Department of Computer Science and Engineering, University of Nebraska, Lincoln, NE 68588-0115, USA.
BMC Genomics. 2013 Jul 31;14:524. doi: 10.1186/1471-2164-14-524.
The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).
A total of 1,007 PAS domains and 686 PDC domains distributed over 1,174 proteins were identified. For 28 Gram-positive bacteria, the distribution, organization, and molecular evolution of PDC/PAS domains were analyzed in greater detail, with a special emphasis on the genus Staphylococcus. Compared to other bacteria the staphylococci have relatively fewer proteins (6-9) containing PDC/PAS domains. As a general rule, the staphylococcal genomes examined in this study contain a core group of seven PDC/PAS domain-containing proteins consisting of WalK, SrrB, PhoR, ArlS, HssS, NreB, and GdpP. The exceptions to this rule are: 1) S. saprophyticus lacks the core NreB protein; 2) S. carnosus has two additional PAS domain containing proteins; 3) S. epidermidis, S. aureus, and S. pseudintermedius have an additional protein with two PDC domains that is predicted to code for a sensor histidine kinase; 4) S. lugdunensis has an additional PDC containing protein predicted to be a sensor histidine kinase.
This comprehensive analysis demonstrates that variation in PDC/PAS domains among bacteria has limited correlations to the genome size or pathogenicity; however, our analysis established that bacteria having a motile phase in their life cycle have significantly more PDC/PAS-containing proteins. In addition, our analysis revealed a tremendous amount of variation in the number of PDC/PAS-containing proteins within genera. This variation extended to the Staphylococcus genus, which had between 6 and 9 PDC/PAS proteins and some of these appear to be previously undescribed signaling proteins. This latter point is important because most staphylococcal proteins that contain PDC/PAS domains regulate virulence factor synthesis or antibiotic resistance.
Per-Arnt-Sim（PAS）结构域代表一种普遍存在的结构折叠，涉及细菌感应和适应系统，包括几种与毒力相关的功能。尽管 PAS 结构域和 PhoQ-DcuS-CitA（PDC）结构域子类具有共同的结构，但氨基酸序列相似性有限。为了更深入地了解细菌王国和葡萄球菌中存在的 PDC/PAS 结构域的进化，使用基于 HMM-to-HMM 比较（HHblits）的敏感搜索方法，从代表 5 个门的 48 种细菌的基因组序列中鉴定了 PDC/PAS 结构域。
总共鉴定了 1007 个 PAS 结构域和 686 个 PDC 结构域，分布在 1174 种蛋白质上。对于 28 种革兰氏阳性菌，更详细地分析了 PDC/PAS 结构域的分布、组织和分子进化，特别强调了葡萄球菌属。与其他细菌相比，葡萄球菌含有相对较少的（6-9）种含有 PDC/PAS 结构域的蛋白质。一般来说，本研究中检查的葡萄球菌基因组包含一组由 WalK、SrrB、PhoR、ArlS、HssS、NreB 和 GdpP 组成的七个含有 PDC/PAS 结构域的核心蛋白。但有例外：1）S. saprophyticus 缺乏核心 NreB 蛋白；2）S. carnosus 有两个额外的含有 PAS 结构域的蛋白质；3）S. epidermidis、S. aureus 和 S. pseudintermedius 有一个额外的含有两个 PDC 结构域的蛋白质，预测编码传感器组氨酸激酶；4）S. lugdunensis 有一个额外的含有 PDC 结构域的蛋白质，预测为传感器组氨酸激酶。
这项全面的分析表明，细菌之间 PDC/PAS 结构域的变异与基因组大小或致病性的相关性有限；然而，我们的分析确定，在其生命周期中具有运动阶段的细菌具有更多的含有 PDC/PAS 的蛋白质。此外，我们的分析显示，属内含有 PDC/PAS 的蛋白质数量存在巨大差异。这种变异扩展到葡萄球菌属，该属有 6 到 9 种 PDC/PAS 蛋白，其中一些似乎是以前未描述的信号蛋白。这一点很重要，因为大多数含有 PDC/PAS 结构域的葡萄球菌蛋白调节毒力因子合成或抗生素耐药性。
