scholarly journals Complete DNA Sequence and Detailed Analysis of the Yersinia pestis KIM5 Plasmid Encoding Murine Toxin and Capsular Antigen

1998 ◽  
Vol 66 (12) ◽  
pp. 5731-5742 ◽  
Author(s):  
Luther E. Lindler ◽  
Gregory V. Plano ◽  
Valerie Burland ◽  
George F. Mayhew ◽  
Frederick R. Blattner
Keyword(s):  
Yersinia Pestis ◽  
Dna Sequence ◽  
Virulence Factors ◽  
Acute Onset ◽  
Open Reading Frames ◽  
Mammalian Host ◽  
Virulence Plasmid ◽  
Origin Of Replication ◽  
Putative Origin ◽  
Species Specific

ABSTRACT Yersinia pestis, the causative agent of plague, harbors at least three plasmids necessary for full virulence of the organism, two of which are species specific. One of the Y. pestis-specific plasmids, pMT1, is thought to promote deep tissue invasion, resulting in more acute onset of symptoms and death. We determined the entire nucleotide sequence of Y. pestis KIM5 pMT1 and identified potential open reading frames (ORFs) encoded by the 100,990-bp molecule. Based on codon usage for known yersinial genes, homology with known proteins in the databases, and potential ribosome binding sites, we determined that 115 of the potential ORFs which we considered could encode polypeptides in Y. pestis. Five of these ORFs were genes previously identified as being necessary for production of the classic virulence factors, murine toxin (MT), and the fraction 1 (F1) capsule antigen. The regions of pMT1 encoding MT and F1 were surrounded by remnants of multiple transposition events and bacteriophage, respectively, suggesting horizontal gene transfer of these virulence factors. We identified seven new potential virulence factors that might interact with the mammalian host or flea vector. Forty-three of the remaining 115 putative ORFs did not display any significant homology with proteins in the current databases. Furthermore, DNA sequence analysis allowed the determination of the putative replication and partitioning regions of pMT1. We identified a single 2,450-bp region within pMT1 that could function as the origin of replication, including a RepA-like protein similar to RepFIB, RepHI1B, and P1 and P7 replicons. Plasmid partitioning function was located ca. 36 kb from the putative origin of replication and was most similar to the parABS bacteriophage P1 and P7 system. Y. pestis pMT1 encoded potential genes with a high degree of similarity to a wide variety of organisms, plasmids, and bacteriophage. Accordingly, our analysis of the pMT1 DNA sequence emphasized the mosaic nature of this large bacterial virulence plasmid and provided implications as to its evolution.

scholarly journals Poly-N-Acetylglucosamine Expression by Wild-Type Yersinia pestis Is Maximal at Mammalian, Not Flea, Temperatures

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Pauline Yoong ◽  
Colette Cywes-Bentley ◽  
Gerald B. Pier
Keyword(s):  
Yersinia Pestis ◽  
Congo Red ◽  
Biofilm Formation ◽  
Mammalian Host ◽  
Virulence Plasmid ◽  
Insect Vector ◽  
Wild Type ◽  
Content Type ◽  
Higher Temperature ◽  
Mammalian Infection

ABSTRACTNumerous bacteria, includingYersinia pestis, express the poly-N-acetylglucosamine (PNAG) surface carbohydrate, a major component of biofilms often associated with a specific appearance of colonies on Congo red agar. Biofilm formation and PNAG synthesis byY. pestishave been reported to be maximal at 21 to 28°C or “flea temperatures,” facilitating the regurgitation ofY. pestisinto a mammalian host during feeding, but production is diminished at 37°C and thus presumed to be decreased during mammalian infection. Most studies of PNAG expression and biofilm formation byY. pestishave used a low-virulence derivative of strain KIM, designated KIM6+, that lacks the pCD1 virulence plasmid, and an isogenic mutant without the pigmentation locus, which contains the hemin storage genes that encode PNAG biosynthetic proteins. Using confocal microscopy, fluorescence-activated cell sorter analysis and growth on Congo red agar, we confirmed prior findings regarding PNAG production with the KIM6+ strain. However, we found that fully virulent wild-type (WT) strains KIM and CO92 had maximal PNAG expression at 37°C, with lower PNAG production at 28°C both in broth medium and on Congo red agar plates. Notably, the typical dark colony morphology appearing on Congo red agar was maintained at 28°C, indicating that this phenotype is not associated with PNAG expression in WTY. pestis. Extracts of WT sylvaticY. pestisstrains from the Russian Federation confirmed the maximal expression of PNAG at 37°C. PNAG production by WTY. pestisis maximal at mammalian and not insect vector temperatures, suggesting that this factor may have a role during mammalian infection.IMPORTANCEYersinia pestistransitions from low-temperature residence and replication in insect vectors to higher-temperature replication in mammalian hosts. Prior findings based primarily on an avirulent derivative of WT (wild-type) KIM, named KIM6+, showed that biofilm formation associated with synthesis of poly-N-acetylglucosamine (PNAG) is maximal at 21 to 28°C and decreased at 37°C. Biofilm formation was purported to facilitate the transmission ofY. pestisfrom fleas to mammals while having little importance in mammalian infection. Here we found that for WT strains KIM and CO92, maximal PNAG production occurs at 37°C, indicating that temperature regulation of PNAG production in WTY. pestisis not mimicked by strain KIM6+. Additionally, we found that Congo red binding does not always correlate with PNAG production, despite its widespread use as an indicator of biofilm production. Taken together, the findings show that a role for PNAG in WTY. pestisinfection should not be disregarded and warrants further study.

scholarly journals Isolation of a Minireplicon of the Virulence Plasmid pXO2 of Bacillus anthracis and Characterization of the Plasmid-Encoded RepS Replication Protein

2004 ◽  
Vol 186 (9) ◽  
pp. 2717-2723 ◽  
Author(s):  
Eowyn Tinsley ◽  
Asma Naqvi ◽  
Agathe Bourgogne ◽  
Theresa M. Koehler ◽  
Saleem A. Khan
Keyword(s):  
Bacillus Anthracis ◽  
Replication Initiation ◽  
Open Reading Frame ◽  
Virulence Plasmid ◽  
Origin Of Replication ◽  
Mobility Shift ◽  
Reading Frame ◽  
Amino Terminal ◽  
Central Regions ◽  
Putative Origin

ABSTRACT A minireplicon of plasmid pXO2 of Bacillus anthracis was isolated by molecular cloning in Escherichia coli and shown to replicate in B. anthracis, Bacillus cereus, and Bacillus subtilis. The pXO2 replicon included (i) an open reading frame encoding the putative RepS replication initiation protein and (ii) the putative origin of replication. The RepS protein was expressed as a fusion with the maltose binding protein (MBP) at its amino-terminal end and purified by affinity chromatography. Electrophoretic mobility shift assays showed that the purified MBP-RepS protein bound specifically to a 60-bp region corresponding to the putative origin of replication of pXO2 located immediately downstream of the RepS open reading frame. Competition DNA binding experiments showed that the 5′ and central regions of the putative origin were important for RepS binding. MBP-RepS also bound nonspecifically to single-stranded DNA with a lower affinity.

scholarly journals Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

2004 ◽  
Vol 186 (18) ◽  
pp. 6298-6305 ◽  
Author(s):  
Vladimir L. Motin ◽  
Anca M. Georgescu ◽  
Joseph P. Fitch ◽  
Pauline P. Gu ◽  
David O. Nelson ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Dna Microarrays ◽  
Open Reading Frames ◽  
Mammalian Host ◽  
Global Changes ◽  
Temperature Transition ◽  
Entire Genome ◽  
Regulatory Changes ◽  
Chromosomal Genes ◽  
Reading Frames

ABSTRACT DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca2+. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca2+. In contrast, Ca2+ had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

scholarly journals A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Open Biology ◽  
2015 ◽  
Vol 5 (4) ◽  
pp. 140218 ◽  
Author(s):  
Luis Quintales ◽  
Ignacio Soriano ◽  
Enrique Vázquez ◽  
Mónica Segurado ◽  
Francisco Antequera
Keyword(s):  
Amino Acids ◽  
Protein Composition ◽  
Open Reading Frames ◽  
Yeast Genome ◽  
Relative Distribution ◽  
Periodic Distribution ◽  
Wide Range ◽  
Average Distribution ◽  
Species Specific ◽  
High Degree

Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

DNA sequence heterogeneity within the Epstein–Barr virus family of repeats in the latent origin of replication

Gene ◽  
2001 ◽  
Vol 265 (1-2) ◽  
pp. 165-173 ◽  
Author(s):  
Alberto Fruscalzo ◽  
Giulia Marsili ◽  
Vincenzo Busiello ◽  
Luisa Bertolini ◽  
Domenico Frezza
Keyword(s):  
Dna Sequence ◽  
Epstein Barr Virus ◽  
Origin Of Replication ◽  
Virus Family ◽  
Sequence Heterogeneity ◽  
Barr Virus ◽  
Epstein Barr

scholarly journals Virulence factors and antibiotic resistance in enterococci isolated from food-stuffs

2011 ◽  
Vol 56 (No. 7) ◽  
pp. 352-357 ◽  
Author(s):  
K. Trivedi ◽  
S. Cupakova ◽  
R. Karpiskova
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Diffusion Method ◽  
Haemolytic Activity ◽  
Virulence Determinants ◽  
Disk Diffusion Method ◽  
Specific Pcr ◽  
Virulence Potential ◽  
Enterococcal Species ◽  
Species Specific

A collection of 250 enterococci isolated from various food-stuffs were used to investigate seven virulence determinants and the microbial susceptibility of eight antibiotics. Species-specific PCR revealed the presence of E. faecalis (127 isolates), E. faecium (77 isolates), E. casseliflavus (21 isolates), E. mundtii (19 isolates) and E. durans (six isolates). Multiplex PCR for virulence factors showed that from a total 250 isolates, 221 (88.4%) carried one or more virulence-encoding genes. β-Haemolytic activity was also evident in enterococcal species other than E. faecalis and E. faecium. Species other than E. faecalis and E. faecium isolated from food are also seen to harbour the potential for virulence. Antimicrobial susceptibility testing using the disk diffusion method showed that of the total 250 isolates, 114 (46%) were resistant to cephalothin and 94 (38%) to ofloxacin. Lower antibiotic resistance was seen with ampicillin, chloramphenicol, gentamicin and teicoplanin. None of the isolates was found to be resistant to vancomycin. The results of this study show that food can play an important role in the spread of enterococci with virulence potential through the food chain to the human population.

scholarly journals 1127. Genomic Analysis of Biofilm-Forming Enteroinvasive E. coli Emergent Pathogen

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S337-S338
Author(s):  
Oscar Gomez-Duarte ◽  
Julio Guerra ◽  
Ricky Ko
Keyword(s):  
Virulence Factors ◽  
Dna Sequences ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Coli Strain ◽  
Virulence Plasmid ◽  
E Coli ◽  
Query Coverage

Abstract Background Enteroinvasive Escherichia coli (EIEC) are involved in dysenteric diarrhea among children in low- and middle-income countries. EIEC strains isolated in Colombia, South America were shown to form biofilms and to be invasive in vitro. The O96:H19 serotypes and biofilm formation (BF) are not common phenotypes among EIEC, and the role they may play in diarrhea is at present unknown. The main goal of this study was to identify virulence and BF genes from EIEC genomic data. We hypothesize that EIEC O96:H19 strain 52.1 originated from horizontal transfer of a Shigella-like virulence plasmid into a non-EIEC pathogenic E coli strain. Methods WGS was performed on the BF-EIEC 52.1 strain using NextGen Illumina and Pacific Biosciences (PacBio) platforms. Publically available genomes from other EIEC O96H19 and Shigella genomes previously published were analyzed using online available software and databases including NCBI, BLAST, Mauve, among others. This analysis was tailored to identify virulence factors from the virulence factor database (VFDB). BLASTn was used to determine identity and query coverage of genes encoding the Shigella virulence factors. EIEC and Shigella genomes were analyzed on a multiple genome alignment software (Mauve) to verify results from BLASTn and to determine pseudogenes. Results The genome of EIEC O96:H19 strain 52.1 was 5,193,449 bp in size, containing 5,050 coding DNA sequences (CDSs). O96:H19 strain 52.1 carries three plasmids, the invasion plasmid (pINV) contains all type 3 secretion system (TTSS) and TTSS effectors genes previously described for Shigella and EIEC O96:H19 CFSAN029787 Italian strain. Non-TTSS virulence genes were also identified, including: long polar fimbrial gene (IpfA), enterotoxin (senB), and antibiotic resistance genes. Conclusion The EIEC O96:H19 strain 52.1 genome carries TTSS genes within a virulence plasmid, protein effector genes, and enterotoxin genes known to be associated with EIEC virulence. The EIEC O96:H19 stain 52.1 is an emergent diarrheagenic pathogen likely derived from an E. coli O96:H19 strain that acquired a Shigella-like virulence plasmid by horizontal transfer. Disclosures All authors: No reported disclosures.

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