The dif/Xer Recombination Systems in Proteobacteria
The dif/Xer Recombination Systems in Proteobacteria
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DOI：
10.1371/journal.pone.0006531
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发表时间：
2009-09-03
期刊：
影响因子：
3.7
通讯作者：
Roten, Claude-Alain
中科院分区：
文献类型：
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作者：
Carnoy, Christophe;Roten, Claude-Alain
在大肠在大肠杆菌中，10%到15%的生长细菌在DNA复制过程中产生二聚体染色体。这些二聚体被XerC和XerD分解，XerC和XerD是两种酪氨酸重组酶，靶向与染色体复制末端相关的28个核苷酸基序（dif）。在链球菌和乳球菌中，另一种系统是由一种独特的Xer-like重组酶（XerS）与位于复制末端的dif-like基序（dif（SL））遗传连接组成。初步观察表明，dif/Xer系统通常存在于具有圆形染色体的细菌中，但这一假设尚未在详尽的分析中得到证实。本研究的目的是广泛的特点的dif/Xer系统中的变形菌，因为这个分类占大多数的基因组测序的日期。为此，我们分析了来自156种变形菌的234条染色体，结果表明大多数种类（87.8%）携带XerC和XerD样重组酶和一个dif相关序列，该序列（i）位于非编码序列中，（ii）靠近复制末端（如由累积GC偏斜所定义）（iii）具有回文结构，（iv）由低G+C含量编码，和（v）含有高度保守的XerD结合位点。然而，并非所有的变形菌都显示这种dif/XerCD系统。事实上，致病性ε-变形菌的亚组（包括螺杆菌属和弯曲杆菌属）具有不同的重组系统，其由单个重组酶（XerH）和基序（dif（H））组成，所述单个重组酶（XerH）在遗传学上与其他Xer重组酶不同，所述基序（dif（H））与dif（SL）共享同源性。此外，在小的内共生体基因组或某些具有较大染色体的细菌（如军团菌目）中没有检测到dif或Xer重组酶的同源物。这就提出了在这些物种中存在其他染色体解连锁系统的问题。我们的研究突出了dif/Xer重组酶系统在变形菌的复杂性，并为系统检测这些组件在原核生物铺平了道路。
In E. coli, 10 to 15% of growing bacteria produce dimeric chromosomes during DNA replication. These dimers are resolved by XerC and XerD, two tyrosine recombinases that target the 28-nucleotide motif (dif) associated with the chromosome's replication terminus. In streptococci and lactococci, an alternative system is composed of a unique, Xer-like recombinase (XerS) genetically linked to a dif-like motif (dif(SL)) located at the replication terminus. Preliminary observations have suggested that the dif/Xer system is commonly found in bacteria with circular chromosomes but that assumption has not been confirmed in an exhaustive analysis. The aim of the present study was to extensively characterize the dif/Xer system in the proteobacteria, since this taxon accounts for the majority of genomes sequenced to date. To that end, we analyzed 234 chromosomes from 156 proteobacterial species and showed that most species (87.8%) harbor XerC and XerD-like recombinases and a dif-related sequence which (i) is located in non-coding sequences, (ii) is close to the replication terminus (as defined by the cumulative GC skew) (iii) has a palindromic structure, (iv) is encoded by a low G+C content and (v) contains a highly conserved XerD binding site. However, not all proteobacteria display this dif/XerCD system. Indeed, a sub-group of pathogenic epsilon-proteobacteria (including Helicobacter sp and Campylobacter sp) harbors a different recombination system, composed of a single recombinase (XerH) which is phylogenetically distinct from the other Xer recombinases and a motif (dif(H)) sharing homologies with dif(SL). Furthermore, no homologs to dif or Xer recombinases could be detected in small endosymbiont genomes or in certain bacteria with larger chromosomes like the Legionellales. This raises the question of the presence of other chromosomal deconcatenation systems in these species. Our study highlights the complexity of dif/Xer recombinase systems in proteobacteria and paves the way for systematic detection of these components in prokaryotes.