Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution

Abstract

BackgroundThe caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Although previous studies of this protein family have been reported for Arabidopsis and other species, understanding of the evolution of the caleosin gene family in plants remains inadequate.ResultsIn this study, comparative genomic analysis was performed to investigate the phylogenetic relationships, evolutionary history, functional divergence, positive selection, and coevolution of caleosins. First, 84 caleosin genes were identified from five main lineages that included 15 species. Phylogenetic analysis placed these caleosins into five distinct subfamilies (sub I–V), including two subfamilies that have not been previously identified. Among these subfamilies, sub II coincided with the distinct P-caleosin isoform recently identified in the pollen oil bodies of lily; caleosin genes from the same lineage tended to be clustered together in the phylogenetic tree. A special motif was determined to be related with the classification of caleosins, which may have resulted from a deletion in sub I and sub III occurring after the evolutionary divergence of monocot and dicot species. Additionally, several segmentally and tandem-duplicated gene pairs were identified from seven species, and further analysis revealed that caleosins of different species did not share a common expansion model. The ages of each pair of duplications were calculated, and most were consistent with the time of genome-wide duplication events in each species. Functional divergence analysis showed that changes in functional constraints have occurred between subfamilies I/IV, II/IV, and II/V, and some critical amino acid sites were identified during the functional divergence. Additional analyses revealed that caleosins were under positive selection during evolution, and seven candidate amino acid sites (70R, 74G, 88 L, 89G, 100 K, 106A, 107S) for positive selection were identified. Interestingly, the critical amino acid residues of functional divergence and positive selection were mainly located in C-terminal domain. Finally, three groups of coevolved amino acid sites were identified. Among these coevolved sites, seven from group 2 were located in the Ca2+-binding region of crucial importance.ConclusionIn this study, the evolutionary and expansion patterns of the caleosin gene family were predicted, and a series of amino acid sites relevant to their functional divergence, adaptive evolution, and coevolution were identified. These findings provide data to facilitate further functional analysis of caleosin gene families in the plant lineage.

Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

“…The sequence number in this research was increased and two different phylogeny-based approaches were used to assess functional divergence or redundancy between MSP7 members; one involved using DIVERGE v.3 software [55] to estimate type-I functional divergence [5] which is an indicator of functional changes between members of a multigene family [5, 6, 56–61]. This method is based on (site-specific) shifted evolutionary rates.…”

CaM and CML emergence in the green lineage

“…The expanding list of sequenced genomes among the green lineage, from algae to cultivated crops, has facilitated comparative phylogenomics that can provide insight into the evolution and functional significance of protein families [32][33][34][35]. Land plants, such as angiosperms, gymnosperms, or bryophytes, originated from green algae, referred as charophytes, approximately 450 million year ago ( Figure 1) [36].…”

Plant Lipid Droplets and Their Associated Proteins: Potential for Rapid Advances

“…Caleosin and steroleosin (Chen et al, 1999;Naested et al, 2000;Frandsen et al, 2001;Lin et al, 289 2002; Song et al 2014) are likely partly associated with LDs and also ER. Caleosin was first 290 reported in microsomes (Frandsen et al, 1996), and their transcripts are ubiquitous in diverse 291 tissues or organs with or without known LDs (Table I).…”

“…These hairpins would be analogous to the 298 hairpin of oleosin. However, they are substantially shorter (longest being 21 residues for caleosin 299 and 24 residues for steroleosin, both one-third the length of the oleosin hairpin), and the hairpin 300 residues are only mildly conserved among isoforms within the same and among diverse species 301 (Song et al, 2014;Pasaribu et al, 2016). Two of the proline resides in the caleosin hairpin loop 302 are not essential for LD binding (Muller et al, 2017 monoacylglycerol hydrolase (to be described), possess no long hydrophobic or predicted 358 membrane-insertion segment (Gidda et al, 2016;Lopez-Ribera et al, 2014;Shimada et al, 2014 …”