Nature of the genome of the saprophytic spirochete Spirochaeta aurantia and its ribosomal RNA operons

2004 ◽  
Vol 50 (11) ◽  
pp. 967-971 ◽  
Author(s):  
Richard McLaughlin ◽  
David M Secko ◽  
Catherine J Paul ◽  
Andrew M Kropinski
Keyword(s):  
Ribosomal Rna ◽  
Gel Electrophoresis ◽  
Large Subunit ◽  
Complete Sequence ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pulsed Field ◽  
23S Rrna Gene ◽  
Intergenic Regions

Using restriction endonucleases DraI, AseI, and I-CeuI in conjunction with pulsed-field gel electrophoresis, we have shown that Spirochaeta aurantia M1 possesses a circular 3.98-Mb genome. This is the second largest spirochete chromosome yet analyzed. The observation that the latter enzyme cuts in 3 places suggests the presence of 3 copies of the large subunit (23S) rRNA gene (rrl), which was confirmed by Southern hybridizations. The complete sequence of 2 of the ribosomal RNA operons was determined, revealing that their structure resembled that of the typical member of the bacterial superkingdom: rrs (16S; 1561 bp), tRNA, rrl (23S; 2972 bp), and rrf (5S; 110 bp). The S. aurantia rrs–rrl intergenic regions, as with Treponema denticola, contain genes specifying a 73-nt tRNAAla (anticodon TGC) and a 77-nt tRNAIle (anticodon GAT).Key words: spirochete, pulsed-field gel electrophoresis, ribosomal RNA, operon, Spirochaeta aurantia.

scholarly journals Genotypic Characterization of Clarithromycin-Resistant and -Susceptible Helicobacter pylori Strains from the Same Patient Demonstrates Existence of Two Unrelated Isolates

1998 ◽  
Vol 36 (9) ◽  
pp. 2730-2731 ◽  
Author(s):  
Ge Wang ◽  
Qin Jiang ◽  
Diane E. Taylor
Keyword(s):  
Helicobacter Pylori ◽  
Gel Electrophoresis ◽  
Genomic Dna ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Clarithromycin Resistance ◽  
23S Rrna Gene ◽  
Mode Of Development

Clarithromycin-susceptible and clarithromycin-resistantHelicobacter pylori isolates from the same patient were investigated for the mode of development and mechanism of clarithromycin resistance. The clarithromycin-resistant strain UA1182 harbors homozygous A-to-G mutations at position 2143 in both copies of the 23S rRNA gene and has a phenotype of resistance to clarithromycin and clindamycin but no significant resistance to streptogramin B. Pulsed-field gel electrophoresis patterns of NruI- andNotI-digested genomic DNA from the Clas and Clar isolates demonstrated that they are genetically distinct, suggesting that the development of clarithromycin resistance is not from the mutation of the existing Clas strain but from a completely new strain.

scholarly journals Epidemiological Investigation ofSalmonella Tileneby Pulsed-Field Gel Electrophoresis and Polymerase Chain Reaction

1997 ◽  
Vol 8 (6) ◽  
pp. 318-322 ◽  
Author(s):  
Chandar M Anand ◽  
Kevin Fonseca ◽  
Ken Longmore ◽  
Robert Rennie ◽  
Linda Chui ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Gel Electrophoresis ◽  
Washington State ◽  
Pulsed Field Gel Electrophoresis ◽  
Dna Fingerprint ◽  
Rrna Genes ◽  
23S Rrna ◽  
Chain Reaction ◽  
Pulsed Field ◽  
Polymerase Chain

Pulsed-field gel electrophoresis (PFGE) and DNA fingerprinting by the polymerase chain reaction (PCR) were performed on 11 isolates ofSalmonella tilene. Five strains were from a cluster of human patients, six from sugar gliders and pygmy hedgehogs kept as family pets or from local pet retailers, and one isolate from the first North American case ofS tilenedescribed in Washington State in 1994. The PFGE restriction patterns showed all isolates to be similar. However, PCR using primers to the 16S and 23S rRNA genes ofEscherichia colidemonstrated that the Washington State isolate differed from the rest of the other isolates, which were all similar based upon their DNA fingerprint. This study indicates that reliance on one technique alone may be insufficient to show nuances between strains that are, in many respects, closely related.

Genome size ofEperythrozoon suisand hybridization with 16S rRNA gene

2000 ◽  
Vol 46 (11) ◽  
pp. 1082-1086 ◽  
Author(s):  
Joanne B Messick ◽  
Geoffrey Smith ◽  
Linda Berent ◽  
Sandra Cooper
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Size ◽  
Gel Electrophoresis ◽  
Restriction Enzymes ◽  
Strand Break ◽  
Pulsed Field Gel Electrophoresis ◽  
Rrna Gene ◽  
Pulsed Field ◽  
Full Length Genome

The genome size of Eperythrozoon suis, an unculturable haemotropic mycoplasma, was estimated using pulsed-field gel electrophoresis (PFGE). Gamma irradiation was used to introduce one (on the average) double-strand break in the E. suis Illinois chromosome. Restriction enzymes that cut infrequently were also used to analyze genome size. The size estimate for the full-length genome was 745 kilobases (kb), whereas the size estimates based on the summation of restriction fragments ranged from 730 to 770 kb. The 16S rRNA gene was located on the 120-kb MluI fragment, 128-kb NruI fragment, 25-kb SacII fragment, and 217-kb SalI fragment by Southern blotting.Key words: Eperythrozoon suis, 16S rRNA, Mycoplasma pneumoniae group, pulsed-field gel electrophoresis, genome size.

scholarly journals Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

2015 ◽  
Vol 82 (1) ◽  
pp. 384-393 ◽  
Author(s):  
Kristin M. Schill ◽  
Yun Wang ◽  
Robert R. Butler ◽  
Jean-François Pombert ◽  
N. Rukma Reddy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
High Throughput Sequencing ◽  
Pulsed Field Gel Electrophoresis ◽  
Rrna Gene ◽  
Snp Analysis ◽  
Whole Genome ◽  
Clostridium Sporogenes ◽  
Content Type ◽  
Pulsed Field

ABSTRACTClostridium sporogenesPA 3679 is a nonpathogenic, nontoxic model organism for proteolyticClostridium botulinumused in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates ofC. sporogenesPA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. AllC. sporogenesPA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolyticC. botulinumstrains, with clade I forming a distinct cluster with otherC. sporogenesnon-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession numberAGAH00000000.1) than clade II isolates were. The genomic referenceC. sporogenesPA 3679 (NCTC8594) genome and clade IC. sporogenesisolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use ofC. sporogenesPA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization ofC. sporogenesPA 3679 are of critical importance.

The photosynthetic endosymbiont in cryptomonad cells produces both chloroplast and cytoplasmic-type ribosomes

1994 ◽  
Vol 107 (2) ◽  
pp. 649-657
Author(s):  
G.I. McFadden ◽  
P.R. Gilson ◽  
S.E. Douglas
Keyword(s):  
In Situ Hybridization ◽  
Gel Electrophoresis ◽  
Small Volume ◽  
Pulsed Field Gel Electrophoresis ◽  
Rrna Gene ◽  
Pulsed Field ◽  
Host Cytoplasm ◽  
Cytoplasmic Type ◽  
Host Nucleus

Cryptomonad algae contain a photosynthetic, eukaryotic endosymbiont. The endosymbiont is much reduced but retains a small nucleus. DNA from this endosymbiont nucleus encodes rRNAs, and it is presumed that these rRNAs are incorporated into ribosomes. Surrounding the endosymbiont nucleus is a small volume of cytoplasm proposed to be the vestigial cytoplasm of the endosymbiont. If this compartment is indeed the endosymbiont's cytoplasm, it would be expected to contain ribosomes with components encoded by the endosymbiont nucleus. In this paper, we used in situ hybridization to localize rRNAs encoded by the endosymbiont nucleus of the cryptomonad alga, Cryptomonas phi. Transcripts of the endosymbiont rRNA gene were observed within the endosymbiont nucleus, and in the compartment thought to represent the endosymbiont's cytoplasm. These results indicate that the endosymbiont produces its own set of cytoplasmic translation machinery. We also localized transcripts of the host nucleus rRNA gene. These transcripts were found in the nucleolus of the host nucleus, and throughout the host cytoplasm, but never in the endosymbiont compartment. Our rRNA localizations indicate that the cryptomonad cell produces two different of sets of cytoplasmic-type ribosomes in two separate subcellular compartments. The results suggest that there is no exchange of rRNAs between these compartments. We also used the probe specific for the endosymbiont rRNA gene to identify chromosomes from the endosymbiont nucleus in pulsed field gel electrophoresis. Like other cryptomonads, the endosymbiont nucleus of Cryptomonas phi contains three small chromosomes.

Sign in / Sign up

Export Citation Format

Share Document