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Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato.
J Exp Bot. 2014 Mar; 65(4):1013-23.JE

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+Show Affiliations

University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruit, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24399174

Citation

Hao, Yanwei, et al. "Genome-wide Identification, Phylogenetic Analysis, Expression Profiling, and Protein-protein Interaction Properties of TOPLESS Gene Family Members in Tomato." Journal of Experimental Botany, vol. 65, no. 4, 2014, pp. 1013-23.
Hao Y, Wang X, Li X, et al. Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. J Exp Bot. 2014;65(4):1013-23.
Hao, Y., Wang, X., Li, X., Bassa, C., Mila, I., Audran, C., Maza, E., Li, Z., Bouzayen, M., van der Rest, B., & Zouine, M. (2014). Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. Journal of Experimental Botany, 65(4), 1013-23. https://doi.org/10.1093/jxb/ert440
Hao Y, et al. Genome-wide Identification, Phylogenetic Analysis, Expression Profiling, and Protein-protein Interaction Properties of TOPLESS Gene Family Members in Tomato. J Exp Bot. 2014;65(4):1013-23. PubMed PMID: 24399174.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. AU - Hao,Yanwei, AU - Wang,Xinyu, AU - Li,Xian, AU - Bassa,Carole, AU - Mila,Isabelle, AU - Audran,Corinne, AU - Maza,Elie, AU - Li,Zhengguo, AU - Bouzayen,Mondher, AU - van der Rest,Benoit, AU - Zouine,Mohamed, Y1 - 2014/01/07/ PY - 2014/1/9/entrez PY - 2014/1/9/pubmed PY - 2014/11/5/medline KW - Aux/IAA KW - Solanum lycopersicum KW - TOPLESS. KW - auxin signalling KW - co-repressor KW - multigenic family KW - protein–protein interactions KW - tomato SP - 1013 EP - 23 JF - Journal of experimental botany JO - J Exp Bot VL - 65 IS - 4 N2 - 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. SN - 1460-2431 UR - https://www.unboundmedicine.com/medline/citation/24399174/Genome_wide_identification_phylogenetic_analysis_expression_profiling_and_protein_protein_interaction_properties_of_TOPLESS_gene_family_members_in_tomato_ L2 - https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert440 DB - PRIME DP - Unbound Medicine ER -