Evolution of competence and DNA uptake specificity in the Pasteurellaceae.
Evolution of competence and DNA uptake specificity in the Pasteurellaceae.
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DOI：
10.1186/1471-2148-6-82
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发表时间：
2006-10-12
影响因子：
3.4
通讯作者：
Nash JH
中科院分区：
文献类型：
--
作者：
Redfield RJ;Findlay WA;Bossé J;Kroll JS;Cameron AD;Nash JH
许多细菌可以吸收DNA，但进化历史和自然能力和转化的功能仍然不清楚。零星分布的能力表明，它经常丢失和/或获得，但这还没有被检查在明确的系统发育背景下。其他见解可能来自物种（如流感嗜血杆菌）摄取的序列特异性，其中9 bp摄取信号序列（USS）重复在基因组中高度过量，并且需要有效的DNA摄取。我们利用感受态基因的分布和H.流感的家庭，巴斯德菌科，检查祖先的能力。巴氏杆菌科的一个系统发生学基于12个蛋白质编码基因，这些基因来自具有测序基因组的物种，显示出两个强有力的支持的亚支：Hin亚支（H。流感杆菌、伴放线放线杆菌、多杀性巴氏杆菌、产琥珀酸曼氏杆菌和H. somnus）和Apl亚支（A. pleuropneumoniae、M. haemolytica和H. ducreyi）。所有物种都含有所有已知H.流感病毒感受态基因，与感受态的祖先起源一致。在三个物种中鉴定出感受态基因缺陷（H. somnus，H. ducreyi和M.溶血性）;每个似乎是最近的起源。USS是由突变而不是复制产生的假设首先通过H的比对得到证实。流感病毒蛋白与远缘同源物。在所有8个巴氏杆菌基因组中均发现了丰富的USS样重复序列，Hin亚支中的物种重复序列一致性与H.流感（AAGTGCGGT），而Apl亚进化枝的成员共享共识ACAAGCGGT。所有物种的USS都具有H的强一致性和侧翼富含AT的重复序列。流感病毒DNA摄取和竞争实验表明，Apl型重复序列是一个真正的USS，不同于Hin型USS：A。胸膜肺炎杆菌优先摄取含有Apl型USS的DNA片段，而不是H.流感病毒和无关DNA，以及H.流感病毒更喜欢自己的USS而不是APL型。感受态和DNA摄取特异性是巴斯德菌科的祖先特性，不同的USS和摄取特异性仅区分两个主要的亚分支。在该家族约3.5亿年的历史中，大多数能力基因都得到了保存，这表明失去能力的谱系可能是进化的死胡同。
Many bacteria can take up DNA, but the evolutionary history and function of natural competence and transformation remain obscure. The sporadic distribution of competence suggests it is frequently lost and/or gained, but this has not been examined in an explicitly phylogenetic context. Additional insight may come from the sequence specificity of uptake by species such as Haemophilus influenzae, where a 9 bp uptake signal sequence (USS) repeat is both highly overrepresented in the genome and needed for efficient DNA uptake. We used the distribution of competence genes and DNA uptake specificity in H. influenzae's family, the Pasteurellaceae, to examine the ancestry of competence. A phylogeny of the Pasteurellaceae based on 12 protein coding genes from species with sequenced genomes shows two strongly supported subclades: the Hin subclade (H. influenzae, Actinobacillus actinomycetemcomitans, Pasteurella multocida, Mannheimia succiniciproducens, and H. somnus), and the Apl subclade (A. pleuropneumoniae, M. haemolytica, and H. ducreyi). All species contained homologues of all known H. influenzae competence genes, consistent with an ancestral origin of competence. Competence gene defects were identified in three species (H. somnus, H. ducreyi and M. haemolytica); each appeared to be of recent origin. The assumption that USS arise by mutation rather than copying was first confirmed using alignments of H. influenzae proteins with distant homologues. Abundant USS-like repeats were found in all eight Pasteurellacean genomes; the repeat consensuses of species in the Hin subclade were identical to that of H. influenzae (AAGTGCGGT), whereas members of the Apl subclade shared the consensus ACAAGCGGT. All species' USSs had the strong consensus and flanking AT-rich repeats of H. influenzae USSs. DNA uptake and competition experiments demonstrated that the Apl-type repeat is a true USS distinct from the Hin-type USS: A. pleuropneumoniae preferentially takes up DNA fragments containing the Apl-type USS over both H. influenzae and unrelated DNAs, and H. influenzae prefers its own USS over the Apl type. Competence and DNA uptake specificity are ancestral properties of the Pasteurellaceae, with divergent USSs and uptake specificity distinguishing only the two major subclades. The conservation of most competence genes over the ~350 million year history of the family suggests that lineages that lose competence may be evolutionary dead ends.
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影响因子：
14.9
作者：
Karlin, S;Mrazek, J;Campbell, AM
通讯作者：
Campbell, AM
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
3.3
作者：
Bigas, A;Garrido, ME;Llagostera, M
通讯作者：
Llagostera, M
巴斯德菌科 DNA 摄取信号序列的进化稳定性
DOI：
10.1073/pnas.0306366101
发表时间：
2004-03-30
影响因子：
11.1
作者：
Bakkali, M;Chen, TY;Redfield, RJ
通讯作者：
Redfield, RJ
11 个碱基对序列决定了嗜血杆菌转化过程中 DNA 吸收的特异性
影响因子：
3.5
作者：
DANNER, DB;DEICH, RA;SMITH, HO
通讯作者：
SMITH, HO