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At least 865 records · Page 48Linked to original sources
PubMed2001

Complementarity of the 16S rRNA penultimate stem with sequences downstream of the AUG destabilizes the plastid mRNAs.

Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein accumulation without a significant affect on mRNA stability. The objective of this study was to test whether enhancing the complementarity of plastid mRNAs downstream of the AUG (downstream sequence or DS) with the 16S rRNA penultimate stem (anti-DS or ADS region) enhances protein accumulation. The test system was the tobacco plastid rRNA operon promoter fused with the E.coli phage T7 gene 10 (T7g10) 5'-untranslated region (5'-UTR) and DB region. Translation efficiency was tested by measuring neomycin phosphotransferase (NPTII) accumulation in tobacco chloroplasts. We report here that the phage T7g10 5'-UTR and DB region promotes accumulation of NPTII up to approximately 16% of total soluble leaf protein (TSP). Enhanced mRNA stability and an improved NPTII yield ( approximately 23% of TSP) was obtained from a construct in which the T7g10 5'-UTR was linked with the NPTII coding region via a NheI site. However, replacing the T7g10 DB region with the plastid DS sequence reduced NPTII and mRNA levels to 0.16 and 28%, respectively. Reduced NPTII accumulation is in part due to accelerated mRNA turnover.

Bacteriophage T7↗
PubMed1995

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes.

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).

Animals↗
PubMed1989

[The complete nucleotide sequence of Brassica napus chloroplast 16S rRNA gene].

The complete nucleotide sequence of a 16S rRNA gene and its flanking sequence from Brassica napus chloroplast has been determined. The 16S rRNA gene is 1491 bp in length, having 98.5%, and 96.1% homology with those of tobacco and maize chloroplast, respectively. The large stem and loop structure can be constructed from the sequence surrounding the 5' and 3' ends of the 16S rRNA gene. The stem is about half shorter than that of tobacco, due to a 79 bp deletion in Brassica napus chloroplast.

Base Sequence↗
PubMed1993

Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria.

We report the amplification of bacterial genes from uninoculated surface and subsurface sediments by the polymerase chain reaction (PCR). PCR amplification of indigenous bacterial 16S ribosomal DNA genes was unsuccessful when subsurface sediment containing approximately 10(7) cells.g-1 was added directly to a PCR mixture. However, when 10 mg of sediment was inoculated with approximately 10(5) cells of Pseudomonas putida G7, the nahAc naphthalene dioxygenase gene characteristic of the P. putida G7 NAH7 plasmid was detected by PCR amplification. Southern blotting of the PCR amplification product improved sensitivity to 10(3) to 10(4) cells from samples inoculated with P. putida G7, but controls with no sediment added showed that the PCR was partially inhibited by the sediments. Lysozyme-sodium dodecyl sulfate-freeze-thaw DNA extraction was combined with gel electrophoretic partial purification in the presence of polyvinylpyrrolidone to render DNA from indigenous bacteria in surface or subsurface sediment samples amplifiable by PCR using eubacterial 16S ribosomal DNA primers. The nahAc gene could also be amplified from indigenous bacteria by using nahAc-specific primers when PCR conditions were modified by increasing Taq and primer concentrations. Restriction digests of the nahAc amplification products from surface and subsurface sediments revealed polymorphism relative to P. putida G7. The procedures for DNA extraction, purification, and PCR amplification described here demonstrate that the PCR is a potentially useful tool in studies of function- and taxon-specific DNA from indigenous microbial communities in sediment and groundwater environments.

Base Sequence↗
PubMed2004

The bacterial catalase from filarial DNA preparations derives from common pseudomonad contaminants and not from Wolbachia endosymbionts.

Wolbachia are obligatory endosymbionts in many species of filarial nematodes. Certain bacterial molecules induce antibody responses in mammalian hosts infected with filariae, while others activate inflammatory responses that contribute to pathology. These findings, coupled with antibiotic studies demonstrating the dependence of filarial embryogenesis on the presence of Wolbachia, have intensified research on Wolbachia-nematode interactions, and the effects of Wolbachia molecules on the mammalian immune system. By amplification and sequencing of 16S rDNA and catalase sequences, we show that filarial DNA samples prepared from nematodes collected under typical conditions are frequently contaminated with Pseudomonas DNA. Analysis of a published DNA fragment containing a catalase attributed to the Wolbachia of Onchocerca volvulus showed it to be most like Pseudomonas, both in terms of sequence similarity and genomic organization. Additionally, there was no obvious catalase in either of two available Wolbachia genome sequences. Contamination of filarial DNA with bacterial sequences other than Wolbachia can complicate studies of the role of these symbionts in filarial biology.

Animals↗
PubMed2001

A sequence variant of Staphylococcus hominis with a high prevalence of oxacillin and fluoroquinolone resistance.

A newly identified subspecies of Staphylococcus hominis, S. hominis subsp. novobiosepticus, was found to be the cause of several invasive infections at a hospital in New Jersey. This subspecies differs from classical S. hominis, now S. hominis subsp. hominis, by the phenotypic characteristics of novobiocin resistance and the inability to ferment trehalose. DNA sequences of segments of 16S rRNA, DNA gyrase (gyrA), and DNA topoisomerase IV (grlA) genes were determined for the type strains of the 2 subspecies, and for 34 S. hominis clinical isolates. The 16S rRNA sequences of the type strains differed at 3 positions over 410 bp; the grlA sequences differed at 6 positions over 119 bp. These sequence differences define S. hominis subsp. novobiosepticus and S. hominis subsp. hominis "sequevars." Of 34 S. hominis clinical isolates, 31 were S. hominis subsp. novobiosepticus sequevars, 28 of which were resistant to both oxacillin and ciprofloxacin. The clinical microbiology laboratory, using a MicroScan system, identified 7 of the 31S. hominis subsp. novobiosepticus sequevars as S. hominis subsp. hominis on the basis of phenotypic characteristics. Three S. hominis subsp. hominis sequevars were all identified phenotypically as S. hominis subsp. hominis and were oxacillin- and ciprofloxacin-susceptible. Although the precise relationship between the S. hominis sequevars and their phenotypic subspecies remains to be determined, our results indicate that antibiotic-resistant clinical isolates of S. hominis belong almost exclusively to the S. hominis subsp. novobiosepticus sequevar.

Anti-Infective Agents↗
PubMed2001

Classification of a Brevundimonas strain detectable after PCR with a Helicobacter-specific primer pair.

In a study for the isolation of new Helicobacter strains, biopsy samples were taken from the gastric mucosa of dogs and subjected to PCR amplification using a Helicobacter-specific primer pair (H276f and H676r, directed to the 16S rDNA) to identify members of this genus in the specimens. From one Helicobacter positive sample, a bacterial strain was isolated which displayed a characteristic band after PCR amplification with the Helicobacter-specific primer pair. The isolate designated H2/98-FUNDUS was motile, oxidase-, catalase- and aminopeptidase-positive and grew only under microaerophilic conditions at 37 degrees C. The bacterium was classified by a polyphasic approach, including analysis of the isoprenoid quinones, fatty acids, polar lipids and partial 16S rDNA sequence. Analysis of the 16S rDNA sequence (1003 bases) indicated that the strain H2/98-FUNDUS is a member of the genus Brevundimonas and most closely related to Brevundimonas aurantiaca DSM 4731T (99.5% sequence similarity). Isolate H2/98-FUNDUS contained a predominant ubiquinone Q-10 and a fatty acid profile with the major compounds C18:1 and C16:0. In the polar lipid extract, phosphatidylglycerol, six unknown phospholipids, one unknown phosphoglycolipid, two unknown glycolipids and two unknown aminolipids were detected. All these results indicate that H2/98-FUNDUS represents a new member of the genus Brevundimonas which gives a positive signal upon PCR employing the Helicobacter-specific primer pair.

Base Sequence↗
PubMed2003

Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.

The taxonomic position of a chlorophenol-degrading bacterium, strain S37T, was investigated. The 16S rDNA sequence indicated that this strain belongs to the genus Sphingopyxis, exhibiting high sequence similarity to the 16S rDNA sequences of Sphingomonas alaskensis LMG 18877T (98.8%), Sphingopyxis macrogoltabida LMG 17324T (98.2%), Sphingopyxis terrae IFO 15098T (95%) and Sphingomonas adhaesiva GIFU 11458T (92%). These strains (except Sphingopyxis terrae IFO 15098T, which was not investigated) and the novel isolate accumulated polyhydroxyalkanoates consisting of 3-hydroxybutyric acid and 3-hydroxyvaleric acid from glucose as carbon source. The G + C content of the DNA of strain S37T was 65.5 mol%. The major cellular fatty acids of this strain were octadecenoic acid (18 : 1omega7c), heptadecenoic acid (17 : 1omega6c) and hexadecanoic acid (16 : 0). The results of DNA-DNA hybridization experiments and its physiological characteristics clearly distinguished the novel isolate from all known Sphingopyxis species and indicated that the strain represents a novel Sphingopyxis species. Therefore, the species Sphingopyxis chilensis sp. nov. is proposed, with strain S37T (=LMG 20986T =DSM 14889T) as the type strain. The transfer of Sphingomonas alaskensis to the genus Sphingopyxis as Sphingopyxis alaskensis comb. nov. is also proposed.

Alphaproteobacteria↗
PubMed2004

Novel mass spectrometry-based tool for genotypic identification of mycobacteria.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for the identification of mycobacteria. Full-length 16S rDNA reference sequences of 12 type strains of Mycobacterium spp. frequently isolated from clinical specimens were determined by PCR, cloning, and sequencing. For MALDI-TOF MS-based comparative sequence analysis, mycobacterial 16S rDNA signature sequences ( approximately 500 bp) of the 12 type strains and 24 clinical isolates were PCR amplified using RNA promoter-tagged forward primers. T7 RNA polymerase-mediated transcription of forward strands in the presence of 5-methyl ribo-CTP maximized mass differences of fragments generated by base-specific cleavage. In vitro transcripts were subsequently treated with RNase T1, resulting in G-specific cleavage. Sample analysis by MALDI-TOF MS showed a specific mass signal pattern for each of the 12 type strains, allowing unambiguous identification. All 24 clinical isolates were identified unequivocally by comparing their detected mass signal pattern to the reference sequence-derived in silico pattern of the type strains and to the in silico mass patterns of published 16S rDNA sequences. A 16S rDNA microheterogeneity of the Mycobacterium xenopi type strain (DSM 43995) was detected by MALDI-TOF MS and later confirmed by Sanger dideoxy sequencing. In conclusion, analysis of 16S rDNA amplicons by MS after base-specific cleavage of RNA transcripts allowed fast and reliable identification of the Mycobacterium tuberculosis complex and ubiquitous mycobacteria (mycobacteria other than tuberculosis). The technology delivers an open platform for high-throughput microbial identification on the basis of any specific genotypic marker region.

Genotype↗
PubMed2000

Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes.

The nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. However, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. Experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tidal creek for 24 or 72 h. The organisms colonizing these surfaces were examined by using a cultivation-independent approach, amplified ribosomal DNA restriction analysis. The goals of this study were to assess the diversity of bacterial colonists involved in early succession on a variety of surfaces and to determine the phylogenetic affiliations of the most common early colonists. Substantial differences in the representation of different cloned ribosomal DNA sequences were found when the 24- and 72-h incubations were compared, indicating that some new organisms were recruited and some other organisms were lost. Phylogenetic analyses of the most common sequences recovered showed that the colonists were related to organisms known to inhabit surfaces or particles in marine systems. A total of 22 of the 26 clones sequenced were affiliated with the Roseobacter subgroup of the alpha subdivision of the division Proteobacteria (alpha-Proteobacteria), and most of these clones were recovered at a high frequency from all surfaces after 24 or 72 h of incubation. Two clones were affiliated with the Alteromonas group of the gamma-Proteobacteria and appeared to be involved only in the very early stages of colonization (within the first 24 h). A comparison of the colonization patterns on the test surfaces indicated that the early bacterial community succession rate and/or direction may be influenced by surface physicochemical properties. However, organisms belonging to the Roseobacter subgroup are ubiquitous and rapid colonizers of surfaces in coastal environments.

Alphaproteobacteria↗
PubMed2002

Bacteremia due to Moraxella atlantae in a cancer patient.

A gram-negative alkaline phosphatase- and pyrrolidone peptidase-positive rod-shaped bacterium (CCUG 45702) was isolated from two aerobic blood cultures from a female cancer patient. No identification could be reached using phenotypic techniques. Amplification of the tRNA intergenic spacers revealed fragments with lengths of 116, 133, and 270 bp, but no such pattern was present in our reference library. Sequencing of the 16S rRNA gene revealed its identity as Moraxella atlantae, a species isolated only rarely and published only once as causing infection. In retrospect, the phenotypic characteristics fit the identification as M. atlantae (formerly known as CDC group M-3). Comparative 16S rRNA sequence analysis indicates that M. atlantae, M. lincolnii, and M. osloensis might constitute three separate genera within the MORAXELLACEAE: After treatment with amoxicillin-clavulanic acid for 2 days, fever subsided and the patient was dismissed.

Adenocarcinoma↗
PubMed1994

Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria.

Twenty-five isolates of dissimilatory sulfate-reducing bacteria were clustered based on similarity analysis of their phospholipid ester-linked fatty acids (PLFA). Of these, 22 showed that phylogenetic relationships based on the sequence similarity of their 16S rRNA directly paralleled the PLFA relationships. Desulfobacter latus and Desulfobacter curvatus grouped with the other Desulfobacter spp. by 16S rRNA comparison but not with the PLFA analysis as they contained significantly more monoenoic PLFA than the others. Similarly, Desulfovibrio africanus clustered with the Desulfovibrio spp. by 16S rRNA but not with them when analyzed by PLFA patterns because of higher monoenoic PLFA content. Otherwise, clustering obtained with either analysis was essentially congruent. The relationships defined by PLFA patterns appeared robust to shifts in nutrients and terminal electron acceptors. Additional analyses utilizing the lipopolysaccharide-lipid A hydroxy fatty acid patterns appeared not to shift the relationships based on PLFA significantly except when completely absent, as in Gram-positive bacteria. Phylogenetic relationships between isolates defined by 16S rRNA sequence divergence represent a selection clearly different from the multi-enzyme activities responsible for the PLFA patterns. Determination of bacterial relationships based on different selective pressures for various cellular components provides more clues to evolutionary history leading to a more rational nomenclature.

Desulfovibrio↗