Abstract
BackgroundTranslationally controlled tumor protein (TCTP) is a conserved, multifunctional protein involved in numerous cellular processes in eukaryotes. Although the functions of TCTP have been investigated sporadically in animals, invertebrates, and plants, few lineage-specific activities of this molecule, have been reported. An exception is in Arabidopsis thaliana, in which TCTP (AtTCTP1) functions in stomatal closuer by regulating microtubule stability. Further, although the development of next-generation sequencing technologies has facilitated the analysis of many eukaryotic genomes in public databases, inter-kingdom comparative analyses using available genome information are comparatively scarce.MethodologyTo carry out inter-kingdom comparative analysis of TCTP, TCTP genes were identified from 377 species. Then phylogenetic analysis, prediction of protein structure, molecular docking simulation and molecular dynamics analysis were performed to investigate the evolution of TCTP genes and their binding proteins.ResultsA total of 533 TCTP genes were identified from 377 eukaryotic species, including protozoa, fungi, invertebrates, vertebrates, and plants. Phylogenetic and secondary structure analyses reveal lineage-specific evolution of TCTP, and inter-kingdom comparisons highlight the lineage-specific emergence of, or changes in, secondary structure elements in TCTP proteins from different kingdoms. Furthermore, secondary structure comparisons between TCTP proteins within each kingdom, combined with measurements of the degree of sequence conservation, suggest that TCTP genes have evolved to conserve protein secondary structures in a lineage-specific manner. Additional tertiary structure analysis of TCTP-binding proteins and their interacting partners and docking simulations between these proteins further imply that TCTP gene variation may influence the tertiary structures of TCTP-binding proteins in a lineage-specific manner.ConclusionsOur analysis suggests that TCTP has undergone lineage-specific evolution and that structural changes in TCTP proteins may correlate with the tertiary structure of TCTP-binding proteins and their binding partners in a lineage-specific manner.
Highlights
Controlled tumor protein (TCTP) was first discovered in the late 1980s, [1, 2] and has subsequently been identified as a highly conserved protein expressed in all eukaryotic organisms [3,4,5]
Our analysis suggests that Translationally controlled tumor protein (TCTP) has undergone lineage-specific evolution and that structural changes in TCTP proteins may correlate with the tertiary structure of TCTP-binding proteins and their binding partners in a lineage-specific manner
To carry out an inter-kingdom analysis of TCTP genes, we identified a wider set of candidate TCTP genes using Prometheus [23] with two IPR terms for mammalian suppressor of yeast SEC4 (MSS4)/translationally controlled tumor-associated TCTP (IPR011323) and family entry of TCTP (IPR018105) in the three domains of life: Archaea, Bacteria, and Eukarya
Summary
Controlled tumor protein (TCTP) was first discovered in the late 1980s, [1, 2] and has subsequently been identified as a highly conserved protein expressed in all eukaryotic organisms [3,4,5]. The TCTP protein is involved in many cellular processes, including cell growth [3, 4], protein synthesis, cell cycle progression [8], apoptosis [9,10,11,12,13], immune responses [14], and the regulation of pluripotency [15]. Controlled tumor protein (TCTP) is a conserved, multifunctional protein involved in numerous cellular processes in eukaryotes. The development of next-generation sequencing technologies has facilitated the analysis of many eukaryotic genomes in public databases, inter-kingdom comparative analyses using available genome information are comparatively scarce
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