Extended Bibliography: |
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Ref #: |
25447 |
Author(s): |
Conrads,G.;Citron,D.M.;Tyrrell,K.L.;Horz,H.P.;Goldstein,E.J. |
Journal: |
Int J Syst Evol Microbiol |
Title: |
16S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas |
Volume: |
55 |
Page(s): |
607-13 |
Year: |
2005 |
Keyword(s): |
GENBANK/AB034799
GENBANK/AB035460
GENBANK/AF208290
GENBANK/AY546472
GENBANK/AY546473
GENBANK/AY546474
GENBANK/AY546475
GENBANK/AY546476
GENBANK/AY546477
GENBANK/AY546478
GENBANK/AY546479
GENBANK/AY546480
GENBANK/AY546481
GENBANK/AY546482
GENBANK/AY546483
GENBANK/AY546484
GENBANK/AY546485
GENBANK/AY546486
GENBANK/AY546487
GENBANK/AY546488
GENBANK/AY546489
GENBANK/AY546490
Bacterial Typing Techniques
DNA, Ribosomal Spacer/*analysis
Genes, rRNA
Humans
Molecular Sequence Data
*Phylogeny
Porphyromonas/*classification/genetics
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
Sequence Analysis, DNA
Species Specificity
|
Remarks: |
The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260(T) divided the sequences into two clusters, of which one was alpha-fucosidase-positive (like the type strain) while the other was alpha-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of 'Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called 'Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of alpha-fucosidase-negative P. asaccharolytica strains as a new species should also be considered. |
URL: |
15774632 |
|
Ref #: |
69143 |
Author(s): |
Morse,R.;O'Hanlon,K.;Collins,M.D. |
Journal: |
Int J Syst Evol Microbiol |
Title: |
Phylogenetic, amino acid content and indel analyses of the beta subunit of DNA-dependent RNA polymerase of gram-positive and gram-negative bacteria |
Volume: |
52 |
Page(s): |
1477-84 |
Year: |
2002 |
Keyword(s): |
GENBANK/AE001944
GENBANK/Y16466
GENBANK/Y16467
GENBANK/Y16468
GENBANK/Y16469
GENBANK/Y16470
GENBANK/Y16471
GENBANK/Y16472
GENBANK/Y19223
Amino Acid Sequence
Amino Acids/analysis
Base Composition
Base Sequence
DNA Transposable Elements
DNA, Bacterial/chemistry/genetics
DNA-Directed RNA Polymerases/*chemistry/*genetics
Drug Resistance, Bacterial/genetics
Genes, Bacterial
Gram-Negative Bacteria/classification/*enzymology/*genetics
Gram-Positive Bacteria/classification/*enzymology/*genetics
Molecular Sequence Data
Phylogeny
Protein Subunits
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Rifampin/pharmacology
Sequence Deletion
Sequence Homology, Amino Acid
|
Remarks: |
In this study, we have sequenced the rpoB gene, encoding the beta subunit of DNA-dependent RNA polymerase, from a selection of gram-positive and gram-negative bacteria. The presence of insertions and deletions (indels) in the beta subunit separate the gram-positive and gram-negative bacteria from each other and support the division of the gram-positive organisms into two clades based on DNA G+C content. Phylogenetic and amino acid content analyses further separate the clostridia from bacilli, leuconostocs, listeriae and relatives, forming an early branch after the common gram-positive ancestor. The occurrence in the beta subunit of Asn-Ala at positions 471-472 in Porphyromonas cangingivalis and Asn at position 372 in Weissella paramesenteroides are postulated to be the cause of the natural rifampicin resistance of these species. |
URL: |
12361249 |
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