Oligonucleotide Cataloguing Research Articles

The Small Subunit rRNA Modification Database

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods.

Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria

Phylogenetic analysis of the almost complete 16S rDNA sequence of the fimbriate prosthecate bacterium Verrucomicrobium spinosum confirms the unique phylogenetic position of this organism, as previously shown by oligonucleotide cataloguing and partial reverse transcriptase sequencing. Comparative 16S rDNA sequence analysis of V. spinosum with a group of environmental clones, considered to represent a novel phylum, reveals their relatedness, and allows assignment of these clones to a known main line of descent. This phylogenetic relationship is supported by the presence in the 16S rDNA sequence of V. spinosum of signature nucleotides previously considered unique for the environmental clone cluster.

Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine.

A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 microns. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 degrees C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO2, and H2. The major components of the cellular fatty acids were C14:0, C16:0, C16:1, and C17:0 cyc acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752T was most closely related to Haloanaerobium praevalens GSLT (ATCC 33744), the sole member of the genus Haloanaerobium. We propose that strain VS-752 (ATCC 51327) be established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium.

Chemotaxonomy of Bacteroides: a review.

The loose definition of Bacteroides, some species of which are important etiologic agents of oral diseases, has enabled isolates with only marginal similarities to be reposited in this genus. Many attempts have been made over the years to improve the taxonomy of this heterogeneous group of bacteria. The present article reviews major chemotaxonomic characters and techniques that have been used for this purpose: pigmentation, metabolites, whole-cell fatty acids, phospholipids, isoprenoid quinones, carbohydrates of lipopolysaccharide, whole-cell proteins, peptidoglycans, enzymes, pyrolysis mass spectrometry, DNA composition, restriction fragment length polymorphisms of DNA and ribosomal (r) RNA, homology of DNA and RNA, DNA-rRNA hybridization, and 16S and 5S rRNA oligonucleotide cataloging and sequencing. Despite improvements in their taxonomy, some bacteroides are still misclassified. Suggestions for further improvements in the taxonomy of bacteroides are made.

16S rRNA sequences of Bartonella bacilliformis and cat scratch disease bacillus reveal phylogenetic relationships with the alpha-2 subgroup of the class Proteobacteria

The primary structures of 16S rRNAs of Bartonella bacilliformis, an isolate of the cat scratch disease (CSD) bacillus, and a strain phenotypically similar to the CSD bacillus were determined by reverse transcriptase sequencing. These microorganisms were found to be members of the alpha-2 subgroup of the class Proteobacteria. The sequence from B. bacilliformis was most closely related to the rRNA of Rochalimaea quintana (91.7% homology), the etiologic agent of trench fever. The sequence from the isolate of the CSD bacillus showed the greatest homology with Brucella abortus (89.7%) and, when compared with oligonucleotide catalog data, formed a cluster with Rhodopseudomonas palustris, Pseudomonas carboxidovorans, Nitrobacter species, and Bradyrhizobium species. The 16S rRNA sequence was also determined for the Cleveland Clinic isolate, which was previously shown to be phenotypically similar to and approximately 30% related, by DNA hybridization, to the CSD bacillus. The Cleveland Clinic isolate was isolated from a patient not diagnosed with CSD. The rRNAs from these bacteria exhibited 98.2% homology, confirming that this isolate is a second species in the same genus as the CSD bacillus. Our data suggest that neither B. bacilliformis nor the CSD bacillus is the etiologic agent of bacillary epithelioid angiomatosis.

Nucleoside deoxyribosyltransferase and inosine phosphorylase activity in lactic acid bacteria

Phosphate-independent nucleoside deoxyribosyltransferase activity was detected in Aerococcus viridans, Leuconostoc mesenteroides, two species of Pediococcus, eight obligately homofermentative and three obligately heterofermentative lactobacilli. In cellfree extracts of one strain of Lactococcus, one strain of Streptococcus and three strains of facultatively heterofermentative lactobacilli no phosphate-independent nucleoside deoxyribosyltransferase could be detected and inosine nucleoside phosphorylase was the only enzyme catalysing pentosyl transfer to purines. A classification based on the presence or absence of these enzymes separates Streptococcus and Lactococcus from the remaining genera which is in agreement with studies using anti-aldolase sera and 16S rRNA oligonucleotide catalogues.

Natural relationships among sulfate-reducing eubacteria

Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA sequencing. All genera of mesophilic sulfate-reducing eubacteria except the new genus Desulfomicrobium and the gliding Desulfonema species were included. The sporeforming species Desulfotomaculum ruminis and Desulfotomaculum orientis were found to be gram-positive organisms sharing 83% 16S rRNA sequence similarity, indicating that this genus is diverse. The gram-negative nonsporeforming species could be divided into seven natural groups: group 1, Desulfovibrio desulfuricans and other species of this genus that do not degrade fatty acids (this group also included "Desulfomonas" pigra); group 2, the fatty acid-degrading "Desulfovibrio" sapovorans; group 3, Desulfobulbus species; group 4, Desulfobacter species; group 5, Desulfobacterium species and "Desulfococcus" niacini; group 6, Desulfococcus multivorans and Desulfosarcina variabilis; and group 7, the fatty acid-oxidizing "Desulfovibrio" baarsii. (The quotation marks are used to indicate the need for taxonomic revision.) Groups 1 to 3 are incomplete oxidizers that form acetate as an end product; groups 4 to 7 are complete oxidizers. The data were consistent with and refined relationships previously inferred by oligonucleotide catalogs of 16S rRNA. Although the determined relationships are generally consistent with the existing classification based on physiology and other characteristics, the need for some taxonomic revision is indicated.

Analysis and Interpretation of Sequence Data for Bacterial Systematics: The View of a Numerical Taxonomist

The nature of sequence data is considered with particular attention to phenetic and cladistic relationships. The correct use of the terms phylogenetic, phenotypic and genomic is emphasized. Sequence data are genomic, and this is included within the concept of phenetic relationships. The primary aim of taxonomy is to construct phenetic groups, because of their high content of information. Methods of analysis of sequence data are briefly considered. Sequence relationships are subject to statistical sampling error, which is greater for smaller sequences. It is a substantial cause of uncertainty in both phenograms and cladograms. This is illustrated by examples from ribosomal RNA sequences, using a convenient graphic representation of uncertainty. Other sources of uncertainty include similarities between sequences which are not orthologous, i. e. not strictly comparable (such as paralogous similarities between genes that have undergone gene duplication and independent evolution of the duplicates), and imperfect correlation between relationships from oligonucleotide catalogues and the full sequences. Phylogenetic trees of prokaryotes rest heavily on the assumptions that rRNA sequences from different organisms are orthologous and that their evolution has been constant and divergent. There are some instances where 16S and 5S rRNA sequences give discrepancies larger than those expected from sampling error, The explanations are briefly considered. DNA-DNA pairing may be held to reflect the whole genome, and has, in theory, very small sampling error, but its value is limited by the experimental accuracy of the method. If accuracy can be improved the technique may have great potential at all levels of taxonomic rank.

Ectothiorhodospira marismortui sp. nov., an obligately anaerobic, moderately halophilic purple sulfur bacterium from a hypersaline sulfur spring on the shore of the Dead Sea

A novel type of purple sulfur bacterium was isolated from a hypersaline sulfur spring on the shore of the Dead Sea. The cells of the isolate are irregularly rod-shaped or curved, and motile by means of a tuft of polar flagella. The photosynthetic system, containing bacteriochlorophyll a and carotenoids of the spirilloxanthin series, is located on stacks of lamellar membranes in the cell cytoplasm. The organism can grow either photoautotrophically with sulfide as electron donor, which is oxidized via extracellular sulfur to sulfate, or photoheterotrophically, using acetate, succinate, fumarate, malate or pyruvate as carbon sources. The bacterium is obligately anaerobic, and requires a source of reduced sulfur for growth. The isolate is moderately halophilic, and grows optimally at NaCl concentrations between 3 and 8%, temperatures between 30 and 45°C, and neutral pH. 16S ribosomal RNA oligonucleotide cataloging suggests a close relationship to purple sulfur bacteria of the genus Ectothiorhodospira. As the isolate differs greatly from the described members of the genus Ectothiorhodospira, we describe the isolate as a new species, and propose the name Ectothiorhodospira marismortui sp. nov.

The Deinococcus-Thermus Phylum and the Effect of rRNA Composition on Phylogenetic Tree Construction

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Cladistic analysis of blue‐green procaryote interrelationships and chloroplast origin based on 16S rRNA oligonucleotide catalogues

AbstractOligonucleotide catalogues from 16S rRNA have been a major source of information for phylogenetic reconstruction among procaryotes. Several large procaryote groups have been analyzed and phylogenies presented. Catalogues are also available for many chloroplasts. The hypotheses of phylogeny are derived mainly from similarity (phenetic) comparisons of the catalogues and the extent of the homoplasy (parallelisms and reversals) involved has not been estimated properly. Although catalogues are currently being superseded by complete sequence data, an evaluation of the strength of catalogue data, and hence of the strength of the extensive phylogenetic hypotheses derived from them, is in order. Cladistic analysis of 16S rRNA oligonucleotide catalogues from three blue‐green procaryotes, Prochloron, and chloroplasts of a red alga, Euglena, a green alga and two flowering plants shows that there is extensive homoplasy in the catalogues and several phylogenetic trees are possible. The corresponding consensus trees indicate that little or nothing can be said about interrelationships and chloroplast origin on the basis of these particular catalogues, except that Prochloron may be more closely related to the blue‐greens than to chloroplasts.

Verrucomicrobium spinosum, a Eubacterium Representing an Ancient Line of Descent

Summary 16S Ribosomal RNA of Verrucomicrobium spinosum was analysed by oligonucleotide cataloguing and reverse transcriptase sequencing. Similarity coefficients (S AB values) calculated for the RNase T1 catalogue of V. spinosum and about 460 catalogues of eubacterial strains were found to be as low as those separating individual eubacterial phyla (as defined by Woese et al., 1985), indicating that V. spinosum represents a new division. The deep branching point of V. spinosum within the dendrogram of relationships is in accord with its position in the phlyogenetic tree derived from comparisons of two long 16S rRNA sequences of size 285 and 230 nucleotides from V. spinosum and the homologous regions of a variety of eubacteria. V. spinosum is most distantly related only to other eubacteria carrying prosthecates, e.g. members of Frosthecomicrobium, Ancalomicrobium, Stella, Caulobacter, Hyphomicrobium, Pedomicrobium, Hyphomonas and Prosthecochloris .

Proposal to Retain Listeria murrayi and Listeria grayi in the Genus Listeria

The 16S ribosomal ribonucleic acid oligonucleotide catalog of Listeria murrayi was found to be closely related (similarity coefficient, 0.73) to that of L. monocytogenes. These data, together with the phenotypic similarity found among all Listeria strains tested, provide no support for the exclusion of L. murrayi (and the closely related species L. grayi) from the genus Listeria.

Phylogenetic Analysis of Certain Sulfide-Oxidizing and Related Morphologically Conspicuous Bacteria by 5S Ribosomal Ribonucleic Acid Sequences

Comparisons of 5S ribosomal ribonucleic acid (rRNA) nucleotide sequences were used for the phylogenetic characterization of a number of “morphologically conspicuous” sulfide-oxidizing eubacteria and certain of their non-sulfide oxidizing counterparts. Nucleotide sequences were determined for 5S rRNAs isolated from Thiovulum sp., Beggiatoa alba B18LD, Thiothrix nivea JP2, strain 30 (a Thiothrix-like organism), Vitreoscilla beggiatoides B23SS, Vitreoscilla filiformis L1401-7, V.filiformis ATCC 15551, Vitreoscilla stercoraria VT1, and Leptothrix discophora (Stokes). All 5S rRNAs characterized in this study, except that of Thiovulum sp., belong to either the gamma or beta subdivisions of the “purple bacteria,” which form 1 of the 10 major eubacterial divisions so far defined by 16S rRNA oligonucleotide catalog analysis. Although its 5S rRNA is clearly eubacterial in character, Thiovulum sp. appears to have no specific relatives among the eubacteria presently represented in the 5S rRNA data collection.

Structure of clostridial 5 S ribosomal RNAs and bacterial evolution

Summary The nucleotide sequence of the 5 S rRNAs of Clostridium bifermentans, Clostridium pasteurianum, Clostridium butyricum , and Clostridium tyrobutyricum has been determined. The evolutionary position of the Clostridia in the eubacterial primary kingdom was examined by construction of a phylogenetic tree on the basis of 5 S RNA sequences from 115 species and organelles. The tree is comparable to the trees constructed on the basis of SAB values derived from 16 S rRNA oligonucleotide catalogues, as far as the composition of the major clusters is concerned. However there are some notable differences in the deeper branching pattern leading to these clusters. The five Clostridium species for which the 5 S RNA structure is now established are distributed over three different clusters.

16S rRNA analysis and the phylogenetic position ofWolinella succinogenes

The 16S ribosomal RNA of Wolinella succinogenes ATCC29543 was analyzed by the RNase T1 oligonucleotide cataloguing approach. In contrast to its present classification, W. succinogenes is related neither to members of the genus Bacteroides nor to any other genus of the family Bacteroidaceae. As derived from the similarity coefficients (SAB values) calculated on the basis of more than 350 eubacterial species, W. succinogenes appears to be a distantly related member of the division of purple photosynthetic bacteria and their relatives; however, SAB values do not indicate that this species is preferentially related to any representative of the 4 subdivisions.

Evolution of the biochemical pathway for aromatic amino acid biosynthesis in Serpens flexibilis in relationship to its phylogenetic position

Given the availability of a reasonably complete phylogenetic tree constructed by means of modern nucleic acid sequencing techniques, it is sometimes possible to use biochemical-pathway characteristics as a basis to fine-tune the phylogenetic position of certain organisms making up the tree. A case in point in Serpens flexibilis, a helical bacterium shown by oligonucleotide cataloging to belong to the group Ia cluster of pseudomonads. The results show that within the group Ia pseudomonad cluster, S. flexibilis clusters with the Pseudomonas stutzeri/P. mendocina/P. alcaligenes/P. pseudoalcaligenes assemblage, which diverges from a lineage leading to P. aeruginosa and from yet another lineage leading to species of Azomonas and Azotobacter.

Lack of relationship between gliding cyanobacteria and filamentous gliding heterotrophic eubacteria: comparison of 16S rRNA catalogues of Spirulina, Saprospira, Vitreoscilla, Leucothrix, and Herpetosiphon

Spirulina platensis and Spirulina maxima were characterized by 16S ribosomal RNA oligonucleotide cataloguing. Both species are highly related. They fall into the main group of the cyanobacteria, showing a remote relationship to Nostoc, Fischerella, Aphanocapsa, and also to Prochloron. Low similarity coefficients were found between the Spirulina species and certain organotrophic and sulfide oxidizing bacteria, viz. Saprospira grandis, Vitreoscilla stercoraria, Leucothrix mucor, Herpetosiphon aurantiacus, and Beggiatoa leptomitiformis, respectively. This result does not support the classical hypothesis that certain filamentous gliding bacteria are apochlorotic cyanobacteria.

Evolution of the regulatory isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase present in the Escherichia coli genealogy.

The evolutionary history of isozymes for 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase has been constructed in a phylogenetic cluster of procaryotes (superfamily B) that includes Escherichia coli. Members of superfamily B that have been positioned on a phylogenetic tree by oligonucleotide cataloging possess one or more of four distinct isozymes of DAHP synthase. DAHP synthase-0 is insensitive to feedback inhibition, while DAHP synthase-Tyr, DAHP synthase-Trp, and DAHP synthase-Phe are sensitive to feedback inhibition by L-tyrosine, L-tryptophan, and L-phenylalanine, respectively. The evolutionary history of this isozyme family can be deduced within superfamily B by using a cladistic methodology of maximum parsimony (R. A. Jensen, Mol. Biol. Evol. 2:92-108, 1985). DAHP synthase-0 was found in Acinetobacter species and in Oceanospirillum minutulum, organisms that also possess DAHP synthase-Tyr. These two isozymes were apparently present in a common ancestor that predated the evolutionary divergence of contemporary superfamily B sublineages. DAHP synthase-0 is postulated to have been the evolutionary forerunner of DAHP synthase-Trp. The newly evolved DAHP synthase-Trp is postulated to have possessed sensitivity to feedback inhibition by chorismate as well as by L-tryptophan, chorismate sensitivity having been retained in rRNA group I pseudomonads (minor sensitivity), group V pseudomonads (very sensitive), and Lysobacter enzymogenes (ultrasensitive). Organisms constituting the enteric lineage of the phylogenetic tree (including a cluster of four Oceanospirillum species) have all lost the chorismate sensitivity of DAHP synthase-Trp. The absence of DAHP synthase-Phe in the Oceanospirillum cluster of organisms supports the previous conclusion that DAHP synthase-Phe evolved recently within superfamily B, being present only Escherichia coli and its close relatives.

16S rRNA analysis of Sporomusa, selenomonas, and Megasphaera: on the phylogenetic origin of Gram-positive Eubacteria

In order to determine the phylogenetic relationships of representatives of three Gram-negative genera, Sporomusa, Selenomonas, and Megasphaera, the 16S ribosomal RNAs were compared by oligonucleotide cataloguing. Surprisingly, Sporomusa ovata, S. sphaeroides, Selenomonas ruminantium, and Megasphaera elsdenii do not group with any of the 200 Gram-negative eubacterial species investigated so far by this method but show a distinct although remote relationship to Gram-positive eubacteria of the “Clostridium subdivision”. The presence of Gram-negative species within the radiation of the cluster defined by Gram-positive cubacteria reduces the significance the Gram-positive staining behaviour plays in taxonomic and phylogenetic studies. It furthermore supports previous findings showing the Gram-negative and phototrophic species Heliobacterium chlorum to be a member of the Clostridium-Bacillus cluster. The presence of Gram-negative endospore-containing Sporomusa species among the 16S rRNA cluster of Gram-positive endospore-forming eubacteria allow speculations about the evolutionary origin of Gram-positive eubacteria.