title: Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato.
abstract: Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in 'higher-plant' genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein-protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs.
authors.affiliation: University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France.
authors.forename: Yanwei
authors.initials: Y
authors.lastname: Hao
authors.forename: Xinyu
authors.initials: X
authors.lastname: Wang
authors.forename: Xian
authors.initials: X
authors.lastname: Li
authors.forename: Carole
authors.initials: C
authors.lastname: Bassa
authors.forename: Isabelle
authors.initials: I
authors.lastname: Mila
authors.forename: Corinne
authors.initials: C
authors.lastname: Audran
authors.forename: Elie
authors.initials: E
authors.lastname: Maza
authors.forename: Zhengguo
authors.initials: Z
authors.lastname: Li
authors.forename: Mondher
authors.initials: M
authors.lastname: Bouzayen
authors.forename: Benoit
authors.initials: B
authors.lastname: van der Rest
authors.forename: Mohamed
authors.initials: M
authors.lastname: Zouine
mesh_terms: D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017930:Genes, Reporter; D018745:Genome, Plant / Q000235:genetics*; D007210:Indoleacetic Acids / Q000378:metabolism; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics; D011993:Recombinant Fusion Proteins; D014026:Nicotiana / Q000235:genetics / Q000378:metabolism; D020798:Two-Hybrid System Techniques
chemical_list: D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; D010940:Plant Proteins; D018749:RNA, Plant; D011993:Recombinant Fusion Proteins; C030737:indoleacetic acid
keywords: Aux/IAA; Solanum lycopersicum; TOPLESS.; auxin signalling; co-repressor; multigenic family; protein–protein interactions; tomato