Proux Caroline, van Sinderen Douwe, Suarez Juan, Garcia Pilar, Ladero Victor, Fitzgerald Gerald F, Desiere Frank, Brüssow Harald
Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland.
J Bacteriol. 2002 Nov;184(21):6026-36. doi: 10.1128/JB.184.21.6026-6036.2002.
The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared. Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness. This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster. With respect to structural genes, four DNA homology groups could be defined within temperate L. lactis phages. Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics. However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics. For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera. We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system. In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.
本文报道了两种乳源噬菌体——嗜热链球菌噬菌体7201和干酪乳杆菌噬菌体A2的全基因组序列。比较基因组学研究表明，这两种噬菌体均属于最近提出的长尾噬菌体科中Sfi21样噬菌体属，该噬菌体类型在低GC含量的革兰氏阳性菌中广泛分布。在比较不同的Sfi21样噬菌体时，观察到了渐变相关性，这是生物系统进化的标志。在结构模块中，渐变相关性表现为高水平的DNA序列相似性或蛋白质序列相似性，或者在缺乏序列相关性时表现为共享的基因图谱。如乳酸乳球菌菌株IL1403所携带的不同原噬菌体所示，在来自单一物种的Sfi21样噬菌体中发现了这种不同程度的相关性。对11个完整的乳酸乳球菌噬菌体基因组序列进行的系统点阵分析显示，所有温和噬菌体与两类烈性噬菌体明显分离。温和型乳酸乳球菌噬菌体在非结构基因簇上以斑块状方式共享DNA序列同源性。就结构基因而言，在温和型乳酸乳球菌噬菌体中可定义四个DNA同源组。在来自链球菌或李斯特菌的噬菌体中检测到了所有四个DNA同源组的密切相关的结构模块，这表明它们代表了不同的进化谱系，并非仅在乳酸乳球菌中独特进化。基于比较基因组学的数据进行噬菌体分类似乎是合理的。然而，噬菌体进化的特殊模块化性质在通过比较基因组学定义噬菌体分类单元时产生了模糊性。例如，根据分类所基于的模块不同，温和型乳酸乳球菌噬菌体可以被分类为一个单一的噬菌体物种、四个不同的噬菌体物种，或者如果不是三个不同的噬菌体属，也可以被分类为两个。我们建议基于单个结构基因模块（头部或尾部基因）的比较基因组学进行噬菌体分类。这种部分基于系统发育的分类系统仍然反映了当前国际病毒分类委员会分类系统的一些方面。在这个系统中，目前已测序的乳酸乳球菌噬菌体将被分为五个属：c2 - 、sk1、Sfi11 - 、r1t - 和Sfi21样噬菌体。
