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Adema K, Kohlen W. The symbiosome-a transient organelle in evolution. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3209-3213. [PMID: 38845354 PMCID: PMC11156803 DOI: 10.1093/jxb/erae152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
This article comments on: Casaes PA, Ferreira dos Santos JM, Silva VC, Rhem MFK, Teixeira Cota MM, de Faria SM, Rando JG, James EK, Gross E. 2024. The radiation of nodulated Chamaecrista species from the rainforest into more diverse habitats has been accompanied by a reduction in growth form and a shift from fixation threads to symbiosomes. Journal of Experimental Botany 75, 3643-3662.
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Affiliation(s)
- Kelvin Adema
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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2
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. FRONTIERS IN PLANT SCIENCE 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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3
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Libourel C, Keller J, Brichet L, Cazalé AC, Carrère S, Vernié T, Couzigou JM, Callot C, Dufau I, Cauet S, Marande W, Bulach T, Suin A, Masson-Boivin C, Remigi P, Delaux PM, Capela D. Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes. NATURE PLANTS 2023:10.1038/s41477-023-01441-w. [PMID: 37322127 PMCID: PMC10356618 DOI: 10.1038/s41477-023-01441-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Symbiotic interactions such as the nitrogen-fixing root nodule symbiosis (RNS) have structured ecosystems during the evolution of life. Here we aimed at reconstructing ancestral and intermediate steps that shaped RNS observed in extant flowering plants. We compared the symbiotic transcriptomic responses of nine host plants, including the mimosoid legume Mimosa pudica for which we assembled a chromosome-level genome. We reconstructed the ancestral RNS transcriptome composed of most known symbiotic genes together with hundreds of novel candidates. Cross-referencing with transcriptomic data in response to experimentally evolved bacterial strains with gradual symbiotic proficiencies, we found the response to bacterial signals, nodule infection, nodule organogenesis and nitrogen fixation to be ancestral. By contrast, the release of symbiosomes was associated with recently evolved genes encoding small proteins in each lineage. We demonstrate that the symbiotic response was mostly in place in the most recent common ancestor of the RNS-forming species more than 90 million years ago.
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Affiliation(s)
- Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Lukas Brichet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Tatiana Vernié
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Jean-Malo Couzigou
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Isabelle Dufau
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - William Marande
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Tabatha Bulach
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Amandine Suin
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Philippe Remigi
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
| | - Delphine Capela
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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4
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Lee HH, Park J, Jung H, Seo YS. Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. Microorganisms 2021; 9:1123. [PMID: 34067383 PMCID: PMC8224644 DOI: 10.3390/microorganisms9061123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.
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Affiliation(s)
- Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
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Madhaiyan M, See-Too WS, Ee R, Saravanan VS, Wirth JS, Alex THH, Lin C, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:2640-2647. [DOI: 10.1099/ijsem.0.004084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of
Burkholderiaceae
revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family
Burkholderiaceae
. The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1
ω7c /C16 : 1
ω6c) and summed feature 8 (C18 : 1
ω7c /C18 : 1
ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera
Burkholderia
,
Caballeronia
,
Mycetohabitans
,
Mycoavidus
,
Pandoraea
,
Paraburkholderia
,
Robbsia
and
Trinickia
. Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family
Burkholderiaceae
, for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Joseph S. Wirth
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Cai Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
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Roy P, Achom M, Wilkinson H, Lagunas B, Gifford ML. Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides. Genes (Basel) 2020; 11:E348. [PMID: 32218172 PMCID: PMC7230169 DOI: 10.3390/genes11040348] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/11/2020] [Accepted: 03/22/2020] [Indexed: 12/31/2022] Open
Abstract
Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.
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Affiliation(s)
- Proyash Roy
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1205, Bangladesh
| | - Mingkee Achom
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, NY 14853, USA
| | - Helen Wilkinson
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
| | - Beatriz Lagunas
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
| | - Miriam L. Gifford
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK; (P.R.); (M.A.); (H.W.); (B.L.)
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Daubech B, Poinsot V, Klonowska A, Capela D, Chaintreuil C, Moulin L, Marchetti M, Masson-Boivin C. noeM, a New Nodulation Gene Involved in the Biosynthesis of Nod Factors with an Open-Chain Oxidized Terminal Residue and in the Symbiosis with Mimosa pudica. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1635-1648. [PMID: 31617792 DOI: 10.1094/mpmi-06-19-0168-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The β-rhizobium Cupriavidus taiwanensis is a nitrogen-fixing symbiont of Mimosa pudica. Nod factors produced by this species were previously found to be pentameric chitin-oligomers carrying common C18:1 or C16:0 fatty acyl chains, N-methylated and C-6 carbamoylated on the nonreducing terminal N-acetylglucosamine and sulfated on the reducing terminal residue. Here, we report that, in addition, C. taiwanensis LMG19424 produces molecules where the reducing sugar is open and oxidized. We identified a novel nodulation gene located on the symbiotic plasmid pRalta, called noeM, which is involved in this atypical Nod factor structure. noeM encodes a transmembrane protein bearing a fatty acid hydroxylase domain. This gene is expressed during symbiosis with M. pudica and requires NodD and luteolin for optimal expression. The closest noeM homologs formed a separate phylogenetic clade containing rhizobial genes only, which are located on symbiosis plasmids downstream from a nod box. Corresponding proteins, referred to as NoeM, may have specialized in symbiosis via the connection to the nodulation pathway and the spread in rhizobia. noeM was mostly found in isolates of the Mimoseae tribe, and specifically detected in all tested strains able to nodulate M. pudica. A noeM deletion mutant of C. taiwanensis was affected for the nodulation of M. pudica, confirming the role of noeM in the symbiosis with this legume.
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Affiliation(s)
- Benoit Daubech
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Verena Poinsot
- Université de Toulouse 3, UPS CNRS 5623, UMR, Lab IMRCP, F-31062 Toulouse, France
| | | | - Delphine Capela
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Clémence Chaintreuil
- Université Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, LSTM, Montpellier, France
| | - Lionel Moulin
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Marta Marchetti
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Shi C, Beller L, Deboutte W, Yinda KC, Delang L, Vega-Rúa A, Failloux AB, Matthijnssens J. Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics. MICROBIOME 2019; 7:121. [PMID: 31462331 PMCID: PMC6714450 DOI: 10.1186/s40168-019-0734-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/13/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of the viral diversity in individual mosquitoes. To address this issue, we applied our optimized viral metagenomics protocol (NetoVIR) to compare the virome of single and pooled Aedes aegypti and Culex quinquefasciatus mosquitoes collected from different locations in Guadeloupe, in 2016 and 2017. RESULTS The total read number and viral reads proportion of samples containing a single mosquito have no significant difference compared with those of pools containing five mosquitoes, which proved the feasibility of using single mosquito for viral metagenomics. A comparative analysis of the virome revealed a higher abundance and more diverse eukaryotic virome in Aedes aegypti, whereas Culex quinquefasciatus harbors a richer and more diverse phageome. The majority of the identified eukaryotic viruses were mosquito-species specific. We further characterized the genomes of 11 novel eukaryotic viruses. Furthermore, qRT-PCR analyses of the six most abundant eukaryotic viruses indicated that the majority of individual mosquitoes were infected by several of the selected viruses with viral genome copies per mosquito ranging from 267 to 1.01 × 108 (median 7.5 × 106) for Ae. aegypti and 192 to 8.69 × 106 (median 4.87 × 104) for Cx. quinquefasciatus. Additionally, in Cx. quinquefasciatus, a number of phage contigs co-occurred with several marker genes of Wolbachia sp. strain wPip. CONCLUSIONS We firstly demonstrate the feasibility to use single mosquito for viral metagenomics, which can provide much more precise virome profiles of mosquito populations. Interspecific comparisons show striking differences in abundance and diversity between the viromes of Ae. aegypti and Cx. quinquefasciatus. Those two mosquito species seem to have their own relatively stable "core eukaryotic virome", which might have important implications for the competence to transmit important medically relevant arboviruses. The presence of Wolbachia in Cx. quinquefasciatus might explain (1) the lower overall viral load compared to Ae. aegypti, (2) the identification of multiple unknown phage contigs, and (3) the difference in competence for important human pathogens. How these viruses, phages, and bacteria influence the physiology and vector competence of mosquito hosts warrants further research.
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Affiliation(s)
- Chenyan Shi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Leen Beller
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Kwe Claude Yinda
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Anubis Vega-Rúa
- Institut Pasteur of Guadeloupe, Laboratory of Vector Control Research, Unit Transmission, Reservoirs and Pathogen Diversity, Les Abymes, Guadeloupe
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jelle Matthijnssens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
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9
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Cherni AE, Perret X. Deletion of rRNA Operons of Sinorhizobium fredii Strain NGR234 and Impact on Symbiosis With Legumes. Front Microbiol 2019; 10:154. [PMID: 30814981 PMCID: PMC6381291 DOI: 10.3389/fmicb.2019.00154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/22/2019] [Indexed: 01/08/2023] Open
Abstract
During their lifecycle, from free-living soil bacteria to endosymbiotic nitrogen-fixing bacteroids of legumes, rhizobia must colonize, and cope with environments where nutrient concentrations and compositions vary greatly. Bacterial colonization of legume rhizospheres and of root surfaces is subject to a fierce competition for plant exudates. By contrast root nodules offer to rhizobia sheltered nutrient-rich environments within which the cells that successfully propagated via infection threads can rapidly multiply. To explore the effects on symbiosis of a slower rhizobia growth and metabolism, we deleted one or two copies of the three functional rRNA operons of the promiscuous Sinorhizobium fredii strain NGR234 and examined the impact of these mutations on free-living and symbiotic lifestyles. Strains with two functional rRNA operons (NGRΔrRNA1 and NGRΔrRNA3) grew almost as rapidly as NGR234, and NGRΔrRNA1 was as proficient as the parent strain on all of the five legume species tested. By contrast, the NGRΔrRNA1,3 double mutant, which carried a single rRNA operon and grew significantly slower than NGR234, had a reduced symbiotic proficiency on Cajanus cajan, Macroptilium atropurpureum, Tephrosia vogelii, and Vigna unguiculata. In addition, while NGRΔrRNA1 and NGR234 equally competed for nodulation of V. unguiculata, strain NGRΔrRNA1,3 was clearly outcompeted by wild-type. Surprisingly, on Leucaena leucocephala, NGRΔrRNA1,3 was the most proficient strain and competed equally NGR234 for nodule occupation. Together, these results indicate that for strains with otherwise identical repertoires of symbiotic genes, a faster growth on roots and/or inside plant tissues may contribute to secure access to nodules of some hosts. By contrast, other legumes such as L. leucocephala appear as less selective and capable of providing symbiotic environments susceptible to accommodate strains with a broader spectrum of competences.
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Affiliation(s)
- Ala Eddine Cherni
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
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10
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Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C. Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont. Mol Biol Evol 2017; 34:2503-2521. [PMID: 28535261 DOI: 10.1093/molbev/msx165] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here, we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes. We show that a regulatory pathway of the recipient R. solanacearum genome involved in extracellular infection of natural hosts was reused to improve intracellular symbiosis with the Mimosa pudica legume. Optimization of intracellular infection capacity was gained through mutations affecting two components of a new regulatory pathway, the transcriptional regulator efpR and a region upstream from the RSc0965-0967 genes of unknown functions. Adaptive mutations caused the downregulation of efpR and the over-expression of a downstream regulatory module, the three unknown genes RSc3146-3148, two of which encoding proteins likely associated to the membrane. This over-expression led to important metabolic and transcriptomic changes and a drastic qualitative and quantitative improvement of nodule intracellular infection. In addition, these adaptive mutations decreased the virulence of the original pathogen. The complete efpR/RSc3146-3148 pathway could only be identified in the genomes of the pathogenic R. solanacearum species complex. Our findings illustrate how the rewiring of a genetic network regulating virulence allows a radically different type of symbiotic interaction and contributes to ecological transitions and trade-offs.
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Affiliation(s)
- Delphine Capela
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marta Marchetti
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Camille Clérissi
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.,Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Anthony Perrier
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Dorian Guetta
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Carine Gris
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marc Valls
- Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Spain
| | - Alain Jauneau
- Fédération de Recherches Agrobiosciences, Interactions, Biodiversity, Plateforme d'Imagerie TRI, CNRS, UPS, Castanet-Tolosan, France
| | - Stéphane Cruveiller
- CNRS-UMR8030 and Commissariat à l'Energie Atomique et aux Energies Alternatives CEA/DRF/IG/GEN LABGeM, Evry, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
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11
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Daubech B, Remigi P, Doin de Moura G, Marchetti M, Pouzet C, Auriac MC, Gokhale CS, Masson-Boivin C, Capela D. Spatio-temporal control of mutualism in legumes helps spread symbiotic nitrogen fixation. eLife 2017; 6:e28683. [PMID: 29022875 PMCID: PMC5687860 DOI: 10.7554/elife.28683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/11/2017] [Indexed: 01/01/2023] Open
Abstract
Mutualism is of fundamental importance in ecosystems. Which factors help to keep the relationship mutually beneficial and evolutionarily successful is a central question. We addressed this issue for one of the most significant mutualistic interactions on Earth, which associates plants of the leguminosae family and hundreds of nitrogen (N2)-fixing bacterial species. Here we analyze the spatio-temporal dynamics of fixers and non-fixers along the symbiotic process in the Cupriavidus taiwanensis-Mimosa pudica system. N2-fixing symbionts progressively outcompete isogenic non-fixers within root nodules, where N2-fixation occurs, even when they share the same nodule. Numerical simulations, supported by experimental validation, predict that rare fixers will invade a population dominated by non-fixing bacteria during serial nodulation cycles with a probability that is function of initial inoculum, plant population size and nodulation cycle length. Our findings provide insights into the selective forces and ecological factors that may have driven the spread of the N2-fixation mutualistic trait.
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Affiliation(s)
- Benoit Daubech
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
| | - Philippe Remigi
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Ginaini Doin de Moura
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
| | - Marta Marchetti
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
| | - Cécile Pouzet
- Fédération de Recherches Agrobiosciences, Interactions et Biodiversité, Plateforme d’Imagerie TRI, CNRS - UPSCastanet-TolosanFrance
| | - Marie-Christine Auriac
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
- Fédération de Recherches Agrobiosciences, Interactions et Biodiversité, Plateforme d’Imagerie TRI, CNRS - UPSCastanet-TolosanFrance
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary TheoryMax Planck Institute for Evolutionary BiologyPlönGermany
| | - Catherine Masson-Boivin
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
| | - Delphine Capela
- The Laboratory of Plant-Microbe InteractionsUniversité de Toulouse, INRA, CNRSCastanet-TolosanFrance
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12
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Marchetti M, Clerissi C, Yousfi Y, Gris C, Bouchez O, Rocha E, Cruveiller S, Jauneau A, Capela D, Masson-Boivin C. Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime. Mol Ecol 2016; 26:1818-1831. [PMID: 27770459 DOI: 10.1111/mec.13895] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/11/2016] [Accepted: 10/18/2016] [Indexed: 01/09/2023]
Abstract
Experimental evolution is a powerful approach to study the process of adaptation to new environments, including the colonization of eukaryotic hosts. Facultative endosymbionts, including pathogens and mutualists, face changing and spatially structured environments during the symbiotic process, which impose diverse selection pressures. Here, we provide evidence that different selection regimes, involving different times spent in the plant environment, can result in either intra- or extracellular symbiotic adaptations. In previous work, we introduced the symbiotic plasmid of Cupriavidus taiwanensis, the rhizobial symbiont of Mimosa pudica, into the phytopathogen Ralstonia solanacearum and selected three variants able to form root nodules on M. pudica, two (CBM212 and CBM349) being able to rudimentarily infect nodule cells and the third one (CBM356) only capable of extracellular infection of nodules. Each nodulating ancestor was further challenged to evolve using serial ex planta-in planta cycles of either 21 (three short-cycle lineages) or 42 days (three long-cycle lineages). In this study, we compared the phenotype of the 18 final evolved clones. Evolution through short and long cycles resulted in similar adaptive paths on lineages deriving from the two intracellularly infectious ancestors, CBM212 and CBM349. In contrast, only short cycles allowed a stable acquisition of intracellular infection in lineages deriving from the extracellularly infecting ancestor, CBM356. Long cycles, instead, favoured improvement of extracellular infection. Our work highlights the importance of the selection regime in shaping desired traits during host-mediated selection experiments.
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Affiliation(s)
- Marta Marchetti
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan Cedex, France
| | - Camille Clerissi
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan Cedex, France.,Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, 75015, Paris, France.,CNRS, UMR3525, 25-28 rue Dr Roux, 75015, Paris, France
| | - Yasmine Yousfi
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan Cedex, France
| | - Carine Gris
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GeT-PlaGe, INRA, 31326, Castanet-Tolosan Cedex, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet-Tolosan Cedex, France
| | - Eduardo Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, 75015, Paris, France.,CNRS, UMR3525, 25-28 rue Dr Roux, 75015, Paris, France
| | - Stéphane Cruveiller
- CNRS-UMR8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, 2 rue gaston Crémieux, 91057, Evry, France
| | - Alain Jauneau
- Fédération de Recherches Agrobiosciences, Interactions, Biodiversity, Plateforme d'Imagerie TRI, CNRS, UPS, 31326, Castanet-Tolosan Cedex, France
| | - Delphine Capela
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan Cedex, France
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13
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Crespo-Rivas JC, Guefrachi I, Mok KC, Villaécija-Aguilar JA, Acosta-Jurado S, Pierre O, Ruiz-Sainz JE, Taga ME, Mergaert P, Vinardell JM. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis. Environ Microbiol 2015; 18:2392-404. [PMID: 26521863 DOI: 10.1111/1462-2920.13101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/20/2015] [Indexed: 11/28/2022]
Abstract
In rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation.
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Affiliation(s)
- Juan C Crespo-Rivas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - Kenny C Mok
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - José A Villaécija-Aguilar
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain.,Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - Sebastián Acosta-Jurado
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - José E Ruiz-Sainz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - José M Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
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14
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Marchetti M, Jauneau A, Capela D, Remigi P, Gris C, Batut J, Masson-Boivin C. Shaping bacterial symbiosis with legumes by experimental evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:956-964. [PMID: 25105803 DOI: 10.1094/mpmi-03-14-0083-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.
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15
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Guan SH, Gris C, Cruveiller S, Pouzet C, Tasse L, Leru A, Maillard A, Médigue C, Batut J, Masson-Boivin C, Capela D. Experimental evolution of nodule intracellular infection in legume symbionts. ISME JOURNAL 2013; 7:1367-77. [PMID: 23426010 DOI: 10.1038/ismej.2013.24] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Soil bacteria known as rhizobia are able to establish an endosymbiosis with legumes that takes place in neoformed nodules in which intracellularly hosted bacteria fix nitrogen. Intracellular accommodation that facilitates nutrient exchange between the two partners and protects bacteria from plant defense reactions has been a major evolutionary step towards mutualism. Yet the forces that drove the selection of the late event of intracellular infection during rhizobium evolution are unknown. To address this question, we took advantage of the previous conversion of the plant pathogen Ralstonia solanacearum into a legume-nodulating bacterium that infected nodules only extracellularly. We experimentally evolved this draft rhizobium into intracellular endosymbionts using serial cycles of legume-bacterium cocultures. The three derived lineages rapidly gained intracellular infection capacity, revealing that the legume is a highly selective environment for the evolution of this trait. From genome resequencing, we identified in each lineage a mutation responsible for the extracellular-intracellular transition. All three mutations target virulence regulators, strongly suggesting that several virulence-associated functions interfere with intracellular infection. We provide evidence that the adaptive mutations were selected for their positive effect on nodulation. Moreover, we showed that inactivation of the type three secretion system of R. solanacearum that initially allowed the ancestral draft rhizobium to nodulate, was also required to permit intracellular infection, suggesting a similar checkpoint for bacterial invasion at the early nodulation/root infection and late nodule cell entry levels. We discuss our findings with respect to the spread and maintenance of intracellular infection in rhizobial lineages during evolutionary times.
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Affiliation(s)
- Su Hua Guan
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
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16
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Kereszt A, Mergaert P, Kondorosi E. Bacteroid development in legume nodules: evolution of mutual benefit or of sacrificial victims? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1300-9. [PMID: 21995798 DOI: 10.1094/mpmi-06-11-0152] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Symbiosomes are organelle-like structures in the cytoplasm of legume nodule cells which are composed of the special, nitrogen-fixing forms of rhizobia called bacteroids, the peribacteroid space and the enveloping peribacteroid membrane of plant origin. The formation of these symbiosomes requires a complex and coordinated interaction between the two partners during all stages of nodule development as any failure in the differentiation of either symbiotic partner, the bacterium or the plant cell prevents the subsequent transcriptional and developmental steps resulting in early senescence of the nodules. Certain legume hosts impose irreversible terminal differentiation onto bacteria. In the inverted repeat-lacking clade (IRLC) of legumes, host dominance is achieved by nodule-specific cysteine-rich peptides that resemble defensin-like antimicrobial peptides, the known effector molecules of animal and plant innate immunity. This article provides an overview on the bacteroid and symbiosome development including the terminal differentiation of bacteria in IRLC legumes as well as the bacterial and plant genes and proteins participating in these processes.
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