Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria
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.
Main Authors: | , , , , , , , , |
---|---|
Other Authors: | |
Format: | artículo biblioteca |
Published: |
American Society for Microbiology
2021
|
Subjects: | MCP, Chemoreceptor, Chemotaxis, Methyl-accepting chemotaxis protein, Plant-associated bacteria, |
Online Access: | http://hdl.handle.net/10261/252786 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100011011 http://dx.doi.org/10.13039/501100003329 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-inia-es-10261-252786 |
---|---|
record_format |
koha |
spelling |
dig-inia-es-10261-2527862021-12-20T13:41:18Z Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria Sanchis-López, Claudia Cerna-Vargas, Jean Santamaria-Hernando, Saray Ramos, Cayo Krell, Tino Rodríguez-Palenzuela, Pablo López-Solanilla, Emilia Huerta-Cepas, Jaime Rodriguez-Herva, José Ministerio de Ciencia, Innovación y Universidades (España) European Commission Junta de Andalucía Ministerio de Economía y Competitividad (España) MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria 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). 2021-10-21T11:30:03Z 2021-10-21T11:30:03Z 2021 2021-10-21T11:30:03Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1128/mSystems.00951-21 issn: 2379-5077 mSystems 6: e00951-21 (2021) http://hdl.handle.net/10261/252786 10.1128/mSystems.00951-21 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100011011 http://dx.doi.org/10.13039/501100003329 #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-098073-A-I00 info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2016-76779-P info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2017-82492-C2-1-R info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-095222-B-I00 Publisher's version http://dx.doi.org/10.1128/mSystems.00951-21 Sí open American Society for Microbiology |
institution |
INIA ES |
collection |
DSpace |
country |
España |
countrycode |
ES |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-inia-es |
tag |
biblioteca |
region |
Europa del Sur |
libraryname |
Biblioteca del INIA España |
topic |
MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria |
spellingShingle |
MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria Sanchis-López, Claudia Cerna-Vargas, Jean Santamaria-Hernando, Saray Ramos, Cayo Krell, Tino Rodríguez-Palenzuela, Pablo López-Solanilla, Emilia Huerta-Cepas, Jaime Rodriguez-Herva, José Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
description |
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. |
author2 |
Ministerio de Ciencia, Innovación y Universidades (España) |
author_facet |
Ministerio de Ciencia, Innovación y Universidades (España) Sanchis-López, Claudia Cerna-Vargas, Jean Santamaria-Hernando, Saray Ramos, Cayo Krell, Tino Rodríguez-Palenzuela, Pablo López-Solanilla, Emilia Huerta-Cepas, Jaime Rodriguez-Herva, José |
format |
artículo |
topic_facet |
MCP Chemoreceptor Chemotaxis Methyl-accepting chemotaxis protein Plant-associated bacteria |
author |
Sanchis-López, Claudia Cerna-Vargas, Jean Santamaria-Hernando, Saray Ramos, Cayo Krell, Tino Rodríguez-Palenzuela, Pablo López-Solanilla, Emilia Huerta-Cepas, Jaime Rodriguez-Herva, José |
author_sort |
Sanchis-López, Claudia |
title |
Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
title_short |
Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
title_full |
Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
title_fullStr |
Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
title_full_unstemmed |
Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
title_sort |
prevalence and specificity of chemoreceptor profiles in plant-associated bacteria |
publisher |
American Society for Microbiology |
publishDate |
2021 |
url |
http://hdl.handle.net/10261/252786 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100011011 http://dx.doi.org/10.13039/501100003329 |
work_keys_str_mv |
AT sanchislopezclaudia prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT cernavargasjean prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT santamariahernandosaray prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT ramoscayo prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT krelltino prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT rodriguezpalenzuelapablo prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT lopezsolanillaemilia prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT huertacepasjaime prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria AT rodriguezhervajose prevalenceandspecificityofchemoreceptorprofilesinplantassociatedbacteria |
_version_ |
1767602869651898368 |