Similarities and dissimilarities of phage genomes
Similarities and dissimilarities of phage genomes
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DOI：
10.1073/pnas.93.12.5854
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发表时间：
1996-06-11
影响因子：
11.1
通讯作者：
Karlin, S
中科院分区：
文献类型：
--
作者：
Blaisdell, BE;Campbell, AM;Karlin, S
基因组的相似性和对比度进行了研究，在收集的23个噬菌体，包括温和的，裂解的，寄生的生活史，不同的序列组织和不同的主机和不同的形态，比较使用相对丰度的二，三，和tetranucleotides从整个基因组。我们强调几个具体的调查结果。(i)如前所述，每个病毒基因组都有一个独特的短寡核苷酸丰度特征，遍布整个基因组，并将其与其他基因组区分开来。(ii)肠温和双链（ds）噬菌体，如肠细菌，表现出显着高的GpC = GC相对丰度和显着低的TA值，但ds裂解噬菌体中不存在这样的极端情况。(iii)四核苷酸CTAG在大多数哺乳动物中具有统计学上较低的相对丰度。(iv)DAM甲基化酶位点GATC在大多数P1中具有统计学上较低的相对丰度，但在P1中没有。这种差异可能与对复制的控制有关（例如，宿主SeqA基因产物的作用）和大肠杆菌DAM错配修复系统的MutH切割潜力。（v）肠温性dsDNA酶形成连贯组：它们在二核苷酸相对丰度值的平均差异上彼此相对接近并且与它们的细菌宿主相对接近。相比之下，裂解性dsDNA酶不形成连贯组。这种差异可能是因为温带细菌获得了更多的宿主序列特征，因为它们使用宿主复制和修复机制，而分析的裂解型细菌是通过它们的olm机制复制的。(Fi)具有支原体和分枝杆菌宿主的非肠温性嗜热菌与其各自的宿主相对较近，与任何肠宿主和其他嗜热菌相对较远。(vii)单链RNA的相对丰度值最接近随机序列的相对丰度值，这可能是由于RNA的突变率远大于DNA的突变率。
Genomic similarities and contrasts are investigated in a collection of 23 bacteriophages, including phages with temperate, lytic, and parasitic life histories, with varied sequence organizations and with different hosts and with different morphologies, Comparisons use relative abundances of di-, tri-, and tetranucleotides from entire genomes. We highlight several specific findings. (i) As previously shown for cellular genomes, each viral genome has a distinctive signature of short oligonucleotide abundances that pervade the entire genome and distinguish it from other genomes. (ii) The enteric temperate double-stranded (ds) phages, like enterobacteria, exhibit signif icantly high relative abundances of GpC = GC and significantly low values of TA, but no such extremes exist in ds lytic phages. (iii) The tetranucleotide CTAG is of statistically low relative abundance in most phages. (iv) The DAM methylase site GATC is of statistically low relative abundance in most phages, but not in P1. This difference may relate to controls on replication (e,g., actions of the host SeqA gene product) and to MutH cleavage potential of the Escherichia coli DAM mismatch repair system, (v) The enteric temperate dsDNA phages form a coherent group: they are relatively dose to each other and to their bacterial hosts in average differences of dinucleotide relative abundance values, By contrast, the lytic dsDNA phages do not form a coherent group. This difference may come about because the temperate phages acquire more sequence characteristics of the host because they use the host replication and repair machinery, whereas the analyzed lytic phages are replicated by their olm machinery. (Fi) The nonenteric temperate phages with mycoplasmal and myco-bacterial hosts are relatively close to their respective hosts and relatively distant from any of the enteric hosts and from the other phages. (vii) The single-stranded RNA phages have dinucleotide relative abundance values closest to those for random sequences, presumably attributable to the mutation rates of RNA phages being much greater than those of DNA phages.