Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]

GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins...

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Autores: Forbes, Gillian, Schilde, Christina, Lawal, Hajara, Kin, Koryu, Du, Qingyou, Chen, Zhi-Hui, Rivero, Francisco, Schaap, Pauline
Tipo de recurso: conjunto de datos
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/311040
Acceso en línea:http://hdl.handle.net/10261/311040
Access Level:acceso abierto
Palabra clave:GTP binding proteins
Guanine nucleotide exchange factors
GTPase activating proteins
Stage- and cell-type specific transcriptomics
Hierarchical clustering
Interactome
Vesicle trafficking
Cell signalling
Cytokinesis
Cell motility
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spelling Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]Forbes, GillianSchilde, ChristinaLawal, HajaraKin, KoryuDu, QingyouChen, Zhi-HuiRivero, FranciscoSchaap, PaulineGTP binding proteinsGuanine nucleotide exchange factorsGTPase activating proteinsStage- and cell-type specific transcriptomicsHierarchical clusteringInteractomeVesicle traffickingCell signallingCytokinesisCell motilityGTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for Dictyostelium species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.This research was funded by the European Research Council under grant 742288 and by The Wellcome Trust under grant 100293/Z/12/Z; European Research Council [742288].Peer reviewedFigshareEuropean Research CouncilWellcome TrustConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232021info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1application/pdfapplication/vnd.ms-excelhttp://hdl.handle.net/10261/311040reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/742288Forbes, Gillian; Schilde, Christina; Lawal, Hajara; Kin, Koryu; Du, Qingyou; Chen, Zhi-Hui; Rivero, Francisco; Schaap, Pauline. Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators. https://doi.org/10.1080/21541248.2021.1984829 . http://hdl.handle.net/10261/271987https://doi.org/10.6084/m9.figshare.16699108.v2Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3110402026-05-22T06:33:51Z
dc.title.none.fl_str_mv Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
title Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
spellingShingle Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
Forbes, Gillian
GTP binding proteins
Guanine nucleotide exchange factors
GTPase activating proteins
Stage- and cell-type specific transcriptomics
Hierarchical clustering
Interactome
Vesicle trafficking
Cell signalling
Cytokinesis
Cell motility
title_short Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
title_full Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
title_fullStr Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
title_full_unstemmed Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
title_sort Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators [Dataset]
dc.creator.none.fl_str_mv Forbes, Gillian
Schilde, Christina
Lawal, Hajara
Kin, Koryu
Du, Qingyou
Chen, Zhi-Hui
Rivero, Francisco
Schaap, Pauline
author Forbes, Gillian
author_facet Forbes, Gillian
Schilde, Christina
Lawal, Hajara
Kin, Koryu
Du, Qingyou
Chen, Zhi-Hui
Rivero, Francisco
Schaap, Pauline
author_role author
author2 Schilde, Christina
Lawal, Hajara
Kin, Koryu
Du, Qingyou
Chen, Zhi-Hui
Rivero, Francisco
Schaap, Pauline
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Research Council
Wellcome Trust
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv GTP binding proteins
Guanine nucleotide exchange factors
GTPase activating proteins
Stage- and cell-type specific transcriptomics
Hierarchical clustering
Interactome
Vesicle trafficking
Cell signalling
Cytokinesis
Cell motility
topic GTP binding proteins
Guanine nucleotide exchange factors
GTPase activating proteins
Stage- and cell-type specific transcriptomics
Hierarchical clustering
Interactome
Vesicle trafficking
Cell signalling
Cytokinesis
Cell motility
description GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for Dictyostelium species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.
publishDate 2021
dc.date.none.fl_str_mv 2021
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/311040
url http://hdl.handle.net/10261/311040
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/742288
Forbes, Gillian; Schilde, Christina; Lawal, Hajara; Kin, Koryu; Du, Qingyou; Chen, Zhi-Hui; Rivero, Francisco; Schaap, Pauline. Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators. https://doi.org/10.1080/21541248.2021.1984829 . http://hdl.handle.net/10261/271987
https://doi.org/10.6084/m9.figshare.16699108.v2
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/vnd.ms-excel
dc.publisher.none.fl_str_mv Figshare
publisher.none.fl_str_mv Figshare
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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