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Quelas JI, Cabrera JJ, Díaz-Peña R, Sánchez-Schneider L, Jiménez-Leiva A, Tortosa G, Delgado MJ, Pettinari MJ, Lodeiro AR, del Val C, Mesa S. Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism. Int J Mol Sci 2024; 25:2157. [PMID: 38396833 PMCID: PMC10888616 DOI: 10.3390/ijms25042157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this bacterium. To deeply uncover the function of PhaR, we applied a multipronged approach, including the expression profile of a phaR mutant at the transcriptional and protein levels under microaerobic conditions, and the identification of direct targets and of proteins associated with PHA granules. Our results confirmed a pleiotropic function of PhaR, affecting several phenotypes, in addition to PHA cycle control. These include growth deficiency, regulation of carbon and nitrogen allocation, and bacterial motility. Interestingly, PhaR may also modulate the microoxic-responsive regulatory network by activating the expression of fixK2 and repressing nifA, both encoding two transcription factors relevant for microaerobic regulation. At the molecular level, two PhaR-binding motifs were predicted and direct control mediated by PhaR determined by protein-interaction assays revealed seven new direct targets for PhaR. Finally, among the proteins associated with PHA granules, we found PhaR, phasins, and other proteins, confirming a dual function of PhaR in microoxia.
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Affiliation(s)
- Juan I. Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- YPF Tecnología S.A. (Y-TEC), Avenida. del Petróleo Argentino s/n (1923), Berisso 1923, Argentina
| | - Juan J. Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Rocío Díaz-Peña
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Lucía Sánchez-Schneider
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - María J. Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - M. Julia Pettinari
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Aníbal R. Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- Cátedra de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Coral del Val
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
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Holland BL, Matthews ML, Bota P, Sweetlove LJ, Long SP, diCenzo GC. A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost-benefit of nitrogen fixation. THE NEW PHYTOLOGIST 2023; 240:744-756. [PMID: 37649265 DOI: 10.1111/nph.19203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/05/2023] [Indexed: 09/01/2023]
Abstract
Nitrogen-fixing symbioses allow legumes to thrive in nitrogen-poor soils at the cost of diverting some photoassimilate to their microsymbionts. Effort is being made to bioengineer nitrogen fixation into nonleguminous crops. This requires a quantitative understanding of its energetic costs and the links between metabolic variations and symbiotic efficiency. A whole-plant metabolic model for soybean (Glycine max) with its associated microsymbiont Bradyrhizobium diazoefficiens was developed and applied to predict the cost-benefit of nitrogen fixation with varying soil nitrogen availability. The model predicted a nitrogen-fixation cost of c. 4.13 g C g-1 N, which when implemented into a crop scale model, translated to a grain yield reduction of 27% compared with a non-nodulating plant receiving its nitrogen from the soil. Considering the lower nitrogen content of cereals, the yield cost to a hypothetical N-fixing cereal is predicted to be less than half that of soybean. Soybean growth was predicted to be c. 5% greater when the nodule nitrogen export products were amides versus ureides. This is the first metabolic reconstruction in a tropical crop species that simulates the entire plant and nodule metabolism. Going forward, this model will serve as a tool to investigate carbon use efficiency and key mechanisms within N-fixing symbiosis in a tropical species forming determinate nodules.
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Affiliation(s)
- Bethany L Holland
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Megan L Matthews
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pedro Bota
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stephen P Long
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
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Taboada-Castro H, Gil J, Gómez-Caudillo L, Escorcia-Rodríguez JM, Freyre-González JA, Encarnación-Guevara S. Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network. Front Microbiol 2022; 13:947678. [PMID: 36312930 PMCID: PMC9611204 DOI: 10.3389/fmicb.2022.947678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF’s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF’s, Transcriptional Regulatory networks (TRN´s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF’s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
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Affiliation(s)
- Hermenegildo Taboada-Castro
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Jeovanis Gil
- Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden
| | - Leopoldo Gómez-Caudillo
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sergio Encarnación-Guevara
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
- *Correspondence: Sergio Encarnacion Guevara,
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4
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Investigating plant-microbe interactions within the root. Arch Microbiol 2022; 204:639. [PMID: 36136275 DOI: 10.1007/s00203-022-03257-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants' control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant-microbe interaction.
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Ferreira EGC, Gomes DF, Delai CV, Barreiros MAB, Grange L, Rodrigues EP, Henning LMM, Barcellos FG, Hungria M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiol 2022; 22:122. [PMID: 35513812 PMCID: PMC9069715 DOI: 10.1186/s12866-022-02527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. RESULTS A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. CONCLUSIONS All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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Affiliation(s)
- Everton Geraldo Capote Ferreira
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
| | | | - Caroline Vanzzo Delai
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | | | - Luciana Grange
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | - Elisete Pains Rodrigues
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | | | - Fernando Gomes Barcellos
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | - Mariangela Hungria
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
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6
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Buoso S, Zamboni A, Franco A, Commisso M, Guzzo F, Varanini Z, Pinton R, Tomasi N, Zanin L. Nodulating white lupins take advantage of the reciprocal interplay between N and P nutritional responses. PHYSIOLOGIA PLANTARUM 2022; 174:e13607. [PMID: 34837246 PMCID: PMC9303408 DOI: 10.1111/ppl.13607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
The low bioavailability of nutrients, especially nitrogen (N) and phosphorus (P), is one of the most limiting factors for crop production. In this study, under N- and P-free nutrient solution (-N-P), nodulating white lupin plants developed some nodules and analogous cluster root structures characterized by different morphological, physiological, and molecular responses than those observed upon single nutrient deficiency (strong acidification of external media, a better nutritional status than -N+P and +N-P plants). The multi-elemental analysis highlighted that the concentrations of nutrients in white lupin plants were mainly affected by P availability. Gene-expression analyses provided evidence of interconnections between N and P nutritional pathways that are active to promote N and P balance in plants. The root exudome was mainly characterized by N availability in nutrient solution, and, in particular, the absence of N and P in the nutrient solution triggered a high release of phenolic compounds, nucleosides monophosphate and saponines by roots. These morphological, physiological, and molecular responses result from a close interplay between N and P nutritional pathways. They contribute to the good development of nodulating white lupin plants when grown on N- and P-free media. This study provides evidence that limited N and P availability in the nutrient solution can promote white lupin-Bradyrhizobium symbiosis, which is favourable for the sustainability of legume production.
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Affiliation(s)
- Sara Buoso
- Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
| | - Anita Zamboni
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Alessandro Franco
- Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
| | - Mauro Commisso
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Flavia Guzzo
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Zeno Varanini
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Roberto Pinton
- Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
| | - Nicola Tomasi
- Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
| | - Laura Zanin
- Department of Agricultural, Food, Environmental and Animal SciencesUniversity of UdineUdineItaly
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7
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Yuan S, Zhou S, Feng Y, Zhang C, Huang Y, Shan Z, Chen S, Guo W, Yang H, Yang Z, Qiu D, Chen H, Zhou X. Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence. Front Microbiol 2021; 12:754837. [PMID: 34858367 PMCID: PMC8632152 DOI: 10.3389/fmicb.2021.754837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Legume nodule development and senescence directly affect nitrogen fixation efficiency and involve a programmed series of molecular events. These molecular events are carried out synchronously by legumes and rhizobia. The characteristics and molecular mechanisms of nitrogen fixation at soybean important developmental stages play critical roles in soybean cultivation and fertilizer application. Although the gene expression of soybean were analyzed in nodules at five important soybean developmental stages, information on the expression of rhizobial genes in these nodule samples is limited. In the present study, we investigated the expression of Bradyrhizobium diazoefficiens 113-2 genes in the nodule samples from five developmental stages of soybean (Branching stage, flowering stage, fruiting stage, pod stage and harvest stage). Similar gene expression patterns of B. diazoefficiens 113-2 were existed during optimal symbiotic functioning, while different expression patterns were found among early nodule development, nitrogen fixation progress and nodule senescence. Besides, we identified 164 important different expression genes (DEGs) associated with nodule development and senescence. These DEGs included those encoding nod, nif, fix proteins and T3SS secretion system-related proteins, as well as proteins involved in nitrogen metabolism, ABC transporters and two-component system pathways. Gene Ontology, KEGG pathway and homology analysis of the identified DEGs revealed that most of these DEGs are uncharacterized genes associated with nodule development and senescence, and they are not core genes among the rhizobia genomes. Our results provide new clues for the understanding of the genetic determinants of soil rhizobia in nodule development and senescence, and supply theoretical basis for the creation of high efficiency soybean cultivation technology.
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Shunxin Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
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Yurgel SN, Qu Y, Rice JT, Ajeethan N, Zink EM, Brown JM, Purvine S, Lipton MS, Kahn ML. Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1409-1422. [PMID: 34402628 DOI: 10.1094/mpmi-07-21-0180-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Svetlana N Yurgel
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Yi Qu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Jennifer T Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Nivethika Ajeethan
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Faculty of Technology, University of Jaffna, Sri Lanka
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Joseph M Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Sam Purvine
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Mary S Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Michael L Kahn
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, U.S.A
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9
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Ma JX, Yang Y, Li G, Ma BG. Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. Int J Mol Sci 2021; 22:11907. [PMID: 34769335 PMCID: PMC8584416 DOI: 10.3390/ijms222111907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of B. diazoefficiens USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of B. diazoefficiens USDA110 by computational approaches. Based on the comparison of interactomes between B. diazoefficiens USDA110 and other rhizobia, we inferred that the slow growth of B. diazoefficiens USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of B. diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.
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Affiliation(s)
| | | | | | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (J.-X.M.); (Y.Y.); (G.L.)
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10
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Mandon K, Nazaret F, Farajzadeh D, Alloing G, Frendo P. Redox Regulation in Diazotrophic Bacteria in Interaction with Plants. Antioxidants (Basel) 2021; 10:antiox10060880. [PMID: 34070926 PMCID: PMC8226930 DOI: 10.3390/antiox10060880] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/23/2022] Open
Abstract
Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance nutrient acquisition. Nitrogen-fixing bacteria, either as endophytes or as endosymbionts, specifically improve the growth and development of plants by supplying them with nitrogen, a key macro-element. Survival and proliferation of these bacteria require their adaptation to the rhizosphere and host plant, which are particular ecological environments. This adaptation highly depends on bacteria response to the Reactive Oxygen Species (ROS), associated to abiotic stresses or produced by host plants, which determine the outcome of the plant-bacteria interaction. This paper reviews the different antioxidant defense mechanisms identified in diazotrophic bacteria, focusing on their involvement in coping with the changing conditions encountered during interaction with plant partners.
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Affiliation(s)
- Karine Mandon
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Fanny Nazaret
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Davoud Farajzadeh
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz 5375171379, Iran;
- Center for International Scientific Studies and Collaboration (CISSC), Ministry of Science, Research and Technology, Tehran 158757788, Iran
| | - Geneviève Alloing
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
| | - Pierre Frendo
- Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France; (K.M.); (F.N.); (G.A.)
- Correspondence:
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11
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Durán D, Albareda M, García C, Marina AI, Ruiz-Argüeso T, Palacios JM. Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells. Mol Cell Proteomics 2020; 20:100009. [PMID: 33214187 PMCID: PMC7950203 DOI: 10.1074/mcp.ra120.002276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/15/2020] [Accepted: 11/19/2020] [Indexed: 11/06/2022] Open
Abstract
The Rhizobium-legume symbiosis is a beneficial interaction in which the bacterium converts atmospheric nitrogen into ammonia and delivers it to the plant in exchange for carbon compounds. This symbiosis implies the adaptation of bacteria to live inside host plant cells. In this work, we apply RP-LC-MS/MS and isobaric tags as relative and absolute quantitation techniques to study the proteomic profile of endosymbiotic cells (bacteroids) induced by Rhizobium leguminosarum bv viciae strain UPM791 in legume nodules. Nitrogenase subunits, tricarboxylic acid cycle enzymes, and stress-response proteins are among the most abundant from over 1000 rhizobial proteins identified in pea (Pisum sativum) bacteroids. Comparative analysis of bacteroids induced in pea and in lentil (Lens culinaris) nodules revealed the existence of a significant host-specific differential response affecting dozens of bacterial proteins, including stress-related proteins, transcriptional regulators, and proteins involved in the carbon and nitrogen metabolisms. A mutant affected in one of these proteins, homologous to a GntR-like transcriptional regulator, showed a symbiotic performance significantly impaired in symbiosis with pea but not with lentil plants. Analysis of the proteomes of bacteroids isolated from both hosts also revealed the presence of different sets of plant-derived nodule-specific cysteine-rich peptides, indicating that the endosymbiotic bacteria find a host-specific cocktail of chemical stressors inside the nodule. By studying variations of the bacterial response to different plant cell environments, we will be able to identify specific limitations imposed by the host that might give us clues for the improvement of rhizobial performance.
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Affiliation(s)
- David Durán
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carlos García
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC Campus Cantoblanco, Madrid, Spain
| | - Ana-Isabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC Campus Cantoblanco, Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Jose-Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.) UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
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12
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Sharma M, Sudheer S, Usmani Z, Rani R, Gupta P. Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights. Curr Genomics 2020; 21:343-362. [PMID: 33093798 PMCID: PMC7536805 DOI: 10.2174/1389202921999200515140420] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/29/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. Conclusion This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.
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Affiliation(s)
- Minaxi Sharma
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Surya Sudheer
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Zeba Usmani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Rupa Rani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Pratishtha Gupta
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
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13
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Flores-Tinoco CE, Tschan F, Fuhrer T, Margot C, Sauer U, Christen M, Christen B. Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation. Mol Syst Biol 2020; 16:e9419. [PMID: 32490601 PMCID: PMC7268258 DOI: 10.15252/msb.20199419] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.
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Affiliation(s)
| | - Flavia Tschan
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Margot
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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14
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
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Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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15
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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16
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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17
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Speck JJ, James EK, Sugawara M, Sadowsky MJ, Gyaneshwar P. An Alkane Sulfonate Monooxygenase Is Required for Symbiotic Nitrogen Fixation by Bradyrhizobium diazoefficiens (syn. Bradyrhizobium japonicum) USDA110 T. Appl Environ Microbiol 2019; 85:e01552-19. [PMID: 31562172 PMCID: PMC6881790 DOI: 10.1128/aem.01552-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023] Open
Abstract
Sulfur (S)-containing molecules play an important role in symbiotic nitrogen fixation and are critical components of nitrogenase and other iron-S proteins. S deficiency inhibits symbiotic nitrogen fixation by rhizobia. However, despite its importance, little is known about the sources of S that rhizobia utilize during symbiosis. We previously showed that Bradyrhizobium diazoefficiens USDA110T can assimilate both inorganic and organic S and that genes involved in organic S utilization are expressed during symbiosis. Here, we show that a B. diazoefficiens USDA110T mutant with a sulfonate monooxygenase (ssuD) insertion is defective in nitrogen fixation. Microscopy analyses revealed that the ΔssuD mutant was defective in root hair infection and that ΔssuD mutant bacteroids showed degradation compared to the wild-type strain. Moreover, the ΔssuD mutant was significantly more sensitive to hydrogen peroxide-mediated oxidative stress than the wild-type strain. Taken together, these results show that the ability of rhizobia to utilize organic S plays an important role in symbiotic nitrogen fixation. Since nodules have been reported to be an important source of reduced S used during symbiosis and nitrogen fixation, further research will be needed to determine the mechanisms involved in the regulation of S assimilation by rhizobia.IMPORTANCE Rhizobia form symbiotic associations with legumes that lead to the formation of nitrogen-fixing nodules. Sulfur-containing molecules play a crucial role in nitrogen fixation; thus, the rhizobia inside nodules require large amounts of sulfur. Rhizobia can assimilate both inorganic (sulfate) and organic (sulfonates) sources of sulfur. However, very little is known about rhizobial sulfur metabolism during symbiosis. In this report, we show that sulfonate utilization by Bradyrhizobium diazoefficiens is important for symbiotic nitrogen fixation in both soybean and cowpea. The symbiotic defect is probably due to increased sensitivity to oxidative stress from sulfur deficiency in the mutant strain defective for sulfonate utilization. The results of this study can be extended to other rhizobium-legume symbioses, as sulfonate utilization genes are widespread in these bacteria.
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Affiliation(s)
- Justin J Speck
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | | | - Masayuki Sugawara
- Biotechnology Institute, Department of Soil, Water & Climate, University of Minnesota, Saint Paul, Minnesota, USA
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Biotechnology Institute, Department of Plant & Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Michael J Sadowsky
- Biotechnology Institute, Department of Soil, Water & Climate, University of Minnesota, Saint Paul, Minnesota, USA
- Biotechnology Institute, Department of Plant & Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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18
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Barros-Carvalho GA, Hungria M, Lopes FM, Van Sluys MA. Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation. FEMS Microbiol Lett 2019; 366:fnz046. [PMID: 30860585 DOI: 10.1093/femsle/fnz046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/15/2019] [Indexed: 11/14/2022] Open
Abstract
Bradyrhizobium diazoefficiens CPAC 7 and Bradyrhizobium japonicum CPAC 15 are broadly used in commercial inoculants in Brazil, contributing to most of the nitrogen required by the soybean crop. These strains differ in their symbiotic properties: CPAC 7 is more efficient in fixing nitrogen, whereas CPAC 15 is more competitive. Comparative genomics revealed many transposases close to genes associated with symbiosis in the symbiotic island of these strains. Given the importance that insertion sequences (IS) elements have to bacterial genomes, we focused on identifying the local impact of these elements in the genomes of these and other related Bradyrhizobium strains to further understand their phenotypic differences. Analyses were performed using bioinformatics approaches. We found IS elements disrupting and inserted at regulatory regions of genes involved in symbiosis. Further comparative analyses with 21 Bradyrhizobium genomes revealed insertional polymorphism with distinguishing patterns between B. diazoefficiens and B. japonicum lineages. Finally, 13 of these potentially impacted genes are differentially expressed under symbiotic conditions in B. diazoefficiens USDA 110. Thus, IS elements are associated with the diversity of Bradyrhizobium, possibly by providing mechanisms for natural variation of symbiotic effectiveness.
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Affiliation(s)
- Gesiele Almeida Barros-Carvalho
- GaTE Lab; Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, 277 Matão Street, 05508-090, São Paulo, SP, Brazil
- Instituto de Matemática e Estatística, Universidade de São Paulo, 1010 Matão Street, 05508-090, São Paulo, SP, Brazil
| | | | - Fabrício Martins Lopes
- Universidade Tecnológica Federal do Paraná, 1640 Alberto Carazzai Avenue, 86300-000, Cornélio Procópio, Pr, Brazil
| | - Marie-Anne Van Sluys
- GaTE Lab; Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, 277 Matão Street, 05508-090, São Paulo, SP, Brazil
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19
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Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S. An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. Front Microbiol 2019; 10:924. [PMID: 31134003 PMCID: PMC6515984 DOI: 10.3389/fmicb.2019.00924] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 01/31/2023] Open
Abstract
The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.
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Affiliation(s)
- Noemí Fernández
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland.,Department of Health Sciences and Technology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | | | - Bernd Roschitzki
- Functional Genomics Center Zurich, ETH & UZH Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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20
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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21
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Strodtman KN, Frank S, Stevenson S, Thelen JJ, Emerich DW. Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules. Int J Mol Sci 2018; 19:E3947. [PMID: 30544819 PMCID: PMC6320959 DOI: 10.3390/ijms19123947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
The form and physiology of Bradyrhizobium diazoefficiens after the decline of symbiotic nitrogen fixation has been characterized. Proteomic analyses showed that post-symbiotic B. diazoefficiens underwent metabolic remodeling as well-defined groups of proteins declined, increased or remained unchanged from 56 to 119 days after planting, suggesting a transition to a hemibiotrophic-like lifestyle. Enzymatic analysis showed distinct patterns in both the cytoplasm and the periplasm. Similar to the bacteroid, the post-symbiotic bacteria rely on a non-citric acid cycle supply of succinate and, although viable, they did not demonstrate the ability to grow within the senescent nodule.
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Affiliation(s)
- Kent N Strodtman
- Department of Science, Columbia College, Columbia, MO 65216, USA.
| | - Sooyoung Frank
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | | | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - David W Emerich
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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22
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Atieno M, Lesueur D. Opportunities for improved legume inoculants: enhanced stress tolerance of rhizobia and benefits to agroecosystems. Symbiosis 2018. [DOI: 10.1007/s13199-018-0585-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Levy A, Conway JM, Dangl JL, Woyke T. Elucidating Bacterial Gene Functions in the Plant Microbiome. Cell Host Microbe 2018; 24:475-485. [DOI: 10.1016/j.chom.2018.09.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Zhang L, Liu JY, Gu H, Du Y, Zuo JF, Zhang Z, Zhang M, Li P, Dunwell JM, Cao Y, Zhang Z, Zhang YM. Bradyrhizobium diazoefficiens USDA 110- Glycine max Interactome Provides Candidate Proteins Associated with Symbiosis. J Proteome Res 2018; 17:3061-3074. [PMID: 30091610 DOI: 10.1021/acs.jproteome.8b00209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the legume-rhizobium symbiosis is a most-important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog- and domain-based approaches, we constructed an interspecies protein interactome containing 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was further validated by the expression pattern analysis in nodules, gene ontology term semantic similarity, co-expression analysis, and luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top 10 highly interacting proteins (hubs) for each species. Kyoto Encyclopedia of Genes and Genomes pathway analysis for each hub showed that a pair of 14-3-3 proteins (SGF14g and SGF14k) and 5 heat shock proteins in G. max are possibly involved in symbiosis, and 10 hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related soluble N-ethylmaleimide sensitive factor attachment protein receptor proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome provide a valuable basis for understanding the molecular mechanism of nodulation in soybean.
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Affiliation(s)
- Li Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
- School of Public Health , Xinxiang Medical University , Xinxiang 453003 , China
| | - Jin-Yang Liu
- College of Agriculture, Nanjing Agricultural University , Nanjing 210095 , China
| | - Huan Gu
- College of Agriculture, Nanjing Agricultural University , Nanjing 210095 , China
| | - Yanfang Du
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Jian-Fang Zuo
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Zhibin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Menglin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Pan Li
- School of Public Health , Xinxiang Medical University , Xinxiang 453003 , China
| | - Jim M Dunwell
- School of Agriculture, Policy and Development , University of Reading , Reading RG6 6AR , United Kingdom
| | - Yangrong Cao
- College of Life Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Zuxin Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
| | - Yuan-Ming Zhang
- Crop Information Center , College of Plant Science and Technology, Huazhong Agricultural University , Wuhan 430070 , China
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25
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López SMY, Sánchez MDM, Pastorino GN, Franco MEE, García NT, Balatti PA. Nodulation and Delayed Nodule Senescence: Strategies of Two Bradyrhizobium Japonicum Isolates with High Capacity to Fix Nitrogen. Curr Microbiol 2018; 75:997-1005. [PMID: 29546586 DOI: 10.1007/s00284-018-1478-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/12/2018] [Indexed: 01/04/2023]
Abstract
The purpose of this work was to study further two Bradyrhizobium japonicum strains with high nitrogen-fixing capacity that were identified within a collection of approximately 200 isolates from the soils of Argentina. Nodulation and nitrogen-fixing capacity and the level of expression of regulatory as well as structural genes of nitrogen fixation and the 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene of the isolates were compared with that of E109-inoculated plants. Both isolates of B. japonicum, 163 and 366, were highly efficient to fix nitrogen compared to commercial strain E109. Isolate 366 developed a higher number and larger biomass of nodules and because of this fixed more nitrogen. Isolate 163 developed the same number and nodule biomass than E109. However, nodules developed by isolate 163 had red interiors for a longer period, had a higher leghemoglobin content, and presented high levels of expression of acdS gene, that codes for an ACC deaminase. In conclusion, naturalized rhizobia of the soils of Argentina hold a diverse population that might be the source of highly active nitrogen-fixing rhizobia, a process that appears to be based on different strategies.
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Affiliation(s)
- Silvina M Y López
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Centro de Investigaciones de Fitopatología (CIDEFI - CICBA-UNLP), Buenos Aires, Argentina
| | - Ma Dolores Molina Sánchez
- Grupo de Ecología Genética de la Rizosfera, Dpto. Microbiología y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Graciela N Pastorino
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calle 60 y 119, La Plata, 1900, Argentina
| | - Mario E E Franco
- Centro de Investigaciones de Fitopatología (CIDEFI - CICBA-UNLP), Buenos Aires, Argentina
| | - Nicolás Toro García
- Grupo de Ecología Genética de la Rizosfera, Dpto. Microbiología y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Pedro A Balatti
- Centro de Investigaciones de Fitopatología (CIDEFI - CICBA-UNLP), Buenos Aires, Argentina.
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, Calle 60 y 119, La Plata, 1900, Argentina.
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26
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Thal B, Braun HP, Eubel H. Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology. PLANT MOLECULAR BIOLOGY 2018; 97:233-251. [PMID: 29779088 DOI: 10.1007/s11103-018-0736-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/08/2018] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.
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Affiliation(s)
- Beate Thal
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany.
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27
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Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia. High Throughput 2018; 7:ht7020015. [PMID: 29783718 PMCID: PMC6023288 DOI: 10.3390/ht7020015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 01/24/2023] Open
Abstract
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).
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28
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Lardi M, Liu Y, Giudice G, Ahrens CH, Zamboni N, Pessi G. Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ 54 During Symbiosis with Phaseolus vulgaris. Int J Mol Sci 2018; 19:ijms19041049. [PMID: 29614780 PMCID: PMC5979394 DOI: 10.3390/ijms19041049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 12/20/2022] Open
Abstract
RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T formed root nodules on Phaseolus vulgaris cv. Negro jamapa, which were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by a P. phymatumrpoN Fix− mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix− and Fix+ nodules—combined with a search for RpoN binding sequences in promoter regions of regulated genes—confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also allowed us to identify additional target genes, whose differential expression was able to explain the observed metabolite changes in numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant, and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype, as fewer but heavier nodules were formed on P. vulgaris roots.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Gaetano Giudice
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), CH-8820 Wädenswil, Switzerland.
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
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29
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Identification of AHL- and BDSF-Controlled Proteins in Burkholderia cenocepacia by Proteomics. Methods Mol Biol 2018; 1673:193-202. [PMID: 29130174 DOI: 10.1007/978-1-4939-7309-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We used comparative proteome analysis to determine the target genes of the two quorum sensing (QS) circuits in the opportunistic pathogen Burkholderia cenocepacia: the N-acyl homoserine lactone (AHL)-based CepIR system and the BDSF (B urkholderia diffusible signal factor, cis-2-dodecenoic acid)-based RpfFR system. In this book chapter, we focus on the description of the practical procedure we currently use in the laboratory to perform a sensitive GeLC-MS/MS shotgun proteomics experiment; we also briefly describe the downstream bioinformatic data analysis.
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30
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Lardi M, Liu Y, Purtschert G, Bolzan de Campos S, Pessi G. Transcriptome Analysis of Paraburkholderia phymatum under Nitrogen Starvation and during Symbiosis with Phaseolus Vulgaris. Genes (Basel) 2017; 8:genes8120389. [PMID: 29244728 PMCID: PMC5748707 DOI: 10.3390/genes8120389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 01/31/2023] Open
Abstract
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils. Among the genes upregulated under nitrogen limitation, we found genes involved in exopolysaccharides production and in motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly upregulated during symbiosis, we identified—besides the nif gene cluster—an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities, suggesting an important role of the cytochrome for respiration inside the nodule. The analysis of mutant strains for the RNA polymerase transcription factor RpoN (σ54) and its activator NifA indicated that—similar to the situation in α-rhizobia—P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Gabriela Purtschert
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
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31
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Strodtman KN, Stevenson SE, Waters JK, Mawhinney TP, Thelen JJ, Polacco JC, Emerich DW. The Bacteroid Periplasm in Soybean Nodules Is an Interkingdom Symbiotic Space. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:997-1008. [PMID: 29028412 DOI: 10.1094/mpmi-12-16-0264-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The functional role of the periplasm of nitrogen-fixing bacteroids has not been determined. Proteins were isolated from the periplasm and cytoplasm of Bradyrhizobium diazoefficiens bacteroids and were analyzed using liquid chromatography tandem mass spectrometry proteomics. Identification of bacteroid periplasmic proteins was aided by periplasm prediction programs. Approximately 40% of all the proteins identified as periplasmic in the B. diazoefficiens genome were found expressed in the bacteroid form of the bacteria, indicating the periplasm is a metabolically active symbiotic space. The bacteroid periplasm possesses many fatty acid metabolic enzymes, which was in contrast to the bacteroid cytoplasm. Amino acid analysis of the periplasm revealed an abundance of phosphoserine, phosphoethanolamine, and glycine, which are metabolites of phospholipid metabolism. These results suggest the periplasm is a unique space and not a continuum with the peribacteroid space. A number of plant proteins were found in the periplasm fraction, which suggested contamination. However, antibodies to two of the identified plant proteins, histone H2A and lipoxygenase, yielded immunogold labeling that demonstrated the plant proteins were specifically targeted to the bacteroids. This suggests that the periplasm is an interkingdom symbiotic space containing proteins from both the bacteroid and the plant.
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Affiliation(s)
- Kent N Strodtman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - Severin E Stevenson
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - James K Waters
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - Thomas P Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - Joseph C Polacco
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
| | - David W Emerich
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, U.S.A
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32
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Liu Y, Jiang X, Guan D, Zhou W, Ma M, Zhao B, Cao F, Li L, Li J. Transcriptional analysis of genes involved in competitive nodulation in Bradyrhizobium diazoefficiens at the presence of soybean root exudates. Sci Rep 2017; 7:10946. [PMID: 28887528 PMCID: PMC5591287 DOI: 10.1038/s41598-017-11372-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/23/2017] [Indexed: 01/22/2023] Open
Abstract
Nodulation competition is a key factor that limits symbiotic nitrogen fixation between rhizobia and their host legumes. Soybean root exudates (SREs) are thought to act as signals that influence Bradyrhizobium ability to colonize roots and to survive in the rhizosphere, and thus they act as a key determinant of nodulation competitiveness. In order to find the competitiveness-related genes in B. diazoefficiens, the transcriptome of two SREs treated B. diazoefficiens with completely different nodulation abilities (B. diazoefficiens 4534 and B. diazoefficiens 4222) were sequenced and compared. In SREs treated strain 4534 (SREs-4534), 253 unigenes were up-regulated and 204 unigenes were down-regulated. In SREs treated strain 4534 (SREs-4222), the numbers of up- and down-regulated unigenes were 108 and 185, respectively. There were considerable differences between the SREs-4534 and SREs-4222 gene expression profiles. Some differentially expressed genes are associated with a two-component system (i.g., nodW, phyR-σEcfG), bacterial chemotaxis (i.g., cheA, unigene04832), ABC transport proteins (i.g., unigene02212), IAA (indole-3-acetic acid) metabolism (i.g., nthA, nthB), and metabolic fitness (i.g., put.), which may explain the higher nodulation competitiveness of B. diazoefficiens in the rhizosphere. Our results provide a comprehensive transcriptomic resource for SREs treated B. diazoefficiens and will facilitate further studies on competitiveness-related genes in B. diazoefficiens.
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Affiliation(s)
- Yao Liu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality&Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality&Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, China
| | - Baisuo Zhao
- Laboratory of Quality&Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality&Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality&Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, China.
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33
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Larrainzar E, Wienkoop S. A Proteomic View on the Role of Legume Symbiotic Interactions. FRONTIERS IN PLANT SCIENCE 2017; 8:1267. [PMID: 28769967 PMCID: PMC5513976 DOI: 10.3389/fpls.2017.01267] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/05/2017] [Indexed: 05/04/2023]
Abstract
Legume plants are key elements in sustainable agriculture and represent a significant source of plant-based protein for humans and animal feed worldwide. One specific feature of the family is the ability to establish nitrogen-fixing symbiosis with Rhizobium bacteria. Additionally, like most vascular flowering plants, legumes are able to form a mutualistic endosymbiosis with arbuscular mycorrhizal (AM) fungi. These beneficial associations can enhance the plant resistance to biotic and abiotic stresses. Understanding how symbiotic interactions influence and increase plant stress tolerance are relevant questions toward maintaining crop yield and food safety in the scope of climate change. Proteomics offers numerous tools for the identification of proteins involved in such responses, allowing the study of sub-cellular localization and turnover regulation, as well as the discovery of post-translational modifications (PTMs). The current work reviews the progress made during the last decades in the field of proteomics applied to the study of the legume-Rhizobium and -AM symbioses, and highlights their influence on the plant responses to pathogens and abiotic stresses. We further discuss future perspectives and new experimental approaches that are likely to have a significant impact on the field including peptidomics, mass spectrometric imaging, and quantitative proteomics.
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Affiliation(s)
- Estíbaliz Larrainzar
- Department of Environmental Sciences, Universidad Pública de NavarraPamplona, Spain
- *Correspondence: Estíbaliz Larrainzar
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Stefanie Wienkoop
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Yang Y, Hu XP, Ma BG. Construction and simulation of the Bradyrhizobium diazoefficiens USDA110 metabolic network: a comparison between free-living and symbiotic states. MOLECULAR BIOSYSTEMS 2017; 13:607-620. [DOI: 10.1039/c6mb00553e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The first genome-scale metabolic network forBradyrhizobiumwas constructed and the metabolic properties were compared between the free-living and symbiotic physiological states.
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Affiliation(s)
- Yi Yang
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
| | - Xiao-Pan Hu
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
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Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E. Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. PLoS One 2016; 11:e0165429. [PMID: 27788207 PMCID: PMC5082802 DOI: 10.1371/journal.pone.0165429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria.
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Affiliation(s)
- Julia Hahn
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Olga V. Tsoy
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
| | - Sebastian Thalmann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Jelena Čuklina
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- ETH, Institute of Molecular Systems Biology, Zürich, Switzerland
| | - Mikhail S. Gelfand
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- Skolkovo Institute of Science and Technology, Nobel Str. 3, Moscow, 143026, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Vorobyevy Gory 1–73, Moscow, 119234, Russia
- Faculty of Computer Science, Higher School of Economics, Kochnovsky Dr. 3, Moscow, 125319, Russia
- * E-mail: (EEH); (MSG)
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
- * E-mail: (EEH); (MSG)
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Kumar D, Bansal G, Narang A, Basak T, Abbas T, Dash D. Integrating transcriptome and proteome profiling: Strategies and applications. Proteomics 2016; 16:2533-2544. [PMID: 27343053 DOI: 10.1002/pmic.201600140] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/12/2016] [Accepted: 06/23/2016] [Indexed: 12/17/2022]
Abstract
Discovering the gene expression signature associated with a cellular state is one of the basic quests in majority of biological studies. For most of the clinical and cellular manifestations, these molecular differences may be exhibited across multiple layers of gene regulation like genomic variations, gene expression, protein translation and post-translational modifications. These system wide variations are dynamic in nature and their crosstalk is overwhelmingly complex, thus analyzing them separately may not be very informative. This necessitates the integrative analysis of such multiple layers of information to understand the interplay of the individual components of the biological system. Recent developments in high throughput RNA sequencing and mass spectrometric (MS) technologies to probe transcripts and proteins made these as preferred methods for understanding global gene regulation. Subsequently, improvements in "big-data" analysis techniques enable novel conclusions to be drawn from integrative transcriptomic-proteomic analysis. The unified analyses of both these data types have been rewarding for several biological objectives like improving genome annotation, predicting RNA-protein quantities, deciphering gene regulations, discovering disease markers and drug targets. There are different ways in which transcriptomics and proteomics data can be integrated; each aiming for different research objectives. Here, we review various studies, approaches and computational tools targeted for integrative analysis of these two high-throughput omics methods.
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Affiliation(s)
- Dhirendra Kumar
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Gourja Bansal
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Ankita Narang
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Trayambak Basak
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India
| | - Tahseen Abbas
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India
| | - Debasis Dash
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA. , .,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India. ,
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Lardi M, Murset V, Fischer HM, Mesa S, Ahrens CH, Zamboni N, Pessi G. Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures. Int J Mol Sci 2016; 17:E815. [PMID: 27240350 PMCID: PMC4926349 DOI: 10.3390/ijms17060815] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/13/2016] [Accepted: 05/19/2016] [Indexed: 01/17/2023] Open
Abstract
Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots from four different B. diazoefficiens host plants; (ii) soybean nodules harvested at different time points during nodule development; and (iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by independent transcriptomics data. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland.
| | - Valérie Murset
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
| | - Hans-Martin Fischer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-18080 Granada, Spain.
| | - Christian H Ahrens
- Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), CH-8820 Wädenswil, Switzerland.
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland.
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland.
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Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E. Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 2016; 17:302. [PMID: 27107716 PMCID: PMC4842269 DOI: 10.1186/s12864-016-2602-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/25/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. RESULTS A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. CONCLUSIONS The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.
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Affiliation(s)
- Jelena Čuklina
- />AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051 Russia
- />Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudnyy, Moscow region 141700 Russia
- />Present Address: Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard Hof 1, CH-8093 Zürich, Switzerland
| | - Julia Hahn
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Maxim Imakaev
- />Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139 USA
| | - Ulrich Omasits
- />Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Konrad U. Förstner
- />Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Str. 2 Bau D15, D-97080 Würzburg, Germany
| | - Nikolay Ljubimov
- />Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Leninskie Gory, 2-nd educational building, Moscow, 119991 Russia
| | - Melanie Goebel
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriella Pessi
- />ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
- />Present Address: Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Hans-Martin Fischer
- />ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Christian H. Ahrens
- />Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Mikhail S. Gelfand
- />AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051 Russia
- />Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobievy Gory 73-1, Moscow, 119991 Russia
| | - Elena Evguenieva-Hackenberg
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Nambu M, Tatsukami Y, Morisaka H, Kuroda K, Ueda M. Quantitative time-course proteome analysis of Mesorhizobium loti during nodule maturation. J Proteomics 2015; 125:112-20. [DOI: 10.1016/j.jprot.2015.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 11/30/2022]
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Guo Gao T, Yuan Xu Y, Jiang F, Zhen Li B, Shui Yang J, Tao Wang E, Li Yuan H. Nodulation Characterization and Proteomic Profiling of Bradyrhizobium liaoningense CCBAU05525 in Response to Water-Soluble Humic Materials. Sci Rep 2015; 5:10836. [PMID: 26054030 PMCID: PMC4650689 DOI: 10.1038/srep10836] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/14/2015] [Indexed: 12/16/2022] Open
Abstract
The lignite biodegradation procedure to produce water-soluble humic materials (WSHM) with a Penicillium stain was established by previous studies in our laboratory. This study researched the effects of WSHM on the growth of Bradyrhizobium liaoningense CCBAU05525 and its nodulation on soybean. Results showed that WSHM enhanced the cell density of CCBAU05525 in culture, and increased the nodule number, nodule fresh weight and nitrogenase activity of the inoculated soybean plants. Then the chemical compounds of WSHM were analyzed and flavonoid analogues were identified in WSHM through tetramethyl ammonium hydroxide (TMAH)-py-GC/MS analysis. Protein expression profiles and nod gene expression of CCBAU05525 in response to WSHM or genistein were compared to illustrate the working mechanism of WSHM. The differently expressed proteins in response to WSHM were involved in nitrogen and carbon metabolism, nucleic acid metabolism, signaling, energy production and some transmembrane transports. WSHM was found more effective than genistein in inducing the nod gene expression. These results demonstrated that WSHM stimulated cell metabolism and nutrient transport, which resulted in increased cell density of CCBAU05525 and prepared the bacteria for better bacteroid development. Furthermore, WSHM had similar but superior functions to flavone in inducing nod gene and nitrogen fixation related proteins expression in CCBAU05525.
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Affiliation(s)
- Tong Guo Gao
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
- College of Life Science, Agricultural University of Hebei, Baoding 071001, P. R. China
| | - Yuan Yuan Xu
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Feng Jiang
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Bao Zhen Li
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - Jin Shui Yang
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F. 11340, Mexico
| | - Hong Li Yuan
- State Key Laboratory of AgroBiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, P. R. China
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σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111. Appl Environ Microbiol 2015; 81:4077-89. [PMID: 25841012 DOI: 10.1128/aem.00694-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/31/2015] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression levels. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins, and the two-component regulatory system NtrBC, B. cenocepacia H111 also upregulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen-responsive genes identified a σ(54) consensus sequence. The mapping of the σ(54) regulon as well as the characterization of a σ(54) mutant suggests an important role of σ(54) not only in control of nitrogen metabolism but also in the virulence of this organism.
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Chapman B, Bellgard M. High-throughput parallel proteogenomics: A bacterial case study. Proteomics 2014; 14:2780-9. [DOI: 10.1002/pmic.201400185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/11/2014] [Accepted: 10/22/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Brett Chapman
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
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Yang P, Chen XM. Protein profiles of Chinese white wax scale, Ericerus pela, at the male pupal stage by high-throughput proteomics. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2014; 87:214-233. [PMID: 25186183 DOI: 10.1002/arch.21191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The Chinese white wax scale insect (Ericerus pela) is sexually dimorphic with holometabolous males and hemimetabolous females. Holometabolous insects were assumed to originate from hemimetabolous ancestors. Therefore, the male pupal stage is a major innovation compared with hemimetabolous female insects. Here, the protein profiles of the male pupae were obtained by high-throughput proteomics and analyzed using bioinformatics methods. A total of 1,437 peptides were identified and assigned to 677 protein groups. Most of the proteins had molecular weights below 40 kDa and isoelectric points from 4 to 7. Gene Ontology terms were assigned to 331 proteins, including metabolic process, developmental process, and cellular process. Kyoto Encyclopedia of Genes and Genomes annotations identified 142 pathways and most proteins were assigned to metabolism events. Pathways involved in cell growth and death, signal transduction, folding, and sorting and degradation were also identified. Six proteins that had undergone positive selection were classified into four groups, protein biosynthesis, protein degeneration, signal transduction, and detoxification. Many of the high-abundance proteins were enzymes involved in carbohydrate, lipid, and amino acid metabolism; signal transduction; degradation; and immunization, which indicated that metabolism, disruption, and development occurred intensely at the pupal stage. These processes are closely related to the physiological status of pupae. The results also suggested that these related proteins may be fundamental factors in the formation of pupae. This study describes pupal characterization at the molecular level and provides a basis for further physiological studies.
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Affiliation(s)
- Pu Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, China
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Gomes DF, da Silva Batista JS, Rolla AAP, da Silva LP, Bloch C, Galli-Terasawa LV, Hungria M. Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis. BMC Genomics 2014; 15:643. [PMID: 25086822 PMCID: PMC4287336 DOI: 10.1186/1471-2164-15-643] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/25/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Strain CPAC 7 (=SEMIA 5080) was recently reclassified into the new species Bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [Glycine max (L.) Merr.] in Brazil and other South American countries. Although the efficiency of B. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available. RESULTS We provided a two-dimensional proteomic reference map of CPAC 7 obtained under free-living conditions, with the successful identification of 115 spots, representing 95 different proteins. The results highlighted the expression of molecular determinants potentially related to symbiosis establishment (e.g. inositol monophosphatase, IMPase), fixation of atmospheric nitrogen (N2) (e.g. NifH) and defenses against stresses (e.g. chaperones). By using bioinformatic tools, it was possible to attribute probable functions to ten hypothetical proteins. For another ten proteins classified as "NO related COG" group, we analyzed by RT-qPCR the relative expression of their coding-genes in response to the nodulation-gene inducer genistein. Six of these genes were up-regulated, including blr0227, which may be related to polyhydroxybutyrate (PHB) biosynthesis and competitiveness for nodulation. CONCLUSIONS The proteomic map contributed to the identification of several proteins of B. diazoefficiens under free-living conditions and our approach-combining bioinformatics and gene-expression assays-resulted in new information about unknown genes that might play important roles in the establishment of the symbiosis with soybean.
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Affiliation(s)
| | | | | | | | | | | | - Mariangela Hungria
- Embrapa Soja, Embrapa Soja, C,P, 231, 86001-970 Londrina, Paraná, Brazil.
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Abstract
Symbiosomes are a unique structural entity that performs the role of biological nitrogen fixation, an energy-demanding process that is the primary entryway of fixed nitrogen into the biosphere. Symbiosomes result from the infection of specific rhizobial strains into the roots of an appropriate leguminous host plant forming an organ referred to as a nodule. Within the infected plant cells of the nodule, the rhizobia are encased within membrane-bounded structures that develop into symbiosomes. Mature symbiosomes create an environment that allows the rhizobia to differentiate into a nitrogen-fixing form called bacteroids. The bacteroids are surrounded by the symbiosome space, which is populated by proteins from both eukaryotic and prokaryotic symbionts, suggesting this space is the quintessential component of symbiosis: an inter-kingdom environment with the single purpose of symbiotic nitrogen fixation. Proteins associated with the symbiosome membrane are largely plant-derived proteins and are non-metabolic in nature. The proteins of the symbiosome space are mostly derived from the bacteroid with annotated functions of carbon metabolism, whereas relatively few are involved in nitrogen metabolism. An appreciable portion of both the eukaryotic and prokaryotic proteins in the symbiosome are also ‘moonlighting’ proteins, which are defined as proteins that perform roles unrelated to their annotated activities when found in an unexpected physiological environment. The essential functions of symbiotic nitrogen fixation of the symbiosome are performed by co-operative interactions of proteins from both symbionts some of which may be performing unexpected roles.
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Delmotte N, Mondy S, Alunni B, Fardoux J, Chaintreuil C, Vorholt JA, Giraud E, Gourion B. A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis. Int J Mol Sci 2014; 15:3660-70. [PMID: 24590127 PMCID: PMC3975360 DOI: 10.3390/ijms15033660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/28/2022] Open
Abstract
Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency.
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Affiliation(s)
- Nathanael Delmotte
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Samuel Mondy
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Benoit Alunni
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Joel Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Julia A Vorholt
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Benjamin Gourion
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
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A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum. Appl Environ Microbiol 2014; 80:2094-101. [PMID: 24463964 DOI: 10.1128/aem.03314-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.
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Carlier AL, Omasits U, Ahrens CH, Eberl L. Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1325-1333. [PMID: 23902262 DOI: 10.1094/mpmi-05-13-0152-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several plant species of the genus Psychotria (Rubiaceae) harbor Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted vertically between plant generations and have not yet been cultured outside of their host. This symbiosis is considered to be obligatory because plants devoid of symbionts fail to develop into mature individuals. The genome of 'Candidatus Burkholderia kirkii' has been sequenced recently and has revealed evidence of reductive genome evolution, as shown by the proliferation of insertion sequences and the presence of numerous pseudogenes. We employed shotgun proteomics to investigate the expression of 'Ca. B. kirkii' proteins in the leaf nodule. Drawing from this dataset and refined comparative genomics analyses, we designed a new pseudogene prediction algorithm and improved the genome annotation. We also found conclusive evidence that nodule bacteria allocate vast resources to synthesis of secondary metabolites, possibly of the C7N aminocyclitol family. Expression of a putative 2-epi-5-valiolone synthase, a key enzyme of the C7N aminocyclitol synthesis, is high in the nodule population but downregulated in bacteria residing in the shoot apex, suggesting that production of secondary metabolites is particularly important in the leaf nodule.
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Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics 2013; 12:3388-97. [PMID: 23882027 PMCID: PMC3820949 DOI: 10.1074/mcp.m112.027169] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/19/2013] [Indexed: 11/06/2022] Open
Abstract
We present GenoSuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (MS) data from prokaryotes. To demonstrate the effectiveness of GenoSuite, we analyzed proteomics data of Bradyrhizobium japonicum (USDA110), a model organism to study agriculturally important rhizobium-legume symbiosis. Our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (TIS) and discovered 59 novel protein coding genes. Notably, a novel protein which redefined the boundary of a crucial cytochrome P450 system related operon was discovered, known to be highly expressed in the anaerobic symbiotic bacteroids. A focused analysis on N-terminally acetylated peptides indicated downstream TIS for gene blr0594. Finally, ortho-proteogenomic analysis revealed three novel genes in recently sequenced B. japonicum USDA6(T) genome. The discovery of large number of missing genes and correction of gene models have expanded the proteomic landscape of B. japonicum and presents an unparalleled utility of proteogenomic analyses and versatility of GenoSuite for annotating prokaryotic genomes including pathogens.
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Affiliation(s)
- Dhirendra Kumar
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Amit Kumar Yadav
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Puneet Kumar Kadimi
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Shivashankar H. Nagaraj
- §Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sean M. Grimmond
- §Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Debasis Dash
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
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Pessi G, Braunwalder R, Grunau A, Omasits U, Ahrens CH, Eberl L. Response of Burkholderia cenocepacia H111 to micro-oxia. PLoS One 2013; 8:e72939. [PMID: 24023794 PMCID: PMC3759415 DOI: 10.1371/journal.pone.0072939] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/15/2013] [Indexed: 12/20/2022] Open
Abstract
B. cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis (CF). In the CF lung bacteria grow to high densities within the viscous mucus that is limited in oxygen. Pseudomonas aeruginosa, the dominant pathogen in CF patients, is known to grow and survive under oxygen-limited to anaerobic conditions by using micro-oxic respiration, denitrification and fermentative pathways. In contrast, inspection of the genome sequences of available B. cenocepacia strains suggested that B. cenocepacia is an obligate aerobic and non-fermenting bacterium. In accordance with the bioinformatics analysis we observed that B. cenocepacia H111 is able to grow with as little as 0.1% O2 but not under strictly anoxic conditions. Phenotypic analyses revealed that H111 produced larger amounts of biofilm, pellicle and proteases under micro-oxic conditions (0.5%–5% O2, i.e. conditions that mimic those encountered in CF lung infection), and was more resistant to several antibiotics. RNA-Seq and shotgun proteomics analyses of cultures of B. cenocepacia H111 grown under micro-oxic and aerobic conditions showed up-regulation of genes involved in the synthesis of the exopolysaccharide (EPS) cepacian as well as several proteases, two isocitrate lyases and other genes potentially important for life in micro-oxia. Data deposition: RNA-Seq raw data files are accessible through the GEO Series accession number GSE48585. MS data have been deposited in the ProteomeXchange database (PXD000270).
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Affiliation(s)
- Gabriella Pessi
- Department of Microbiology, University of Zurich, Zürich, Switzerland
- * E-mail:
| | | | - Alexander Grunau
- Department of Microbiology, University of Zurich, Zürich, Switzerland
| | - Ulrich Omasits
- Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Christian H. Ahrens
- Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Leo Eberl
- Department of Microbiology, University of Zurich, Zürich, Switzerland
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