Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus.
Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus.
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DOI：
10.1186/1471-2164-14-524
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发表时间：
2013-07-31
期刊：
影响因子：
4.4
通讯作者：
Somerville GA
中科院分区：
文献类型：
--
作者：
Shah N;Gaupp R;Moriyama H;Eskridge KM;Moriyama EN;Somerville GA
Per-Arnt-Sim（PAS）结构域代表参与细菌传感和适应系统的普遍存在的结构折叠，包括几种毒力相关功能。虽然PAS结构域和PhoQ-DcuS-CitA（PDC）结构域的亚类具有共同的结构，但存在有限的氨基酸序列相似性。为了更深入地了解细菌界和葡萄球菌中存在的PDC/PAS结构域的进化，使用基于HMM到HMM比较（HHblits）的灵敏搜索方法从代表5个门的48种细菌的基因组序列中鉴定PDC/PAS结构域。共鉴定了1，007个PAS结构域和686个PDC结构域，分布在1，174个蛋白质中。对于28个革兰氏阳性菌，PDC/PAS结构域的分布，组织和分子进化进行了更详细的分析，特别强调葡萄球菌属。与其他细菌相比，葡萄球菌具有相对较少的含有PDC/PAS结构域的蛋白质（6-9）。作为一般规则，在这项研究中检查的葡萄球菌基因组包含一个核心组的7个PDC/PAS结构域的蛋白质组成的WalK，SrrB，PhoR，ArlS，HssS，NreB，和GdpP。这个规则的例外是：1）S。2）S. saguticus缺乏核心NreB蛋白;肉样链球菌具有两个额外的PAS结构域蛋白; epidermidis、S. aureus和S. pseudintermedius具有另外的蛋白质，该蛋白质具有两个PDC结构域，预测其编码传感器组氨酸激酶; 4）S. lugdunensis具有另外的含PDC的蛋白质，该蛋白质被预测为传感器组氨酸激酶。这种全面的分析表明，PDC/PAS结构域的细菌之间的变化有有限的相关性，基因组大小或致病性，然而，我们的分析建立了细菌在其生命周期中具有运动阶段有显着更多的PDC/PAS含蛋白质。此外，我们的分析揭示了一个巨大的量的变化，在属内的PDC/PAS含蛋白质的数量。这种变化延伸到葡萄球菌属，其具有6至9个PDC/PAS蛋白，其中一些似乎是以前未描述的信号蛋白。后一点很重要，因为大多数含有PDC/PAS结构域的葡萄球菌蛋白质调节毒力因子合成或抗生素抗性。
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.
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DOI：
10.1007/0-387-30744-3_1
发表时间：
2006
期刊：
The Prokaryotes
影响因子：
--
作者：
Götz F;Bannerman T;Schleifer KH
通讯作者：
Schleifer KH
影响因子：
3.2
作者：
Fedtke, I;Kamps, A;Götz, F
通讯作者：
Götz, F
影响因子：
3.6
作者：
Dubrac, Sarah;Bisicchia, Paola;Msadek, Tarek
通讯作者：
Msadek, Tarek
影响因子：
3.2
作者：
CALOGERO, S;GARDAN, R;DEBARBOUILLE, M
通讯作者：
DEBARBOUILLE, M
影响因子：
3.7
作者：
Burnside K;Lembo A;de Los Reyes M;Iliuk A;Binhtran NT;Connelly JE;Lin WJ;Schmidt BZ;Richardson AR;Fang FC;Tao WA;Rajagopal L
通讯作者：
Rajagopal L