分析原核生物基因體複製起點與終點的反向對偶對稱現象

Analyzing Inverse Symmetry with Original and Terminal Sites of Prokaryotic Genomes

許梓亭(Tzu-Ting Hsu)

指導教授 ： 李弘謙

國立中央大學/理學院/生物資訊與系統生物研究所/碩士(2008年)

摘要

片段複製在基因體的成長與演化上被認為是一個十分重要的機制［1］，在酵母菌的染色體上已經證實曾經發生全基因體的複製［2］；藉著廣泛地分析許多原核生物，包含 18 個古細菌與 140 個細菌，我們發現一個相當有趣的現象，在這些原核生物的複製起點與終點，有相當顯著的反向對偶對稱性，我們認為在大部分的原核生物曾經發生全基因體的反向對偶複製，這種複製機制發生在複製起點與終點附近；我們利用原核生物的全基因體序列資料，來進行反向對偶對稱性的研究，並且提出證據；不但利用計算鹼基的字串出現頻率來進行分析，還利用同源基因的分佈來觀察驗證；將反向對偶對稱性當作一項特徵，可以應用來預測複製起點與終點的位置；除此之外，藉由比較各種原核生物反向對偶對稱性的差異性，可以將其分成四個種類的類型生物，並且觀察各類型生物和親緣關係樹與系統分類學之間的關係。

關鍵字

基因體複製 ； 原核生物基因體 ； 複製終止點 ； 複製起始點 ； 反向對偶對稱

並列摘要

Segmental duplication has long been known to be an important mechanism for genome growth and evolution [1]. Beyond that, recent study has spotted occurrence of whole-genome duplication on yeast [2]. In this work we investigate possible association of inverse symmetry with origin sites and terminal sites on genomes. Our findings, through analyses of word-frequency nucleotides and distributions of homologous genes on publicly available complete genomes of 18 archaea and 140 bacteria, are positive. These findings suggest, first, that whole-genome inverse duplications have occurred in most prokaryotic chromosomes near original sites and terminal sites. Secondly, inverse symmetry can be taken as a feature to predict loci of original sites and terminal sites in prokaryotic chromosomes. Thirdly, prokaryotic organisms can be classified into four categories by diversity of inverse symmetry in prokaryotic chromosomes. Phylogeny and taxonomy among the four categories have also been investigated.

並列關鍵字

Replication ； Prokaryotic Genome ； Inverse Symmetry ； Terminal Site ； Original Site

參考文獻

[1] Lynch M. Genomics. Gene duplication and evolution. (2002) Science 297:945-7.

[2] Wolfe, KH, DC. Molecular evidence for an ancient duplication of the entire yeast genome. (1997) Nature 387:708-13.

[3] Forsdyke DR, Mortimer JR. Chargaff''s legacy. (2000) Gene 261:127-37.

[4] Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. (1950) Experientia 6:201-9.

[6] Watson JD, Crick FH. Genetical implications of the structure of deoxyribonucleic acid (1953) Nature 171:964-7.