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Zorin EA, Kliukova MS, Afonin AM, Gribchenko ES, Gordon ML, Sulima AS, Zhernakov AI, Kulaeva OA, Romanyuk DA, Kusakin PG, Tsyganova AV, Tsyganov VE, Tikhonovich IA, Zhukov VA. A variable gene family encoding nodule-specific cysteine-rich peptides in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884726. [PMID: 36186063 PMCID: PMC9515463 DOI: 10.3389/fpls.2022.884726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume Medicago truncatula Gaertn., while in many other legumes relevant information is still fragmentary. Here, we characterize the NCR gene family in pea (Pisum sativum L.) using genomic and transcriptomic data. We found 360 genes encoding NCR peptides that are expressed in nodules. The sequences of pea NCR genes and putative peptides are highly variable and differ significantly from NCR sequences of M. truncatula. Indeed, only one pair of orthologs (PsNCR47-MtNCR312) has been identified. The NCR genes in the pea genome are located in clusters, and the expression patterns of NCR genes from one cluster tend to be similar. These data support the idea of independent evolution of NCR genes by duplication and diversification in related legume species. We also described spatiotemporal expression profiles of NCRs and identified specific transcription factor (TF) binding sites in promoters of "early" and "late" NCR genes. Further, we studied the expression of NCR genes in nodules of Fix- mutants and predicted potential regulators of NCR gene expression, one among them being the TF ERN1 involved in the early steps of nodule organogenesis. In general, this study contributes to understanding the functions of NCRs in legume nodules and contributes to understanding the diversity and potential antibiotic properties of pea nodule-specific antimicrobial molecules.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Emma S. Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Mikhail L. Gordon
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | | | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Pyotr G. Kusakin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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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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3
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Green RT, East AK, Karunakaran R, Downie JA, Poole PS. Transcriptomic analysis of Rhizobium leguminosarum bacteroids in determinate and indeterminate nodules. Microb Genom 2019; 5:e000254. [PMID: 30777812 PMCID: PMC6421345 DOI: 10.1099/mgen.0.000254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 01/25/2023] Open
Abstract
Two common classes of nitrogen-fixing legume root nodules are those that have determinate or indeterminate meristems, as in Phaseolus bean and pea, respectively. In indeterminate nodules, rhizobia terminally differentiate into bacteroids with endoreduplicated genomes, whereas bacteroids from determinate nodules are less differentiated and can regrow. We used RNA sequencing to compare bacteroid gene expression in determinate and indeterminate nodules using two Rhizobium leguminosarum strains whose genomes differ due to replacement of the symbiosis (Sym) plasmid pRP2 (strain Rlp4292) with pRL1 (strain RlvA34), thereby switching symbiosis hosts from Phaseolus bean (determinate nodules) to pea (indeterminate nodules). Both bacteroid types have gene expression patterns typical of a stringent response, a stressful environment and catabolism of dicarboxylates, formate, amino acids and quaternary amines. Gene expression patterns were indicative that bean bacteroids were more limited for phosphate, sulphate and iron than pea bacteroids. Bean bacteroids had higher levels of expression of genes whose products are predicted to be associated with metabolite detoxification or export. Pea bacteroids had increased expression of genes associated with DNA replication, membrane synthesis and the TCA (tricarboxylic acid) cycle. Analysis of bacteroid-specific transporter genes was indicative of distinct differences in sugars and other compounds in the two nodule environments. Cell division genes were down-regulated in pea but not bean bacteroids, while DNA synthesis was increased in pea bacteroids. This is consistent with endoreduplication of pea bacteroids and their failure to regrow once nodules senesce.
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Affiliation(s)
- R. T. Green
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - A. K. East
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - R. Karunakaran
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - J. A. Downie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - P. S. Poole
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Kereszt A, Mergaert P, Montiel J, Endre G, Kondorosi É. Impact of Plant Peptides on Symbiotic Nodule Development and Functioning. FRONTIERS IN PLANT SCIENCE 2018; 9:1026. [PMID: 30065740 PMCID: PMC6056668 DOI: 10.3389/fpls.2018.01026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/25/2018] [Indexed: 05/20/2023]
Abstract
Ribosomally synthesized peptides have wide ranges of functions in plants being, for example, signal molecules, transporters, alkaloids, or antimicrobial agents. Legumes are an unprecedented rich source of peptides, which are used to control the symbiosis of these plants with the nitrogen-fixing Rhizobium bacteria. Here, we discuss the function and the evolution of these peptides playing an important role in the formation or functioning of the symbiotic organs, the root nodules. We distinguish peptides that can be either cell-autonomous or secreted short-range or long-range signals, carrying messages in or between plant cells or that can act as effectors interacting with the symbiotic bacteria. Peptides are further classified according to the stage of the symbiotic process where they act. Several peptide classes, including RALF, DLV, ENOD40, and others, control Rhizobium infection and the initiation of cell divisions and the formation of nodule primordia. CLE and CEP peptides are implicated in systemic and local control of nodule initiation during autoregulation of nodulation and in response to the nutritional demands of the plant. Still other peptides act at later stages of the symbiosis. The PSK peptide is thought to be involved in the suppression of immunity in nodules and the nodule-specific cysteine-rich, GRP, and SNARP (LEED..PEED) peptide families are essential in the functioning of the nitrogen fixing root nodules. The NCRs and possibly also the GRP and SNARPs are targeted to the endosymbionts and play essential roles in the terminal differentiation of these bacteria.
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Affiliation(s)
- Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Peter Mergaert
- Institute of Integrative Biology of the Cell, UMR 9198, CNRS – CEA – Université Paris-Sud, Gif-sur-Yvette, France
| | - Jesús Montiel
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gabriella Endre
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Éva Kondorosi
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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5
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Morphotype of bacteroids in different legumes correlates with the number and type of symbiotic NCR peptides. Proc Natl Acad Sci U S A 2017; 114:5041-5046. [PMID: 28438996 DOI: 10.1073/pnas.1704217114] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In legume nodules, rhizobia differentiate into nitrogen-fixing forms called bacteroids, which are enclosed by a plant membrane in an organelle-like structure called the symbiosome. In the Inverted Repeat-Lacking Clade (IRLC) of legumes, this differentiation is terminal due to irreversible loss of cell division ability and is associated with genome amplification and different morphologies of the bacteroids that can be swollen, elongated, spherical, and elongated-branched, depending on the host plant. In Medicago truncatula, this process is orchestrated by nodule-specific cysteine-rich peptides (NCRs) delivered into developing bacteroids. Here, we identified the predicted NCR proteins in 10 legumes representing different subclades of the IRLC with distinct bacteroid morphotypes. Analysis of their expression and predicted sequences establishes correlations between the composition of the NCR family and the morphotypes of bacteroids. Although NCRs have a single origin, their evolution has followed different routes in individual lineages, and enrichment and diversification of cationic peptides has resulted in the ability to impose major morphological changes on the endosymbionts. The wide range of effects provoked by NCRs such as cell enlargement, membrane alterations and permeabilization, and biofilm and vesicle formation is dependent on the amino acid composition and charge of the peptides. These effects are strongly influenced by the rhizobial surface polysaccharides that affect NCR-induced differentiation and survival of rhizobia in nodule cells.
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6
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Montiel J, Szűcs A, Boboescu IZ, Gherman VD, Kondorosi É, Kereszt A. Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:210-9. [PMID: 26713350 DOI: 10.1094/mpmi-09-15-0213-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Medicago and closely related legume species from the inverted repeat-lacking clade (IRLC) impose terminal differentiation onto their bacterial endosymbionts, manifested in genome endoreduplication, cell enlargement, and loss of cell-division capacity. Nodule-specific cysteine-rich (NCR) secreted host peptides are plant effectors of this process. As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids in species from these genera as well as in four other species representing distinct genera of the phylogenetic tree for this clade. Bacteroids in all tested legumes proved to be larger in size and DNA content than cultured cells; however, the degree of cell elongation was rather variable in the different species. In addition, the reproductive ability of the bacteroids isolated from these legumes was remarkably reduced. In all IRLC species with available sequence data, the existence of NCR genes was found. These results indicate that IRLC legumes provoke terminal differentiation of their endosymbionts with different morphotypes, probably with the help of NCR peptides.
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Affiliation(s)
- Jesús Montiel
- 1 Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Attila Szűcs
- 1 Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Iulian Z Boboescu
- 1 Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
- 2 Research Institute for Renewable Energy, Polytechnic University of Timisoara. Piaţa Victoriei Nr. 2, 300006 Timisoara, Romania
| | - Vasile D Gherman
- 2 Research Institute for Renewable Energy, Polytechnic University of Timisoara. Piaţa Victoriei Nr. 2, 300006 Timisoara, Romania
| | - Éva Kondorosi
- 1 Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Attila Kereszt
- 1 Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
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Cao J, Li X, Lv Y, Ding L. Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. FRONTIERS IN PLANT SCIENCE 2015; 6:515. [PMID: 26217366 PMCID: PMC4499708 DOI: 10.3389/fpls.2015.00515] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/26/2015] [Indexed: 05/18/2023]
Abstract
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.
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Affiliation(s)
- Jun Cao
- *Correspondence: Jun Cao, Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Jiangsu, Zhenjiang 212013, China,
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8
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Kondorosi E, Mergaert P, Kereszt A. A paradigm for endosymbiotic life: cell differentiation of Rhizobium bacteria provoked by host plant factors. Annu Rev Microbiol 2014; 67:611-28. [PMID: 24024639 DOI: 10.1146/annurev-micro-092412-155630] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Symbiosis between Rhizobium bacteria and legumes leads to the formation of the root nodule. The endosymbiotic bacteria reside in polyploid host cells as membrane-surrounded vesicles where they reduce atmospheric nitrogen to support plant growth by supplying ammonia in exchange for carbon sources and energy. The morphology and physiology of endosymbionts, despite their common function, are highly divergent in different hosts. In galegoid plants, the endosymbionts are terminally differentiated, uncultivable polyploid cells, with remarkably elongated and even branched Y-shaped cells. Bacteroid differentiation is controlled by host peptides, many of which have antibacterial activity and require the bacterial function of BacA. Although the precise and combined action of several hundred host peptides and BacA has yet to be discovered, similarities, especially to certain insect-bacterium symbioses involving likewise host peptides for manipulation of endosymbionts, suggest convergent evolution. Rhizobium-legume symbiosis provides a rich source of information for understanding host-controlled endosymbiotic life in eukaryotic cells.
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Affiliation(s)
- Eva Kondorosi
- Institut des Sciences du Végétal, CNRS UPR 2355, Gif sur Yvette 91198, France; ,
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium–legume symbiosis. FEMS Microbiol Rev 2013; 37:364-83. [DOI: 10.1111/1574-6976.12003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/12/2012] [Accepted: 09/14/2012] [Indexed: 01/09/2023] Open
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10
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The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis. Mol Genet Genomics 2012; 288:1-20. [DOI: 10.1007/s00438-012-0726-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/07/2012] [Indexed: 02/07/2023]
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11
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium-legume symbiosis. FEMS Microbiol Rev 2012. [DOI: 10.1111/1574-6976.2012.12003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Markus F. F. Arnold
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Kamila K. Myka
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Sergio Dall'Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | | | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique; Gif-sur-Yvette Cedex; France
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
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Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011; 480:520-4. [PMID: 22089132 PMCID: PMC3272368 DOI: 10.1038/nature10625] [Citation(s) in RCA: 767] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 10/13/2011] [Indexed: 11/09/2022]
Abstract
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
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Affiliation(s)
- Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA.
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Alunni B, Kevei Z, Redondo-Nieto M, Kondorosi A, Mergaert P, Kondorosi E. Genomic organization and evolutionary insights on GRP and NCR genes, two large nodule-specific gene families in Medicago truncatula. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1138-48. [PMID: 17849716 DOI: 10.1094/mpmi-20-9-1138] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Deciphering the mechanisms leading to symbiotic nitrogen-fixing root nodule organogenesis in legumes resulted in the identification of numerous nodule-specific genes and gene families. Among them, NCR and GRP genes encode short secreted peptides with potential antimicrobial activity. These genes appear to form large multigenic families in Medicago truncatula and other closely related legume species, whereas no similar genes were found in databases of Lotus japonicus and Glycine max. We analyzed the genomic organization of these genes as well as their evolutionary dynamics in the M. truncatula genome. A total of 108 NCR and 23 GRP genes have been mapped that were often clustered in the genome. These included 29 new NCR and 17 new GRP genes. Reverse transcription-polymerase chain reaction analyses of the novel genes confirmed their exclusive nodule-specific expression similar to the previously identified members. Protein alignments and phylogenetic analyses revealed traces of several duplication events in the history of GRP and NCR genes. Moreover, microsyntenic evidences between M. truncatula and L. japonicus validated the hypothesis that these genes are specific for the inverted repeat-lacking clade of hologalegoid legumes, which allowed dating the appearance of these two gene families during the evolution of legume plants.
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Affiliation(s)
- Benoit Alunni
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique UPR2355, Bat 23, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
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Chen DS, Li YG, Zhou JC. The symbiosis phenotype and expression patterns of five nodule-specific genes of Astragalus sinicus under ammonium and salt stress conditions. PLANT CELL REPORTS 2007; 26:1421-30. [PMID: 17415569 DOI: 10.1007/s00299-007-0346-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 03/04/2007] [Accepted: 03/10/2007] [Indexed: 05/14/2023]
Abstract
In previous works, we isolated 14 nodule-specific or nodule-enhanced genes from Astragalus sinicus by suppressive subtractive hybridization. In this study, we have further identified the expression patterns of five nodule-specific genes of A. sinicus under salt and ammonium stress. Transcription levels of genes tested were quantified by quantitative fluorescence real-time RT-PCR. Results showed that: (1) About 80 mM NaCl and all stress treatments containing (NH(4))(2)SO(4) significantly inhibited nitrogen-fixing capacity of inoculated plants. About 40 mM NaCl showed relative lighter inhibition. (2) Compare with positive control at normal conditions, the expressions of all genes were significantly reduced by all ammonium stress. (3) Under salt stress without exogenous nitrogen, transcription levels of AsIIA255 and AsE246 were significantly increased after treatment for 3 days. But expressions of AsG2411, AsIIC2512, and AsB2510 were suppressed by 80 mM NaCl and not significantly affected by 40 mM NaCl. (4) Under salt stress with exogenous nitrogen, expressions of AsG2411, AsIIC2512, AsB2510, and AsIIA255 were significantly suppressed. While, the transcription level of AsE246 under 80 mM NaCl containing 1 mM (NH(4))(2)SO(4) was still higher than that of positive control. The correlation of the expression profiles of three cysteine cluster protein (CCP) genes (AsG2411, AsIIC2512, AsIIA255) and one lipid transfer protein (LTP) gene (AsE246) with the nitrogen-fixing capacities of nodules in each treatments may explain the molecular mechanisms of their supposed functions in symbiosis and nitrogen-fixing process. Our results also implied that AsIIA255 and AsE246 might play a role in the response of A. sinicus to salt stress to facilitate the nitrogen-fixation process.
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Affiliation(s)
- Da-Song Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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15
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Suganuma N, Yamamoto A, Itou A, Hakoyama T, Banba M, Hata S, Kawaguchi M, Kouchi H. cDNA macroarray analysis of gene expression in ineffective nodules induced on the Lotus japonicus sen1 mutant. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2004; 17:1223-1233. [PMID: 15553247 DOI: 10.1094/mpmi.2004.17.11.1223] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Lotus japonicus sen1 mutant forms ineffective nodules in which development is arrested at the stage of bacterial differentiation into nitrogen-fixing bacteroids. Here, we used cDNA macroarray systems to compare gene expression in ineffective nodules induced on the sen1 mutant with gene expression in wild-type nodules, in order to identify the host plant genes that are involved in nitrogen fixation. Macroarray analysis coupled with Northern blot analysis revealed that the expression of 18 genes was significantly enhanced in ineffective sen1 nodules, whereas the expression of 30 genes was repressed. Many of the enhanced genes encoded hydrolase enzymes, such as cysteine proteinase and asparaginase, that might function in the early senescence of sen1 nodules. By contrast, the repressed genes encoded nodulins, enzymes that are involved in carbon and nitrogen metabolism, membrane transporters, enzymes involved in phytohormone metabolism and secondary metabolism, and regulatory proteins. These proteins might have a role in the establishment of nitrogen fixation. In addition, we discovered two novel genes that encoded glutamate-rich proteins and were localized in the vascular bundles of the nodules. The expression of these genes was repressed in the ineffective nodules, which had lower levels of nitrogenase activity.
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Affiliation(s)
- Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448-8542, Japan.
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Brewin NJ. Plant Cell Wall Remodelling in the Rhizobium–Legume Symbiosis. CRITICAL REVIEWS IN PLANT SCIENCES 2004; 23:293-316. [PMID: 0 DOI: 10.1080/07352680490480734] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Patriarca EJ, Tatè R, Ferraioli S, Iaccarino M. Organogenesis of legume root nodules. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 234:201-62. [PMID: 15066376 DOI: 10.1016/s0074-7696(04)34005-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The N(2)-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.
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Affiliation(s)
- Eduardo J Patriarca
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, Consiglio Nazionale delle Ricerche, 80125 Naples, Italy
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Mergaert P, Nikovics K, Kelemen Z, Maunoury N, Vaubert D, Kondorosi A, Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. PLANT PHYSIOLOGY 2003; 132:161-73. [PMID: 12746522 PMCID: PMC166962 DOI: 10.1104/pp.102.018192] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2002] [Revised: 02/09/2003] [Accepted: 02/09/2003] [Indexed: 05/18/2023]
Abstract
Transcriptome analysis of Medicago truncatula nodules has led to the discovery of a gene family named NCR (nodule-specific cysteine rich) with more than 300 members. The encoded polypeptides were short (60-90 amino acids), carried a conserved signal peptide, and, except for a conserved cysteine motif, displayed otherwise extensive sequence divergence. Family members were found in pea (Pisum sativum), broad bean (Vicia faba), white clover (Trifolium repens), and Galega orientalis but not in other plants, including other legumes, suggesting that the family might be specific for galegoid legumes forming indeterminate nodules. Gene expression of all family members was restricted to nodules except for two, also expressed in mycorrhizal roots. NCR genes exhibited distinct temporal and spatial expression patterns in nodules and, thus, were coupled to different stages of development. The signal peptide targeted the polypeptides in the secretory pathway, as shown by green fluorescent protein fusions expressed in onion (Allium cepa) epidermal cells. Coregulation of certain NCR genes with genes coding for a potentially secreted calmodulin-like protein and for a signal peptide peptidase suggests a concerted action in nodule development. Potential functions of the NCR polypeptides in cell-to-cell signaling and creation of a defense system are discussed.
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Affiliation(s)
- Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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Fedorova M, van de Mortel J, Matsumoto PA, Cho J, Town CD, VandenBosch KA, Gantt JS, Vance CP. Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. PLANT PHYSIOLOGY 2002; 130:519-37. [PMID: 12376622 PMCID: PMC166584 DOI: 10.1104/pp.006833] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable.
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Affiliation(s)
- Maria Fedorova
- Department of Agronomy and Plant Genetics, 1991 Upper Bedford Circle, University of Minnesota, St. Paul, MN 55108, USA
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