Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Chen, Zehua; Schneider, Thomas D.

doi:10.1093/nar/gki915

Cited by 41 publications

(29 citation statements)

References 91 publications

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“…A bioinformatic search, by following an existing reference for finding T7-like promoters (11), failed to identify a T7 RNAP promoter-like sequence in the phiL7 genome, although phiL7 has a T7-like RNAP. This result is consistent with the previous report, showing that a group of T7-like phages (e.g., phiKMV, Xp10, and PaP3) encoded a T7-like RNAP but contained no T7 RNAP promoter-like sequence (9). Based on known Xp10 promoter sequences and Ϫ35 to Ϫ10 consensus sequences for E. coli 70 , seven phiL7 promoters were predicted, in the 5Ј-flanking regions of p07, p20, p24, p35, p38, p49, and p57 ( Fig.…”

Section: Resultssupporting

confidence: 93%

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Lee

Lin

Weng

et al. 2009

Appl Environ Microbiol

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The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear doublestranded DNA genome (44,080 bp, 56% G؉C) with a 3-protruding cos site (5-TTACCGGAC-3) and 59 possible genes. Among the deduced proteins, 32 have homologs with known functions and 18 show no database similarities; moreover, the genes encoding these 18 proteins mostly have varying G؉C contents and form clusters dispersed along the genome. Only 39 genes have sequences related (27% to 78%) to those of sequenced genes of X. oryzae pv. oryzae phages, although the genome size and architecture of these Xanthomonas phages are similar. These findings suggest that phiL7 acquired genes by horizontal transfer, followed by evolution via various types of mutations. Major differences were found between phiL7 and the X. oryzae pv. oryzae phages: (i) phiL7 has a group I intron inserted in the DNA polymerase gene, the first such intron observed in Xanthomonas phages; (ii) although infection of phiL7 exerted inhibition to the host RNA polymerase, similar to the situations in X. oryzae pv. oryzae phages Xp10 and Xop411, sequence analysis did not identify a homologue of the Xp10 p7 that controls the shift from host RNA polymerase (RNAP) to viral RNAP during transcription; and (iii) phiL7 lacks the tail fiber protein gene that exhibits domain duplications thought to be important for host range determination in OP1, and sequence analysis suggested that p20 (tail protein III) instead has the potential to play this role.The genus Xanthomonas in the gamma subdivision of the Proteobacteria is a diverse and economically important group of bacterial plant pathogens consisting of 27 species (35), causing tremendous loss in agriculture worldwide. Individual species of this genus comprise multiple pathogenic variants (pathovars) and collectively cause diseases on at least 124 monocot species and 268 dicot species: for example, Xanthomonas campestris pv. campestris causes black rot in crucifers, X. campestris pv. vesicatoria causes spot disease in peppers and tomatoes, X. axonopodis pv. citri causes citrus canker, and X. oryzae pv. oryzae causes bacterial leaf blight on rice plants (17). In addition, members of the genus Xanthomonas commonly produce great amounts of an exopolysaccharide (xanthan gum) and X. campestris pv. campestris has been the organism of choice in industry for production of xanthan, which is useful in food, agriculture, industry and cosmetics (55).For controlling bacterial plant diseases, chemical control with antibiotics and copper compounds has been the standard (31, 46). However, many agrochemicals are toxic and may pose significant environmental and health risks (14). Therefore, there has been a resurgence of interest recently in using bacteriophages to replace the currently prevalent chemical measures, in which phages can be used effectively as part of integrated disease management strategies (12,15,16,32). Although pha...

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Section: Resultssupporting

confidence: 93%

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Lee

Lin

Weng

et al. 2009

Appl Environ Microbiol

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“…Another common feature is their transcription system. The phages encode their own RNAP that initiate transcription at conserved promoters distributed along the genome (25,26). Bioinformatics identified a 12 bp sequence 5Ј-CCTTAATTAACT-3Ј in the middle/late portion of the Syn5 genome, the only sequence that appears several times within the genome (13).…”

Section: Resultsmentioning

confidence: 99%

The RNA Polymerase of Marine Cyanophage Syn5

Zhu

Tabor

Raytcheva

et al. 2013

Journal of Biological Chemistry

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Background: Cyanophages are dominant viruses in the ocean while little has been known on their nucleic acid metabolism. Results: The RNA polymerase of cyanophage Syn5 has been purified and characterized and the Syn5 promoters identified. Conclusion: The Syn5 RNA polymerase and promoters have unique and ocean-adapted features. Significance: The first characterized single-subunit RNA polymerase from marine organisms.

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“…Promoter sequences that are recognized by the phage-encoded RNAP are found in all the members of the T7 group for which genome data are available (11). The genome of EcoM-GJ1 has nine genes with upstream motifs reminiscent of T7-like promoters (11,29).…”

Section: Discussionmentioning

confidence: 99%

“…The genome of EcoM-GJ1 has nine genes with upstream motifs reminiscent of T7-like promoters (11,29). EcoM-GJ1 is also similar to members of the T7 supergroup of phages (T7, SP6 and KMV) in that all the predicted genes are transcribed from one strand (45).…”

Section: Discussionmentioning

confidence: 99%

Complete Genomic Sequence of Bacteriophage φEcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase

Jamalludeen

Kropinski

Johnson

et al. 2008

Appl Environ Microbiol

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The complete genome of EcoM-GJ1, a lytic phage that attacks porcine enterotoxigenic Escherichia coli of serotype O149:H10:F4, was sequenced and analyzed. The morphology of the phage and the identity of the structural proteins were also determined. The genome consisted of 52,975 bp with a G؉C content of 44% and was terminally redundant and circularly permuted. Seventy-five potential open reading frames (ORFs) were identified and annotated, but only 29 possessed homologs. The proteins of five ORFs showed homology with proteins of phages of the family Myoviridae, nine with proteins of phages of the family Podoviridae, and six with proteins of phages of the family Siphoviridae. ORF 1 encoded a T7-like single-subunit RNA polymerase and was preceded by a putative E. coli 70 -like promoter. Nine putative phage promoters were detected throughout the genome. The genome included a tRNA gene of 95 bp that had a putative 18-bp intron. The phage morphology was typical of phages of the family Myoviridae, with an icosahedral head, a neck, and a long contractile tail with tail fibers. The analysis shows that EcoM-GJ1 is unique, having the morphology of the Myoviridae, a gene for RNA polymerase, which is characteristic of phages of the T7 group of the Podoviridae, and several genes that encode proteins with homology to proteins of phages of the family Siphoviridae.Postweaning diarrhea (PWD) due to enterotoxigenic Escherichia coli (ETEC) is a major problem for the swine industry (2, 17, 36). The ETEC strains that cause this disease typically produce F4 (K88) or F18 fimbriae and belong to a small number of O serogroups, with O149 being dominant worldwide (2,17,19). Strains of this serogroup were responsible for recent exceptionally severe outbreaks of disease in pigs in Ontario (2,26,38). The outbreak strains were almost all O149:H10:F4, whereas O149 strains from earlier periods were all O149: H43:F4 (38). Since multidrug resistance is common among these ETEC strains (2,32,38), and the problem persists despite traditional approaches such as vaccination, antibiotic treatment, feed additives, and management strategies, it was decided to investigate the use of bacteriophages for prophylaxis and therapy.Phage therapy has been effective in the prevention and treatment of experimentally induced diarrhea due to ETEC in neonatal pigs (46) but has never been investigated for PWD. We therefore used a mixture of 10 strains of O149:H10 ETEC from PWD as host strains in order to isolate phages by standard procedures from pig sewage (9). Six phages (EcoM-GJ1 to EcoM-GJ6) were isolated and characterized on the bases of morphology and spectrum of activity against O149:H10:F4 and O149:H43:F4 ETEC strains, strains of other serotypes of ETEC, and the 72 strains of the ECOR collection. The phages were also compared with respect to DNA fragment patterns resulting from digestion with three restriction enzymes. The six phages were similar morphologically and in their restriction enzyme digestion patterns as well as in their ability to lyse all or almost ...

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Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Cited by 41 publications

References 91 publications

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

The RNA Polymerase of Marine Cyanophage Syn5

Complete Genomic Sequence of Bacteriophage φEcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase

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