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Dallachiesa D, Aguilar OM, Lozano MJ. Improved detection and phylogenetic analysis of plant proteins containing LysM domains. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:NULL. [PMID: 38007819 DOI: 10.1071/fp23131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/31/2023] [Indexed: 11/28/2023]
Abstract
Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, through cell-surface receptors containing a tight bundle of three LysM domains in their extracellular region. However, the identification of LysM domains of receptor-like kinases (RLK)/receptor-like proteins (RLP) using sequence based methods has led to some ambiguity, as some proteins have been annotated with only one or two LysM domains. This missing annotation was likely produced by the failure of the LysM hidden Markov model (HMM) from the Pfam database to correctly identify some LysM domains in proteins of plant origin. In this work, we provide improved HMMs for LysM domain detection in plants, that were built from the structural alignment of manually curated LysM domain structures from the Protein Data Bank and AlphaFold Protein Structure Database. Furthermore, we evaluated different sets of ligand-specific HMMs that were able to correctly classify a limited set of fully characterised RLK/Ps by their ligand specificity. In contrast, the phylogenetic analysis of the extracellular region of RLK/Ps, or of their individual LysM domains, was unable to discriminate these proteins by their ligand specificity. The HMMs reported here will allow a more sensitive detection of plant proteins containing LysM domains and help improve their characterisation.
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Affiliation(s)
- Dardo Dallachiesa
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
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Cullimore J, Fliegmann J, Gasciolli V, Gibelin-Viala C, Carles N, Luu TB, Girardin A, Cumener M, Maillet F, Pradeau S, Fort S, Bono JJ, Gough C, Lefebvre B. Evolution of lipochitooligosaccharide binding to a LysM-RLK for nodulation in Medicago truncatula. PLANT & CELL PHYSIOLOGY 2023:pcad033. [PMID: 37098213 DOI: 10.1093/pcp/pcad033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 06/19/2023]
Abstract
Lysin motif receptor like kinases (LysM-RLKs) are involved in the perception of chitooligosaccharides (COs) and related lipochitooligosaccharides (LCOs) in plants. Expansion and divergence of the gene family during evolution have led to various roles in symbiosis and defence. By studying proteins of the LYR-IA subclass of LysM-RLKs of the Poaceae, we show here that they are high affinity LCO binding proteins with a lower affinity for COs, consistent with a role in LCO perception to establish arbuscular mycorrhiza (AM). In Papilionoid legumes whole genome duplication has resulted in two LYR-IA paralogs, MtLYR1 and MtNFP in Medicago truncatula, with MtNFP playing an essential role in the root nodule symbiosis with nitrogen-fixing rhizobia. We show that MtLYR1 has retained the ancestral LCO binding characteristic and is dispensable for AM. Domain swapping between the three Lysin motifs (LysMs) of MtNFP and MtLYR1 and mutagenesis in MtLYR1 suggest that the MtLYR1 LCO binding site is on the second LysM, and that divergence in MtNFP led to better nodulation, but surprisingly with decreased LCO binding. These results suggest that divergence of the LCO binding site has been important for the evolution of a role of MtNFP in nodulation with rhizobia.
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Affiliation(s)
- Julie Cullimore
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Judith Fliegmann
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Virginie Gasciolli
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Chrystel Gibelin-Viala
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Noémie Carles
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Thi-Bich Luu
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Ariane Girardin
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Marie Cumener
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Fabienne Maillet
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | | | - Sébastien Fort
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Jean-Jacques Bono
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Clare Gough
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Benoit Lefebvre
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
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Luu TB, Ourth A, Pouzet C, Pauly N, Cullimore J. A newly evolved chimeric lysin motif receptor-like kinase in Medicago truncatula spp. tricycla R108 extends its Rhizobia symbiotic partnership. THE NEW PHYTOLOGIST 2022; 235:1995-2007. [PMID: 35611584 DOI: 10.1111/nph.18270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Rhizobial lipochitooligosaccharidic Nod factors (NFs), specified by nod genes, are the primary determinants of host specificity in the legume-Rhizobia symbiosis. We examined the nodulation ability of Medicago truncatula cv Jemalong A17 and M. truncatula ssp. tricycla R108 with the Sinorhizobium meliloti nodF/nodL mutant, which produces modified NFs. We then applied genetic and functional approaches to study the genetic basis and mechanism of nodulation of R108 by this mutant. We show that the nodF/nodL mutant can nodulate R108 but not A17. Using genomics and reverse genetics, we identified a newly evolved, chimeric LysM receptor-like kinase gene in R108, LYK2bis, which is responsible for the phenotype and can allow A17 to gain nodulation with the nodF/nodL mutant. We found that LYK2bis is involved in nodulation by mutants producing nonO-acetylated NFs and interacts with the key receptor protein NFP. Many, but not all, natural S. meliloti and S. medicae strains tested require LYK2bis for efficient nodulation of R108. Our findings reveal that a newly evolved gene in R108, LYK2bis, extends nodulation specificity to mutants producing nonO-acetylated NFs and is important for nodulation by many natural Sinorhizobia. Evolution of this gene may present an adaptive advantage to allow nodulation by a greater variety of strains.
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Affiliation(s)
- Thi-Bich Luu
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326, Castanet-Tolosan Cedex, France
| | - Anna Ourth
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326, Castanet-Tolosan Cedex, France
| | - Cécile Pouzet
- FRAIB-TRI Imaging Platform Facilities, FR AIB, Université de Toulouse, CNRS, 31320, Castanet-Tolosan, France
| | - Nicolas Pauly
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326, Castanet-Tolosan Cedex, France
- Institut Sophia Agrobiotech, Université Côte d'Azur, INRAE, CNRS, 06903, Sophia Antipolis Cedex, France
| | - Julie Cullimore
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326, Castanet-Tolosan Cedex, France
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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