scholarly journals Complete Sequence of the Enterocin Q-Encoding Plasmid pCIZ2 from the Multiple Bacteriocin Producer Enterococcus faecium L50 and Genetic Characterization of Enterocin Q Production and Immunity

2006 ◽  
Vol 72 (10) ◽  
pp. 6653-6666 ◽  
Author(s):  
Raquel Criado ◽  
Dzung B. Diep ◽  
Ågot Aakra ◽  
Jorge Gutiérrez ◽  
Ingolf F. Nes ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Genetic Determinants ◽  
Significant Similarity ◽  
Minimum Requirement ◽  
Initiator Protein ◽  
Bacteriocin Producer ◽  
Origin Region ◽  
Transfer Origin

ABSTRACT The locations of the genetic determinants for enterocin L50 (EntL50A and EntL50B), enterocin Q (EntQ), and enterocin P (EntP) in the multiple bacteriocin producer Enterococcus faecium strain L50 were determined. These bacteriocin genes occur at different locations; entL50AB (encoding EntL50A and EntL50B) are on the 50-kb plasmid pCIZ1, entqA (encoding EntQ) is on the 7.4-kb plasmid pCIZ2, and entP (encoding EntP) is on the chromosome. The complete nucleotide sequence of pCIZ2 was determined to be 7,383 bp long and contains 10 putative open reading frames (ORFs) organized in three distinct regions. The first region contains three ORFs: entqA preceded by two divergently oriented genes, entqB and entqC. EntqB shows high levels of similarity to bacterial ATP-binding cassette (ABC) transporters, while EntqC displays no significant similarity to any known protein. The second region encompasses four ORFs (orf4 to orf7), and ORF4 and ORF5 display high levels of similarity to mobilization proteins from E. faecium and Enterococcus faecalis. In addition, features resembling a transfer origin region (oriT) were found in the promoter area of orf4. The third region contains three ORFs (orf8 to orf10), and ORF8 and ORF9 exhibit similarity to the replication initiator protein RepE from E. faecalis and to RepB proteins, respectively. To clarify the minimum requirement for EntQ synthesis, we subcloned and heterologously expressed a 2,371-bp fragment from pCIZ2 that encompasses only the entqA, entqB, and entqC genes in Lactobacillus sakei, and we demonstrated that this fragment is sufficient for EntQ production. Moreover, we also obtained experimental results indicating that EntqB is involved in ABC transporter-mediated EntQ secretion, while EntqC confers immunity to this bacteriocin.

scholarly journals The Genes Coding for Enterocin EJ97 Production by Enterococcus faecalis EJ97 Are Located on a Conjugative Plasmid

2003 ◽  
Vol 69 (3) ◽  
pp. 1633-1641 ◽  
Author(s):  
Marina Sánchez-Hidalgo ◽  
Mercedes Maqueda ◽  
Antonio Gálvez ◽  
Hikmate Abriouel ◽  
Eva Valdivia ◽  
...  
Keyword(s):  
Amino Acid ◽  
Enterococcus Faecalis ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Leader Peptide ◽  
Genetic Determinants ◽  
Significant Similarity ◽  
New Class ◽  
Strong Homology

ABSTRACT Enterococcus faecalis EJ97 produces a cationic bacteriocin (enterocin EJ97) of low molecular mass (5,327.7 Da). The complete amino acid sequence of enterocin EJ97 was elucidated after automated microsequencing of oligopeptides generated by endoproteinase GluC digestion and cyanogen bromide treatment. Transfer of the 60-kb conjugative plasmid pEJ97 from the bacteriocinogenic strain E. faecalis EJ97 to E. faecalis OG1X conferred bacteriocin production and resistance on the recipient. The genetic determinants of enterocin EJ97 were located in an 11.3-kb EcoRI-BglII DNA fragment of pEJ97. This region was cloned and sequenced. It contains the ej97A structural gene plus three open reading frames (ORFs) (ej97B, ej97C, and ej97D) and three putative ORFs transcribed in the opposite direction (orfA, orfB, and orfC). The gene ej97A translated as a 44-amino-acid residue mature protein lacking a leader peptide with no homology to other bacteriocins described so far. The product of ej97B (Ej97B) shows strong homology in its C-terminal domain to the superfamily of bacterial ATP-binding cassette transporters. The products of ej97C (Ej97C) and ej97D (Ej97D) could be proteins with 71 and 64 residues, respectively, of unknown functions and with no significant similarity to known proteins. There are two additional ORFs (ORF1 and ORF6) flanking the ej97 module, which have been identified as a transposon-like structure (tnp). ORF1 shows similarities to transposase of the Lactococcus lactis element ISS1 and is up to 50% identical to IS1216. This is flanked by two 18-bp inverted repeats (IRs) that are almost identical to those of ISS1 and IS1216. ORF6 (resEJ97) shows strong homology to the resolvase of plasmid pAM373 and up to 40 to 50% homology with the recombinase of several multiresistant plasmids and transposons from Staphylococcus aureus and E. faecalis. These data suggest that EJ97 could represent a new class of bacteriocins with a novel secretion mechanism and that the whole structure could be a composite transposon. Furthermore, two additional gene clusters were found: one cluster is probably related to the region responsible for the replication of plasmid pEJ97, and the second cluster is related to the sex pheromone response. These regions showed a high homology to the corresponding regions of the conjugative plasmids pAM373, pPD1, and pAD1 of E. faecalis, suggesting that they have a common origin.

scholarly journals Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

2013 ◽  
Vol 57 (8) ◽  
pp. 3775-3782 ◽  
Author(s):  
Jianhui Xiong ◽  
David C. Alexander ◽  
Jennifer H. Ma ◽  
Maxime Déraspe ◽  
Donald E. Low ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Carbapenem Resistance ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Content Type ◽  
Conserved Sequence ◽  
Carbapenem Resistant ◽  
Class 1 ◽  
Usage Analysis ◽  
Type 3

ABSTRACTPseudomonas aeruginosa96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 ofPseudomonas fluorescensSBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. TheblaIMP-9-carrying integron containedaacA4→blaIMP-9→aacA4, flanked upstream by Tn21 tnpMRAand downstream by a completetnioperon of Tn402and amermodule, named Tn6016. The second integron carriedaacA4→catB8a→blaOXA-10and was flanked by Tn1403-liketnpRAand asul1-type 3′ conserved sequence (3′-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and twopiloperons. The replication and maintenance systems exhibit similarity to a genomic island ofRalstonia solanacearumGM1000. Codon usage analysis suggests the recent acquisition ofblaIMP-9. The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.

scholarly journals Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Alena Karaseva ◽  
Anna Tsapieva ◽  
Justin Pachebat ◽  
Alexander Suvorov
Keyword(s):  
Genome Sequence ◽  
Russian Federation ◽  
Enterococcus Faecium ◽  
Draft Genome ◽  
Bacteriocin Production ◽  
Draft Genome Sequence ◽  
Bacteriocin Producer ◽  
Probiotic Preparation ◽  
The Russian Federation ◽  
Faecium Strain

We report here the draft genome sequence of the bacteriocin producer Enterococcus faecium strain L-3, isolated from a probiotic preparation, Laminolact, which is widely used in the Russian Federation. The draft genome sequence is composed of 74 contigs for a total of 2,643,001 bp, with 2,646 coding genes. Five clusters for bacteriocin production were found.

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

Molecular analysis of the replication region of the pCIZ2 plasmid from the multiple bacteriocin producer strain Enterococcus faecium L50

Plasmid ◽  
2008 ◽  
Vol 60 (3) ◽  
pp. 181-189 ◽  
Author(s):  
R. Criado ◽  
J. Gutiérrez ◽  
A. Budin-Verneuil ◽  
P.E. Hernández ◽  
A. Hartke ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Enterococcus Faecium ◽  
Producer Strain ◽  
Bacteriocin Producer ◽  
Replication Region

An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

2021 ◽  
Author(s):  
Juan F Cornejo-Franco ◽  
Francisco Flores ◽  
Dimitre Mollov ◽  
diego fernando quito-avila
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Genomic Features ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

scholarly journals Isolation and Characterization of Two Cryptic Plasmids in the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain ENI-11

1999 ◽  
Vol 181 (11) ◽  
pp. 3375-3381 ◽  
Author(s):  
Akira Yamagata ◽  
Junichi Kato ◽  
Ryuichi Hirota ◽  
Akio Kuroda ◽  
Tsukasa Ikeda ◽  
...  
Keyword(s):  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Nucleotide Sequences ◽  
Open Reading Frames ◽  
Homologous Region ◽  
Significant Similarity ◽  
Physical Maps ◽  
Isolation And Characterization ◽  
Ammonia Oxidizing Bacterium ◽  
Cryptic Plasmids

ABSTRACT Two plasmids were discovered in the ammonia-oxidizing bacteriumNitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designated pAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. The complete nucleotide sequences of pAYS and pAYL were determined, and their physical maps were constructed. There existed two major open reading frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significant similarity to any known protein sequences was detected with the predicted product of ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp. The overall identity was 98% between the two nucleotide sequences. Interestingly, HHR-homologous sequences were also detected in the genomes of ENI-11 and the plasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential for plasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the first plasmids found in the ammonia-oxidizing autotrophic bacteria.

scholarly journals Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

scholarly journals Genetic Determinants of Reutericyclin Biosynthesis in Lactobacillus reuteri

2015 ◽  
Vol 81 (6) ◽  
pp. 2032-2041 ◽  
Author(s):  
Xiaoxi B. Lin ◽  
Christopher T. Lohans ◽  
Rebbeca Duar ◽  
Jinshui Zheng ◽  
John C. Vederas ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Genomic Island ◽  
Lactobacillus Reuteri ◽  
Acyl Carrier Protein ◽  
Open Reading Frames ◽  
Protein Domain ◽  
Regulatory Proteins ◽  
Tetramic Acid ◽  
Genetic Determinants ◽  
Content Type

ABSTRACTReutericyclin is a unique antimicrobial tetramic acid produced by some strains ofLactobacillus reuteri. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producingL. reuteristrains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded byrtcNis composed of a condensation domain, an adenylation domain likely specific ford-leucine, and a thiolation domain.rtcKcodes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products ofrtcA,rtcB, andrtcCare homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion ofrtcNorrtcABCinL. reuteriTMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negativeL. reuteristrain TMW1.656ΔrtcN, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteriaStreptococcus mutansandLactobacillus plantarum, suggesting that the genes in these organisms and those inL. reuterishare an evolutionary origin.

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