title: A novel BLAST-Based Relative Distance (BBRD) method can effectively group members of protein arginine methyltransferases and suggest their evolutionary relationship.
abstract: We developed a novel BLAST-Based Relative Distance (BBRD) method by Pearson's correlation coefficient to avoid the problems of tedious multiple sequence alignment and complicated outgroup selection. We showed its application on reconstructing reliable phylogeny for nucleotide and protein sequences as exemplified by the fmr-1 gene and dihydrolipoamide dehydrogenase, respectively. We then used BBRD to resolve 124 protein arginine methyltransferases (PRMTs) that are homologues of nine mammalian PRMTs. The tree placed the uncharacterized PRMT9 with PRMT7 in the same clade, outside of all the Type I PRMTs including PRMT1 and its vertebrate paralogue PRMT8, PRMT3, PRMT6, PRMT2 and PRMT4. The PRMT7/9 branch then connects with the type II PRMT5. Some non-vertebrates contain different PRMTs without high sequence homology with the mammalian PRMTs. For example, in the case of Drosophila arginine methyltransferase (DART) and Trypanosoma brucei methyltransferases (TbPRMTs) in the analyses, the BBRD program grouped them with specific clades and thus suggested their evolutionary relationships. The BBRD method thus provided a great tool to construct a reliable tree for members of protein families through evolution.
authors.affiliation: Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan. Electronic address: ycw@csmu.edu.tw.
authors.forename: Yi-Chun
authors.initials: YC
authors.lastname: Wang
authors.affiliation: Department of Computer Science and Information Engineering, Asia University, No. 500, Lioufeng Rd., Wufeng District, Taichung 41354, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.
authors.forename: Jing-Doo
authors.initials: JD
authors.lastname: Wang
authors.affiliation: Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan.
authors.forename: Chin-Han
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Department of Life Science, Tunghai University, No. 1727, Sec. 4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan.
authors.forename: Yi-Wen
authors.initials: YW
authors.lastname: Chen
authors.affiliation: Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan. Electronic address: cli@csmu.edu.tw.
authors.forename: Chuan
authors.initials: C
authors.lastname: Li
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000201:enzymology; D010802:Phylogeny; D011484:Protein-Arginine N-Methyltransferases / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014346:Trypanosoma brucei brucei / Q000201:enzymology
chemical_list: D011484:Protein-Arginine N-Methyltransferases
keywords: BLAST; Evolutionary relationship; Pearson’s correlation coefficient