Prophages and bacterial genomics: what have we learned so far?

Abstract

EpigraphThere is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact. Mark Twain 1883 Life on the Mississippi SummaryBacterial genome nucleotide sequences are being completed at a rapid and increasing rate. Integrated virus genomes (prophages) are common in such genomes. Fifty-one of the 82 such genomes published to date carry prophages, and these contain 230 recognizable putative prophages. Prophages can constitute as much as 10-20% of a bacterium's genome and are major contributors to differences between individuals within species. Many of these prophages appear to be defective and are in a state of mutational decay. Prophages, including defective ones, can contribute important biological properties to their bacterial hosts. Therefore, if we are to comprehend bacterial genomes fully, it is essential that we are able to recognize accurately and understand their prophages from nucleotide sequence analysis. Analysis of the evolution of prophages can shed light on the evolution of both bacteriophages and their hosts. Comparison of the Rac prophages in the sequenced genomes of three Escherichia coli strains and the Pnm prophages in two Neisseria meningitidis strains suggests that some prophages can lie in residence for very long times, perhaps millions of years, and that recombination events have occurred between related prophages that reside at different locations in a bacterium's genome. In addition, many genes in defective prophages remain functional, so a significant portion of the temperate bacteriophage gene pool resides in prophages.Prophage biology

Subunit Conformations and Assembly States of a DNA-translocating Motor: The Terminase of Bacteriophage P22

“…47 The terminase large subunit of phage P22 belongs to a "sequence type" subfamily that differs from that of phage T4 and is considered only a distant relative of the phage SPP1 terminase (about 14% amino acid sequence identity, despite being in the same subfamily). 45 Terminases of the P22 and SPP1 subfamily are very common among known phages, yet very limited information is available on their structures and molecular mechanisms of function.…”

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

“…The 'phage structural supermodule' of Phage H105/1, responsible for phage assembly and structure, is syntenous with the morphogenetic operon of other temperate phages and prophages (Figure 2a) (Botstein and Matz, 1970;Canchaya et al, 2003). Typical of a l-like morphogenetic operon (Casjens, 2003), ORF 20, encoding a putative head morphogenesis protein, is found in the 'DNA packaging and head formation' module with genes encoding the large and small terminases (ORFs 18 and 19), ATPbinding proteins that cut the concatenated phage DNA to prepare it for packaging (Black, 1989) (Figure 2a). The large terminase protein sequence of H105/1 falls outside the known function-based phage terminase clusters (Figure 3b), and is most related to the terminase of a marine Silibacter prophage, with similarity to other known lambdoid phages (SO-1 and KS5).…”

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…However, phage lifestyle and experimental preparation of water samples dictate that this may not be the case. Lysogeny, the capacity of phages to lie dormant within bacterial genomes, has led to a 'mislabelling' problem in the databases serving tools such as BLAST, and the genetic material of prophages is often classified as being bacterial (Casjens 2003). Furthermore, the presence of prophages is not identified by water-sample processing methods, designed to capture viral diversity.…”