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Abstract

Comparative phage genomics has become possible due to the availability of more than 100 complete phage genome sequences and the development of powerful bioinformatics tools. This technology, profiting from classical molecular-biology knowledge, has opened avenues of research for topics, which were difficult to address in the past. Now, it is possible to retrace part of the evolutionary history of phage modules by comparative genomics. The diagnosis of relatedness is hereby not uniquely based on sequence similarity alone, but includes topological considerations of genome organization. Detailed transcription maps have allowed in silico predictions of genome organization to be verified and refined. This comparative knowledge is providing the basis for a new taxonomic classification concept for bacteriophages infecting low G + C-content Gram-positive bacteria based on the genetic organization of the structural gene module. An Sfi21-like and an Sfi11-like genus of Siphoviridae is proposed. The gene maps of many phages show remarkable synteny in their structural genes defining a lambda super-group within Siphoviridae. A hierarchy of relatedness within the lambda super-group suggests elements of vertical evolution in Siphoviridae. Tailed phages are the result of both vertical and horizontal evolution and are thus fascinating objects for the study of molecular evolution. Prophage sequences integrated into the genomes of their bacterial host present theoretical challenges for evolutionary biologists. Prophages represent up to 10% of the genome in some LAB. In pathogenic streptococci prophages confer genes of selective value for the lysogenic cell. The lysogenic conversion genes are located between the lysin gene and the right phage attachment site. Non-attributed genes were found at the same genome position of prophages from lactic streptococci. These genes belong to the few prophage genes transcribed in the lysogen. Prophages from dairy bacteria might therefore also contribute to the evolutionary fitness of non-pathogenic LAB.

Isolation and Characterization of vB_ArS-ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome

“…As was observed in other siphoviruses [61] , [65] , the packaging module in ArV2 is followed by a large genome cluster (∼18 kb) that contains genes encoding structural components of the virion. Bioinformatics analysis allowed us to identify 9 structural proteins of ArV2, including those coding for head (ORF03, ORF06), tail (ORF11, ORF15–ORF18), tail fiber (ORF20, ORF24), as well as a capsid maturation protease (ORF04) and a scaffolding protein (ORF05).…”

Complete genome sequence of the probiotic lactic acid bacteriumLactobacillus acidophilusNCFM

“…Prophages are a common feature among prokaryotic genomes and several phages have been reported in LAB (20,21). In silico analysis of the genome of L. acidophilus NCFM did not reveal any complete prophages.…”

Bacteriophages and dairy fermentations

“…delbrueckii phages being the first to be classified in the 1980s 64 . Later, several completely sequenced Lactobacillus genome phages were assigned to a classification scheme based on the organization of the structural gene module of the siphophages 65 . Further proposals for classification of Lactobacillus phages were based on the deduced proteomic trees, disregarding phage morphology, but the under-representation of Lactobacillus phages in these schemes might distort the impact of those phylogenetic trees 66 …”