標題: Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations
作者: Lin, Tiao-Yin
生物科技學系
Department of Biological Science and Technology
關鍵字: Simple sequence repeat;Insertion and deletion;Genome evolution;Molecular mechanism;Phage divergence;Human gene mutations
公開日期: 七月-2016
摘要: Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage phi YeO3-12, and Salmonella phage phi SG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications. (C) 2016 Elsevier B.V. All rights reserved.
URI: http://dx.doi.org/10.1016/j.mrfmmm.2016.04.001
http://hdl.handle.net/11536/133905
ISSN: 0027-5107
DOI: 10.1016/j.mrfmmm.2016.04.001
期刊: MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
Volume: 789
起始頁: 48
結束頁: 56
顯示於類別:期刊論文