Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network

This article belongs to the Special Issue Regulatory Mechanisms of Development and Abiotic Stress Response by Transcriptional Regulators in Plants: 2nd Edition.

Detalles Bibliográficos
Autores: Landaeta-Sepúlveda, Diego, Johnson, Nathan, Morales-Espinoza, Jonathan, Tobar, Mariola, Sánchez, Evelyn, Fernández, José D., Olivares-Yáñez, Consuelo, Medina, Joaquín, Canales, Javier, Vidal, Elena A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/399036
Acceso en línea:http://hdl.handle.net/10261/399036
Access Level:acceso abierto
Palabra clave:MicroRNAs
Sulfur
Sulfate deficiency
Tomato
id ES_0b07d0ecbe22daeafa9989d7d3c6b048
oai_identifier_str oai:digital.csic.es:10261/399036
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
title Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
spellingShingle Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
Landaeta-Sepúlveda, Diego
MicroRNAs
Sulfur
Sulfate deficiency
Tomato
title_short Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
title_full Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
title_fullStr Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
title_full_unstemmed Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
title_sort Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
dc.creator.none.fl_str_mv Landaeta-Sepúlveda, Diego
Johnson, Nathan
Morales-Espinoza, Jonathan
Tobar, Mariola
Sánchez, Evelyn
Fernández, José D.
Olivares-Yáñez, Consuelo
Medina, Joaquín
Canales, Javier
Vidal, Elena A.
author Landaeta-Sepúlveda, Diego
author_facet Landaeta-Sepúlveda, Diego
Johnson, Nathan
Morales-Espinoza, Jonathan
Tobar, Mariola
Sánchez, Evelyn
Fernández, José D.
Olivares-Yáñez, Consuelo
Medina, Joaquín
Canales, Javier
Vidal, Elena A.
author_role author
author2 Johnson, Nathan
Morales-Espinoza, Jonathan
Tobar, Mariola
Sánchez, Evelyn
Fernández, José D.
Olivares-Yáñez, Consuelo
Medina, Joaquín
Canales, Javier
Vidal, Elena A.
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Agencia Nacional de Investigación y Desarrollo (Chile)
Fondo Nacional de Desarrollo Científico y Tecnológico (Chile)
Agencia Estatal de Investigación (España)
Ministerio de Ciencia e Innovación (España)
European Commission
Fernández, José D. [0009-0000-9920-860X]
Vidal, Elena A. [0000-0002-8208-7327]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv MicroRNAs
Sulfur
Sulfate deficiency
Tomato
topic MicroRNAs
Sulfur
Sulfate deficiency
Tomato
description This article belongs to the Special Issue Regulatory Mechanisms of Development and Abiotic Stress Response by Transcriptional Regulators in Plants: 2nd Edition.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/399036
url http://hdl.handle.net/10261/399036
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/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114165RR-C21
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/ijms26178392
https://doi.org/10.3390/ijms26178392
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
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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
_version_ 1869403197630578688
spelling Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory NetworkLandaeta-Sepúlveda, DiegoJohnson, NathanMorales-Espinoza, JonathanTobar, MariolaSánchez, EvelynFernández, José D.Olivares-Yáñez, ConsueloMedina, JoaquínCanales, JavierVidal, Elena A.MicroRNAsSulfurSulfate deficiencyTomatoThis article belongs to the Special Issue Regulatory Mechanisms of Development and Abiotic Stress Response by Transcriptional Regulators in Plants: 2nd Edition.[Data Availability Statement] The sRNA-Seq datasets generated and analyzed during the current study are available in the NCBI Sequence Read Archive (SRA) repository, accession PRJNA1214914, available at https://www.ncbi.nlm.nih.gov/sra/PRJNA1214914, accessed on 1 August 2025. All other data generated during this study are included in this published article and its Supplementary Information files.Sulfate availability critically influences plant growth, yet the role of small RNAs, particularly microRNAs (miRNAs), in regulating responses to sulfate deficiency remains poorly understood. Here, we conducted a temporal analysis of sulfate deficiency-responsive miRNAs in the roots and leaves of Solanum lycopersicum (tomato), using an updated miRNA annotation in the SL4.0 genome. We found 40 differentially expressed miRNAs, including 2 novel, tomato-specific miRNAs. Tomato miRNAs showed an important time- and organ-specific regulation, similar to the described response of the mRNA transcriptome. Integration with transcriptomic data and Degradome-seq analysis highlighted both canonical and non-canonical targets for sulfate-responsive miRNAs. miR395, the most extensively studied miRNA, was found to control not only its conserved targets involved in sulfate transport and assimilation, but also genes involved in redox homeostasis, photosynthesis and chloride transport. Notably, most targets were repressed in leaves, suggesting miRNA-mediated downregulation of energy-intensive processes, while root targets were predominantly upregulated, including genes related to protein remodeling and antioxidant defense. Comparative analysis with Arabidopsis thaliana revealed a broader functional repertoire in tomato, suggesting species-specific adaptations to sulfate deficiency. Overall, our results underscore the critical role of miRNAs in fine-tuning organ-specific metabolic reprogramming during nutrient stress, expanding the current understanding of the regulatory landscape underlying sulfate deficiency in plants.This research was funded by the Agencia Nacional de Investigación y Desarrollo (ANID)-Millennium Science Initiative, Millennium Institute for Integrative Biology—iBio, grant number ICN17_022 to N.R.J., C.O.-Y., J.C., and E.A.V.; the ANID-Millennium Nucleus in Data Science for Plant Resilience—Phytolearning, grant number NCN2024_047 to E.A.V.; the ANID-Fondo Nacional de Investigación Científica y Tecnológica (FONDECYT), grant numbers 1211130 and 1250631 to E.A.V., 3210312 to M.T., 11240968 to C.O.-Y., and 1230833 to J.C.; the ANID-Vinculación Internacional, grant number FOVI230159 to J.M., J.C., and E.A.V.; the ANID-Anillo, grant number ACT210007 to E.A.V.; the ANID-Beca de Doctorado Nacional, grant numbers 21230478 to J.D.F. and 21230939 to D.L.-S.; and the Ministerio de Ciencia e Innovación (MCIN) and the Agencia Estatal de Investigación, grant number PID2020-114165RRC21 to J.M. These funding agencies were not involved in the design of the study; the collection, analysis, and interpretation of the data; or in the writing of the manuscript.Peer reviewedMultidisciplinary Digital Publishing InstituteAgencia Nacional de Investigación y Desarrollo (Chile)Fondo Nacional de Desarrollo Científico y Tecnológico (Chile)Agencia Estatal de Investigación (España)Ministerio de Ciencia e Innovación (España)European CommissionFernández, José D. [0009-0000-9920-860X]Vidal, Elena A. [0000-0002-8208-7327]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2025202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/399036reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114165RR-C21The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/ijms26178392https://doi.org/10.3390/ijms26178392Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3990362026-05-22T06:33:51Z
score 15,811543

Similares en LA Referencia