance liquid chromatography-tandem mass spectrometry, we pinpoint the presence of SA in the fern. Comparative genomics and phylogenetics on SA biosynthesis genes across Chloroplastida reveal that the entire Phenylalanine ammonia-lyase-dependent pathway likely existed in the last common ancestor of land plants. Indeed, Azolla filiculoides secondarily lost its isochorismate synthase but has the genetic competence to derive SA from benzoic acid; the presence of SA in artificially cyanobiont-free Azolla supports the existence of this route. Global gene expression data and SA levels from cyanobiont-containing and -free A. filiculoides link SA synthesis with the symbioses: SA appears to induce cyanobacterial proliferation, whereas removal of the symbiont results in reduced SA levels in a nitrogen-dependent manner.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
- Goettingen Metabolomics and Lipidomics Laboratory, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, USA
- Plant Biology Section, Cornell University, Ithaca, New York, USA
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
- Goettingen Metabolomics and Lipidomics Laboratory, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
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Zhou Y, Wang L, Rubio MC, Pérez-Rontomé C, Zhou Y, Qi Y, Tian T, Zhang W, Fan Q, Becana M, Duanmu D. Heme catabolism mediated by heme oxygenase in uninfected interstitial cells enables efficient symbiotic nitrogen fixation in Lotus japonicus nodules. New Phytol 2023. [PMID: 37329247 DOI: 10.1111/nph.19074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Legume nodules produce large quantities of heme required for the synthesis of leghemoglobin (Lb) and other hemoproteins. Despite the crucial function of Lb in nitrogen fixation and the toxicity of free heme, the mechanisms of heme homeostasis remain elusive. Biochemical, cellular, and genetic approaches were used to study the role of heme oxygenases (HOs) in heme degradation in the model legume Lotus japonicus. Heme and biliverdin were quantified and localized, HOs were characterized, and knockout LORE1 and CRISPR/Cas9 mutants for LjHO1 were generated and phenotyped. We show that LjHO1, but not the LjHO2 isoform, is responsible for heme catabolism in nodules and identify biliverdin as the in vivo product of the enzyme in senescing green nodules. Spatiotemporal expression analysis revealed that LjHO1 expression and biliverdin production are restricted to the plastids of uninfected interstitial cells. The nodules of ho1 mutants showed decreased nitrogen fixation, and the development of brown, rather than green, nodules during senescence. Increased superoxide production was observed in ho1 nodules, underscoring the importance of LjHO1 in antioxidant defense. We conclude that LjHO1 plays an essential role in degradation of Lb heme, uncovering a novel function of nodule plastids and uninfected interstitial cells in nitrogen fixation.
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Affiliation(s)
- Yu Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longlong Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maria Carmen Rubio
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, Zaragoza, 50059, Spain
| | - Carmen Pérez-Rontomé
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, Zaragoza, 50059, Spain
| | - Yumiao Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongmei Qi
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Tian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiqing Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiuling Fan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manuel Becana
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, Zaragoza, 50059, Spain
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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Feng J, Song Y, Zhu B. Ecosystem-dependent responses of soil carbon storage to phosphorus enrichment. New Phytol 2023; 238:2363-2374. [PMID: 36960561 DOI: 10.1111/nph.18907] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
Phosphorus deposition can stimulate both plant carbon inputs and microbial carbon outputs. However, how P enrichment affects soil organic carbon (SOC) storage and the underlying mechanisms remain unclear. We conducted a meta-analysis of 642 SOC observations from 213 field P addition experiments world-wide and explored the regulations of plant inputs, microbial outputs, plant characteristics, and environmental and experimental factors on SOC responses. We found that, globally, P addition stimulated SOC by 4.0% (95% CI: 2.0-6.0%), but the stimulation only occurred in forest and cropland rather than in grassland. Across sites, the response of SOC correlated with that of plant aboveground rather than belowground biomass, suggesting that the change in plant inputs from aboveground was more important than that from belowground in regulating SOC changes due to P addition. Among multiple factors, plant N fixation status and mean annual temperature were the best predictors for SOC responses to P addition, with SOC stimulation being higher in ecosystems dominated by symbiotic nitrogen fixers and ecosystems in high-temperature regions like tropical forests. Our findings highlight the differential and ecosystem-dependent responses of SOC to P enrichment and can contribute to accurate predictions of soil carbon dynamics in a P-enriched world.
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Affiliation(s)
- Jiguang Feng
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, 100871, China
| | - Yanjun Song
- University of Bordeaux, INRAE, BIOGECO, Pessac, 33615, France
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, 100871, China
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Liyanage DK, Torkamaneh D, Belzile F, Balasubramanian P, Hill B, Thilakarathna MS. The Genotypic Variability among Short-Season Soybean Cultivars for Nitrogen Fixation under Drought Stress. Plants (Basel) 2023; 12:1004. [PMID: 36903865 PMCID: PMC10005650 DOI: 10.3390/plants12051004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Soybean fixes atmospheric nitrogen through the symbiotic rhizobia bacteria that inhabit root nodules. Drought stress negatively affect symbiotic nitrogen fixation (SNF) in soybean. The main objective of this study was to identify allelic variations associated with SNF in short-season Canadian soybean varieties under drought stress. A diversity panel of 103 early-maturity Canadian soybean varieties was evaluated under greenhouse conditions to determine SNF-related traits under drought stress. Drought was imposed after three weeks of plant growth, where plants were maintained at 30% field capacity (FC) (drought) and 80% FC (well-watered) until seed maturity. Under drought stress, soybean plants had lower seed yield, yield components, seed nitrogen content, % nitrogen derived from the atmosphere (%Ndfa), and total seed nitrogen fixed compared to those under well-watered conditions. Significant genotypic variability among soybean varieties was found for yield, yield parameters, and nitrogen fixation traits. A genome-wide association study (GWAS) was conducted using 2.16 M single nucleotide single nucleotide polymorphisms (SNPs) for different yield and nitrogen fixation related parameters for 30% FC and their relative performance (30% FC/80% FC). In total, five quantitative trait locus (QTL) regions, including candidate genes, were detected as significantly associated with %Ndfa under drought stress and relative performance. These genes can potentially aid in future breeding efforts to develop drought-resistant soybean varieties.
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Affiliation(s)
- Dilrukshi Kombala Liyanage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Parthiba Balasubramanian
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Brett Hill
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Malinda S. Thilakarathna
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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12
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Chen WF, Meng XF, Jiao YS, Tian CF, Sui XH, Jiao J, Wang ET, Ma SJ. Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens. Microbiol Spectr 2023; 11:e0107922. [PMID: 36656008 PMCID: PMC9927569 DOI: 10.1128/spectrum.01079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
Bradyrhizobium arachidis strain CCBAU 051107 could differentiate into swollen and nonswollen bacteroids in determinate root nodules of peanut (Arachis hypogaea) and indeterminate nodules of Sophora flavescens, respectively, with different N2 fixation efficiencies. To reveal the mechanism of bacteroid differentiation and symbiosis efficiency in association with different hosts, morphologies, transcriptomes, and nitrogen fixation efficiencies of the root nodules induced by strain CCBAU 051107 on these two plants were compared. Our results indicated that the nitrogenase activity of peanut nodules was 3 times higher than that of S. flavescens nodules, demonstrating the effects of rhizobium-host interaction on symbiotic effectiveness. With transcriptome comparisons, genes involved in biological nitrogen fixation (BNF) and energy metabolism were upregulated, while those involved in DNA replication, bacterial chemotaxis, and flagellar assembly were significantly downregulated in both types of bacteroids compared with those in free-living cells. However, expression levels of genes involved in BNF, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, hydrogenase synthesis, poly-β-hydroxybutyrate (PHB) degradation, and peptidoglycan biosynthesis were significantly greater in the swollen bacteroids of peanut than those in the nonswollen bacteroids of S. flavescens, while contrasting situations were found in expression of genes involved in urea degradation, PHB synthesis, and nitrogen assimilation. Especially higher expression of ureABEF and aspB genes in bacteroids of S. flavescens might imply that the BNF product and nitrogen transport pathway were different from those in peanut. Our study revealed the first differences in bacteroid differentiation and metabolism of these two hosts and will be helpful for us to explore higher-efficiency symbiosis between rhizobia and legumes. IMPORTANCE Rhizobial differentiation into bacteroids in leguminous nodules attracts scientists to investigate its different aspects. The development of bacteroids in the nodule of the important oil crop peanut was first investigated and compared to the status in the nodule of the extremely promiscuous medicinal legume Sophora flavescens by using just a single rhizobial strain of Bradyrhizobium arachidis, CCBAU 051107. This strain differentiates into swollen bacteroids in peanut nodules and nonswollen bacteroids in S. flavescens nodules. The N2-fixing efficiency of the peanut nodules is three times higher than that of S. flavescens. By comparing the transcriptomes of their bacteroids, we found that they have similar gene expression spectra, such as nitrogen fixation and motivity, but different spectra in terms of urease activity and peptidoglycan biosynthesis. Those altered levels of gene expression might be related to their functions and differentiation in respective nodules. Our studies provided novel insight into the rhizobial differentiation and metabolic alteration in different hosts.
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Affiliation(s)
- Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xiang Fei Meng
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Yin Shan Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, Beijing, People’s Republic of China
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, People’s Republic of China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Sheng Jun Ma
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
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13
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Singh J, Valdés-López O. A nodule peptide confiscates haem to promote iron uptake in rhizobia. Trends Plant Sci 2023; 28:125-127. [PMID: 36443185 DOI: 10.1016/j.tplants.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Nodule cysteine-rich (NCR) peptides have a major role in the differentiation of endocytosed bacteria into nitrogen-fixing bacteroids. A recent paper by Sankari et al. indicates that NCR247 is essential for the uptake of iron, a mineral nutrient required for nitrogenase activity. Furthermore, the special ability of NCR247 to sequester haem suggests potential applications for human health.
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Affiliation(s)
- Jawahar Singh
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, México
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, México.
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14
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Kong X, Lv N, Liu S, Xu H, Huang J, Xie X, Tao Q, Wang B, Ji R, Zhang Q, Jiang J. Phytoremediation of isoproturon-contaminated sites by transgenic soybean. Plant Biotechnol J 2023; 21:342-353. [PMID: 36278914 PMCID: PMC9884020 DOI: 10.1111/pbi.13951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The widespread application of isoproturon (IPU) can cause serious pollution to the environment and threaten ecological functions. In this study, the IPU bacterial N-demethylase gene pdmAB was transferred and expressed in the chloroplast of soybean (Glycine max L. 'Zhonghuang13'). The transgenic soybeans exhibited significant tolerance to IPU and demethylated IPU to a less phytotoxic metabolite 3-(4-isopropylphenyl)-1-methylurea (MDIPU) in vivo. The transgenic soybeans removed 98% and 84% IPU from water and soil within 5 and 14 days, respectively, while accumulating less IPU in plant tissues compared with the wild-type (WT). Under IPU stress, transgenic soybeans showed a higher symbiotic nitrogen fixation performance (with higher total nodule biomass and nitrogenase activity) and a more stable rhizosphere bacterial community than the WT. This study developed a transgenic (TS) soybean capable of efficiently removing IPU from its growing environment and recovering a high-symbiotic nitrogen fixation capacity under IPU stress, and provides new insights into the interactions between rhizosphere microorganisms and TS legumes under herbicide stress.
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Affiliation(s)
- Xiangkun Kong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Na Lv
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Songmeng Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Hui Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Junwei Huang
- College of Resources and Environment, Key Laboratory of Agri‐food Safety of Anhui ProvinceAnhui Agricultural UniversityHefeiChina
| | | | - Qing Tao
- Beijing DaBeiNong Technology Co., Ltd.BeijingChina
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the EnvironmentNanjing UniversityNanjingChina
| | - Qun Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
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15
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Liu Y, Lin Y, Guan N, Song Y, Li Y, Xie X. A Lipopolysaccharide Synthesis Gene rfaD from Mesorhizobium huakuii Is Involved in Nodule Development and Symbiotic Nitrogen Fixation. Microorganisms 2022; 11:microorganisms11010059. [PMID: 36677351 PMCID: PMC9866225 DOI: 10.3390/microorganisms11010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Rhizobium lipopolysaccharide (LPS) is an important component of the cell wall of gram-negative bacteria and serves as a signal molecule on the surface of rhizobia, participating in the symbiosis during rhizobia-legume interaction. In this study, we constructed a deletion mutant of ADP-L-glycerol-D-mannoheptosyl-6-exoisomerase (rfaD) of Mesorhizobium huakuii 7653R and a functional complementary strain. The results showed that the deletion of rfaD did not affect the free-living growth rate of 7653R, but that it did affect the LPS synthesis and that it increased sensitivity to abiotic stresses. The rfaD promoter-GUS reporter assay showed that the gene was mainly expressed in the infection zone of the mature nodules. The root nodules formation of the rfaD mutant was delayed during symbiosis with the host plant of Astragalus sinicus. The symbiotic phenotype analyses showed that the nodules of A. sinicus lost symbiotic nitrogen fixation ability, when inoculated with the rfaD mutant strain. In conclusion, our results reveal that the 7653R rfaD gene plays a crucial role in the LPS synthesis involved in the symbiotic interaction between rhizobia and A. sinicus. This study also provides new insights into the molecular mechanisms by which the rhizobia regulate their own gene expression and cell wall components enabling nodulation in legumes.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ye Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Guan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuting Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
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16
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Batstone RT, Lindgren H, Allsup CM, Goralka LA, Riley AB, Grillo MA, Marshall-Colon A, Heath KD. Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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17
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Zarrabian M, Montiel J, Sandal N, Ferguson S, Jin H, Lin YY, Klingl V, Marín M, James EK, Parniske M, Stougaard J, Andersen SU. A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera. Mol Plant Microbe Interact 2022; 35:1006-1017. [PMID: 35852471 DOI: 10.1094/mpmi-06-22-0124-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mohammad Zarrabian
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico. Cuernavaca, Mexico
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Yen-Yu Lin
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Verena Klingl
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Macarena Marín
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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18
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Huang R, Snedden WA, diCenzo GC. Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. Plant Direct 2022; 6:e408. [PMID: 35774624 PMCID: PMC9219011 DOI: 10.1002/pld3.408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 05/10/2023]
Abstract
Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ∼2-fold more abundant in M. sativa than in M. officinalis, and ∼27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.
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Affiliation(s)
- Rui Huang
- Department of BiologyQueen's UniversityKingstonOntarioCanada
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19
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Weisberg AJ, Sachs JL, Chang JH. Dynamic interactions between mega symbiosis ICEs and bacterial chromosomes maintain genome architecture. Genome Biol Evol 2022; 14:6593308. [PMID: 35639596 PMCID: PMC9174649 DOI: 10.1093/gbe/evac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Acquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome–symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA.,Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
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20
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. Front Plant Sci 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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21
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Yi X, Liu J, Chen S, Wu H, Liu M, Xu Q, Lei L, Lee S, Zhang B, Kudrna D, Fan W, Wing RA, Wang X, Zhang M, Zhang J, Yang C, Chen N. Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. G3 (Bethesda) 2022; 12:jkac017. [PMID: 35188189 PMCID: PMC8982393 DOI: 10.1093/g3journal/jkac017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022]
Abstract
Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromosome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with 3 published soybeans (WM82, ZH13, and W05), which identified 5 large inversions and 2 large translocations specific to JD17, 20,984-46,912 presence-absence variations spanning 13.1-46.9 Mb in size. A total of 1,695,741-3,664,629 SNPs and 446,689-800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.
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Affiliation(s)
- Xinxin Yi
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jing Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Hao Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Min Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qing Xu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lingshan Lei
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Seunghee Lee
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Bao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Dave Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Wei Fan
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Rod A Wing
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Mengchen Zhang
- Institute of Food and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, Hebei, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Chunyan Yang
- Institute of Food and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, Hebei, China
| | - Nansheng Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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22
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Wang L, Zhou Y, Li R, Liang J, Tian T, Ji J, Chen R, Zhou Y, Fan Q, Ning G, Larkin RM, Becana M, Duanmu D. Single cell-type transcriptome profiling reveals genes that promote nitrogen fixation in the infected and uninfected cells of legume nodules. Plant Biotechnol J 2022; 20:616-618. [PMID: 35038375 PMCID: PMC8989494 DOI: 10.1111/pbi.13778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/24/2021] [Accepted: 01/07/2022] [Indexed: 06/12/2023]
Affiliation(s)
- Longlong Wang
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yu Zhou
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Runhui Li
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Jianjun Liang
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Tao Tian
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Jie Ji
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Runzhou Chen
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Yumiao Zhou
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Qiuling Fan
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Guogui Ning
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Manuel Becana
- Departamento de Nutrición VegetalEstación Experimental de Aula DeiConsejo Superior de Investigaciones CientíficasZaragozaSpain
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural MicrobiologyHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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23
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Wang Y, Yang P, Zhou Y, Hu T, Zhang P, Wu Y. A proteomic approach to understand the impact of nodulation on salinity stress response in alfalfa (Medicago sativa L.). Plant Biol (Stuttg) 2022; 24:323-332. [PMID: 34870352 DOI: 10.1111/plb.13369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Symbiotic nitrogen fixation in legumes is an important source of nitrogen supply in sustainable agriculture. Salinity is a key abiotic stress that negatively affects host plant growth, rhizobium-legume symbiosis and nitrogen fixation. This work investigates how the symbiotic relationship impacts plant response to salinity stress. We assayed the physiological changes and the proteome profile of alfalfa plants with active nodules (NA), inactive nodules (NI) or without nodules (NN) when plants were subjected to salinity stress. Our data suggest that NA plants respond to salinity stress through some unique signalling regulations. NA plants showed upregulation of proteins related to cell wall remodelling and reactive oxygen species scavenging, and downregulation of proteins involved in protein synthesis and degradation. The data also show that NA plants, together with NI plants, upregulated proteins involved in photosynthesis, carbon fixation and respiration, anion transport and plant defence against pathogens. The study suggests that the symbiotic relationship gave the host plant a better capacity to adjust key processes, probably to more efficiently use energy and resources, deal with oxidative stress, and maintain ion homeostasis and health during salinity stress.
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Affiliation(s)
- Y Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - P Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Y Zhou
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, Australia
| | - T Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - P Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Y Wu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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24
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Zhu J, Jiang X, Guan D, Kang Y, Li L, Cao F, Zhao B, Ma M, Zhao J, Li J. Effects of rehydration on physiological and transcriptional responses of a water-stressed rhizobium. J Microbiol 2022; 60:31-46. [PMID: 34826097 DOI: 10.1007/s12275-022-1325-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023]
Abstract
As a microsymbiont of soybean, Bradyrhizobium japonicum plays an important role in symbiotic nitrogen fixation and sustainable agriculture. However, the survival of B. japonicum cells under water-deplete (e.g., drought) and water-replete (e.g., flood) conditions is a major concern affecting their nitrogen-fixing ability by establishing the symbiotic relationship with the host. In this study, we isolated a water stress tolerant rhizobium from soybean root nodules and tested its survival under water-deplete conditions. The rhizobium was identified as Bradyrhizobium japonicum and named strain 5038. Interestingly, both plate counting and live/dead fluorescence staining assays indicate that a number of viable but non-culturable cells exist in the culture medium upon the rehydration process which could cause dilution stress. Bradyrhizobium japonicum 5038 cells increased production of exopolysaccharide (EPS) and trehalose when dehydrated, suggesting that protective responses were stimulated. As expected, cells reduced their production upon the subsequent rehydration. To examine differential gene expression of B. japonicum 5038 when exposed to water-deplete and subsequent water-replete conditions, whole-genome transcriptional analysis was performed under 10% relative humidity (RH), and subsequent 100% RH, respectively. A total of 462 differentially expressed genes (DEGs, > 2.0-fold) were identified under the 10% RH condition, while 3,776 genes showed differential expression during the subsequent rehydration (100% RH) process. Genes involved in signal transduction, inorganic ion transport, energy production and metabolisms of carbohydrates, amino acids, and lipids were far more up-regulated than down-regulated in the 10% RH condition. Notably, trehalose biosynthetic genes (otsAB, treS, and treYZ), genes ligD, oprB, and a sigma factor rpoH were significantly induced by 10% RH. Under the subsequent 100% RH condition, genes involved in transcription, translation, cell membrane regulation, replication and repair, and protein processing were highly up-regulated. Interestingly, most of 10%-RH inducible genes displayed rehydration-repressed, except three genes encoding heat shock (Hsp20) proteins. Therefore, this study provides molecular evidence for the switch of gene expression of B. japonicum cells when encountered the opposite water availability from water-deplete to water-replete conditions.
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Affiliation(s)
- Jie Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yaowei Kang
- Life Sciences College of Zhaoqing University, Zhaoqing, 526061, P. R. China
| | - Li Li
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
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25
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de Vries S, de Vries J. Evolutionary genomic insights into cyanobacterial symbioses in plants. Quant Plant Biol 2022; 3:e16. [PMID: 37077989 PMCID: PMC10095879 DOI: 10.1017/qpb.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria-plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
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26
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Aguirre-Noyola JL, Rosenblueth M, Santiago-Martínez MG, Martínez-Romero E. Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System. Front Microbiol 2021; 12:740818. [PMID: 34777287 PMCID: PMC8581550 DOI: 10.3389/fmicb.2021.740818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Corn and common bean have been cultivated together in Mesoamerica for thousands of years in an intercropping system called "milpa," where the roots are intermingled, favoring the exchange of their microbiota, including symbionts such as rhizobia. In this work, we studied the genomic expression of Rhizobium phaseoli Ch24-10 (by RNA-seq) after a 2-h treatment in the presence of root exudates of maize and bean grown in monoculture and milpa system under hydroponic conditions. In bean exudates, rhizobial genes for nodulation and degradation of aromatic compounds were induced; while in maize, a response of genes for degradation of mucilage and ferulic acid was observed, as well as those for the transport of sugars, dicarboxylic acids and iron. Ch24-10 transcriptomes in milpa resembled those of beans because they both showed high expression of nodulation genes; some genes that were expressed in corn exudates were also induced by the intercropping system, especially those for the degradation of ferulic acid and pectin. Beans grown in milpa system formed nitrogen-fixing nodules similar to monocultured beans; therefore, the presence of maize did not interfere with Rhizobium-bean symbiosis. Genes for the metabolism of sugars and amino acids, flavonoid and phytoalexin tolerance, and a T3SS were expressed in both monocultures and milpa system, which reveals the adaptive capacity of rhizobia to colonize both legumes and cereals. Transcriptional fusions of the putA gene, which participates in proline metabolism, and of a gene encoding a polygalacturonase were used to validate their participation in plant-microbe interactions. We determined the enzymatic activity of carbonic anhydrase whose gene was also overexpressed in response to root exudates.
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Affiliation(s)
- José Luis Aguirre-Noyola
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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27
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Ficano N, Porder S, McCulloch LA. Tripartite legume-rhizobia-mycorrhizae relationship is influenced by light and soil nitrogen in Neotropical canopy gaps. Ecology 2021; 102:e03489. [PMID: 34292601 DOI: 10.1002/ecy.3489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 11/09/2022]
Abstract
Plants and their soil microbial symbionts influence ecosystem productivity and nutrient cycling, but the controls on these symbioses remain poorly understood. This is particularly true for plants in the Fabaceae family (hereafter legumes), which can associate with both arbuscular mycorrhizal fungi (AMF) and nitrogen (N) -fixing bacteria. Here we report results of the first manipulated field experiment to explore the abiotic and biotic controls of this tripartite symbiosis in Neotropical canopy gaps (hereafter gaps). We grew three species of Neotropical N-fixing legume seedlings under different light (gap-full light, gap-shadecloth, and understory) and soil nitrogen (20 g N·m-2 ·yr-1 vs. 0 g N·m-2 ·yr-1 ) conditions across a lowland tropical forest at La Selva Biological Station, Costa Rica. We harvested the seedlings after 4 months of growth in the field and measured percent AMF root colonization (%AMF), nodule and seeding biomass, and seedling aboveground:belowground biomass ratios. Our expectation was that seedlings in gaps would grow larger and, as a result of higher light, invest more carbon in both AMF and N-fixing bacteria. Indeed, seedlings in gaps had higher total biomass, nodule biomass (a proxy for N-fixing bacteria investment) and rates of AMF root colonization, and the three were significantly positively correlated. However, we only found a significant positive effect of light availability on %AMF when seedlings were fertilized with N. Furthermore, when we statistically controlled for treatment, species, and site effects, we found %AMF and seedling biomass had a negative relationship. This was likely driven by the fact that seedlings invested relatively less in AMF as they increased in biomass (lower %AMF per gram of seedling). Taken together, these results challenge the long-held assumption that high light conditions universally increase carbon investment in AMF and demonstrate that this tripartite symbiosis is influenced by soil nutrient and light conditions.
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Affiliation(s)
- Nikayla Ficano
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, 02912, USA
| | - Stephen Porder
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, 02912, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, 02912, USA
| | - Lindsay A McCulloch
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, 02912, USA
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28
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Wang L, Liang J, Zhou Y, Tian T, Zhang B, Duanmu D. Molecular Characterization of Carbonic Anhydrase Genes in Lotus japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation. Int J Mol Sci 2021; 22:ijms22157766. [PMID: 34360533 PMCID: PMC8346106 DOI: 10.3390/ijms22157766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 12/28/2022] Open
Abstract
Carbonic anhydrase (CA) plays a vital role in photosynthetic tissues of higher plants, whereas its non-photosynthetic role in the symbiotic root nodule was rarely characterized. In this study, 13 CA genes were identified in the model legume Lotus japonicus by comparison with Arabidopsis CA genes. Using qPCR and promoter-reporter fusion methods, three previously identified nodule-enhanced CA genes (LjαCA2, LjαCA6, and LjβCA1) have been further characterized, which exhibit different spatiotemporal expression patterns during nodule development. LjαCA2 was expressed in the central infection zone of the mature nodule, including both infected and uninfected cells. LjαCA6 was restricted to the vascular bundle of the root and nodule. As for LjβCA1, it was expressed in most cell types of nodule primordia but only in peripheral cortical cells and uninfected cells of the mature nodule. Using CRISPR/Cas9 technology, the knockout of LjβCA1 or both LjαCA2 and its homolog, LjαCA1, did not result in abnormal symbiotic phenotype compared with the wild-type plants, suggesting that LjβCA1 or LjαCA1/2 are not essential for the nitrogen fixation under normal symbiotic conditions. Nevertheless, the nodule-enhanced expression patterns and the diverse distributions in different types of cells imply their potential functions during root nodule symbiosis, such as CO2 fixation, N assimilation, and pH regulation, which await further investigations.
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29
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Yu YC, Dickstein R, Longo A. Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules. Front Plant Sci 2021; 12:685334. [PMID: 34276736 PMCID: PMC8282211 DOI: 10.3389/fpls.2021.685334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/17/2021] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation is a complex and regulated process that takes place in root nodules of legumes and allows legumes to grow in soils that lack nitrogen. Nitrogen is mostly acquired from the soil as nitrate and its level in the soil affects nodulation and nitrogen fixation. The mechanism(s) by which legumes modulate nitrate uptake to regulate nodule symbiosis remain unclear. In Medicago truncatula, the MtNPF1.7 transporter has been shown to control nodulation, symbiosis, and root architecture. MtNPF1.7 belongs to the nitrate/peptide transporter family and is a symporter with nitrate transport driven by proton(s). In this study we combined in silico structural predictions with in planta complementation of the severely defective mtnip-1 mutant plants to understand the role of a series of distinct amino acids in the transporter's function. Our results support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. Results reveal that Motif A, a motif conserved among major facilitator transport (MFS) proteins, is essential for function. We hypothesize that it participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. Our results also question the existence of a putative TMH4-TMH10 salt bridge. These results are discussed in the context of potential nutrient transport functions for MtNPF1.7. Our findings add to the knowledge of the mechanism of alternative conformational changes as well as symport transport in NPFs and enhance our knowledge of the mechanisms for nitrate signaling.
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Ayra L, Reyero-Saavedra MDR, Isidra-Arellano MC, Lozano L, Ramírez M, Leija A, Fuentes SI, Girard L, Valdés-López O, Hernández G. Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors. Front Plant Sci 2021; 12:679463. [PMID: 34163511 PMCID: PMC8216239 DOI: 10.3389/fpls.2021.679463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/25/2023]
Abstract
Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.
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Affiliation(s)
- Litzy Ayra
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María del Rocio Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Luis Lozano
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara-Isabel Fuentes
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Castro-Rodríguez R, Escudero V, Reguera M, Gil-Díez P, Quintana J, Prieto RI, Kumar RK, Brear E, Grillet L, Wen J, Mysore KS, Walker EL, Smith PMC, Imperial J, González-Guerrero M. Medicago truncatula Yellow Stripe-Like7 encodes a peptide transporter participating in symbiotic nitrogen fixation. Plant Cell Environ 2021. [PMID: 33797764 DOI: 10.1101/2020.03.26.009159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Yellow Stripe-Like (YSL) proteins are a family of plant transporters that are typically involved in transition metal homeostasis. Three of the four YSL clades (I, II and IV) transport metals complexed with the non-proteinogenic amino acid nicotianamine or its derivatives. No such capability has been shown for any member of clade III, but the link between these YSLs and metal homeostasis could be masked by functional redundancy. We studied the role of the clade III YSL protein MtSYL7 in Medicago truncatula nodules. MtYSL7, which encodes a plasma membrane-bound protein, is mainly expressed in the pericycle and cortex cells of the root nodules. Yeast complementation assays revealed that MtSYL7 can transport short peptides. M. truncatula transposon insertion mutants with decreased expression of MtYSL7 had lower nitrogen fixation rates and showed reduced plant growth whether grown in symbiosis with rhizobia or not. YSL7 mutants accumulated more copper and iron in the nodules, which is likely to result from the increased expression of iron uptake and delivery genes in roots. Taken together, these data suggest that MtYSL7 plays an important role in the transition metal homeostasis of nodules and symbiotic nitrogen fixation.
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Affiliation(s)
- Rosario Castro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - María Reguera
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Patricia Gil-Díez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Julia Quintana
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Rakesh K Kumar
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Ella Brear
- Department of Animal, Plant, and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Louis Grillet
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jiangqi Wen
- Noble Research Institute, LLC., Ardmore, Oklahoma, USA
| | | | - Elsbeth L Walker
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Penelope M C Smith
- Department of Animal, Plant, and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Juan Imperial
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Castro-Rodríguez R, Escudero V, Reguera M, Gil-Díez P, Quintana J, Prieto RI, Kumar RK, Brear E, Grillet L, Wen J, Mysore KS, Walker EL, Smith PMC, Imperial J, González-Guerrero M. Medicago truncatula Yellow Stripe-Like7 encodes a peptide transporter participating in symbiotic nitrogen fixation. Plant Cell Environ 2021; 44:1908-1920. [PMID: 33797764 DOI: 10.1111/pce.14059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Yellow Stripe-Like (YSL) proteins are a family of plant transporters that are typically involved in transition metal homeostasis. Three of the four YSL clades (I, II and IV) transport metals complexed with the non-proteinogenic amino acid nicotianamine or its derivatives. No such capability has been shown for any member of clade III, but the link between these YSLs and metal homeostasis could be masked by functional redundancy. We studied the role of the clade III YSL protein MtSYL7 in Medicago truncatula nodules. MtYSL7, which encodes a plasma membrane-bound protein, is mainly expressed in the pericycle and cortex cells of the root nodules. Yeast complementation assays revealed that MtSYL7 can transport short peptides. M. truncatula transposon insertion mutants with decreased expression of MtYSL7 had lower nitrogen fixation rates and showed reduced plant growth whether grown in symbiosis with rhizobia or not. YSL7 mutants accumulated more copper and iron in the nodules, which is likely to result from the increased expression of iron uptake and delivery genes in roots. Taken together, these data suggest that MtYSL7 plays an important role in the transition metal homeostasis of nodules and symbiotic nitrogen fixation.
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Affiliation(s)
- Rosario Castro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - María Reguera
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Patricia Gil-Díez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Julia Quintana
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Rakesh K Kumar
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Ella Brear
- Department of Animal, Plant, and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Louis Grillet
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jiangqi Wen
- Noble Research Institute, LLC., Ardmore, Oklahoma, USA
| | | | - Elsbeth L Walker
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Penelope M C Smith
- Department of Animal, Plant, and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Juan Imperial
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Huo H, Wang X, Liu Y, Chen J, Wei G. A Nod factor- and type III secretion system-dependent manner for Robinia pseudoacacia to establish symbiosis with Mesorhizobium amorphae CCNWGS0123. Tree Physiol 2021; 41:817-835. [PMID: 33219377 DOI: 10.1093/treephys/tpaa160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/15/2020] [Indexed: 06/11/2023]
Abstract
Under nitrogen-limiting conditions, symbiotic nodulation promotes the growth of legume plants via the fixation of atmospheric nitrogen to ammonia by rhizobia in root nodules. The rhizobial Nod factor (NF) and type III secretion system (T3SS) are two key signaling pathways for establishing the legume-rhizobium symbiosis. However, whether NF signaling is involved in the nodulation of Robinia pseudoacacia and Mesorhizobium amorphae CCNWGS0123, and its symbiotic differences compared with T3SS signaling remain unclear. Therefore, to elucidate the function of NF signaling in nodulation, we mutated nodC in M. amorphae CCNWGS0123, which aborted NF synthesis. Compared with the plants inoculated with the wild type strain, the plants inoculated with the NF-deficient strain exhibited shorter shoots with etiolated leaves. These phenotypic characteristics were similar to those of the plants inoculated with the T3SS-deficient strain, which served as a Nod- (non-effective nodulation) control. The plants inoculated with both the NF- and T3SS-deficient strains formed massive root hair swellings, but no normal infection threads were detected. Sections of the nodules showed that inoculation with the NF- and T3SS-deficient strains induced small, white bumps without any rhizobia inside. Analyzing the accumulation of 6 plant hormones and the expression of 10 plant genes indicated that the NF- and T3SS-deficient strains activated plant defense reactions while suppressing plant symbiotic signaling during the perception and nodulation processes. The requirement for NF signaling appeared to be conserved in two other leguminous trees that can establish symbiosis with M. amorphae CCNWGS0123. In contrast, the function of the T3SS might differ among species, even within the same subfamily (Faboideae). Overall, this work demonstrated that nodulation of R. pseudoacacia and M. amorphae CCNWGS0123 was both NF and T3SS dependent.
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Affiliation(s)
- Haibo Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Yao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Juan Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water conservation, Northwest A&F University, 26 Xinong Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
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Hu A, Chen X, Luo S, Zou Q, Xie J, He D, Li X, Cheng G. Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation. Front Microbiol 2021; 12:627562. [PMID: 33633710 PMCID: PMC7900000 DOI: 10.3389/fmicb.2021.627562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
Glutathione (GSH) plays a key role in regulating the cellular Redox Homeostasis, and appears to be essential for initiation and development of root nodules. Glutathione peroxidase (Gpx) catalyzes the reduction of H2O2 and organic hydroperoxides by oxidation of GSH to oxidized GSH (GSSG), which in turn is reduced by glutathione reductase (GR). However, it has not been determined whether the Rhizobium leguminosarum Gpx or GR is required during symbiotic interactions with pea. To characterize the role of glutathione-dependent enzymes in the symbiotic process, single and double mutants were made in gpxA (encoding glutathione peroxidase) and gshR (encoding glutathione reductase) genes. All the mutations did not affect the rhizobial growth, but they increased the sensitivity of R. leguminosarum strains to H2O2. Mutant in GpxA had no effect on intracellular GSH levels, but can increase the expression of the catalase genes. The gshR mutant can induce the formation of normal nodules, while the gpxA single and double mutants exhibited a nodulation phenotype coupled to more than 50% reduction in the nitrogen fixation capacity, these defects in nodulation were characterized by the formation of ineffective nodules. In addition, the gpxA and gshR double mutant was severely impaired in rhizosphere colonization and competition. Quantitative proteomics using the TMT labeling method was applied to study the differential expression of proteins in bacteroids isolated from pea root nodules. A total of 27 differentially expressed proteins were identified in these root bacteroids including twenty down-regulated and seven up-regulated proteins. By sorting the down-regulated proteins, eight are transporter proteins, seven are dehydrogenase, deoxygenase, oxidase, and hydrolase. Moreover, three down-regulating proteins are directly involved in nodule process.
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Affiliation(s)
- Aiqi Hu
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Xiaohong Chen
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Sha Luo
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Qian Zou
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Jing Xie
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Donglan He
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Xiaohua Li
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
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Zou Q, Zhou Y, Cheng G, Peng Y, Luo S, Wu H, Yan C, Li X, He D. Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841. Appl Environ Microbiol 2021; 87:AEM. [PMID: 33277272 DOI: 10.1128/AEM.01956-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Glutaredoxins (Grx) are redoxin family proteins that reduce disulfides and mixed disulfides between glutathione and proteins. Rhizobium leguminosarum bv. Viciae 3841 contains three genes coding for glutaredoxins: RL4289 (grxA) codes for a dithiolic glutaredoxin, RL2615 (grxB) codes for a monothiol glutaredoxin, while RL4261 (grxC) codes for a glutaredoxin-like NrdH protein. We generated mutants interrupted in one, two, or three glutaredoxin genes. These mutants had no obvious differences in growth phenotypes from the wild type RL3841. However, while a mutant of grxC did not affect the antioxidant or symbiotic capacities of R. leguminosarum, grxA-derived or grxB mutants decreased antioxidant and nitrogen fixation capacities. Furthermore, grxA mutants were severely impaired in rhizosphere colonization, and formed smaller nodules with defects of bacteroid differentiation, whereas nodules induced by grxB mutants contained abnormally thick cortices and prematurely senescent bacteroids. The grx triple mutant had the greatest defect in antioxidant and symbiotic capacities of R. leguminosarum and quantitative proteomics revealed it had 56 up-regulated and 81 down-regulated proteins relative to wildtype. Of these proteins, twenty-eight are involved in transporter activity, twenty are related to stress response and virulence, and sixteen are involved in amino acid metabolism. Overall, R. leguminosarum glutaredoxins behave as antioxidant proteins mediating root nodule symbiosis.IMPORTANCE Glutaredoxin catalyzes glutathionylation/deglutathionylation reactions, protects SH-groups from oxidation and restores functionally active thiols. Three glutaredoxins exist in R. leguminosarum and their properties were investigated in free-living bacteria and during nitrogen-fixing symbiosis. All the glutaredoxins were necessary for oxidative stress defense. Dithiol GrxA affects nodulation and nitrogen fixation of bacteroids by altering deglutathionylation reactions, monothiol GrxB is involved in symbiotic nitrogen fixation by regulating Fe-S cluster biogenesis, and GrxC may participate in symbiosis by an unknown mechanism. Proteome analysis provides clues to explain the differences between the grx triple mutant and wild-type nodules.
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de Borja Reis AF, Moro Rosso L, Purcell LC, Naeve S, Casteel SN, Kovács P, Archontoulis S, Davidson D, Ciampitti IA. Environmental Factors Associated With Nitrogen Fixation Prediction in Soybean. Front Plant Sci 2021; 12:675410. [PMID: 34211487 PMCID: PMC8239404 DOI: 10.3389/fpls.2021.675410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/06/2021] [Indexed: 05/10/2023]
Abstract
Biological nitrogen (N)-fixation is the most important source of N for soybean [Glycine max (L.) Merr.], with considerable implications for sustainable intensification. Therefore, this study aimed to investigate the relevance of environmental factors driving N-fixation and to develop predictive models defining the role of N-fixation for improved productivity and increased seed protein concentration. Using the elastic net regularization of multiple linear regression, we analyzed 40 environmental factors related to weather, soil, and crop management. We selected the most important factors associated with the relative abundance of ureides (RAU) as an indicator of the fraction of N derived from N-fixation. The most relevant RAU predictors were N fertilization, atmospheric vapor pressure deficit (VPD) and precipitation during early reproductive growth (R1-R4 stages), sowing date, drought stress during seed filling (R5-R6), soil cation exchange capacity (CEC), and soil sulfate concentration before sowing. Soybean N-fixation ranged from 60 to 98% across locations and years (n = 95). The predictive model for RAU showed relative mean square error (RRMSE) of 4.5% and an R2 value of 0.69, estimated via cross-validation. In addition, we built similar predictive models of yield and seed protein to assess the association of RAU and these plant traits. The variable RAU was selected as a covariable for the models predicting yield and seed protein, but with a small magnitude relative to the sowing date for yield or soil sulfate for protein. The early-reproductive period VPD affected all independent variables, namely RAU, yield, and seed protein. The elastic net algorithm successfully depicted some otherwise challenging empirical relationships to assess with bivariate associations in observational data. This approach provides inference about environmental variables while predicting N-fixation. The outcomes of this study will provide a foundation for improving the understanding of N-fixation within the context of sustainable intensification of soybean production.
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Affiliation(s)
- André Froes de Borja Reis
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: André Froes de Borja Reis, ; Ignacio A. Ciampitti,
| | - Luiz Moro Rosso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Larry C. Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Seth Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Shaun N. Casteel
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Péter Kovács
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | | | - Dan Davidson
- Davidson Agronomics and Consulting, Omaha, NE, United States
| | - Ignacio A. Ciampitti
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: André Froes de Borja Reis, ; Ignacio A. Ciampitti,
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García-Soto I, Boussageon R, Cruz-Farfán YM, Castro-Chilpa JD, Hernández-Cerezo LX, Bustos-Zagal V, Leija-Salas A, Hernández G, Torres M, Formey D, Courty PE, Wipf D, Serrano M, Tromas A. The Lotus japonicus ROP3 Is Involved in the Establishment of the Nitrogen-Fixing Symbiosis but Not of the Arbuscular Mycorrhizal Symbiosis. Front Plant Sci 2021; 12:696450. [PMID: 34868100 PMCID: PMC8636059 DOI: 10.3389/fpls.2021.696450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/25/2021] [Indexed: 05/17/2023]
Abstract
Legumes form root mutualistic symbioses with some soil microbes promoting their growth, rhizobia, and arbuscular mycorrhizal fungi (AMF). A conserved set of plant proteins rules the transduction of symbiotic signals from rhizobia and AMF in a so-called common symbiotic signaling pathway (CSSP). Despite considerable efforts and advances over the past 20 years, there are still key elements to be discovered about the establishment of these root symbioses. Rhizobia and AMF root colonization are possible after a deep cell reorganization. In the interaction between the model legume Lotus japonicus and Mesorhizobium loti, this reorganization has been shown to be dependent on a SCAR/Wave-like signaling module, including Rho-GTPase (ROP in plants). Here, we studied the potential role of ROP3 in the nitrogen-fixing symbiosis (NFS) as well as in the arbuscular mycorrhizal symbiosis (AMS). We performed a detailed phenotypic study on the effects of the loss of a single ROP on the establishment of both root symbioses. Moreover, we evaluated the expression of key genes related to CSSP and to the rhizobial-specific pathway. Under our experimental conditions, rop3 mutant showed less nodule formation at 7- and 21-days post inoculation as well as less microcolonies and a higher frequency of epidermal infection threads. However, AMF root colonization was not affected. These results suggest a role of ROP3 as a positive regulator of infection thread formation and nodulation in L. japonicus. In addition, CSSP gene expression was neither affected in NFS nor in AMS condition in rop3 mutant. whereas the expression level of some genes belonging to the rhizobial-specific pathway, like RACK1, decreased in the NFS. In conclusion, ROP3 appears to be involved in the NFS, but is neither required for intra-radical growth of AMF nor arbuscule formation.
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Affiliation(s)
- Ivette García-Soto
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Ivette García-Soto,
| | - Raphael Boussageon
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | | | | | | | - Victor Bustos-Zagal
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija-Salas
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Mario Serrano,
| | - Alexandre Tromas
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- La Cité College, Bureau de la Recherche et de l’Innovation, Ottawa, ON, Canada
- Alexandre Tromas,
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Castro-Rodríguez R, Abreu I, Reguera M, Novoa-Aponte L, Mijovilovich A, Escudero V, Jiménez-Pastor FJ, Abadía J, Wen J, Mysore KS, Álvarez-Fernández A, Küpper H, Imperial J, González-Guerrero M. The Medicago truncatula Yellow Stripe1-Like3 gene is involved in vascular delivery of transition metals to root nodules. J Exp Bot 2020; 71:7257-7269. [PMID: 32841350 DOI: 10.1093/jxb/eraa390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Symbiotic nitrogen fixation carried out in legume root nodules requires transition metals. These nutrients are delivered by the host plant to the endosymbiotic nitrogen-fixing bacteria living within the nodule cells, a process in which vascular transport is essential. As members of the Yellow Stripe-Like (YSL) family of metal transporters are involved in root to shoot transport, they should also be required for root to nodule metal delivery. The genome of the model legume Medicago truncatula encodes eight YSL proteins, four of them with a high degree of similarity to Arabidopsis thaliana YSLs involved in long-distance metal trafficking. Among them, MtYSL3 is a plasma membrane protein expressed by vascular cells in roots and nodules and by cortical nodule cells. Reducing the expression level of this gene had no major effect on plant physiology when assimilable nitrogen was provided in the nutrient solution. However, nodule functioning was severely impaired, with a significant reduction of nitrogen fixation capabilities. Further, iron and zinc accumulation and distribution changed. Iron was retained in the apical region of the nodule, while zinc became strongly accumulated in the nodule veins in the ysl3 mutant. These data suggest a role for MtYSL3 in vascular delivery of iron and zinc to symbiotic nitrogen fixation.
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Affiliation(s)
- Rosario Castro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Crta. M-40 km 38, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Crta. M-40 km 38, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - María Reguera
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Crta. M-40 km 38, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Ana Mijovilovich
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Česke Budějovice, Czech Republic
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Crta. M-40 km 38, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Francisco J Jiménez-Pastor
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana 1005, Zaragoza, Spain
| | - Javier Abadía
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana 1005, Zaragoza, Spain
| | | | | | - Ana Álvarez-Fernández
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana 1005, Zaragoza, Spain
| | - Hendrik Küpper
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Česke Budějovice, Czech Republic
- University of South Bohemia, Department of Experimental Plant Biology, Branišovská 31/1160, 370 05 České Budějovice, Czech Republic
| | - Juan Imperial
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (ICA-CSIC), Serrano, 115 bis, 28006 Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Crta. M-40 km 38, 28223 Pozuelo de Alarcón (Madrid), Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY. Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae. Genome Biol Evol 2020; 12:2002-2014. [PMID: 32687170 PMCID: PMC7719263 DOI: 10.1093/gbe/evaa152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.
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Affiliation(s)
- Ling-Ling Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, PR China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City D.F., México
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
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Escudero V, Abreu I, Tejada-Jiménez M, Rosa-Núñez E, Quintana J, Prieto RI, Larue C, Wen J, Villanova J, Mysore KS, Argüello JM, Castillo-Michel H, Imperial J, González-Guerrero M. Medicago truncatula Ferroportin2 mediates iron import into nodule symbiosomes. New Phytol 2020; 228:194-209. [PMID: 32367515 DOI: 10.1111/nph.16642] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Iron is an essential cofactor for symbiotic nitrogen fixation, required by many of the enzymes involved, including signal transduction proteins, O2 homeostasis systems, and nitrogenase itself. Consequently, host plants have developed a transport network to deliver essential iron to nitrogen-fixing nodule cells. Ferroportin family members in model legume Medicago truncatula were identified and their expression was determined. Yeast complementation assays, immunolocalization, characterization of a tnt1 insertional mutant line, and synchrotron-based X-ray fluorescence assays were carried out in the nodule-specific M. truncatula ferroportin Medicago truncatula nodule-specific gene Ferroportin2 (MtFPN2) is an iron-efflux protein. MtFPN2 is located in intracellular membranes in the nodule vasculature and in inner nodule tissues, as well as in the symbiosome membranes in the interzone and early-fixation zone of the nodules. Loss-of-function of MtFPN2 alters iron distribution and speciation in nodules, reducing nitrogenase activity and biomass production. Using promoters with different tissular activity to drive MtFPN2 expression in MtFPN2 mutants, we determined that expression in the inner nodule tissues is sufficient to restore the phenotype, while confining MtFPN2 expression to the vasculature did not improve the mutant phenotype. These data indicate that MtFPN2 plays a primary role in iron delivery to nitrogen-fixing bacteroids in M. truncatula nodules.
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Affiliation(s)
- Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Manuel Tejada-Jiménez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Elena Rosa-Núñez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Julia Quintana
- Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Camille Larue
- EcoLab, CNRS, Université de Toulouse, Toulouse, 31326, France
| | - Jiangqi Wen
- Noble Research Institute, Ardmore, OK, 73401, USA
| | - Julie Villanova
- ID16 Beamline. European Synchrotron Radiation Facility, Grenoble, 38043, France
| | | | | | | | - Juan Imperial
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, 28006, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), 28223, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, 28040, Spain
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Liu A, Ku YS, Contador CA, Lam HM. The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi. Front Genet 2020; 11:583954. [PMID: 33193716 PMCID: PMC7554533 DOI: 10.3389/fgene.2020.583954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/08/2020] [Indexed: 12/03/2022] Open
Abstract
Legumes are unique among plants as they can obtain nitrogen through symbiosis with nitrogen-fixing rhizobia that form root nodules in the host plants. Therefore they are valuable crops for sustainable agriculture. Increasing nitrogen fixation efficiency is not only important for achieving better plant growth and yield, but it is also crucial for reducing the use of nitrogen fertilizer. Arbuscular mycorrhizal fungi (AMF) are another group of important beneficial microorganisms that form symbiotic relationships with legumes. AMF can promote host plant growth by providing mineral nutrients and improving the soil ecosystem. The trilateral legume-rhizobia-AMF symbiotic relationships also enhance plant development and tolerance against biotic and abiotic stresses. It is known that domestication and agricultural activities have led to the reduced genetic diversity of cultivated germplasms and higher sensitivity to nutrient deficiencies in crop plants, but how domestication has impacted the capability of legumes to establish beneficial associations with rhizospheric microbes (including rhizobia and fungi) is not well-studied. In this review, we will discuss the impacts of domestication and agricultural practices on the interactions between legumes and soil microbes, focusing on the effects on AMF and rhizobial symbioses and hence nutrient acquisition by host legumes. In addition, we will summarize the genes involved in legume-microbe interactions and studies that have contributed to a better understanding of legume symbiotic associations using metabolic modeling.
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Affiliation(s)
| | | | | | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Komaitis F, Kalliampakou K, Botou M, Nikolaidis M, Kalloniati C, Skliros D, Du B, Rennenberg H, Amoutzias GD, Frillingos S, Flemetakis E. Molecular and physiological characterization of the monosaccharide transporters gene family in Medicago truncatula. J Exp Bot 2020; 71:3110-3125. [PMID: 32016431 DOI: 10.1093/jxb/eraa055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Monosaccharide transporters (MSTs) represent key components of the carbon transport and partitioning mechanisms in plants, mediating the cell-to-cell and long-distance distribution of a wide variety of monosaccharides. In this study, we performed a thorough structural, molecular, and physiological characterization of the monosaccharide transporter gene family in the model legume Medicago truncatula. The complete set of MST family members was identified with a novel bioinformatic approach. Prolonged darkness was used as a test condition to identify the relevant transcriptomic and metabolic responses combining MST transcript profiling and metabolomic analysis. Our results suggest that MSTs play a pivotal role in the efficient partitioning and utilization of sugars, and possibly in the mechanisms of carbon remobilization in nodules upon photosynthate-limiting conditions, as nodules are forced to acquire a new role as a source of both C and N.
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Affiliation(s)
- Fotios Komaitis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Kalliampakou
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Maria Botou
- Laboratory of Biological Chemistry, Department of Medicine, University of Ioannina, Ioannina, Greece
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Chrysanthi Kalloniati
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Baoguo Du
- Institute of Forest Sciences, Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Freiburg, Germany
| | - Heinz Rennenberg
- Institute of Forest Sciences, Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Freiburg, Germany
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Grigoris D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, Department of Medicine, University of Ioannina, Ioannina, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
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Harris JM, Pawlowski K, Mathesius U. Editorial: Evolution of Signaling in Plant Symbioses. Front Plant Sci 2020; 11:456. [PMID: 32411157 PMCID: PMC7198894 DOI: 10.3389/fpls.2020.00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/27/2020] [Indexed: 05/29/2023]
Affiliation(s)
- Jeanne Marie Harris
- Department of Plant Biology, University of Vermont, Burlington, VT, United States
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
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Zou Q, Luo S, Wu H, He D, Li X, Cheng G. A GMC Oxidoreductase GmcA Is Required for Symbiotic Nitrogen Fixation in Rhizobium leguminosarum bv. viciae. Front Microbiol 2020; 11:394. [PMID: 32265862 PMCID: PMC7105596 DOI: 10.3389/fmicb.2020.00394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
GmcA is a FAD-containing enzyme belonging to the GMC (glucose-methanol-choline oxidase) family of oxidoreductases. A mutation in the Rhizobium leguminosarum gmcA gene was generated by homologous recombination. The mutation in gmcA did not affect the growth of R. leguminosarum, but it displayed decreased antioxidative capacity at H2O2 conditions higher than 5 mM. The gmcA mutant strain displayed no difference of glutathione reductase activity, but significantly lower level of the glutathione peroxidase activity than the wild type. Although the gmcA mutant was able to induce the formation of nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 30% reduction in the nitrogen fixation capacity. The observation on ultrastructure of 4-week pea nodules showed that the mutant bacteroids tended to start senescence earlier and accumulate poly-β-hydroxybutyrate (PHB) granules. In addition, the gmcA mutant was severely impaired in rhizosphere colonization. Real-time quantitative PCR showed that the gmcA gene expression was significantly up-regulated in all the detected stages of nodule development, and statistically significant decreases in the expression of the redoxin genes katG, katE, and ohrB were found in gmcA mutant bacteroids. LC-MS/MS analysis quantitative proteomics techniques were employed to compare differential gmcA mutant root bacteroids in response to the wild type infection. Sixty differentially expressed proteins were identified including 33 up-regulated and 27 down-regulated proteins. By sorting the identified proteins according to metabolic function, 15 proteins were transporter protein, 12 proteins were related to stress response and virulence, and 9 proteins were related to transcription factor activity. Moreover, nine proteins related to amino acid metabolism were over-expressed.
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Affiliation(s)
- Qian Zou
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Sha Luo
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hetao Wu
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Donglan He
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Xiaohua Li
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
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Maillet F, Fournier J, Mendis HC, Tadege M, Wen J, Ratet P, Mysore KS, Gough C, Jones KM. Sinorhizobium meliloti succinylated high-molecular-weight succinoglycan and the Medicago truncatula LysM receptor-like kinase MtLYK10 participate independently in symbiotic infection. Plant J 2020; 102:311-326. [PMID: 31782853 PMCID: PMC9327734 DOI: 10.1111/tpj.14625] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
The formation of nitrogen-fixing nodules on legume hosts is a finely tuned process involving many components of both symbiotic partners. Production of the exopolysaccharide succinoglycan by the nitrogen-fixing bacterium Sinorhizobium meliloti 1021 is needed for an effective symbiosis with Medicago spp., and the succinyl modification to this polysaccharide is critical. However, it is not known when succinoglycan intervenes in the symbiotic process, and it is not known whether the plant lysin-motif receptor-like kinase MtLYK10 intervenes in recognition of succinoglycan, as might be inferred from work on the Lotus japonicus MtLYK10 ortholog, LjEPR3. We studied the symbiotic infection phenotypes of S. meliloti mutants deficient in succinoglycan production or producing modified succinoglycan, in wild-type Medicago truncatula plants and in Mtlyk10 mutant plants. On wild-type plants, S. meliloti strains producing no succinoglycan or only unsuccinylated succinoglycan still induced nodule primordia and epidermal infections, but further progression of the symbiotic process was blocked. These S. meliloti mutants induced a more severe infection phenotype on Mtlyk10 mutant plants. Nodulation by succinoglycan-defective strains was achieved by in trans rescue with a Nod factor-deficient S. meliloti mutant. While the Nod factor-deficient strain was always more abundant inside nodules, the succinoglycan-deficient strain was more efficient than the strain producing only unsuccinylated succinoglycan. Together, these data show that succinylated succinoglycan is essential for infection thread formation in M. truncatula, and that MtLYK10 plays an important, but different role in this symbiotic process. These data also suggest that succinoglycan is more important than Nod factors for bacterial survival inside nodules.
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Affiliation(s)
- Fabienne Maillet
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Joëlle Fournier
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Hajeewaka C. Mendis
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
| | - Million Tadege
- Department of Plant and Soil SciencesInstitute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
| | - Jiangqi Wen
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Pascal Ratet
- IPS2Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-SaclayBâtiment 63091405OrsayFrance
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-CitéBâtiment 63091405OrsayFrance
| | | | - Clare Gough
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Kathryn M. Jones
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
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Couchoud M, Salon C, Girodet S, Jeudy C, Vernoud V, Prudent M. Pea Efficiency of Post-drought Recovery Relies on the Strategy to Fine-Tune Nitrogen Nutrition. Front Plant Sci 2020; 11:204. [PMID: 32174946 PMCID: PMC7056749 DOI: 10.3389/fpls.2020.00204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/11/2020] [Indexed: 05/03/2023]
Abstract
As drought is increasingly frequent in the context of climate change it is a major constraint for crop growth and yield. The ability of plants to maintain their yield in response to drought depends not only on their ability to tolerate drought, but also on their capacity to subsequently recover. Post-stress recovery can indeed be decisive for drought resilience and yield stability. Pea (Pisum sativum), as a legume, has the capacity to fix atmospheric nitrogen through its symbiotic interaction with soil bacteria within root nodules. Biological nitrogen fixation is highly sensitive to drought which can impact plant nitrogen nutrition and growth. Our study aimed at dynamically evaluating whether the control of plant N status after drought could affect nodulated pea plant's ability to recover. Two pea genotypes, Puget and Kayanne, displaying different drought resilience abilities were compared for their capacity to tolerate to, and to recover from, a 2-weeks water-deficit period applied before flowering. Physiological processes were studied in this time-series experiment using a conceptual structure-function analysis framework focusing on whole plant carbon, nitrogen, and water fluxes combined to two 13CO2 and 15N2 labeling experiments. While Puget showed a yield decrease compared to well-watered plants, Kayanne was able to maintain its yield. During the recovery period, genotype-dependent strategies were observed. The analysis of the synchronization of carbon, nitrogen, and water related traits dynamics during the recovery period and at the whole plant level, revealed that plant growth recovery was tightly linked to N nutrition. In Puget, the initiation of new nodules after water deficit was delayed compared to control plants, and additional nodules developed, while in Kayanne the formation of nodules was both rapidly and strictly re-adjusted to plant growth needs, allowing a full recovery. Our study suggested that a rapid re-launch of N acquisition, associated with a fine-tuning of nodule formation during the post-stress period is essential for efficient drought resilience in pea leading to yield stability.
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Reinprecht Y, Schram L, Marsolais F, Smith TH, Hill B, Pauls KP. Effects of Nitrogen Application on Nitrogen Fixation in Common Bean Production. Front Plant Sci 2020; 11:1172. [PMID: 32849727 PMCID: PMC7424037 DOI: 10.3389/fpls.2020.01172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/20/2020] [Indexed: 05/13/2023]
Abstract
The nitrogen fixing ability of common bean (Phaseolus vulgaris L.) in association with rhizobia is often characterized as poor compared to other legumes, and nitrogen fertilizers are commonly used in bean production to achieve high yields, which in general inhibits nitrogen fixation. In addition, plants cannot take up all the nitrogen applied to the soil as a fertilizer leading to runoff and groundwater contamination. The overall objective of this work is to reduce use of nitrogen fertilizer in common bean production. This would be a major advance in profitability for the common bean industry in Canada and would significantly improve the ecological footprint of the crop. In the current work, 22 bean genotypes [including recombinant inbred lines (RILs) from the Mist × Sanilac population and a non-nodulating mutant (R99)] were screened for their capacity to fix atmospheric nitrogen under four nitrogen regimes. The genotypes were evaluated in replicated field trials on N-poor soils over three years for the percent nitrogen derived from atmosphere (%Ndfa), yield, and a number of yield-related traits. Bean genotypes differed for all analyzed traits, and the level of nitrogen significantly affected most of the traits, including %Ndfa and yield in all three years. In contrast, application of rhizobia significantly affected only few traits, and the effect was inconsistent among the years. Nitrogen application reduced symbiotic nitrogen fixation (SNF) to various degrees in different bean genotypes. This variation suggests that SNF in common bean can be improved through breeding and selection for the ability of bean genotypes to fix nitrogen in the presence of reduced fertilizer levels. Moreover, genotypes like RIL_38, RIL_119, and RIL_131, being both high yielding and good nitrogen fixers, have potential for simultaneous improvement of both traits. However, breeding advancement might be slow due to an inconsistent correlation between these traits.
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Affiliation(s)
- Yarmilla Reinprecht
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- *Correspondence: Yarmilla Reinprecht,
| | - Lyndsay Schram
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Thomas H. Smith
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Brett Hill
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Woliy K, Degefu T, Frostegård Å. Host Range and Symbiotic Effectiveness of N 2O Reducing Bradyrhizobium Strains. Front Microbiol 2019; 10:2746. [PMID: 31849890 PMCID: PMC6896821 DOI: 10.3389/fmicb.2019.02746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Emissions of the potent greenhouse gas N2O is one of the environmental problems associated with intensive use of synthetic N fertilizers, and novel N2O mitigation strategies are needed to minimize fertilizer applications and N2O release without affecting agricultural efficiencies. Increased incorporation of legume crops in agricultural practices offers a sustainable alternative. Legumes, in their symbiosis with nitrogen fixing bacteria, rhizobia, reduce the need for fertilizers and also respond to the need for increased production of plant-based proteins. Not all combinations of rhizobia and legumes result in efficient nitrogen fixation, and legume crops therefore often need to be inoculated with compatible rhizobial strains. Recent research has demonstrated that some rhizobia are also very efficient N2O reducers. Several nutritionally and economically important legumes form root nodules in symbiosis with bacteria belonging to Bradyrhizobium. Here, the host-ranges of fourteen N2O reducing Bradyrhizobium strains were tested on six legume hosts; cowpea, groundnut, mung bean, haricot bean, soybean, and alfalfa. The plants were grown for 35 days in pots in sterile sand supplemented with N-free nutrient solution. Cowpea was the most promiscuous host nodulated by all test strains, followed by groundnut (11 strains) and mungbean (4 strains). Three test strains were able to nodulate all these three legumes, while none nodulated the other three hosts. For cowpea, five strains increased the shoot dry weight and ten strains the shoot nitrogen content (pairwise comparison; p < 0.05). For groundnut the corresponding results were three and nine strains. The symbiotic effectiveness for the different strains ranged from 45 to 98% in cowpea and 34 to 95% in groundnut, relative to fertilized controls. The N2O reduction capacity of detached nodules from cowpea plants inoculated with one of these strains confirmed active N2O reduction inside the nodules. When released from senescent nodules such strains are expected to also act as sinks for N2O produced by denitrifying organisms in the soil microbial community. Our strategy to search among known N2O-reducing Bradyrhizobium strains for their N2-fixation effectiveness successfully identified several strains which can potentially be used for the production of legume inoculants with the dual capacities of efficacious N2-fixation and N2O reduction.
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Affiliation(s)
- Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Chu Q, Sha Z, Maruyama H, Yang L, Pan G, Xue L, Watanabe T. Metabolic reprogramming in nodules, roots, and leaves of symbiotic soybean in response to iron deficiency. Plant Cell Environ 2019; 42:3027-3043. [PMID: 31283836 DOI: 10.1111/pce.13608] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 05/28/2023]
Abstract
To elucidate the mechanism of adaptation of leguminous plants to iron (Fe)-deficient environment, comprehensive analyses of soybean (Glycine max) plants (sampled at anthesis) were conducted under Fe-sufficient control and Fe-deficient treatment using metabolomic and physiological approach. Our results show that soybeans grown under Fe-deficient conditions showed lower nitrogen (N) fixation efficiency; however, ureides increased in different tissues, indicating potential N-feedback inhibition. N assimilation was inhibited as observed in the repressed amino acids biosynthesis and reduced proteins in roots and nodules. In Fe-deficient leaves, many amino acids increased, accompanied by the reduction of malate, fumarate, succinate, and α-ketoglutarate, which implies the N reprogramming was stimulated by the anaplerotic pathway. Accordingly, many organic acids increased in roots and nodules; however, enzymes involved in the related metabolic pathway (e.g., Krebs cycle) showed opposite activity between roots and nodules, indicative of different mechanisms. Sugars increased or maintained at constant level in different tissues under Fe deficiency, which probably relates to oxidative stress, cell wall damage, and feedback regulation. Increased ascorbate, nicotinate, raffinose, galactinol, and proline in different tissues possibly helped resist the oxidative stress induced by Fe deficiency. Overall, Fe deficiency induced the coordinated metabolic reprogramming in different tissues of symbiotic soybean plants.
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Affiliation(s)
- Qingnan Chu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Centre of Integrated Water-Energy-Food Studies, School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Nottinghamshire, NG25 0QF, UK
| | - Zhimin Sha
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Graduate School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hayato Maruyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Linzhang Yang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Gang Pan
- Centre of Integrated Water-Energy-Food Studies, School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Nottinghamshire, NG25 0QF, UK
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Toshihiro Watanabe
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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Hashimoto S, Wongdee J, Songwattana P, Greetatorn T, Goto K, Tittabutr P, Boonkerd N, Teaumroong N, Uchiumi T. Homocitrate Synthase Genes of Two Wide-Host-Range Bradyrhizobium Strains are Differently Required for Symbiosis Depending on Host Plants. Microbes Environ 2019; 34:393-401. [PMID: 31597890 PMCID: PMC6934396 DOI: 10.1264/jsme2.me19078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nifV gene encodes homocitrate synthase, the enzyme that catalyzes the formation of homocitrate, which is essential for arranging the FeMo-cofactor in the catalytic center of nitrogenase. Some host plants, such as Lotus japonicus, supply homocitrate to their symbionts, in this case, Mesorhizobium loti, which lacks nifV. In contrast, Bradyrhizobium ORS285, a symbiont of Aeschynomene cross-inoculation (CI) groups 2 and 3, requires nifV for symbiosis with Aeschynomene species that belong to CI group 3, and some species belonging to CI group 2. However, it currently remains unclear whether rhizobial nifV is required for symbiosis with Aeschynomene species belonging to CI group 1 or with other legumes. We generated nifV-disruption (ΔnifV) mutants of two wide-host-range rhizobia, Bradyrhizobium SUTN9-2 and DOA9, to investigate whether they require nifV for symbiosis. Both ΔnifV mutant strains showed significantly less nitrogenase activity in a free-living state than the respective wild-type strains. The symbiotic phenotypes of SUTN9-2, DOA9, and their ΔnifV mutants were examined with four legumes, Aeschynomene americana, Stylosanthes hamata, Indigofera tinctoria, and Desmodium tortuosum. nifV was required for the efficient symbiosis of SUTN9-2 with A. americana (CI group 1), but not for that of DOA9. SUTN9-2 established symbiosis with all three other legumes; nifV was required for symbiosis with I. tinctoria and D. tortuosum. These results suggest that, in addition to Aeschynomene CI groups 2 and 3, CI group 1 and several other legumes require the rhizobial nifV for symbiosis.
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Affiliation(s)
- Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Kohki Goto
- Graduate School of Science and Engineering, Kagoshima University
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University
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