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

By Sherwood R. Casjens. Molecular Microbiology, 2003

882 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0bf78ed69aecfa907e0c458fbba62914b6fd8b05

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Citations in the corpus

In vivo recombineering of bacteriophage λ by PCR fragments and single-strand oligonucleotides (2004, background): “Casjens (2003) estimated the presence of 230 prophages in 51 bacterial genomes whose sequence was deciphered.”
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models (2006, neutral): “The largest GIs included the cryptic prophages CP4-6 (262 – 297 kbp), DLP12 (557 – 584 kbp), e14 (1,196 – 1,221), Rac (1,410 – 1,433 kbp), Qin (1,631 – 1,651 kbp), CP4-44 (2,064 – 2,069 kbp), CPS-53 (2,465 – 2,475 kbp), Eut (2,556 – 2,563 kbp), CP4-57 (2,752 – 2,775 kbp), and the phagelike element K”
PHAST: A Fast Phage Search Tool (2011, background): “As the most abundant biological entity on Earth (1), phages are also thought to play a crucial role in cycling nutrients and boosting photosynthesis in the world’s oceans (4).”
Varieties of Living Things: Life at the Intersection of Lineage and Metabolism (2009, background): “Some viruses have an extra developmental stage in which they remain dormant in the host cell or genome as prophages or proviruses and are inherited (Casjens 2003; Bannert et al. 2004).”
Lysogeny in nature: mechanisms, impact and ecology of temperate phages (2017, background): “Here, we complement efforts to specifically review lysogeny which have largely focused on prophage genomics and impacts of lysogeny on either microbial cells (Casjens, 2003; Brussow et al., 2004; Canchaya et al., 2004; Abedon and LeJeune, 2005; Fortier and Sekulovic, 2013; Hargreaves et al., 2014; F”
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences (2006, methodology): “The pipeline was tested against a set of manually-defined prophage regions ( 20 ).”
Genomic analysis of bacteriophage ε34 of Salmonella enterica serovar Anatum (15+) (2008, background): “In theory, point mutations could have inactivated nearly any of these prophage genes, but there are many examples of fully functional genes, even in quite highly degraded prophages that are very likely much older than Scho1 and Para1 [ 10 ].”
Cryptic prophages help bacteria cope with adverse environments (2010, background): “Because of their prevalence, acquisition of prophages contributes most to the horizontal gene transfer, as phage-like elements have been identified in almost all sequenced pathogenic and non-pathogenic bacterial genomes, and can constitute up to 20% of the DN”
Cloning Serratia entomophila Antifeeding Genes—a Putative Defective Prophage Active against the Grass Grub Costelytra zealandica (2004, background): “Typically, viruses of gram-negative bacteria have highly mosaic structures, with many viruses encoding the same genes but at different locations in their genomes (10).”
PHASTER: a better, faster version of the PHAST phage search tool (2016, background): “Bacterial genomes and plasmids can contain a large fraction ( > 20% in some cases) of functional and non-functional bacteriophage genes (1).”