Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms
Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms
复制标题
DOI：
10.1016/s0378-1119(00)00459-5
复制
发表时间：
2000-12-23
期刊：
影响因子：
3.5
通讯作者：
Kobayashi, I
中科院分区：
文献类型：
--
作者：
Chinen, A;Uchiyama, I;Kobayashi, I
最近的研究表明，限制性修饰基因复合物是可移动的遗传元件，它们将自身插入到基因组中并引起各种基因组重排。在目前的工作中，对超嗜热古菌（古细菌）属中的两个物种——Pyrococcus horikoshii 和 Pyrococcus abyssi 的完整基因组序列进行了比较，以检测与限制性修饰基因同源物相关的大基因组多态性。序列比对、GC 含量分析和密码子使用分析证明了这些同源物的多样性，并揭示了相对较新的获取（水平转移）的可能情况。在确定的六个大多态性中的两个案例中，插入了带有修饰基因同源物的 DNA 片段，并伴有目标删除（简单替换）。在另外两种情况下：携带修饰基因同源物的同源 DNA 片段存在于两个基因组的不同位置（转座）。在这两种情况下，两个基因座之一的取代（插入/删除）都伴随着相邻染色体片段的倒位。在第五种情况中，被携带I型限制性、修饰性和特异性基因同源物的DNA片段取代同样伴随着相邻的倒位。在最后一种情况下，在两个基因组的不同位点（转座）发现了两个同源 DNA 片段，但只有其中一个插入了修饰同源物和未知的 ORF。将讨论这些多态性与染色体上限制性酶攻击的可能关系。 (C) 2000 Elsevier Science B.V. 保留所有权利。
Recent work suggests that restriction-modification gene complexes are mobile genetic elements that insert themselves into the genome and cause various genome rearrangements. In the present work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect large genome polymorphisms linked with restriction-modification gene homologs. Sequence alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these homologs and revealed a possible case of relatively recent acquisition (horizontal transfer). In two cases out of the six large polymorphisms identified, there was insertion of a DNA segment with a modification gene homolog, accompanied by target deletion (simple substitution). In two other cases: homologous DNA segments carrying a modification gene homolog were present at different locations in the two genomes (transposition), In both cases, substitution (insertion/deletion) in one of the two loci was accompanied by inversion of adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I restriction, modification, and specificity gene homologs was likewise accompanied by adjacent inversion. In the last case, two homologous DNA segments, were found at different loci in the two genomes (transposition), but only one of them had insertion of a modification homolog and an unknown ORF. The possible relationship of these polymorphisms to attack by restriction enzymes on the chromosome will be discussed. (C) 2000 Elsevier Science B.V. All rights reserved.