Phylogenomics and signature proteins for the alpha proteobacteria and its main groups.
Phylogenomics and signature proteins for the alpha proteobacteria and its main groups.
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DOI：
10.1186/1471-2180-7-106
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发表时间：
2007-11-28
期刊：
影响因子：
4.2
通讯作者：
Mok, Amy
中科院分区：
文献类型：
--
作者：
Gupta, Radhey S.;Mok, Amy
阿尔法变形菌是细菌中最大和最广泛研究的群体之一。然而，对于这些细菌作为一个整体，并为所有主要亚群（即根瘤菌目，杜鹃花科，杜鹃花科，立克次氏体目，鞘氨醇单胞菌目和柄杆菌目），很少或没有独特的分子或生物化学特征是已知的。我们利用Blastp和PSI-Blast对几种α-变形菌基因组中的开放阅读框进行了全面的PCR基因组分析（即日本慢生根瘤菌、猪布鲁氏菌、新月柄杆菌、氧化葡萄糖酸杆菌、中根瘤菌、温氏硝化杆菌、食芳香新鞘氨醇菌、类球红杆菌2.4.1、硅杆菌属TM 1040，红杜鹃和沃尔巴克氏体（果蝇）内共生体）。这些研究已经鉴定了几种蛋白质，它们是所有α-变形菌的独特特征，以及许多蛋白质，它们是其所有主要目（即根瘤菌目、红酵母目、红酵母目、立克次体目、鞘氨醇单胞菌目和柄杆菌目）和许多科（即立克次体科、无形体科、红酵母科、醋杆菌科、慢生菌科、布鲁氏菌科和巴尔通体科）的独特库。在α-变形菌中存在于不同系统发育深度的许多其他蛋白质提供了关于它们进化的重要信息。从这些研究中推断的α-变形菌之间的进化关系与它们在系统发育树中的分支模式和基于许多保守蛋白质的串联序列的特征相容性集团非常一致。这些研究提供的证据表明，α-变形菌中的主要类群已按以下顺序分化：（立克次体目（红球菌目（鞘氨醇单胞菌目（红球菌目（柄杆菌目-小菌目（根瘤菌目）。我们还描述了两个保守的插入DNA旋转酶B和RNA聚合酶β亚基的鞘氨醇单胞菌目和Rhodosprilllales物种的独特特征，分别。这里提出的结果也提供了支持的分组丝孢菌科和Parvularcula种与柄杆菌目和放置Stappia aggregata与根瘤菌科组。本文所描述的α-变形菌特异性蛋白和插入缺失为这些细菌的分类学、生物化学和分子生物学研究提供了新的有力手段。它们的功能研究应该证明有助于确定这些细菌所特有的新的生化和生理特征。
Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales)))))). We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the Sphingomonadales and Rhodosprilllales species, respectively. The results presented here also provide support for the grouping of Hyphomonadaceae and Parvularcula species with the Caulobacterales and the placement of Stappia aggregata with the Rhizobiaceae group. The α-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.
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影响因子：
4.5
作者：
Dunning Hotopp JC;Lin M;Madupu R;Crabtree J;Angiuoli SV;Eisen JA;Seshadri R;Ren Q;Wu M;Utterback TR;Smith S;Lewis M;Khouri H;Zhang C;Niu H;Lin Q;Ohashi N;Zhi N;Nelson W;Brinkac LM;Dodson RJ;Rosovitz MJ;Sundaram J;Daugherty SC;Davidsen T;Durkin AS;Gwinn M;Haft DH;Selengut JD;Sullivan SA;Zafar N;Zhou L;Benahmed F;Forberger H;Halpin R;Mulligan S;Robinson J;White O;Rikihisa Y;Tettelin H
通讯作者：
Tettelin H
影响因子：
10.7
作者：
Castresana, J
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Castresana, J
影响因子：
3.1
作者：
Chain, PSG;Comerci, DJ;Garcia, E
通讯作者：
Garcia, E
DOI：
10.1073/pnas.221575398
发表时间：
2002-01-08
影响因子：
11.1
作者：
DelVecchio, VG;Kapatral, V;Overbeek, R
通讯作者：
Overbeek, R
DOI：
10.1098/rstb.2002.1193
发表时间：
2003-01-29
影响因子：
6.3
作者：
Andersson, SGE;Karlberg, O;Kurland, CG
通讯作者：
Kurland, CG