Snapshot of the genome of the pseudo-T-even bacteriophage RB49
Snapshot of the genome of the pseudo-T-even bacteriophage RB49
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DOI：
10.1128/jb.184.10.2789-2804.2002
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发表时间：
2002-05-01
影响因子：
3.2
通讯作者：
Krisch, HM
中科院分区：
文献类型：
--
作者：
Desplats, C;Dez, C;Krisch, HM
RB49 是一种感染大肠杆菌的剧毒噬菌体。其病毒体形态与众所周知的T-even噬菌体T4没有区别，但DNA杂交表明它在系统发育上与T4相距甚远，因此被归类为伪T-even噬菌体。为了进一步表征 RB49，我们对大约 170 kb 基因组中约 20% 的小片段进行了随机测序。大多数这些核苷酸序列与 T4 缺乏足够的同源性，无法在 NCBI BlastN 分析中检测到。然而，当翻译后，其中大约 70% 编码与 T4 蛋白同源的蛋白。这些序列包括病毒颗粒和噬菌体 DNA 复制装置的众多成分。绘制 RB49 基因图谱表明，其中许多基因具有与 T4 基因组中相同的相对顺序。确定了 RB49 基因组的两个区域的完整核苷酸序列，这两个区域包含大部分参与 DNA 复制的基因。该测序表明 RB49 具有所有必需 T4 复制基因的同源物，但正如预期的那样，它们的序列与其 T4 同源物有很大差异。 RB49 中缺少许多非必需 T4 基因，并已被未知序列取代。 RB49 的基因间序列不如编码序列保守，至少在某些情况下，RB49 已经进化出替代的调控策略。例如，对 RB49 转录的分析揭示了比 T4 更简单的调控模式，只有两类而不是三类时间控制的启动子。这些结果表明 RB49 和 T4 与其最后的共同祖先有很大差异。不同的T4型噬菌体似乎包含一组共同基因，可以通过调节序列的可塑性和大量兼性基因的精确选择来以不同的方式利用这些基因。
RB49 is a virulent bacteriophage that infects Escherichia coli. Its virion morphology is indistinguishable from the well-known T-even phage T4, but DNA hybridization indicated that it was phylogenetically distant from T4 and thus it was classified as a pseudo-T-even phage. To further characterize RB49, we randomly sequenced small fragments corresponding to about 20% of the approximate to170-kb genome. Most of these nucleotide sequences lacked sufficient homology to T4 to be detected in an NCBI BlastN analysis. However, when translated, about 70% of them encoded proteins with homology to T4 proteins. Among these sequences were the numerous components of the virion and the phage DNA replication apparatus. Mapping the RB49 genes revealed that many of them had the same relative order found in the T4 genome. The complete nucleotide sequence was determined for the two regions of RB49 genome that contain most of the genes involved in DNA replication. This sequencing revealed that RB49 has homologues of all the essential T4 replication genes, but, as expected, their sequences diverged considerably from their T4 homologues. Many of the nonessential T4 genes are absent from RB49 and have been replaced by unknown sequences. The intergenic sequences of RB49 are less conserved than the coding sequences, and in at least some cases, RB49 has evolved alternative regulatory strategies. For example, an analysis of transcription in RB49 revealed a simpler pattern of regulation than in T4, with only two, rather than three, classes of temporally controlled promoters. These results indicate that RB49 and T4 have diverged substantially from their last common ancestor. The different T4-type phages appear to contain a set of common genes that can be exploited differently, by means of plasticity in the regulatory sequences and the precise choice of a large group of facultative genes.