Desplats Carine, Dez Christophe, Tétart Françoise, Eleaume Heïdy, Krisch H M
Laboratoire de Microbiologie et Génétique Moléculaire du CNRS, UMR 5100, 118 Route de Norbonne, 31062 Toulouse Cedex, France.
J Bacteriol. 2002 May;184(10):2789-804. doi: 10.1128/JB.184.10.2789-2804.2002.
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 approximately 170-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 Many of the nonessential T4 genes are absent from RB49 and have been replaced by unknown sequences.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.
RB49是一种能感染大肠杆菌的烈性噬菌体。其病毒体形态与著名的T偶数噬菌体T4无法区分，但DNA杂交表明它在系统发育上与T4相距甚远，因此被归类为假T偶数噬菌体。为了进一步表征RB49，我们随机测序了约170 kb基因组中约20%的小片段。在NCBI BlastN分析中，这些核苷酸序列中的大多数与T4缺乏足够的同源性而无法被检测到。然而，翻译后，其中约70%编码与T4蛋白具有同源性的蛋白质。这些序列中包括病毒体的众多成分和噬菌体DNA复制装置。绘制RB49基因图谱发现，其中许多基因在T4基因组中的相对顺序相同。确定了RB49基因组中包含大部分参与DNA复制基因的两个区域的完整核苷酸序列。该测序结果表明，RB49具有所有必需的T4复制基因的同源物，但正如预期的那样，它们的序列与T4同源物有很大差异。RB49中缺少许多非必需的T4基因，已被未知序列取代。RB49的基因间序列比编码序列的保守性更低，并且至少在某些情况下，RB49已经进化出替代的调控策略。例如，对RB49转录的分析揭示了一种比T4更简单的调控模式，只有两类而非三类时间控制启动子。这些结果表明，RB49和T4与其最后的共同祖先已经有了很大的分歧。不同的T4型噬菌体似乎包含一组共同的基因，这些基因可以通过调控序列的可塑性和大量兼性基因的精确选择而被不同地利用。
