scholarly journals A Novel Putative Enterococcal Pathogenicity Island Linked to the esp Virulence Gene of Enterococcus faecium and Associated with Epidemicity

2004 ◽  
Vol 186 (3) ◽  
pp. 672-682 ◽  
Author(s):  
Helen Leavis ◽  
Janetta Top ◽  
Nathan Shankar ◽  
Katrine Borgen ◽  
Marc Bonten ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Virulence Gene ◽  
Surface Protein ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Regulation Of Transcription ◽  
Genetic Element ◽  
Virulence Regulation ◽  
Flanking Regions ◽  
Reading Frames

ABSTRACT Enterococcus faecalis harbors a virulence-associated surface protein encoded by the esp gene. This gene has been shown to be part of a 150-kb putative pathogenicity island. A gene similar to esp has recently been found in Enterococcus faecium isolates recovered from hospitalized patients. In the present study we analyzed the polymorphism in the esp gene of E. faecium, and we investigated the association of esp with neighboring chromosomal genes. The esp gene showed considerable sequence heterogeneity in the regions encoding the nonrepeat N- and C-terminal domains of the Esp protein as well as differences in the number of repeats. DNA sequencing of chromosomal regions flanking the esp gene of E. faecium revealed seven open reading frames, representing putative genes implicated in virulence, regulation of transcription, and antibiotic resistance. These flanking regions were invariably associated with the presence or absence of the esp gene in E. faecium, indicating that esp in E. faecium is part of a distinct genetic element. Because of the presence of virulence genes in this gene cluster, the lower G+C content relative to that of the genome, and the presence of esp in E. faecium isolates associated with nosocomial outbreaks and clinically documented infections, we conclude that this genetic element constitutes a putative pathogenicity island, the first one described in E. faecium. Except for the presence of esp and araC, this pathogenicity island is completely different from the esp-containing pathogenicity island previously disclosed in E. faecalis.

scholarly journals The SPI-3 Pathogenicity Island ofSalmonella enterica

1999 ◽  
Vol 181 (3) ◽  
pp. 998-1004 ◽  
Author(s):  
Anne-Béatrice Blanc-Potard ◽  
Felix Solomon ◽  
Jayson Kayser ◽  
Eduardo A. Groisman
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
Regulatory Protein ◽  
Virulence Gene ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Serovar Typhimurium ◽  
Multistep Process ◽  
The Right ◽  
Reading Frames

ABSTRACT Pathogenicity islands are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. We have determined the molecular genetic structure of SPI-3, a 17-kb pathogenicity island located at the selC tRNA locus of Salmonella enterica serovar Typhimurium. The G+C content of SPI-3 (47.5%) differs from that of the Salmonella genome (52%), consistent with the notion that these sequences have been horizontally acquired. SPI-3 harbors 10 open reading frames organized in six transcriptional units, which include the previously describedmgtCB operon encoding the macrophage survival protein MgtC and the Mg2+ transporter MgtB. Among the newly identified open reading frames, one exhibits sequence similarity to the ToxR regulatory protein of Vibrio cholerae and one is similar to the AIDA-I adhesin of enteropathogenic Escherichia coli. The distribution of SPI-3 sequences varies among the salmonellae: the right end of the island, which harbors the virulence genemgtC, is present in all eight subspecies ofSalmonella; however, a four-gene cluster at the center of SPI-3 is found in only some of the subspecies and is bracketed by remnants of insertion sequences, suggesting a multistep process in the evolution of SPI-3 sequences.

scholarly journals The Bacteroides fragilis Pathogenicity Island Is Contained in a Putative Novel Conjugative Transposon

2004 ◽  
Vol 186 (18) ◽  
pp. 6077-6092 ◽  
Author(s):  
Augusto A. Franco
Keyword(s):  
Blot Hybridization ◽  
Bacteroides Fragilis ◽  
Antibiotic Resistance Genes ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Genetic Element ◽  
Conjugative Transposon ◽  
Conjugative Transposons ◽  
New Family ◽  
Reading Frames

ABSTRACT The genetic element flanking the Bacteroides fragilis pathogenicity island (BfPAI) in enterotoxigenic B. fragilis (ETBF) strain 86-5443-2-2 and a related genetic element in NCTC 9343 were characterized. The results suggested that these genetic elements are members of a new family of conjugative transposons (CTns) not described previously. These putative CTns, designated CTn86 and CTn9343 for ETBF 86-5443-2-2 and NCTC 9343, respectively, differ from previously described Bacteroides species CTns in a number of ways. These new transposons do not carry tetQ, and the excision from the chromosome to form a circular intermediate is not regulated by tetracycline; they are predicted to differ in their mechanism of transposition; and their sequences have very limited similarity with CTnDOT or other described CTns. CTn9343 is 64,229 bp in length, contains 61 potential open reading frames, and both ends contain IS21 transposases. Colony blot hybridization, PCR, and sequence analysis indicated that CTn86 has the same structure as CTn9343 except that CTn86 lacks a ∼7-kb region containing truncated integrase (int2) and rteA genes and it contains the BfPAI integrated between the mob region and the bfmC gene. If these putative CTns were to be demonstrated to be transmissible, this would suggest that the bft gene can be transferred from ETBF to nontoxigenic B. fragilis strains by a mechanism similar to that for the spread of antibiotic resistance genes.

scholarly journals Precise Excision of the Large Pathogenicity Island, SPI7, in Salmonella enterica Serovar Typhi

2004 ◽  
Vol 186 (10) ◽  
pp. 3202-3213 ◽  
Author(s):  
Susan M. Bueno ◽  
Carlos A. Santiviago ◽  
Alejandro A. Murillo ◽  
Juan A. Fuentes ◽  
A. Nicole Trombert ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Pathogenicity Island ◽  
Open Reading Frames ◽  
Epithelial Cell Line ◽  
Direct Repeats ◽  
Salmonella Enterica Serovar Typhi ◽  
Precise Excision ◽  
Join Point ◽  
Reading Frames ◽  
Vi Antigen

ABSTRACT The large pathogenicity island (SPI7) of Salmonella enterica serovar Typhi is a 133,477-bp segment of DNA flanked by two 52-bp direct repeats overlapping the pheU (phenylalanyl-tRNA) gene, contains 151 potential open reading frames, and includes the viaB operon involved in the synthesis of Vi antigen. Some clinical isolates of S. enterica serovar Typhi are missing the entire SPI7, due to its precise excision; these strains have lost the ability to produce Vi antigen, are resistant to phage Vi-II, and invade a human epithelial cell line more rapidly. Excision of SPI7 occurs spontaneously in a clinical isolate of S. enterica serovar Typhi when it is grown in the laboratory, leaves an intact copy of the pheU gene at its novel join point, and results in the same three phenotypic consequences. SPI7 is an unstable genetic element, probably an intermediate in the pathway of lateral transfer of such pathogenicity islands among enteric gram-negative bacteria.

scholarly journals Tranosema rostrale ichnovirus repeat element genes display distinct transcriptional patterns in caterpillar and wasp hosts

2009 ◽  
Vol 90 (6) ◽  
pp. 1505-1514 ◽  
Author(s):  
Asieh Rasoolizadeh ◽  
Catherine Béliveau ◽  
Don Stewart ◽  
Conrad Cloutier ◽  
Michel Cusson
Keyword(s):  
Fat Body ◽  
Gene Dosage ◽  
Choristoneura Fumiferana ◽  
Gene Families ◽  
Transcript Abundance ◽  
Repeat Element ◽  
Open Reading Frames ◽  
Regulation Of Transcription ◽  
Lepidopteran Host ◽  
Reading Frames

The endoparasitic wasp Tranosema rostrale transmits an ichnovirus to its lepidopteran host, Choristoneura fumiferana, during parasitization. As shown for other ichnoviruses, the segmented dsDNA genome of the T. rostrale ichnovirus (TrIV) features several multi-gene families, including the repeat element (rep) family, whose products display no known similarity to non-ichnovirus proteins, except for a homologue encoded by the genome of the Helicoverpa armigera granulovirus; their functions remain unknown. This study applied linear regression of efficiency analysis to real-time PCR quantification of transcript abundance for all 17 TrIV rep open reading frames (ORFs) in parasitized and virus-injected C. fumiferana larvae, as well as in T. rostrale ovaries and head–thorax complexes. Although transcripts were detected for most rep ORFs in infected caterpillars, two of them clearly outnumbered the others in whole larvae, with a tendency for levels to drop over time after infection. The genome segments bearing the three most highly expressed rep genes in parasitized caterpillars were present in higher proportions than other rep-bearing genome segments in TrIV DNA, suggesting a possible role for gene dosage in the regulation of transcription level. TrIV rep genes also showed important differences in the relative abundance of their transcripts in specific tissues (cuticular epithelium, the fat body, haemocytes and the midgut), implying tissue-specific roles for individual members of this gene family. Significantly, no rep transcripts were detected in T. rostrale head–thorax complexes, whereas some were abundant in ovaries. There, the transcription pattern was completely different from that observed in infected caterpillars, suggesting that some rep genes have wasp-specific functions.

scholarly journals Characterization of a Genetic Element Carrying the Macrolide Efflux Gene mef(A) in Streptococcus pneumoniae

2000 ◽  
Vol 44 (9) ◽  
pp. 2585-2587 ◽  
Author(s):  
Maria Santagati ◽  
Francesco Iannelli ◽  
Marco R. Oggioni ◽  
Stefania Stefani ◽  
Gianni Pozzi
Keyword(s):  
Streptococcus Pneumoniae ◽  
Resistance Gene ◽  
Clinical Isolate ◽  
Open Reading Frames ◽  
Genetic Element ◽  
Reading Frames

ABSTRACT The mef(A) gene from a clinical isolate ofStreptococcus pneumoniae exhibiting the M-type resistance to macrolides was found to be part of the 7,244-bp chromosomal element Tn1207.1, which contained 8 open reading frames.orf2 encodes a resolvase/invertase, and orf5 is a homolog of the macrolide-streptogramin B resistance genemsr(SA).

scholarly journals Genetic Identification of the Bacteriocins Produced by Enterococcus faecium IT62 and Evidence that Bacteriocin 32 Is Identical to Enterocin IT

2009 ◽  
Vol 53 (5) ◽  
pp. 1907-1911 ◽  
Author(s):  
Esther Izquierdo ◽  
Yimin Cai ◽  
Eric Marchioni ◽  
Saïd Ennahar
Keyword(s):  
Amino Acids ◽  
Genetic Analysis ◽  
Structural Gene ◽  
Enterococcus Faecium ◽  
Open Reading Frames ◽  
Genetic Identification ◽  
Leader Peptide ◽  
Sequencing Analysis ◽  
The One ◽  
Reading Frames

ABSTRACT Enterococcus faecium IT62, a strain isolated from ryegrass in Japan, produces three bacteriocins (enterocins L50A, L50B, and IT) that have been previously purified and the primary structures of which have been determined by amino acid sequencing (E. Izquierdo, A. Bednarczyk, C. Schaeffer, Y. Cai, E. Marchioni, A. Van Dorsselaer, and S. Ennahar, Antimicrob. Agents Chemother., 52:1917-1923, 2008). Genetic analysis showed that the bacteriocins of E. faecium IT62 are plasmid encoded, but with the structural genes specifying enterocin L50A and enterocin L50B being carried by a plasmid (pTAB1) that is separate from the one (pTIT1) carrying the structural gene of enterocin IT. Sequencing analysis of a 1,475-bp region from pTAB1 identified two consecutive open reading frames corresponding, with the exception of 2 bp, to the genes entL50A and entL50B, encoding EntL50A and EntL50B, respectively. Both bacteriocins are synthesized without N-terminal leader sequences. Genetic analysis of a sequenced 1,380-bp pTIT1 fragment showed that the genes entIT and entIM, encoding enterocin IT and its immunity protein, respectively, were both found in E. faecium VRE200 for bacteriocin 32. Enterocin IT, a 6,390-Da peptide made up of 54 amino acids, has been previously shown to be identical to the C-terminal part of bacteriocin 32, a 7,998-Da bacteriocin produced by E. faecium VRE200 whose structure was deduced from its structural gene (T. Inoue, H. Tomita, and Y. Ike, Antimicrob. Agents Chemother., 50:1202-1212, 2006). By combining the biochemical and genetic data on enterocin IT, it was concluded that bacteriocin 32 is in fact identical to enterocin IT, both being encoded by the same plasmid-borne gene, and that the N-terminal leader peptide for this bacteriocin is 35 amino acids long and not 19 amino acids long as previously reported.

scholarly journals Purification and Molecular Characterization of a Tripeptidase (PepT) from Lactobacillus helveticus

2000 ◽  
Vol 66 (2) ◽  
pp. 794-800 ◽  
Author(s):  
Kirsi Savijoki ◽  
Airi Palva
Keyword(s):  
Maximum Activity ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Transcription Start ◽  
Sequence Analyses ◽  
Repeat Structure ◽  
Flanking Regions ◽  
Dairy Starter ◽  
Reading Frames

ABSTRACT A tripeptidase (PepT) from a thermophilic dairy starter strain ofLactobacillus helveticus was purified by four chromatographic steps. PepT appeared to be a trimeric metallopeptidase with a molecular mass of 150 kDa. PepT exhibited maximum activity against hydrophobic tripeptides, with the highest activity for Met-Gly-Gly (Km , 2.6 mM;V max, 80.2 μmol · min−1 · μg−1). Some of the hydrophobic dipeptides were slowly hydrolyzed, distinguishing theLactobacillus PepT from its counterpart in mesophilicLactococcus lactis. No activity against tetrapeptides or amino acid p-nitroanilide derivatives was observed. ThepepT gene and its flanking regions were isolated by PCR and sequenced by cyclic sequencing. The sequence analyses revealed open reading frames (ORFs) 816 bp (ORF1) and 1,239 bp (ORF2) long. ORF2 encoded a 47-kDa PepT protein which exhibited 53% identity with the PepT from L. lactis. The mRNA analyses indicated thatpepT conforms a novel operon structure with an ORF1 located upstream. Several putative −35/−10 regions preceded the operon, but only one transcription start site located downstream of the first putative −10 region was identified. An inverted repeat structure with ΔG of −64.8 kJ/mol was found downstream of the PepT-encoding region.

scholarly journals The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

2010 ◽  
Vol 192 (20) ◽  
pp. 5289-5303 ◽  
Author(s):  
C. Peter Wolk ◽  
Sigal Lechno-Yossef ◽  
Karin M. Jäger
Keyword(s):  
Transposable Elements ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Direct Repeats ◽  
Homologous Sequences ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Flanking Regions ◽  
Adaptive Role ◽  
Reading Frames

ABSTRACT Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/ ) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.

scholarly journals Specificities of Eleven Different DNA Methyltransferases of Helicobacter pylori Strain 26695

2001 ◽  
Vol 183 (2) ◽  
pp. 443-450 ◽  
Author(s):  
Jolanta Vitkute ◽  
Kornelijus Stankevicius ◽  
Giedre Tamulaitiene ◽  
Zita Maneliene ◽  
Albertas Timinskas ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Dna Methyltransferases ◽  
Open Reading Frames ◽  
Restriction Endonucleases ◽  
Regulation Of Transcription ◽  
Cellular Processes ◽  
Genes Encoding ◽  
Bacterial Genetic ◽  
Restriction Modification ◽  
Reading Frames

ABSTRACT Methyltransferases (MTases) of procaryotes affect general cellular processes such as mismatch repair, regulation of transcription, replication, and transposition, and in some cases may be essential for viability. As components of restriction-modification systems, they contribute to bacterial genetic diversity. The genome ofHelicobacter pylori strain 26695 contains 25 open reading frames encoding putative DNA MTases. To assess which MTase genes are active, strain 26695 genomic DNA was tested for cleavage by 147 restriction endonucleases; 24 were found that did not cleave this DNA. The specificities of 11 expressed MTases and the genes encoding them were identified from this restriction data, combined with the known sensitivities of restriction endonucleases to specific DNA modification, homology searches, gene cloning and genomic mapping of the methylated bases m4C, m5C, and m6A.

scholarly journals Identification and Characterization of a Gene Cluster for Synthesis of the Polyketide Antibiotic 2,4-Diacetylphloroglucinol from Pseudomonas fluorescens Q2-87

1999 ◽  
Vol 181 (10) ◽  
pp. 3155-3163 ◽  
Author(s):  
M. Gita Bangera ◽  
Linda S. Thomashow
Keyword(s):  
Genomic Dna ◽  
Plant Pathogens ◽  
Polyketide Synthase ◽  
Open Reading Frames ◽  
Fungal Plant Pathogens ◽  
Repressor Proteins ◽  
Flanking Regions ◽  
Identification And Characterization ◽  
Reading Frames

The polyketide metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) is produced by many strains of fluorescent Pseudomonas spp. with biocontrol activity against soilborne fungal plant pathogens. Genes required for 2,4-DAPG synthesis by P. fluorescensQ2-87 are encoded by a 6.5-kb fragment of genomic DNA that can transfer production of 2,4-DAPG to 2,4-DAPG-nonproducing recipientPseudomonas strains. In this study the nucleotide sequence was determined for the 6.5-kb fragment and flanking regions of genomic DNA from strain Q2-87. Six open reading frames were identified, four of which (phlACBD) comprise an operon that includes a set of three genes (phlACB) conserved between eubacteria and archaebacteria and a gene (phlD) encoding a polyketide synthase with homology to chalcone and stilbene synthases from plants. The biosynthetic operon is flanked on either side by phlEand phlF, which code respectively for putative efflux and regulatory (repressor) proteins. Expression in Escherichia coli of phlA, phlC, phlB, andphlD, individually or in combination, identified a novel polyketide biosynthetic pathway in which PhlD is responsible for the production of monoacetylphloroglucinol (MAPG). PhlA, PhlC, and PhlB are necessary to convert MAPG to 2,4-DAPG, and they also may function in the synthesis of MAPG.

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