Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.
Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.
复制标题
苏云金芽孢杆菌噬菌体的比较基因组学0305phi8-36：在新的古代噬菌体谱系中定义下降模式。
DOI：
10.1186/1743-422x-4-97
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发表时间：
2007-10-05
期刊：
影响因子：
4.8
通讯作者：
Serwer, Philip
中科院分区：
文献类型：
--
作者：
Hardies, Stephen C.;Thomas, Julie A.;Serwer, Philip
苏云金芽孢杆菌噬菌体0305φ8-36的218 kb基因组序列与已知噬菌体的同源性有限。这种噬菌体唯一已知的亲戚是B染色体上一串称为BtI 1的噬菌体样基因。苏云金杆菌噬菌体基因组的高度分化和新奇对如何从其基因组序列描述噬菌体提出了挑战。噬菌体0305φ8-36和BtI 1估计在20 - 25亿年前已经分离。定位偏倚的Blast搜索比对了0305φ8-36和BtI 1之间保持相同基因顺序的30个同源结构或形态发生基因。基因的功能聚类有助于识别其他基因功能。一个保守的长卷尺基因表明长尾是这种噬菌体谱系的进化稳定特性。一个不寻常的形式的尾部伴侣系统分裂成两个基因的特点，是一个增生的同源T4 gp 27枢纽基因。在该区域内，一些片段被最好地描述为编码与可交换结构域的可变组分融合的结构域的保守阵列。其他片段被最好地描述为参与模块水平交换的多基因单位。0305φ8-36的非结构基因似乎包括两个复制系统的残余，这导致了基因组计划是由两个祖先病毒融合而产生的假设。通过扩展该家族的隐马尔可夫模型，增强了位于0305φ8-36的RNAi RNA指导的RNA聚合酶家族成员的情况。最后，注意到预期的转录启动子从基因组的固定末端开始以从小到大的转录物的梯度分布。可以分析高于单个基因序列比较水平的基因组组织，以帮助理解大噬菌体基因组。分析方法包括1）应用时间尺度，2）用位置信息增加blast评分，3）将基因组重排分类为具有特征速率和结果的几个过程之一，以及4）将表观转录物大小与基因组位置、基因含量和启动子基序相关联。
The recently sequenced 218 kb genome of morphologically atypical Bacillus thuringiensis phage 0305φ8-36 exhibited only limited detectable homology to known bacteriophages. The only known relative of this phage is a string of phage-like genes called BtI1 in the chromosome of B. thuringiensis israelensis. The high degree of divergence and novelty of phage genomes pose challenges in how to describe the phage from its genomic sequences. Phage 0305φ8-36 and BtI1 are estimated to have diverged 2.0 – 2.5 billion years ago. Positionally biased Blast searches aligned 30 homologous structure or morphogenesis genes between 0305φ8-36 and BtI1 that have maintained the same gene order. Functional clustering of the genes helped identify additional gene functions. A conserved long tape measure gene indicates that a long tail is an evolutionarily stable property of this phage lineage. An unusual form of the tail chaperonin system split to two genes was characterized, as was a hyperplastic homologue of the T4gp27 hub gene. Within this region some segments were best described as encoding a conservative array of structure domains fused with a variable component of exchangeable domains. Other segments were best described as multigene units engaged in modular horizontal exchange. The non-structure genes of 0305φ8-36 appear to include the remnants of two replicative systems leading to the hypothesis that the genome plan was created by fusion of two ancestral viruses. The case for a member of the RNAi RNA-directed RNA polymerase family residing in 0305φ8-36 was strengthened by extending the hidden Markov model of this family. Finally, it was noted that prospective transcriptional promoters were distributed in a gradient of small to large transcripts starting from a fixed end of the genome. Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes. Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.