Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
BMC Genomics. 2010 Jan 27;11:67. doi: 10.1186/1471-2164-11-67.
Helicobacter canadensis is an emerging human pathogen and zoonotic agent. The genome of H. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts.
Twenty-one of the repeat-associated coding regions were determined to be potentially transcriptionally or translationally phase variable. In each case the homopolymeric tract was within the predicted promoter region or at the 5' end of the coding region, respectively. However, eight coding sequences were identified with simple sequence repeats toward the 3' end of the open reading frame. In these cases, the repeat tract would be too far into the coding region to be mediating translational phase variation. All of the 29 coding region-associated homopolymeric tracts display variability in tract length in the sequencing read data.
Twenty-nine coding regions have been identified in the genome sequence of Helicobacter canadensis strain NCTC13241 that show variations in homopolymeric tract length in the bacterial population, indicative of phase variation. Five of these are potentially associated with promoter regions, which would lead to transcriptional phase variation. Translational phase variation usually switches expression of a gene ON and OFF due to the repeat region being located sufficiently close to the initiation codon for the resulting frame-shift to lead to a premature termination codon and stop the translation of the protein. Sixteen of the 29 coding regions have homopolymeric tracts characteristic of translational phase variation. For eight coding sequences with repeats located later in the reading frame, changes in the repeat tract length would alter the protein sequence at the C-terminus but not stop the expression of the protein. This mechanism of C-terminal phase variation has implications for stochastic switching of protein sequence in bacterial species that already undergo transcriptional and translational phase variation.
加拿大幽门螺杆菌是一种新兴的人类病原体和人畜共患病原。此前已经对 H. canadensis 的基因组进行了测序，并确定其包含 29 个与长链重复序列相关的注释编码区。
21 个与重复相关的编码区被确定为潜在的转录或翻译阶段可变。在每种情况下，长链重复序列分别位于预测的启动子区域或编码区域的 5'端。然而，有 8 个编码序列在开放阅读框的 3'端被鉴定出具有简单的重复序列。在这些情况下，重复序列会延伸到编码区域的太远，无法介导翻译阶段的变化。29 个与编码区相关的长链重复序列在测序读段数据中显示出重复序列长度的可变性。
在 Helicobacter canadensis 菌株 NCTC13241 的基因组序列中鉴定出 29 个编码区，这些编码区的长链重复序列长度在细菌群体中存在差异，表明存在阶段变化。其中 5 个可能与启动子区域相关，这将导致转录阶段的变化。翻译阶段的变化通常会由于重复区域足够接近起始密码子，导致移码，从而产生提前终止密码子并停止蛋白质的翻译，从而使基因的表达 ON 和 OFF 切换。29 个编码区中有 16 个具有翻译阶段变化的长链重复序列特征。对于 8 个编码序列，其重复序列位于阅读框的后期，重复序列长度的变化会改变蛋白质序列的 C 末端，但不会停止蛋白质的表达。这种 C 末端阶段变化的机制对已经经历转录和翻译阶段变化的细菌物种中的蛋白质序列的随机切换具有影响。
