ライフサイエンスコーパス: prophage

1 f spacers to the integrated phage sequences (prophages).

2 e) or unrelated (heterotypic defence) to the prophage.

3 oter, PRM, which directs CI synthesis by the prophage.

4 er set LJ900f/LJ900r derived from multi-copy prophage.

5 of multiple S. aureus clones via a resident prophage.

6 induction of the integrated Escherichia coli prophage.

7 r proteins encoded by Listeria monocytogenes prophages.

8 he majority of contractile-tailed phages and prophages.

9 sm, in mobile genetic elements and defective prophages.

10 more than 200 genomes of P22-like phages and prophages.

11 ncluding Stx2a, are encoded within temperate prophages.

12 ection exclusion systems normally encoded on prophages.

13 f integrase and transposase genes in cryptic prophages.

14 placed by analogous functions carried by new prophages.

15 t that bacteria frequently domesticate their prophages.

16 articles, gene transfer agents, or satellite prophages.

17 intains lysogeny of defective and functional prophages.

18 , 13 of which harbored one or more predicted prophages.

19 ed in some by immunity conferred by existing prophages.

20 integrative conjugative elements (ICEs), and prophages.

21 he gene repertoires of intact and incomplete prophages.

22 cultivated strains, for evidence of complete prophages.

23 olerae, and Salmonella enterica harbor these prophages.

24 on-to understand the diverse gene content of prophages.

25 32/1206) of ARGs were found to be carried by prophages.

26 One prophage, prophage 1 (PhiV1), encodes the structural genes necessa

27 Here we studied Yersinia ruckeri antifeeding prophage 18 (Afp18), the toxin component of the phage ta

28 d from temperate phages, genomic islands, or prophages (4-8) , and shared properties with the first A

29 Another prophage, prophage 7 (PhiV7), is required for phage infection of s

30 harbour temperate viruses in their genomes (prophage)(7).

31 ated genes and two strains harbored complete prophages, acquired copper tolerance genes, and CRISPR-a

32 ns with T1RMS rearrangements causing CIs and prophage activation across major S. aureus lineages.

33 ting that the decrease in E. coli was due to prophage activation.

34 In Xylella and Xanthomonas, prophage activity is associated with genome rearrangemen

35 Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron

36 The Serratia entomophila antifeeding prophage (Afp) is a bullet-shaped toxin-delivery apparat

37 As a lysogen, the prophage alters the bacterial physiology by increasing t

38 mply lateral transfers between bacteriophage/prophage and animal genomes.

39 ged mutagenesis mutants having insertions in prophage and genomic island genes.

40 us pyogenes, which is encoded by the SF370.1 prophage and is likely to be expressed as a result of pr

41 lutionary strategy entertained by the SPbeta prophage and its Bacillus host, ensuring both stable pro

42 with the stepwise emergence of (i) a unique prophage and mutation of the regulator of the pyrimidine

43 Its genome contains 6 prophages and 5 genomic islands.

44 gulator genes (psr) are found exclusively on prophages and are associated with effector loci and the

45 provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evalua

46 tic features from siphoviruses, podoviruses, prophages and GTAs.

47 marked with insertion elements, transposons, prophages and integrases - paying testament to past geno

48 cholerae to remove all of the GIs, ICEs, and prophages and revealed important interactions between co

49 treptococcus species and identify nearly 800 prophages and satellite prophages (prophages that do not

50 We show that prophages and satellite prophages are widely distributed

51 Individual prophages and the host pneumococcal genetic lineage were

52 lements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the

53 bute to disease development, e.g., flagella, prophages, and salicylic acid hydroxylase.

54 Temperate phages are common, and prophages are abundant residents of sequenced bacterial

55 Evidence that related prophages are broadly distributed in the oceans suggests

56 proteins of the spirochete's ubiquitous cp32 prophages are DNA-binding proteins, required both for ma

57 e Global Ocean Survey database, showing that prophages are found in natural SAR11 populations.

58 Prophages are largely quiescent, but they can alter host

59 Pneumococcal prophages are likely to play a more important role in pn

60 n the human pathogen, Staphylococcus aureus, prophages are omnipresent and are believed to be respons

61 Prophages are phages in lysogeny that are integrated int

62 Prophages are quiescent viruses located in the chromosom

63 This study indicated that induced prophages are unique and have lower overall community di

64 We show that prophages and satellite prophages are widely distributed among streptococci in a

65 Additionally, we report that prophages are widespread among oral-associated TM7, whil

66 Integrated phages (prophages) are major contributors to the diversity of ba

67 y found in the intergenic region between the prophage at the 3' end and the bacterial gene.

68 imately 1/3 of Shewanella isolates harbour a prophage at the tmRNA (ssrA) gene.

69 ut also in a natural isolate that contains a prophage at this site.

70 the Corticoviridae and the Siphoviridae and prophages belonging to the Myoviridae have been reported

71 ed subtle differences in genomic islands and prophages between the species.

72 that may be assessed to improve research in prophage biology and its association with genome evoluti

73 S S. Typhimurium isolates is the presence of prophage BTP1.

74 PhiSpy locates prophages by ranking genomic regions enriched in distinc

75 ere we describe another mechanism by which a prophage can modulate host phenotype.

76 ractions between phages and their hosts, and prophages can confer a variety of systems that defend ag

77 is failed to occur in inductions of isogenic prophages carrying null mutations in the spanin genes.

78 Full-length prophages clustered into four major groups and every gro

79 as limited evidence for genes shared between prophage clusters.

80 vement of mobile genetic elements (including prophages) combined with genomic rearrangements.

81 ge that a locus within a B. cellulosilyticus prophage confers upon its host.

82 show that genome expansion by integration of prophages containing virulence factors is a major route

83 Return of such particles to the prophage-containing population can drive the transfer of

84 ation of S. aureus cells enables the intact, prophage-containing population to acquire beneficial gen

85 However, prophage content is highly variable even within lineages

86 with variations in capsular locus (cps) and prophage content.

87 evant cps variants and allowing for variable prophage content.

88 Intraclonal variants, reflecting different prophage contents, showed differences in major surface a

89 Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution,

90 ibution, and further identification of these prophages corroborated the lineage specificity.

91 Deletion of O-island 51, a 14.93 kb cryptic prophage (CP-933C), resulted in a reduction in LEE expre

92 at PsrA and effectors encoded within cryptic prophage CP933-N are required for persistence in a rumin

93 ably having one or more tandem cholera toxin prophage (CTX) arrays, which potentially affected its vi

94 cted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Twe

95 viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, an

96 patible with described functions of adaptive prophage-derived elements such as bacteriocins, killer p

97 Nonetheless, 933W forms lysogens, and 933W prophage display a threshold response to UV induction si

98 ich is in accordance with the association of prophage DNA carrying ORF6 with invasive meningococcal s

99 gets included a 308-bp deletion (20%) in the prophage DNA packaging Nu1 and a 730-bp insertion of the

100 TspB is encoded by gene ORF6 in prophage DNA, which others have shown is associated with

101 led that every pneumococcal genome contained prophage DNA.

102 f new toxigenic strains by acquiring the CTX prophage either through reinfection with CTXvarphi or by

103 ined a clinical isolate that carries a novel prophage element, designated Spn1, which was detected in

104 The size distribution of prophage elements is bimodal, suggestive of rapid propha

105 We are able to identify active prophage elements through the requirement for their repr

106 The bacterium has acquired four large prophage elements, PhiM23ND.1 to PhiM23ND.4, harboring g

107 tion sequences, conjugative transposons, and prophage elements.

108 ived from two distinct chromosomally encoded prophage elements.

109 synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produ

110 In Listeria monocytogenes, prophages encode two to three distinct anti-Cas9 protein

111 Numerous plasmids and some prophages encode type IV systems, with similar predicted

112 Here, Toyofuku et al. show that a prophage-encoded endolysin can generate holes in the cel

113 We show that the expression of a prophage-encoded endolysin in a sub-population of cells

114 genes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR

115 gh site-specific recombination mediated by a prophage-encoded integrase.

116 ch produces RS1varphi particles by using CTX prophage-encoded morphogenesis proteins.

117 able to identify two previously unannotated prophage-encoded proteins with tertiary structures simil

118 P2 phage production is induced by a prophage-encoded Rep protein and its excision is induced

119 These prophage-encoded secretion regulator genes (psr) are fou

120 fibronectin-binding protein (SfbX49), and a prophage-encoded superantigen, SpeH.

121 lach et al. (2018) show that modification by prophage-encoded TarP diminishes WTA immunogenicity, all

122 This prophage encodes a gtrC gene, implicated in O-antigen mo

123 combination directionality factor (RDF), for prophage excision (attL x attR recombination).

124 rectionality factor is strictly required for prophage excision from the host genome.

125 Prophage excision occurs through site-specific recombina

126 ut with a difference: the 'bla(TEM-1B) type' prophages exhibited a classic Tn2 transposon structure w

127 cteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere

128 ely on the bacterial host and another helper prophage for survival).

129 tail length tape measure protein (TMP) of a prophage found in the genome of the bacteriophage Entero

130 ertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of d

131 phage lambda infection, induction of lambda prophage from cells carrying BREX leads to production of

132 from the chromosome, the elimination of CTX prophage from host cells is driven by the inability to r

133 PhiCAM shared high levels of similarity to a prophage from Salinispora tropica and a putative prophag

134 he prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs t

135 acted DNA of the ambient viruses and induced prophages from the co-occurring, viral-reduced microbial

136 e Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria.

137 RNA sequencing provided clear evidence of prophage gene expression.

138 gated and RNA sequencing was used to explore prophage gene expression.

139 Hence, our results indicate that cryptic prophage genes can be functionally divergent from their

140 In this study, we show that prophage genes coding for T and B cell stimulating prote

141 e the distributions of over 50,000 annotated prophage genes identified in 1384 prophage sequences, co

142 by bicyclomycin allows for the expression of prophage genes that lead to excisive recombination.

143 phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infecti

144 unterselection of nonsynonymous mutations in prophage genes.

145 Many bacteriophage and prophage genomes encode an HNH endonuclease (HNHE) next

146 r provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the ac

147 Furthermore, prophage genomes present a robust phylogeographic patter

148 s have primarily been discovered in phage or prophage genomes.

149 ation in the synthesis genes, it possesses a prophage glucosylation cluster, which modifies the GlcNA

150 d RNA-Seq suggested that disruption of these prophages had a widespread trans-acting effect on the tr

151 Nearly 40% of the prophages harbored insertion sequences (IS) previously d

152 MS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC).

153 , and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene.

154 This gene, carried by the cryptic rac prophage, has been named rcbA for its ability to reduce

155 Several of these conserved prophages have gene repertoires compatible with describe

156 Prophage Hunter provides a one-stop web service to extra

157 We present Prophage Hunter, a tool aimed at hunting for active prop

158 ased on seven distinctive characteristics of prophages, i.e. protein length, transcription strand dir

159 terial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and

160 Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated.

161 port on this type of exclusion mediated by a prophage in P. aeruginosa IMPORTANCE Pseudomonas aerugin

162 r patients, the presence of the enterococcal prophage in stools and expression of a TMP-cross-reactiv

163 hage from Salinispora tropica and a putative prophage in Streptomyces sp. strain C.

164 he host bacterium in the presence of similar prophage in the chromosome.

165 ae chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regu

166 leads to the successful prediction of 94% of prophages in 50 complete bacterial genomes with a 6% fal

167 Thus, prophages in a gut symbiont can be induced by diet and m

168 A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome.

169 Here, we report the discovery of prophages in cultured SAR11, the ocean's most abundant c

170 The absence of prophages in cultures of the dominant lineages of marine

171 However, finding prophages in microbial genomes remains a problem with no

172 ndings highlight the potential importance of prophages in streptococcal biology and pathogenesis.

173 age elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic de

174 d epidemiologically to the presence of novel prophages, including prophage PhiHKU.vir encoding the se

175 ria colonize the infant gut and by one month prophages induced from these bacteria provide the predom

176 Laboratory experiments showed that prophage-induced Halanaerobium lysis releases intracellu

177 ncluding mortality, genetic transduction and prophage-induced viral immunity.

178 own, but rare, states such as competence and prophage induction and also identified unexpected gene e

179 maging activity using the lambda-Microscreen Prophage induction assay.

180 The second area was the classic problem of prophage induction in response to cellular DNA damage, t

181 Intestinal cues driving prophage induction in the microbiota are largely unknown

182 nzymes are required both in the donor (after prophage induction) and in the recipient strain (for inf

183 s minimal effect on lambda lysogenization or prophage induction.

184 and is likely to be expressed as a result of prophage induction.

185 led a rare subpopulation of cells undergoing prophage induction.

186 hich are bacteria containing dormant phages (prophages) inserted within their genomes.

187 CME and the unique signature pattern for the prophage insertion that harbored the PVL genes.

188 arbour prophages, yet it remains unknown why prophages integrate into tRNA-related genes.

189 Here, we discovered a P2-family prophage integrated at the 3'-end of ssrA in the deep-se

190 particularly gene composition and mutations, prophage integrations, unique genomic rearrangements, an

191 y provides new insight into how bacteria and prophages interact and affect bacterial fitness in vivo.

192 cteriophage, CTXvarphi, that integrates as a prophage into the V. cholerae chromosome.

193 Furthermore, a satellite prophage is associated with virulence in a mouse model o

194 ed but suffers from reduced fitness when the prophage is excised.

195 The KplE1 prophage is one of the 10 prophage regions in Escherichi

196 Identifying active prophages is critical for studying coevolution of phage

197 Cross-species transmission of prophages is not uncommon.

198 sters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental

199 type I toxin/antitoxin system located on the prophage-like region P6 of the Bacillus subtilis chromos

200 (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to th

201 t targeting is resumed upon induction of the prophage lytic cycle.

202 and its Bacillus host, ensuring both stable prophage maintenance and a maximal competitive advantage

203 the transcription termination factor Rho in prophage maintenance through control of the synthesis of

204 romosome and the partitioning system confers prophage maintenance.

205 sent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to

206 In addition, we report a new prophage-mediated genome engineering (recombineering) sy

207 Prophage-mediated viral defence offers an efficient mech

208 s hirae Mice bearing E. hirae harboring this prophage mounted a TMP-specific H-2K(b)-restricted CD8(+

209 DNA of infecting phage and in resolution of prophage multimers created by generalized recombination.

210 e-chain protein, YonO, encoded by the SPbeta prophage of Bacillus subtilis.

211 The prophages of S. equi and other streptococci encode intra

212 ve been identified on insertion elements and prophages of the chromosome, we demonstrated in the curr

213 We show that prophages of the gut symbiont Lactobacillus reuteri are

214 of toxigenic Vibrio cholerae, the CTXvarphi prophage often resides adjacent to a chromosomally integ

215 racy than current tools in predicting active prophages on the validation datasets.

216 acteriophage-related sequences, suggesting a prophage origin.

217 Prophages outnumbered lytic phages approximately 2:1 wit

218 le genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal

219 ic lineage were strongly associated and some prophages persisted for many decades.

220 both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell.

221 V pili or contain insertions in genes of the prophage Pf4.

222 pression of a symbiotic filamentous inoviral prophage, Pf4.

223 nce, diversity and molecular epidemiology of prophages (phage DNA integrated within the bacterial gen

224 o the presence of novel prophages, including prophage PhiHKU.vir encoding the secreted superantigens

225 sis of scarlet fever-causing GAS mediated by prophage PhiHKU.vir exotoxins.

226 r tetracycline and macrolide resistance, and prophage PhiHKU.vir, encoding the superantigens SSA and

227 ral ICE-emm12 variants, PhiHKU.vir and a new prophage, PhiHKU.ssa, occurred in three distinct emm12 l

228 olic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome.

229 LukPQ is encoded on a 45 kb prophage (PhiSaeq1) found in six different clonal lineag

230 ers: one African, one Asian and two European prophage populations.

231 72% of prophages possessed the virulence genes pblA and/or pblB

232 ns isolated from DFUs, we brought to light a prophage present in noninfecting bacteria.

233 dolysins, Lc-Lys and Lc-Lys-2, identified in prophages present in the genome of Lactobacillus casei B

234 tine, caused elimination of the resident CTX prophage-producing nontoxigenic derivatives at a high fr

235 One prophage, prophage 1 (PhiV1), encodes the structural gen

236 Another prophage, prophage 7 (PhiV7), is required for phage infe

237 identify nearly 800 prophages and satellite prophages (prophages that do not encode their own struct

238 relative abundances of hundreds of predicted prophage proteins.

239 , the tight association of the CI genes with prophages provides clues to the possible evolutionary or

240 emonstrate that RalR and RalA of the cryptic prophage rac form a type I TA pair in which the antitoxi

241 The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39

242 a coli strain to express an optimized lambda prophage Red recombination system.

243 We also observed a 49-kb deletion of a prophage region that removed an integration site, which

244 Bacteriophage- or prophage-region-encoded anti-CRISPR (acr) gene molecules

245 The KplE1 prophage is one of the 10 prophage regions in Escherichia coli K12 MG1655.

246 redict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes

247 Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulenc

248 Moreover, a Wolbachia prophage-related sequence was identified.

249 solates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistanc

250 gens in Mycobacterium smegmatis in which the prophage replicates at 2.4 copies/chromosome and the par

251 , we demonstrate that functional and cryptic prophages represent a diversity of genetic sequences tha

252 Prophages represent a large fraction of prokaryotic geno

253 Qtip interferes with the prophage repressor (cI(VP882)), leading to host-cell lys

254 ation was detected within the genome of some prophages, resulting in genome mosaics composed by diffe

255 For other pathogens, prophage roles are yet to be established.

256 etic foot ulcers in French patients harbor a prophage, ROSA-like, that is absent from invasive isolat

257 e several mobile genetic elements (SaPI5 and prophage SA3usa) were strongly upregulated.

258 pan-genome-wide association study identified prophage sequences as being associated with decreased ca

259 egrated into their bacterial hosts' genomes, prophage sequences exhibit a wide diversity of length an

260 e, we performed cataloguing of the predicted prophage sequences from the genomes of all currently rec

261 gnificant portion of its genome dedicated to prophage sequences of a virus called WO.

262 yotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and

263 annotated prophage genes identified in 1384 prophage sequences, comparing the gene repertoires of in

264 tical proteins and are within or adjacent to prophage sequences.

265 ellular toxicity caused by Bacillus subtilis prophage SPbeta-encoded toxin BsrG revealed that, surpri

266 nd the sunI immunity gene are encoded by the prophage SPbeta.

267 Integration thus not only confers prophage stability but also is a requirement for lysogen

268 l of the chromosomal inversion (CI) and with prophage stabilization.

269 riophage lambda stably maintains its dormant prophage state but efficiently enters lytic development

270 bacterial DNA polymerases in the integrated prophage state.

271 of bacteriophage lambda determines whether a prophage stays incorporated in the E. coli chromosome or

272 ew tools for identifying phage and potential prophage structural proteins that are difficult or impos

273 One of the circular plasmids is a prophage that exists as several isoforms in each cell an

274 early 800 prophages and satellite prophages (prophages that do not encode their own structural compon

275 re preferentially lost, resulting in shorter prophages that often retain genes that benefit the host.

276 nto their bacterial hosts, existing there as prophages that refrain from killing the host cell until

277 aded cryptic sequences to intact, functional prophages that retain a full complement of lytic-functio

278 of the genomes examined contain at least one prophage, the majority (97%) were found within genomes o

279 Here we focused on prophages, the least characterized mobile elements of H.

280 ing an association between plant disease and prophage transcriptional modulation.

281 2:1 with the most abundant bacteriophage and prophage types being associated with members of the domi

282 Prophages typically integrated in one of five different

283 impact of the well-characterised Shiga toxin-prophage varphi24B on its Escherichia coli host MC1061.

284 Prophages (viral genomes integrated within a host bacter

285 set of 4 pneumococcal genes co-located on a prophage was a confirmed independent predictor of 30-day

286 Overall, pneumococcal prophages were highly prevalent, demonstrated a structur

287 A total of 1105 potential prophages were identified, and the distribution of the g

288 l-length/putatively full-length pneumococcal prophages were identified, of which 163 have not previou

289 No T4-like prophages were identified.

290 nd AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity

291 ects, from the nearly neutral transposons to prophages, which are actively eliminated by selection.

292 have been preferentially lost in incomplete prophages, while tail fiber, transposase and integrase g

293 he lysis of induced lambda lysogens carrying prophages with either the lambda canonical holin-endolys

294 We identified over 300 vertically inherited prophages within enterobacterial genomes.

295 The role of prophages within genomes for cell biology varies.

296 mparative genomics to study the evolution of prophages within the bacterial genome.

297 e characteristics are capable of identifying prophages without any sequence similarity with known pha

298 enes in the eukaryotic association module of prophage WO from Wolbachia strain wMel recapitulate and

299 es cifA and cifB pioneers genetic studies of prophage WO-induced reproductive manipulations and infor

300 Almost all bacterial genomes harbour prophages, yet it remains unknown why prophages integrat