Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria
| Autor: | Cayo Ramos, Jean Paul Cerna-Vargas, Emilia López-Solanilla, Jaime Huerta-Cepas, Pablo Rodríguez-Palenzuela, Tino Krell, Saray Santamaría-Hernando, Claudia Sanchis-López, José J. Rodríguez-Herva |
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| Přispěvatelé: | Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Junta de Andalucía, Ministerio de Economía y Competitividad (España) |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Chemoreceptor
Physiology chemoreceptor Biology Biochemistry Microbiology plant-associated bacteria Genetics chemotaxis Molecular Biology Ecology Evolution Behavior and Systematics Methyl-accepting chemotaxis protein Chemotaxis methyl-accepting chemotaxis protein Plant associated bacteria Editor's Pick QR1-502 Plant-associated bacteria Computer Science Applications Modeling and Simulation MCP hormones hormone substitutes and hormone antagonists Research Article |
| Zdroj: | mSystems, Vol 6, Iss 5 (2021) mSystems Digital.CSIC. Repositorio Institucional del CSIC instname |
| ISSN: | 2379-5077 |
| Popis: | Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs. This research has been supported by grants PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE (to J.H.-C.), BIO2016-76779-P (to T.K.), AGL2017-82492-C2-1-R (to C.R.), and RTI2018-095222-B-I00 (to E.L.-S.) from the Ministerio de Ciencia, Innovación y Universidades, Spain, as well as grant P18-FR-1621 (to T.K.) from the Junta de Andalucía. C.S.-L. was supported by the FPU program (FPU19/06635, MICINN-Spain), and J.P.C.-V. by the FPI program (BES-2016-076452, MINECO-Spain). |
| Databáze: | OpenAIRE |
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