scholarly journals YAPI, a New Yersinia pseudotuberculosis Pathogenicity Island

2004 ◽  
Vol 72 (8) ◽  
pp. 4784-4790 ◽  
Author(s):  
François Collyn ◽  
Alain Billault ◽  
Chantal Mullet ◽  
Michel Simonet ◽  
Michaël Marceau
Keyword(s):  
Gene Cluster ◽  
Yersinia Pseudotuberculosis ◽  
Low Frequency ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Modification System ◽  
Restriction Modification System ◽  
Type Iv ◽  
Genetic Mosaic ◽  
Characteristic Features

ABSTRACT Pathogenicity islands (PAIs) are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. In the Yersinia pseudotuberculosis 32777 chromosome, we characterized a 98-kb segment that has all of the characteristic features of a PAI, including insertion in a (phenylalanine) tRNA gene, the presence of a bacteriophage-like integrase-encoding gene, and direct repeats at the integration sites. The G+C content of the segment ranges from 31 to 60%, reflecting a genetic mosaic: this is consistent with the notion that the sequences were horizontally acquired. The PAI, termed YAPI (for Yersinia adhesion pathogenicity island), carries 95 open reading frames and includes (i) the previously described pil operon, encoding a type IV pilus that contributes to pathogenicity (F. Collyn et al., Infect. Immun. 70:6196-6205, 2002); (ii) a block of genes potentially involved in general metabolism; (iii) a gene cluster for a restriction-modification system; and (iv) a large number of mobile genetic elements. Furthermore, the PAI can excise itself from the chromosome at low frequency and in a precise manner, and deletion does not result in a significant decrease of bacterial virulence compared to inactivation of the fimbrial gene cluster alone. The prevalence and size of the PAI vary from one Y. pseudotuberculosis strain to another, and it can be found integrated into either of the two phe tRNA loci present on the species' chromosome. YAPI was not detected in the genome of the genetically closely related species Y. pestis, whereas a homologous PAI is harbored by the Y. enterocolitica chromosome.

Molecular evolution of Vibrio pathogenicity island-2 (VPI-2): mosaic structure among Vibrio cholerae and Vibrio mimicus natural isolates

Microbiology ◽  
2005 ◽  
Vol 151 (1) ◽  
pp. 311-322 ◽  
Author(s):  
William S. Jermyn ◽  
E. Fidelma Boyd
Keyword(s):  
Vibrio Cholerae ◽  
Gene Cluster ◽  
Gene Tree ◽  
Pathogenicity Island ◽  
Housekeeping Gene ◽  
Gene Trees ◽  
Modification System ◽  
Restriction Modification System ◽  
Vibrio Mimicus ◽  
Natural Isolates

Vibrio cholerae is a Gram-negative rod that inhabits the aquatic environment and is the aetiological agent of cholera, a disease that is endemic in much of Southern Asia. The 57·3 kb Vibrio pathogenicity island-2 (VPI-2) is confined predominantly to toxigenic V. cholerae O1 and O139 serogroup isolates and encodes 52 ORFs (VC1758 to VC1809), which include homologues of an integrase (VC1758), a restriction modification system, a sialic acid metabolism gene cluster (VC1773–VC1783), a neuraminidase (VC1784) and a gene cluster that shows homology to Mu phage. In this study, a 14·1 kb region of VPI-2 comprising ORFs VC1773 to VC1787 was identified by PCR and Southern blot analyses in all 17 Vibrio mimicus isolates examined. The VPI-2 region in V. mimicus was inserted adjacent to a serine tRNA similar to VPI-2 in V. cholerae. In 11 of the 17 V. mimicus isolates examined, an additional 5·3 kb region encoding VC1758 and VC1804 to VC1809 was present adjacent to VC1787. The evolutionary history of VPI-2 was reconstructed by comparative analysis of the nanH (VC1784) gene tree with the species gene tree, deduced from the housekeeping gene malate dehydrogenase (mdh), among V. cholerae and V. mimicus isolates. Both gene trees showed an overall congruence; on both gene trees V. cholerae O1 and O139 serogroup isolates clustered together, whereas non-O1/non-O139 serogroup isolates formed separate divergent branches with similar clustering of strains within the branches. One exception was noted: on the mdh gene tree, V. mimicus sequences formed a distinct divergent lineage from V. cholerae sequences; however, on the nanH gene tree, V. mimicus clustered with V. cholerae non-O1/non-O139 isolates, suggesting horizontal transfer of this region between these species.

scholarly journals Yersinia pseudotuberculosis Harbors a Type IV Pilus Gene Cluster That Contributes to Pathogenicity

2002 ◽  
Vol 70 (11) ◽  
pp. 6196-6205 ◽  
Author(s):  
François Collyn ◽  
Marie-Annick Léty ◽  
Shamila Nair ◽  
Vincent Escuyer ◽  
Amena Ben Younes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Yersinia Pseudotuberculosis ◽  
Open Reading Frames ◽  
Host Cells ◽  
Gram Negative Bacteria ◽  
Type Iv Pilus ◽  
Chromosomal Locus ◽  
Bacterial Surface ◽  
Type Iv ◽  
Reading Frames

ABSTRACT Fimbriae have been shown to play an essential role in the adhesion of pathogenic gram-negative bacteria to host cells. In the enteroinvasive bacterium Yersinia pseudotuberculosis, we characterized a previously unknown 11-kb chromosomal locus involved in the synthesis of type IV pili. The locus consists of 11 open reading frames forming a polycistronic unit and encoding putative Pil proteins, PilLMNOPQRSUVW. When introduced into Escherichia coli, the Y. pseudotuberculosis operon reconstituted bundles of filaments at a pole on the bacterial surface, demonstrating that the pil locus was functional in a heterogenous genetic background. Environmental factors regulated transcription of the Y. pseudotuberculosis operon; in particular, temperature, osmolarity, and oxygen tension were critical cues. Deletion of the type IV pilus gene cluster was associated with a reduction of Y. pseudotuberculosis pathogenicity for mice infected orally. Forty-one percent of Y. pseudotuberculosis strains isolated from human or animal sources harbored the type IV pilus locus. Therefore, the pil locus of Y. pseudotuberculosis might constitute an “adaptation island,” permitting the microorganism to colonize a vast reservoir.

scholarly journals Complete Genome Sequence of Brevibacterium linens SMQ-1335

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Alessandra G. de Melo ◽  
Simon J. Labrie ◽  
Jeannot Dumaresq ◽  
Richard J. Roberts ◽  
Denise M. Tremblay ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Open Reading Frames ◽  
Type I ◽  
Industrial Strain ◽  
Modification System ◽  
Brevibacterium Linens ◽  
Restriction Modification System ◽  
New Type ◽  
Restriction Modification ◽  
Reading Frames

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

scholarly journals Prevalence of the “High-Pathogenicity Island” of Yersinia Species among Escherichia coliStrains That Are Pathogenic to Humans

1998 ◽  
Vol 66 (2) ◽  
pp. 480-485 ◽  
Author(s):  
S. Schubert ◽  
A. Rakin ◽  
H. Karch ◽  
E. Carniel ◽  
J. Heesemann
Keyword(s):  
Gene Cluster ◽  
Yersinia Pseudotuberculosis ◽  
Pathogenicity Island ◽  
Uptake System ◽  
Highly Pathogenic ◽  
E Coli ◽  
Yersinia Species ◽  
The Family ◽  
High Pathogenicity ◽  
Dna Sequence Comparison

ABSTRACT The fyuA-irp gene cluster contributes to the virulence of highly pathogenic Yersinia (Yersinia pestis,Yersinia pseudotuberculosis, and Yersinia enterocolitica 1B). The cluster encodes an iron uptake system mediated by the siderophore yersiniabactin and reveals features of a pathogenicity island. Two evolutionary lineages of this “high pathogenicity island” (HPI) can be distinguished on the basis of DNA sequence comparison: a Y. pestis group and a Y. enterocolitica group. In this study we demonstrate that the HPI of the Y. pestis evolutionary group is disseminated among species of the family Enterobacteriaceae which are pathogenic to humans. It prevails in enteroaggregativeEscherichia coli and in E. coli blood culture isolates (93 and 80%, respectively), but is rarely found in enteropathogenic E. coli, enteroinvasive E. coli, and enterotoxigenic E. coli isolates. In contrast, the HPI was absent from enterohemorrhagic E. coli, Shigella, and Salmonella entericastrains investigated. Polypeptides encoded by the fyuA,irp1, and irp2 genes located on the HPI could be detected in E. coli strains pathogenic to humans. However, these E. coli strains showed a reduced sensitivity to the bacteriocin pesticin, whose uptake is mediated by the FyuA receptor. Escherichia strains do not possess thehms gene locus thought to be a part of the HPI of Y. pestis. Deletions of the fyuA-irp gene cluster affecting solely the fyuA part of the HPI were identified in 3% of the E. coli strains tested. These results suggest horizontal transfer of the HPI between Y. pestis and some pathogenic E. coli strains.

scholarly journals Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A

2021 ◽  
pp. 71-77
Author(s):  
Yulia V. Diubo ◽  
Artur E. Akhremchuk ◽  
Leonid N. Valentovich ◽  
Yevgeny A. Nikolaichik
Keyword(s):  
Methylation Profile ◽  
Type I ◽  
Pectobacterium Carotovorum ◽  
Modification System ◽  
Restriction Modification System ◽  
Type Iv ◽  
Oxford Nanopore ◽  
Dna Methylation Profile ◽  
Restriction Modification ◽  
Restriction Modification Systems

The methylation profile of Pectobacterium carotovorum 2A genome was studied using the Oxford Nanopore sequencing technology. The specificity of the methylase subunits of the three restriction-modification systems of this strain was determined. Analysis of homologous systems showed the uniqueness of the type I restriction-modification system and the type IV restriction system specific to methylated DNA of this strain. The work confirms the applicability of Oxford Nanopore technology to the analysis of bacterial DNA modifications and is also the first example of such an analysis for Pectobacterium spp.

scholarly journals Cloning and Characterization of the Lactococcal Plasmid-Encoded Type II Restriction/Modification System, LlaDII

1998 ◽  
Vol 64 (7) ◽  
pp. 2424-2431 ◽  
Author(s):  
Annette Madsen ◽  
Jytte Josephsen
Keyword(s):  
Shuttle Vector ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Modification System ◽  
Restriction Modification System ◽  
Stem Loop Structure ◽  
Methylase Gene ◽  
Sequences Alignment ◽  
Restriction Modification

ABSTRACT The LlaDII restriction/modification (R/M) system was found on the naturally occurring 8.9-kb plasmid pHW393 inLactococcus lactis subsp. cremoris W39. A 2.4-kb PstI-EcoRI fragment inserted into theEscherichia coli-L. lactis shuttle vector pCI3340 conferred to L. lactis LM2301 and L. lactis SMQ86 resistance against representatives of the three most common lactococcal phage species: 936, P335, and c2. The LlaDII endonuclease was partially purified and found to recognize and cleave the sequence 5′-GC↓NGC-3′, where the arrow indicates the cleavage site. It is thus an isoschizomer of the commercially available restriction endonuclease Fnu4HI. Sequencing of the 2.4-kbPstI-EcoRI fragment revealed two open reading frames arranged tandemly and separated by a 105-bp intergenic region. The endonuclease gene of 543 bp preceded the methylase gene of 954 bp. The deduced amino acid sequence of the LlaDII R/M system showed high homology to that of its only sequenced isoschizomer,Bsp6I from Bacillus sp. strain RFL6, with 41% identity between the endonucleases and 60% identity between the methylases. The genetic organizations of the LlaDII andBsp6I R/M systems are identical. Both methylases have two recognition sites (5′-GCGGC-3′ and 5′-GCCGC-3′) forming a putative stem-loop structure spanning part of the presumed −35 sequence and part of the intervening region between the −35 and −10 sequences. Alignment of the LlaDII andBsp6I methylases with other m5C methylases showed that the protein primary structures possessed the same organization.

scholarly journals Genetic Characterization of a New Type IV-A Pilus Gene Cluster Found in Both Classical and El Tor Biotypes ofVibrio cholerae

1999 ◽  
Vol 67 (3) ◽  
pp. 1393-1404 ◽  
Author(s):  
Karla Jean Fullner ◽  
John J. Mekalanos
Keyword(s):  
Gene Cluster ◽  
Mutational Analysis ◽  
Rapid Identification ◽  
Genome Project ◽  
Open Reading Frames ◽  
Type Iv ◽  
New Type ◽  
K 12 ◽  
El Tor

ABSTRACT The Vibrio cholerae genome contains a 5.4-kbpil gene cluster that resembles the Aeromonas hydrophila tap gene cluster and other type IV-A pilus assembly operons. The region consists of five complete open reading frames designated pilABCD and yacE, based on the nomenclature of related genes from Pseudomonas aeruginosaand Escherichia coli K-12. This cluster is present in both classical and El Tor biotypes, and the pilA andpilD genes are 100% conserved. The pilA gene encodes a putative type IV pilus subunit. However, deletion ofpilA had no effect on either colonization of infant mice or adherence to HEp-2 cells, demonstrating that pilA does not encode the primary subunit of a pilus essential for these processes. The pilD gene product is similar to other type IV prepilin peptidases, proteins that process type IV signal sequences. Mutational analysis of the pilD gene showed that pilD is essential for secretion of cholera toxin and hemagglutinin-protease, mannose-sensitive hemagglutination (MSHA), production of toxin-coregulated pili, and colonization of infant mice. Defects in these functions are likely due to the lack of processing of N termini of four Eps secretion proteins, four proteins of the MSHA cluster, and TcpB, all of which contain type IV-A leader sequences. SomepilD mutants also showed reduced adherence to HEp-2 cells, but this defect could not be complemented in trans, indicating that the defect may not be directly due to a loss ofpilD. Taken together, these data demonstrate the effectiveness of the V. cholerae genome project for rapid identification and characterization of potential virulence factors.

scholarly journals Characterization of the Endogenous Plasmid fromPseudomonas alcaligenes NCIB 9867: DNA Sequence and Mechanism of Transfer

2000 ◽  
Vol 182 (1) ◽  
pp. 81-90 ◽  
Author(s):  
Stephen M. Kwong ◽  
Chew Chieng Yeo ◽  
Antonius Suwanto ◽  
Chit Laa Poh
Keyword(s):  
Transfer Functions ◽  
Plasmid Stability ◽  
Gene Cassette ◽  
Transformation Process ◽  
Open Reading Frames ◽  
Cell Contact ◽  
Modification System ◽  
Restriction Modification System ◽  
Partial Stability ◽  
Reading Frames

ABSTRACT The endogenous plasmid pRA2 from Pseudomonas alcaligenes NCIB 9867 was determined to have 32,743 bp with a G+C content of 59.8%. Sequence analysis predicted a total of 29 open reading frames, with approximately half of them contributing towards the functions of plasmid replication, mobilization, and stability. ThePac25I restriction-modification system and two mobile elements, Tn5563 and IS1633, were physically localized. An additional eight open reading frames with unknown functions were also detected. pRA2 was genetically tagged with the ΩStrr/Spcr gene cassette by homologous recombination. Intrastrain transfer of pRA2-encoded genetic markers between isogenic mutants of P. alcaligenes NCIB 9867 were observed at high frequencies (2.4 × 10−4 per donor). This transfer was determined to be mediated by a natural transformation process that required cell-cell contact and was completely sensitive to DNase I (1 mg/ml). Efficient transformation was also observed when pRA2 DNA was applied directly onto the cells, while transformation with foreign plasmid DNAs was not observed. pRA2 could be conjugally transferred into Pseudomonas putida RA713 and KT2440 recipients only when plasmid RK2/RP4 transfer functions were provided in trans. Plasmid stability analysis demonstrated that pRA2 could be stably maintained in its original host, P. alcaligenes NCIB 9867, as well as in P. putida RA713 after 100 generations of nonselective growth. Disruption of the pRA2pac25I restriction endonuclease gene did not alter plasmid stability, while the pRA2 minireplicon exhibited only partial stability. This indicates that other pRA2-encoded determinants could have significant roles in influencing plasmid stability.

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