{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T04:26:17Z","timestamp":1790742377569,"version":"4.1.0"},"reference-count":136,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T00:00:00Z","timestamp":1669248000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE\/CRT <jats:italic>cis<\/jats:italic>-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in <jats:italic>Solanum lycopersicum<\/jats:italic>. In genome-wide coverage, 58 <jats:italic>Sl<\/jats:italic>DREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron\u2013exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the <jats:italic>Sl<\/jats:italic>DREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in <jats:italic>Sl<\/jats:italic>DREB genes. Ka\/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 <jats:italic>Sl<\/jats:italic>DREB genes were orthologs to <jats:italic>Arabidopsis<\/jats:italic> and <jats:italic>Solanum tuberosum<\/jats:italic>, respectively. Subcellular localization predicted that <jats:italic>Sl<\/jats:italic>DREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 <jats:italic>Sl<\/jats:italic>DREB genes. Five representative <jats:italic>Sl<\/jats:italic>DREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of <jats:italic>Sl<\/jats:italic>DREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the <jats:italic>Sl<\/jats:italic>DREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of <jats:italic>Sl<\/jats:italic>DREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.<\/jats:p>","DOI":"10.3389\/fpls.2022.1031679","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T07:29:41Z","timestamp":1669274981000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":61,"title":["Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum"],"prefix":"10.3389","volume":"13","author":[{"given":"Hajra","family":"Maqsood","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faiza","family":"Munir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rabia","family":"Amir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alvina","family":"Gul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,24]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0261215","article-title":"Genome-wide promoter analysis, homology modeling and protein interaction network of dehydration responsive element binding (DREB) gene family in solanum tuberosum","volume":"16","author":"Ain-Ali","year":"2021","journal-title":"PloS One"},{"key":"B2","article-title":"DNA-Binding motifs in gene regulatory proteins","volume-title":"Molecular biology of the cell","author":"Alberts","year":"2002"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0120848","article-title":"Functional analysis of the molecular interactions of TATA box-containing genes and essential genes","volume":"10","author":"Bae","year":"2015","journal-title":"PloS One"},{"key":"B4","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B5","doi-asserted-by":"publisher","first-page":"D562","DOI":"10.1093\/nar\/gki022","article-title":"NCBI GEO: mining millions of expression profiles\u2013database and tools","volume":"33","author":"Barrett","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1038\/nrm1314","article-title":"The SANT domain: a unique histone-tail-binding module","volume":"5","author":"Boyer","year":"2004","journal-title":"Nat. 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