| Extended Bibliography: |
Show bibliography
| Ref #: |
95515 |
| Author(s): |
Zakharova,N.;Paster,B.J.;Wesley,I.;Dewhirst,F.E.;Berg,D.E.;Severinov,K.V. |
| Journal: |
J Bacteriol |
| Title: |
Fused and overlapping rpoB and rpoC genes in Helicobacters, Campylobacters, and related bacteria |
| Volume: |
181 |
| Page(s): |
3857-9 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AF136503
GENBANK/AF136504
GENBANK/AF136505
GENBANK/AF136506
GENBANK/AF136507
GENBANK/AF136508
GENBANK/AF136509
GENBANK/AF136510
GENBANK/AF136511
GENBANK/AF136512
GENBANK/AF136513
GENBANK/AF136514
GENBANK/AF136515
GENBANK/AF136516
GENBANK/AF136517
GENBANK/AF136518
Amino Acid Sequence
Base Sequence
Campylobacter/classification/*genetics/isolation & purification
DNA-Directed RNA Polymerases/chemistry/*genetics
*Evolution, Molecular
Gastric Mucosa/microbiology
Genes, Bacterial
Genes, Overlapping
Gram-Negative Bacteria/genetics
Helicobacter/classification/*genetics/isolation & purification
Humans
Molecular Sequence Data
*Phylogeny
Sequence Alignment
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Wolinella/genetics
|
| Remarks: |
The genes coding for the beta (rpoB) and beta' (rpoC) subunits of RNA polymerase are fused in the gastric pathogen Helicobacter pylori but separate in other taxonomic groups. To better understand how the unique fused structure evolved, we determined DNA sequences at and around the rpoB-rpoC junction in 10 gastric and nongastric species of Helicobacter and in members of the related genera Wolinella, Arcobacter, Sulfurospirillum, and Campylobacter. We found the fusion to be specific to Helicobacter and Wolinella genera; rpoB and rpoC overlap in the other genera. The fusion may have arisen by a frameshift mutation at the site of rpoB and rpoC overlap. Loss of good Shine-Dalgarno sequences might then have fixed the fusion in the Helicobacteraceae, even if fusion itself did not confer a selective advantage. |
| URL: |
10368167 |
|
| Ref #: |
20722 |
| Author(s): |
Wesley,I.V.;Schroeder-Tucker,L.;Baetz,A.L.;Dewhirst,F.E.;Paster,B.J. |
| Journal: |
J Clin Microbiol |
| Title: |
Arcobacter-specific and Arcobacter butzleri-specific 16S rRNA-based DNA probes |
| Volume: |
33 |
| Page(s): |
1691-8 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/L04312
GENBANK/L04313
GENBANK/L04314
GENBANK/L04315
GENBANK/L04316
GENBANK/L04317
GENBANK/L04318
GENBANK/L04319
GENBANK/L04320
GENBANK/L04321
GENBANK/L04322
GENBANK/L06974
GENBANK/L06978
GENBANK/L14625
GENBANK/L14627
GENBANK/L14628
GENBANK/L14630
GENBANK/L14631
GENBANK/M35048
GENBANK/M65010
GENBANK/M88157
GENBANK/M88159
GENBANK/U25805
Animals
Base Sequence
Campylobacter/classification/*genetics/pathogenicity
DNA Probes/*genetics
Enteritis/microbiology
Female
Gram-Negative Bacteria/classification/*genetics/pathogenicity
Gram-Negative Bacterial Infections/microbiology/veterinary
Helicobacter/classification/genetics
Horse Diseases/microbiology
Horses
Humans
Male
Molecular Sequence Data
Phylogeny
Pregnancy
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
Species Specificity
Swine
Swine Diseases/microbiology
|
| Remarks: |
The genus Arcobacter encompasses gram-negative, aerotolerant, spiral-shaped bacteria formerly designated Campylobacter cryaerophila. Two genus-specific 16S rRNA-based oligonucleotide DNA probes (23-mer and 27-mer) were developed. The probes hybridized with strains of Arcobacter butzleri (n = 58), Arcobacter cryaerophilus (n = 19), and Arcobacter skirrowii (n = 17). The probes did not cross-react with any of the reference strains of Campylobacter, Helicobacter, including "Flexispira rappini," or Wolinella. The 27-mer hybridized with 61 Arcobacter spp. field isolates originating from late-term aborted porcine (n = 54) and equine (n = 2) fetuses and humans with enteritis (n = 5). The species of Arcobacter isolates (n = 56) recovered from aborted livestock fetuses were determined by ribotyping and were as follows: A. cryaerophilus group 1A (11 of 56; 20%), A. cryaerophilus group 1B (37 of 56; 66%), A. butzleri (5 of 56; 9%), and unknown (3 of 56; 5%). The five human field strains were identified as A. butzleri. A species-specific DNA probe (24-mer) for A. butzleri was also developed since there is evidence that this organism may be a human pathogen. This probe hybridized with previously characterized strains of A. butzleri (n = 58), with 10 field strains identified as A. butzleri by ribotyping and with 2 strains having an indeterminate ribotype. The A. butzleri-specific probe did not cross-react with strains of A. skirrowii (n = 17) and A. cryaerophilus (n = 19). |
| URL: |
7545177 |
|
| Ref #: |
50052 |
| Author(s): |
Dewhirst,F.E.;Shen,Z.;Scimeca,M.S.;Stokes,L.N.;Boumenna,T.;Chen,T.;Paster,B.J.;Fox,J.G. |
| Journal: |
J Bacteriol |
| Title: |
Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics |
| Volume: |
187 |
| Page(s): |
6106-18 |
| Year: |
2005 |
| Keyword(s): |
Base Sequence
DNA Primers
Helicobacter/*classification/*genetics
Phylogeny
Polymerase Chain Reaction
RNA, Bacterial/*genetics
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
|
| Remarks: |
Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum. |
| URL: |
16109952 |
|
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