In Silico Prediction Of Selenoproteins In The Genomes Of Anopheles Gambiae, Bombyx Mori And Apis Mellifera

Selenium (Se) is an essential trace element in vivo. It is closely related to Keshan disease, Kaschin-Beck disease, and cancer. It also plays important roles in cell growth, proliferation, aging , as well as in virus propagation. In selenoproteins, Se is incorporated into proteins in the form of selenocysteine (Sec), the 21st amino acid. Selenocysteine is cotranslationally inserted in response to UGA codon (a stop signal in the canonical genetic code). The alternative decoding of UGA is mediated by a special stem-loop structure in the 3'-UTR of selenoprotein mRNA i.e., the Sec insertion sequence (SECIS) element. In addition, most selenoproteins have homologues in which Sec is replaced by cysteine (Cys). Annotation of genomes is the way to build a bridge between genomic sequences and the biological function of organisms. However, for selenoproteins, which mediate the biological functions of selenium, the dual role of UGA codon confounds the automatic annotation methods. In consequence, selenoproteins are misannotated in the majority of genome projects.We download the newest sequences of cDNA, genomic DNA, and all annotated genes of three species, anopheles gambiae, Bombyx mori and apis mellifera. The annotated and released genes were predicted by the software GENSCAN, SNAP or BGI. Those data include 19839, 45058, and 18518 single genes from anopheles gambiae, Bombyx mori and apis mellifera, respectively. They also contain full length DNA sequences from the 5 chromosomes of anopheles gambiae and 16 chromosomes of apis mellifera. The dataset of Bombyx mori are consisted of 23155 scaffold and a great deal of unassembled sequences, including 115360 ESTs. To identify selenoproteins from those data, we edited a series of computer programs via PERL language to search for all genes ended up with TGA codon. Sequences immediately downstream of those genes were extracted from the database, and analyzed for their SECIS elements. Programs were also edited for the alignments of selenoproteins and their Cys-containing homologs. The screened genes were finally analyzed for their initial codon, in-frame TGA, stop codon, and SECIS element in the 3'-UTR to ensure the correction of selenoprotein prediction. Our anlysis of the genomes of anopheles gambiae, the bombyx mori, and the apis mellifera resulted in 9 novel selenoproteins, among them, three were found in the anopheles gambiae, 5 in the Bombyx mori ,and 1 in the apis mellifera One of the 9 predicted genes is glutathione S-transferase (GST) that has been reported as a microbial selenoprotein. The rest of them have not been predicted as selenoproteins up to the present. Thus, they are newly found selenoproteins. Besides GST, the other 2 silkworm selenoproteins were annotated as ATP-binding cassette transporter subfamily A (ABCA), and nuclear VCP-like protein in the database. Linked to the general function of GST, ABCA and VCP, it could be deduced that Se in the silkworm play important roles in redox regulation, selenium storage and transportation, and cell apoptosis. So far, there have been no enough information on the 6 genes from anopheles gambiae and apis mellifera to deduce their functions.This paper re-annotaed the selenoproteins in the anopheles gambiae, Bombyx mori and apis mellifera by considering the dual function of TGA codon. It surpassed the limit of traditional software in predicting selenoproteins in the genome. It also expanded our understanding on the distribution of selenoproteins in different species, and supported the standpoint on the universality and dispersion of selenoproteins distribution. The results provide theoretical bases for further study regarding effects of Se on insects.