Bioinformatic Studies Of Evolution Of The Cold Shock Domain Protein Family

Based on the public databases, the molecular evolution of the proteinsuper-family with cold shock domain was systematical investigated using theories andmethods of bioinformatics and evolutionary genomics. The purposes of present workare to further understand the molecular mechanisms of gene origin and evolution, andthe functions of gene non-coding region, as well as provide new methods forelucidating the evolutionary mechanism of other gene families and/or super-families.The main results of this study were demonstrated as follows:1) The phylogenetic tree of 84 cold shock domain protein sequences wasconstructed using NJ and ML methods, which shows that the topology structurecontains three clades, namely Cladeâ… , Cladeâ…¡and Cladeâ…¢. Cladeâ… contains the mostspecies from Fugu rubripes to Homo sapiens, and almost all genes of this Cladeâ… contain the three kinds of exons of 64bp, 34bp and 90bp in length with nearly uniformphases of intron insertion. Particularly, the location is just the site of encoding coldshock domain, which implies that the cold shock domain is highly conservative in thesuper-family. Cladeâ…¡contains the most species of invertebrate from Trypanosomacruzi to Apis mellifera and Drosophila melanogaster. Comparing with cladeâ… , Cladeâ…¡genes consist of fewer exons with more nucleotide acids. It is also interesting to findthat there are 4 Paralogous proteins i.e.Cey1, Cey2, Cey3 and Cey4 in Caenorhabditiselegans. Cladeâ…¢contains plants with only few or none introns.2) Analyses on the motif in amino acid sequences of cold shock domain proteinsshow that there are much more motifs in higher animals. In addition, the results alsodisplay that there are much less motifs in plants than in animals, but the plants seem tohave more repeats of single motif than the animals do.3) Analyses on structure properties of 3'and 5'UTR of mRNA with cold shockdomains indicate that the functional elements are more in 3'UTR than in 5'UTR.Furthermore, homology sequence alignment shows that relatively less conservedsequences exist in 3'UTR and 5'UTR, and there is high level of nucleic acidmutations in these regions.4) Investigation on the repeat sequences of introns in genes of different coldshock domain proteins shows that repeat elements in the introns are increased sharplyfrom invertebrate to vertebrate during the evolution. However, it should be noted thatthe increased numbers of repeated elements in different species are remarkably different, which suggested that the amount of intron insertion phases is correspondingincrease. In addition, the closer relative species have similar repeated elements ingene structure. Furthermore, the different kinds of repeat elements are closelycorrelative to the length of introns and the content of GC.In conclusion, in the paper, a phylogenetic model on the evolution of cold shockprotein family had been reconstructed. In this model, the orthologous proteins wereoriginally produced by gene duplication and then paralogous proteins were producedby alternative splicing during evolution, which might result in the multifunction ofcold shock protein family. These findings not only illuminated the mechanism ofmolecular evolution of the protein super-family with cold shock domain, but alsoprovided a new method and clue for further studying the evolutionary mechanism ofother gene family and/or super-family.