Abstract
Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.
Highlights
Tubby-like proteins are a family of bipartite transcription factors that were first studied in animals (Boggon et al, 1999; Santagata et al, 2001; Carroll et al, 2004) but have subsequently been identified from single-celled to multicellular organisms (Liu, 2008)
The 19 GaTLPs were named as GaTLP2-GaTLP12 (GaTLP2.1, 2.2, 2.3, 2.4, 5.1, 5.2, 5.3, 6.1, 6.2, 6.3, 7.1, 7.2, 8, 11, 12.1, 12.2, 12.3, 12.4, and 12.5), GrTLPs were classified as GrTLP2-GrTLP12 (GrTLP2.1, 2.2, 2.3, 5.1, 5.2, 5.3, 6.1, 6.2, 6.3, 7.1, 7.2, 7.3, 8, 11, 12.1, 12.2, 12.3, and 12.4)
Our results showed that positively co-expressed genes (PCoEGs) and negatively co-expressed genes (NCoEGs) of GhTLP11A and GhTLP12A.1 genes might have a crucial role in drought-stress tolerance
Summary
Tubby-like proteins are a family of bipartite transcription factors that were first studied in animals (Boggon et al, 1999; Santagata et al, 2001; Carroll et al, 2004) but have subsequently been identified from single-celled to multicellular organisms (Liu, 2008). Tubby-like proteins (TLPs) are characterized by the presence of the conserved C-terminal tubby domain, comprising of 12 antiparallel closed β-barrel strands with a central hydrophobic α-helix (Boggon et al, 1999). The TLP family in plants is much larger with more than 10 members. Unlike animal TLPs, which possess a variable N-terminal region, plant TLP proteins possess a conserved N-terminal F-box domain besides the C-terminal tubby domain (Noben-Trauth et al, 1996; Gagne et al, 2002; Lai et al, 2004; Xu et al, 2016). Fbox-comprising proteins are involved in the ubiquitin-mediated degradation of proteins (Kile et al, 2002), suggesting a role for TLPs in such processes
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