The genome of Bacillus subtilis bacteriophage SPO1.
The genome of Bacillus subtilis bacteriophage SPO1.
复制标题
DOI：
10.1016/j.jmb.2009.03.009
复制
发表时间：
2009-04-24
影响因子：
5.6
通讯作者：
Pedulla, Marisa L.
中科院分区：
文献类型：
--
作者：
Stewart, Charles R.;Casjens, Sherwood R.;Cresawn, Steven G.;Houtz, Jennifer M.;Smith, Alexis L.;Ford, Michael E.;Peebles, Craig L.;Hatfull, Graham F.;Hendrix, Roger W.;Huang, Wai Mun;Pedulla, Marisa L.
我们报告枯草芽孢杆菌噬菌体SPO 1的基因组序列。独特的基因组序列为132，562 bp，包装在病毒体（染色体）中的DNA具有13，185 bp的末端冗余，总共为145，747 bp。我们预测了204个蛋白质编码基因和5个tRNA基因，我们将这些发现与SPO 1的广泛研究相关联，包括对61个先前定义的基因的功能的研究和对病毒体结构的研究。69%的编码蛋白质与任何先前已知的蛋白质没有相似性。我们确定了107个可能的转录启动子;大多数是早期研究中确定的启动子类别的成员，但我们也看到了一个新的类别，具有与宿主sigma K启动子相同的序列。我们发现三个基因编码潜在的新的转录因子，其中之一是一个遥远的同源宿主σ因子K。我们还确定了75个可能的转录终止子结构。启动子和终止子通常位于基因之间，与早期的数据一起给出了噬菌体转录如何调节的相当完整的图片。有完整的基因组序列可用于另外五种革兰氏阳性宿主，它们在基因组大小以及基因的组成和组织方面与SPO 1相似。在这些其他噬菌体的背景下对SPO 1的比较分析产生了关于SPO 1和其他噬菌体的见解，这在单独分析任何一种噬菌体时都是不明显的。这些包括为几个特定的基因分配身份和可能的功能，并推断进化历史中的进化事件。比较分析也使我们能够把SPO 1到系统发育的背景下。我们看到了一种类似于在噬菌体T4及其亲属中所注意到的模式，其中在一组“核心”基因（包括大多数病毒体结构基因和一些DNA代谢基因）之间存在最小程度的成功水平基因交换，但在基因组的其余部分存在广泛的基因水平转移。在这些基因组中快速进化的基因和小基因之间存在相关性。
We report the genome sequence of Bacillus subtilis phage SPO1. The unique genome sequence is 132,562 bp, and DNA packaged in the virion (the chromosome) has a 13,185 bp terminal redundancy, giving a total of 145,747 bp. We predict 204 protein coding genes and five tRNA genes, and we correlate these findings with the extensive body of investigations of SPO1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. 69% of the encoded proteins show no similarity to any previously known protein. We identify 107 probable transcription promoters; most are members of the promoter classes identified in earlier studies, but we also see a new class that has the same sequence as the host sigma K promoters. We find three genes encoding potential new transcription factors, one of which is a distant homologue of the host sigma factor K. We also identify 75 probable transcription terminator structures. Promoters and terminators are generally located between genes and together with earlier data give what appears to be a rather complete picture of how phage transcription is regulated. There are complete genome sequences available for five additional phages of Gram-positive hosts that are similar to SPO1 in genome size and in composition and organization of genes. Comparative analysis of SPO1 in the context of these other phages yields insights about both SPO1 and the other phages that would not be apparent from the analysis of any one phage alone. These include assigning identities and probable functions for several specific genes, and inferring evolutionary events in the phages’ histories. The comparative analysis also allows us to put SPO1 into a phylogenetic context. We see a pattern similar to what has been noted in phage T4 and its relatives, in which there is minimal successful horizontal exchange of genes among a “core” set of genes that includes most of the virion structural genes and some genes of DNA metabolism, but there is extensive horizontal transfer of genes over the remainder of the genome. There is a correlation between genes in rapid evolutionary flux through these genomes and genes that are small.
登录
查看更多内容
DOI：
10.1073/pnas.80.5.1236
发表时间：
1983-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
COSTANZO, M;PERO, J
通讯作者：
PERO, J
影响因子：
3.7
作者：
CURRAN, JF;STEWART, CR
通讯作者：
STEWART, CR
影响因子：
3.7
作者：
CURRAN, JF;STEWART, CR
通讯作者：
STEWART, CR
影响因子：
3.2
作者：
Casjens, SR;Gilcrease, EB;Hendrix, RW
通讯作者：
Hendrix, RW
DOI：
10.1007/978-1-60327-565-1_7
发表时间：
2009
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Casjens, Sherwood R;Gilcrease, Eddie B
通讯作者：
Gilcrease, Eddie B