Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis

Autores
Gitman, Iván Federico Berco; Grossi, Cecilia Eugenia María; Arico, Denise Soledad; Mazzella, Maria Agustina; Ulloa, Rita Maria
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We developed a pipeline to standardize and integrate publicly available transcriptomic,proteomic, and phosphoproteomic datasets from Arabidopsis thaliana etiolatedseedlings. The pipeline is broadly adaptable, as its database schema and processingscripts can be applied to datasets from any organism or experimental condition. Weapplied it to etiolated seedlings to uncover protein kinases and protein phosphatasesrelevant to early skotomorphogenic development, a stage in which seedlings growunderground and rely on precisely regulated signaling networks to ensure survival andsuccessful emergence. This multi-omics approach revealed a comprehensive landscapeof protein expression at this developmental stage; however, we observed widespreaddiscrepancies between transcript and protein abundance, pointing to post-transcriptionaland/or post-translational regulation. This cross-study minimizes experimental bias andallows the detection of phosphorylation events that may have been overlooked in singleconditionstudies. A search of kinase specific motifs revealed that RxxS motifs weresignificantly enriched among phosphorylated peptides in protein phosphatases andmicrotubule-associated proteins, suggesting regulation by calcium dependent proteinkinases (CPKs). CPK3 and CPK9 were identified as the most relevant isoforms in theproteome and phosphokinome, supporting their central role in skotomorphogenesis. Ourresults underscore the importance of phosphorylation-mediated signaling incoordinating early seedling development and provide a resource for dissectingregulatory networks and candidate genes involved in skotomorphogenesis.
Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Arico, Denise Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Mazzella, Maria Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Ulloa, Rita Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Materia
ARABIDOPSIS THALIANA
CALCIUM DEPENDENT PROTEIN KINASES
PROTEIN PHOSPHATASES
SKOTOMORPHOGENESIS
TRANSCRIPTOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC META-ANALYSIS.
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/281145
Acceder
id CONICETDig_4cf3bd1bc51f7a04c6b927974f69da3e
oai_identifier_str oai:ri.conicet.gov.ar:11336/281145
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis SkotomorphogenesisGitman, Iván Federico BercoGrossi, Cecilia Eugenia MaríaArico, Denise SoledadMazzella, Maria AgustinaUlloa, Rita MariaARABIDOPSIS THALIANACALCIUM DEPENDENT PROTEIN KINASESPROTEIN PHOSPHATASESSKOTOMORPHOGENESISTRANSCRIPTOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC META-ANALYSIS.https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1We developed a pipeline to standardize and integrate publicly available transcriptomic,proteomic, and phosphoproteomic datasets from Arabidopsis thaliana etiolatedseedlings. The pipeline is broadly adaptable, as its database schema and processingscripts can be applied to datasets from any organism or experimental condition. Weapplied it to etiolated seedlings to uncover protein kinases and protein phosphatasesrelevant to early skotomorphogenic development, a stage in which seedlings growunderground and rely on precisely regulated signaling networks to ensure survival andsuccessful emergence. This multi-omics approach revealed a comprehensive landscapeof protein expression at this developmental stage; however, we observed widespreaddiscrepancies between transcript and protein abundance, pointing to post-transcriptionaland/or post-translational regulation. This cross-study minimizes experimental bias andallows the detection of phosphorylation events that may have been overlooked in singleconditionstudies. A search of kinase specific motifs revealed that RxxS motifs weresignificantly enriched among phosphorylated peptides in protein phosphatases andmicrotubule-associated proteins, suggesting regulation by calcium dependent proteinkinases (CPKs). CPK3 and CPK9 were identified as the most relevant isoforms in theproteome and phosphokinome, supporting their central role in skotomorphogenesis. Ourresults underscore the importance of phosphorylation-mediated signaling incoordinating early seedling development and provide a resource for dissectingregulatory networks and candidate genes involved in skotomorphogenesis.Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Arico, Denise Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Mazzella, Maria Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Ulloa, Rita Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaBioRxiv2025-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/281145Gitman, Iván Federico Berco; Grossi, Cecilia Eugenia María; Arico, Denise Soledad; Mazzella, Maria Agustina; Ulloa, Rita Maria; Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis; BioRxiv; BioRxiv; 10-2025; 1-402692-8205CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1101/2025.10.22.683993info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/2025.10.22.683993v1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-02-26T10:26:50Zoai:ri.conicet.gov.ar:11336/281145instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-02-26 10:26:50.756CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
title Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
spellingShingle Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
Gitman, Iván Federico Berco
ARABIDOPSIS THALIANA
CALCIUM DEPENDENT PROTEIN KINASES
PROTEIN PHOSPHATASES
SKOTOMORPHOGENESIS
TRANSCRIPTOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC META-ANALYSIS.
title_short Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
title_full Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
title_fullStr Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
title_full_unstemmed Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
title_sort Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis
dc.creator.none.fl_str_mv Gitman, Iván Federico Berco
Grossi, Cecilia Eugenia María
Arico, Denise Soledad
Mazzella, Maria Agustina
Ulloa, Rita Maria
author Gitman, Iván Federico Berco
author_facet Gitman, Iván Federico Berco
Grossi, Cecilia Eugenia María
Arico, Denise Soledad
Mazzella, Maria Agustina
Ulloa, Rita Maria
author_role author
author2 Grossi, Cecilia Eugenia María
Arico, Denise Soledad
Mazzella, Maria Agustina
Ulloa, Rita Maria
author2_role author
author
author
author
dc.subject.none.fl_str_mv ARABIDOPSIS THALIANA
CALCIUM DEPENDENT PROTEIN KINASES
PROTEIN PHOSPHATASES
SKOTOMORPHOGENESIS
TRANSCRIPTOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC META-ANALYSIS.
topic ARABIDOPSIS THALIANA
CALCIUM DEPENDENT PROTEIN KINASES
PROTEIN PHOSPHATASES
SKOTOMORPHOGENESIS
TRANSCRIPTOMIC, PROTEOMIC AND PHOSPHOPROTEOMIC META-ANALYSIS.
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We developed a pipeline to standardize and integrate publicly available transcriptomic,proteomic, and phosphoproteomic datasets from Arabidopsis thaliana etiolatedseedlings. The pipeline is broadly adaptable, as its database schema and processingscripts can be applied to datasets from any organism or experimental condition. Weapplied it to etiolated seedlings to uncover protein kinases and protein phosphatasesrelevant to early skotomorphogenic development, a stage in which seedlings growunderground and rely on precisely regulated signaling networks to ensure survival andsuccessful emergence. This multi-omics approach revealed a comprehensive landscapeof protein expression at this developmental stage; however, we observed widespreaddiscrepancies between transcript and protein abundance, pointing to post-transcriptionaland/or post-translational regulation. This cross-study minimizes experimental bias andallows the detection of phosphorylation events that may have been overlooked in singleconditionstudies. A search of kinase specific motifs revealed that RxxS motifs weresignificantly enriched among phosphorylated peptides in protein phosphatases andmicrotubule-associated proteins, suggesting regulation by calcium dependent proteinkinases (CPKs). CPK3 and CPK9 were identified as the most relevant isoforms in theproteome and phosphokinome, supporting their central role in skotomorphogenesis. Ourresults underscore the importance of phosphorylation-mediated signaling incoordinating early seedling development and provide a resource for dissectingregulatory networks and candidate genes involved in skotomorphogenesis.
Fil: Gitman, Iván Federico Berco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Grossi, Cecilia Eugenia María. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Arico, Denise Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Mazzella, Maria Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Ulloa, Rita Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
description We developed a pipeline to standardize and integrate publicly available transcriptomic,proteomic, and phosphoproteomic datasets from Arabidopsis thaliana etiolatedseedlings. The pipeline is broadly adaptable, as its database schema and processingscripts can be applied to datasets from any organism or experimental condition. Weapplied it to etiolated seedlings to uncover protein kinases and protein phosphatasesrelevant to early skotomorphogenic development, a stage in which seedlings growunderground and rely on precisely regulated signaling networks to ensure survival andsuccessful emergence. This multi-omics approach revealed a comprehensive landscapeof protein expression at this developmental stage; however, we observed widespreaddiscrepancies between transcript and protein abundance, pointing to post-transcriptionaland/or post-translational regulation. This cross-study minimizes experimental bias andallows the detection of phosphorylation events that may have been overlooked in singleconditionstudies. A search of kinase specific motifs revealed that RxxS motifs weresignificantly enriched among phosphorylated peptides in protein phosphatases andmicrotubule-associated proteins, suggesting regulation by calcium dependent proteinkinases (CPKs). CPK3 and CPK9 were identified as the most relevant isoforms in theproteome and phosphokinome, supporting their central role in skotomorphogenesis. Ourresults underscore the importance of phosphorylation-mediated signaling incoordinating early seedling development and provide a resource for dissectingregulatory networks and candidate genes involved in skotomorphogenesis.
publishDate 2025
dc.date.none.fl_str_mv 2025-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/281145
Gitman, Iván Federico Berco; Grossi, Cecilia Eugenia María; Arico, Denise Soledad; Mazzella, Maria Agustina; Ulloa, Rita Maria; Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis; BioRxiv; BioRxiv; 10-2025; 1-40
2692-8205
CONICET Digital
CONICET
url http://hdl.handle.net/11336/281145
identifier_str_mv Gitman, Iván Federico Berco; Grossi, Cecilia Eugenia María; Arico, Denise Soledad; Mazzella, Maria Agustina; Ulloa, Rita Maria; Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis; BioRxiv; BioRxiv; 10-2025; 1-40
2692-8205
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1101/2025.10.22.683993
info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/2025.10.22.683993v1
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioRxiv
publisher.none.fl_str_mv BioRxiv
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1858305882415169536
score 13.176822

Publicaciones similares