ライフサイエンスコーパス: prophage

1 cidin (PVL) lysogenized into its chromosome (prophage).

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

3 lyse attL x attR recombination to excise the prophage.

4 a bacterial attB site to form an integrated prophage.

5 is after induction of a chimeric lambda :: E prophage.

6 chia coli, is encoded by 933W, a lambda-like prophage.

7 ranslational switch carried on a K1-specific prophage.

8 e proteins was linked the lytic cycle of the prophage.

9 ermutation of gene order going from phage to prophage.

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

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

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

13 articles, gene transfer agents, or satellite prophages.

14 intains lysogeny of defective and functional prophages.

15 , 13 of which harbored one or more predicted prophages.

16 erminator RNA sequences in bacteriophages or prophages.

17 he majority of contractile-tailed phages and prophages.

18 sm, in mobile genetic elements and defective prophages.

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

20 ncluding Stx2a, are encoded within temperate prophages.

21 r proteins encoded by Listeria monocytogenes prophages.

22 ection exclusion systems normally encoded on prophages.

23 placed by analogous functions carried by new prophages.

24 t that bacteria frequently domesticate their prophages.

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

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

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

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

29 besides the polymorphisms found in the comK prophage, a single SNP in the tRNA Thr-4 prophage repres

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

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

32 Deletion of cryptic prophages also overcomes the increased BCM sensitivity i

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

34 ary heritage from an N15-like linear plasmid prophage ancestor.

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

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

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

38 ined to a great extent by differences in the prophage and plasmid contents.

39 difference in genome arrangement between the prophage and virion forms.

40 Its genome contains 6 prophages and 5 genomic islands.

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

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

43 ve used a collection of deletions in cryptic prophages and EHEC O157 O-islands to screen for novel re

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

45 MDS42, which is deleted for all cryptic prophages and insertion elements, or W3102 deleted for t

46 large linear DNA including the N15 and PY54 prophages and linear animal viruses, and for assembly of

47 n E. coli that are most repressed by Rho are prophages and other horizontally acquired portions of th

48 genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most

49 Individual prophages and the host pneumococcal genetic lineage were

50 and distributed over five genomic islands, a prophage, and two plasmids.

51 erp operons are located on episomal cp32 prophages, and a single bacterium may contain as many as

52 since 6 of 13 completed genomes have related prophages, and a survey of 100 strains found that about

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

54 Diversification of this prophage appears to have been caused by multiple homolog

55 hB, pchC, and pchX genes of their respective prophage are highly conserved but are nonetheless embedd

56 r proteins encoded by the LEE and in cryptic prophage are injected into the host cell cytoplasm by th

57 sequenced S. pyogenes genomes, three unique prophages are a major source of genetic diversity.

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

59 Moreover, the prophages are beneficial for withstanding osmotic, oxida

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

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

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

63 Prophages are phages in lysogeny that are integrated int

64 Prophages are quiescent viruses located in the chromosom

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

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

67 f EPEC effector proteins, encoded in cryptic prophages, are coordinately regulated with the LEE-encod

68 transcriptional regulator (SPY49_1113), and prophage-associated genes encoding a putative integrase

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

70 n between the recombinant sites flanking the prophage, attL and attR.

71 tion to a pan-Salmonella DNA microarray, and prophage-based multiplex PCR.

72 on chromosome structure and function and on prophage behavior in vivo.

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

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

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

76 s in the recA gene and a deletion of the e14 prophage both demonstrably contribute to and partially e

77 when bound to its single site in the CTX Phi prophage, both represses transcription from P(A) and coa

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

79 PhiSpy locates prophages by ranking genomic regions enriched in distinc

80 tely adjacent to the late regions of the pch prophage carrying pchA, pchB, pchC, and a newly identifi

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

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

83 as limited evidence for genes shared between prophage clusters.

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

85 111(DE3) or DM800(DE3), in which a lambdaDE3 prophage containing a T7 RNA polymerase gene under the c

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

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

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

89 scovery and study of genome architecture and prophage content identified numerous biomarkers to asses

90 However, prophage content is highly variable even within lineages

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

92 We find that cryptic prophages contribute significantly to resistance to sub-

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

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

95 Prophage CPS-53 proteins YfdK, YfdO and YfdS enhanced re

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

97 ency locus, neuO, carried by the K1-specific prophage, CUS-3.

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

99 The variation occurs in prophage-dense regions of the genome that lie immediatel

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

101 , neuO, is carried on a putative K1-specific prophage designated CUS-3.

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

103 ersification beyond plasmid gain or loss and prophage diversification, highlighting the importance of

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

105 multiple sites in the chromosome, including prophage DNA, to influence gene expression.

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

107 led that every pneumococcal genome contained prophage DNA.

108 fdS enhanced resistance to oxidative stress, prophages e14, CPS-53 and CP4-57 increased resistance to

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

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

111 ll physiology by precisely deleting all nine prophage elements (166 kbp) using Escherichia coli.

112 idespread family of X. fastidiosa P2-related prophage elements and a podophage distantly related to p

113 erovar Typhimurium LT2 are due to integrated prophage elements and Salmonella genomic island 1 encodi

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

115 has over 90% nucleotide identity to multiple prophage elements of the sequenced X. fastidiosa strains

116 ction of Shiga toxin and in multiple cryptic prophage elements that can encode effector proteins and

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

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

119 ived from two distinct chromosomally encoded prophage elements.

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

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

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

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

124 rtion elements, or W3102 deleted for the rac prophage-encoded kil gene, are partially resistant to BC

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

126 PblA and PblB are prophage-encoded proteins of Streptococcus mitis strain

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

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

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

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

131 In contrast to Xfas53, each of these prophages encodes head and DNA packaging proteins relate

132 other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of ad

133 th presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A.

134 e, providing genetic information on previous prophage encounters.

135 However, in rapidly growing cells the prophage excises and replicates as an episome, allowing

136 To return to the lytic lifestyle, the prophage excises its DNA by a similar Int-mediated react

137 0 that controls MMR via a dynamic process of prophage excision and reintegration in response to growt

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

139 Prophage excision involves a second site-specific recomb

140 Prophage excision occurs through site-specific recombina

141 n biases the phage-encoded integrase towards prophage excision, whereas absence of the RDF favours in

142 The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to enc

143 adfO here), a gene located in a cryptic EHEC prophage, exhibits similarity to adherence and/or coloni

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

145 ptide inhibits replication of the Salmonella prophage Fels-1 while integrated in the chromosome.

146 sites, attP and attB, to form an integrated prophage flanked by attL and attR.

147 sites, attP and attB, to form an integrated prophage flanked by attL and attR.

148 The linear plasmid prophage form of PhiHAP-1 begins with the protelomerase

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

150 e rate of spontaneous mutation compared with prophage-free strains [10(-9) to 10(-10) mutation/genera

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

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

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

154 RNA sequencing provided clear evidence of prophage gene expression.

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

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

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

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

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

160 unterselection of nonsynonymous mutations in prophage genes.

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

162 Furthermore, prophage genomes present a robust phylogeographic patter

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

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

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

166 s are consistent with the idea that the 933W prophage has a relatively low threshold for induction, w

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

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

169 nts of these genomes (excluding incorporated prophage) have revealed that they are approximately 90%

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

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

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

173 Deletion of the cryptic rac prophage in wild-type E. coli increases bicyclomycin res

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

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

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

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

178 tator phenotype, leads to increased lambdoid prophage induction (selectable in vivo expression techno

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

180 933W prophage induction contributes to Stx2 production, and h

181 No such increase in prophage induction is seen in cells expressing alaVGlu t

182 by the lytic repressor was not required for prophage induction to occur.

183 risingly high levels of Xis immediately upon prophage induction when excision rates are maximal.

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

185 le lysogens, and switch to lytic growth upon prophage induction, showing a threshold response in swit

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

187 r that is controlling excision events during prophage induction.

188 ackbone genome of the four isolates, a 42 kb prophage inserted in the chromosomal comK gene showed ev

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

190 The presence of a prophage integrated into the 5' end of mutL correlates w

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

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

193 I proposed a model for integration of lambda prophage into the bacterial chromosome.

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

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

196 romoting efficient induction of the Phi24(B) prophage is proposed.

197 A notable feature of Xfas53 and related prophages is the presence of 220- to 390-nucleotide dege

198 s ability to inhibit the excision of several prophages (lambda, P22, Gifsy-1, Gifsy-2, Fels-1, Fels-2

199 These multiplex PCR assays, based on prophage-like elements and Salmonella genomic island 1,

200 variable regions of DNA were associated with prophage-like elements.

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

202 logues in EPEC or EHEC) coding sequences, 10 prophage-like regions, and 17 genomic islands, including

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

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

205 romosome and the partitioning system confers prophage maintenance.

206 ion of oxidative stress, protein damage, and prophage-mediated cell lysis during irradiation and reco

207 Prophage-mediated viral defence offers an efficient mech

208 We found that ciprofloxacin induces prophage mobilization as well as significant alterations

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

213 Here, we explore the impact of cryptic prophages on cell physiology by precisely deleting all n

214 acteriophage-related sequences, suggesting a prophage origin.

215 Prophages outnumbered lytic phages approximately 2:1 wit

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

217 ific double-strand break causes induction of prophage PBSX and SOS gene expression in only a small su

218 sponse, including induction of the defective prophage PBSX.

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

220 Moreover, prophage Pf4 integrated into the chromosome of Pseudomon

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

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

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

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

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

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

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

228 72% of prophages possessed the virulence genes pblA and/or pblB

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

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

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

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

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

234 o this defence through mechanisms in which a prophage protects the bacterial population from attack b

235 relative abundances of hundreds of predicted prophage proteins.

236 of the BLAST score ratio (BSR) of the phage/prophage proteomes.

237 Therefore, cryptic prophages provide multiple benefits to the host for surv

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

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

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

241 oswarmer cells, as did genes in a degenerate prophage region situated immediately adjacent to the Rcs

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

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

244 ading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity c

245 of single-nucleotide polymorphisms (SNPs) in prophage regions that differentiated the two ECII outbre

246 The repertoire and variation in prophage regions underpins differences in the pathogenes

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

248 ions within individual SVMs, indicating that prophage remnants played important roles in generating p

249 he present study, we discovered that cryptic prophage remnants, originating from phages in the order

250 3 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element enco

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

252 homologous recombination events or possibly prophage replacement.

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

254 Prophages represent a large fraction of prokaryotic geno

255 omK prophage, a single SNP in the tRNA Thr-4 prophage represents the only SNP that differentiates the

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

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

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

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

260 e pair from each 1988 and 2000 had identical prophage sequence; however, there were significant diffe

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

262 r, there were significant differences in the prophage sequences between the 1988 and 2000 isolates.

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

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

265 in an operon which was flanked by potential prophage sequences.

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

267 Excision of prophage SF370.4 and expression of MutL mRNA occur simul

268 Prophage SF370.4 is integrated between the two genes, bl

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

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

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

272 The prophage state of bacteriophage lambda is extremely stab

273 bacterial DNA polymerases in the integrated prophage state.

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

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

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

277 We suggest that pSOG3 is a prophage that has undergone genome degeneration accompan

278 SNPs in prophages that differentiated the outbreak clones of ECI

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

280 propose that LexA coordinates P(A) and P(R) prophage transcription in a gene regulatory circuit.

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

282 2:1 with the most abundant bacteriophage and prophage types being associated with members of the domi

283 Prophages typically integrated in one of five different

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

285 rrent at the time, which postulated that the prophage was not inserted into the continuity of the chr

286 onstructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST s

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

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 The 933W prophage, which carries Shiga toxin genes that enhance p

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

293 1 DNA indicated a lack of integration of the prophage with the host chromosome and a difference in ge

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

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

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

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

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

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

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