In Sffamily Identification of Genes in Bacteriophage DNA

Kropinski, Andrew M.; Borodovsky, Mark; Carver, Tim; Cerdeño-Tárraga, Ana; Darling, Aaron E.; Lomsadze, Alexandre; Mahadevan, Padmanabhan; Stothard, Paul; Seto, Donald; Domselaar, Gary Van; Wishart, David S.

doi:10.1007/978-1-60327-565-1_6

Cited by 30 publications

(26 citation statements)

References 81 publications

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“…In contrast, Basilisk shares about 35% of its proteome with Staley and Slash. These proteomic similarities are right on the border of the 40% cutoff that is typically used to group phages by relatedness (54,58,59), highlighting the novel nature of our three isolates.…”

Section: Figmentioning

confidence: 90%

“…JL and Shanette also encode their own DNA polymerase, ligase, and topoisomerase as well as two proteins that appear to be involved in DNA partitioning (JL gp67 and a The number of total gene products for each phage listed is given. CoreGenes scores of ϳ40% are typically used to indicate phage families (54,58,59). The CoreGenes scores of ϳ40% are indicated by an asterisk.…”

Section: Figmentioning

confidence: 99%

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The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to wellcharacterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T‫9؍‬ icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. IMPORTANCEThe Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.

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Section: Figmentioning

confidence: 90%

Section: Figmentioning

confidence: 99%

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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“…In questionable cases, PSI-BLAST (2) was also used. Bioinformatic analysis was performed as described previously (13,16) (see also File S1 in the supplemental material).…”

Section: Methodsmentioning

confidence: 99%

Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673

Kropinski

Arutyunov

Foss

et al. 2011

Appl Environ Microbiol

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Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness worldwide, so improvements to current methods used for bacterial detection and disease prevention are needed. We describe here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and the exploitation of its receptor-binding protein for specific bacterial detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673 differs greatly from any other proteobacterial phage genome described (including C. jejuni phages CP220 and CPt10) and instead shows closest homology to the cyanobacterial T4-related myophages. The phage genome contains 172 putative open reading frames, including 12 homing endonucleases, no visible means of packaging, and a putative trans-splicing intein. The phage DNA appears to be strongly associated with a protein that interfered with PCR amplification and estimation of the phage genome mass by pulsed-field gel electrophoresis. Identification and analyses of the receptor-binding protein (Gp48) revealed features common to the Salmonella enterica P22 phage tailspike protein, including the ability to specifically recognize a host organism. Bacteriophage receptor-binding proteins may offer promising alternatives for use in pathogen detection platforms.Campylobacter belongs to the epsilon class of proteobacteria and is the leading cause of bacterial food-borne gastroenteritis worldwide (22). Campylobacter has also been associated with severe neurological disorders such as the Guillain-Barré and Miller-Fisher syndromes, as well as reactive arthritis and irritable bowel syndrome (32). Many Campylobacter phages have been characterized by their host-range characteristics, morphology, genome size, and susceptibility to restriction endonucleases (5,7,24). Only a few of the characterized Campylobacter phages are members of the B1 group of the family Siphoviridae (1), while most belong to the family Myoviridae possessing genomes which fall into three size classes: 110 to 150 kb (class III), 170 to 190 kb (class II), and 320 kb (class I) (24). One interesting characteristic of many of these phages is that their DNA appears to be resistant to cleavage by several common restriction endonucleases, thus making them "refractory to genomic analysis" (34). Two genomes of Campylobacter phages have been sequenced thus far: CPt10 and CP220 (34). Both appear to be closely related to each other and belong to the class II of Campylobacter Myoviridae phage genomes (34).Bacteriophages possess enormous diagnostic and therapeutic potential, which provides promise for the development of a wide range of novel antimicrobials and diagnostic tools (14). Numerous phages have been isolated against Campylobacter for use in phage typing schemes (9,10,12,18,25), but it has only recently been shown that bacteriophages can effectively decrease Campylobacter contamination (4, 20, 36). For example, Campylobacter-specific phages were able to reduce the numbers of Campylobacter coli and Campylobacter jejuni in chickens when added directly to the...

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“…BLASTP was used to determine similarities in the global database at http://www.ncbi.nlm.nih.gov. Genomic comparisons at the proteomic level were made using CoreGenes [69,70]. Transmembrane domains were predicted using TMHMM v2.0 and Phobius [71].…”

Section: Methodsmentioning

confidence: 99%

Characterization of a ViI-like Phage Specific to Escherichia coli O157:H7

Kutter

Skutt-Kakaria

Blasdel

et al. 2011

Virol J

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Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).

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In Sffamily Identification of Genes in Bacteriophage DNA

Cited by 30 publications

References 81 publications

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673

Characterization of a ViI-like Phage Specific to Escherichia coli O157:H7

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