Database on the structure of small ribosomal subunit RNA

18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera

BACKGROUND

18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core structure across eukaryotes exists for this molecule that can help to inform about its evolution in different groups. Using an alignment of 18S rDNA for Rotifera as traditionally recognized (=Bdelloidea, Monogononta, and Seisonacea, but not Acanthocephala), I fitted sequences for three exemplar species (Adineta vaga, Brachionus plicatilis, and Seison nebaliae, respectively) to the core structure and used these maps to reveal patterns of evolution for the remainder of this diverse group of microscopic animals.

RESULTS

The obtained variability maps of the 18S rRNA molecule revealed a pattern of high diversity among the three major rotifer clades coupled with strong conservation within each of bdelloids and monogononts. A majority of individual sites (ca. 60%) were constant even across rotifers as a whole with variable sites showing only intermediate rates of evolution. Although the three structural maps each showed good agreement with the inferred core structure for eukaryotic 18S rRNA and so were highly similar to one another at the secondary and tertiary levels, the overall pattern is of three highly distinct, but conserved motifs within the group at the primary sequence level. A novel finding was that of a variably expressed deletion at the 3' end of the V3 hypervariable region among some bdelloid species that occasionally extended into and included the pseudoknot structure following this region as well as the central "square" of the 18S rRNA molecule. Compared to other groups, levels of variation and rates of evolution for 18S rRNA in Rotifera roughly matched those for Gastropoda and Acanthocephala, despite increasing evidence for the latter being a clade within Rotifera.

CONCLUSIONS

The lack of comparative data for comparable groups makes interpretation of the results (i.e., very low variation within each of the three major rotifer clades, but high variation between them) and their potential novelty difficult. However, these findings in combination with the high morphological diversity within rotifers potentially help to explain why no clear consensus has been reached to date with regard to the phylogenetic relationships among the major groups.

Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

BACKGROUND

Helicobacter pylori (H. pylori) is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of H. pylori strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. Materials and methods. A total of 75 gastric biopsies were taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was performed by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. The evolutionary aspects were analyzed using MEGA7 software.

RESULTS

Molecular detection of H. pylori has shown that 28 (37.33%) of the patients were positive for H. pylori and no significant differences were found in sociodemographic characteristics, endoscopy series, and H. pylori infection. Nucleotide variations were observed at five nucleotide positions (positions 219, 305, 578, 741, and 763-764), and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. These six mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites; 66.67% of them were located in the central domain of 16S rRNA. The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. The presence of Sudanese H. pylori strains resembling Hungarian H. pylori strains could reflect the migration of Hungarian people to Sudan or vice versa.

CONCLUSION

This finding emphasizes the significance of studying the phylogeny of H. pylori strains as a discriminatory tool to mirror human migration patterns. In addition, the 16S rRNA gene amplification method was found useful for bacterial identification and phylogeny.

Characterization of the complete mitochondrial genome of Chinese Triops granarius and implications for species delimitation

The mt genome of T. granarius (15.121 bp), containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and one control region, present the typical pattern of phyllopod mt genomes from the perspective of gene content and order. All PCGs initiate with standard start codon of ATN and share the complete stop codon of TAA or TAG, whereas nd1 initiates with GTG, nd2 terminates with AGA and nd4 terminates with a single T. The secondary structures of rrnL and rrnS comprise of 48 helices and 32 helices, respectively. The patterns of evolutionary rate heterogeneity were observed at different levels in Triops. Phylogenetic analyses were performed based on the nucleotide sequences and amino acid sequences showed that Asian T. granarius was a sister group to (T. longicaudatus + T. australiensis), and T. cancriformis was the basal clade of Triops. Furthermore, we investigated the genetic diversity and phylogenetic relationships of different T. granarius s.l. populations. Ten phylogenetic lineages are separated on species level by mean maximum likelihood distance ≥ 12.2% in the cox1 gene. While the six populations occurring in Inner Mongolia of China, Mongolia and Russia, investigated for haplotypes belonged to the same haplotype networks.

Typification of virulent and low virulence Babesia bigemina clones by 18S rRNA and rap-1c

The population structure of original Babesia bigemina isolates and reference strains with a defined phenotypic profile was assessed using 18S rRNA and rap-1c genes. Two reference strains, BbiS2P-c (virulent) and BbiS1A-c (low virulence), were biologically cloned in vitro. The virulence profile of the strains and clones was assessed in vivo. One fully virulent and one low-virulence clone were mixed in identical proportions to evaluate their growth efficiency in vitro. Each clone was differentiated by two microsatellites and the gene gp45. The 18S rRNA and rap-1c genes sequences from B. bigemina biological clones and their parental strains, multiplied exclusively in vivo or in vitro, were compared with strain JG-29. The virulence of clones derived from the BbiS2P-c strain was variable. Virulent clone Bbi9P1 grew more efficiently in vitro than did the low-virulence clone Bbi2A1. The haplotypes generated by the nucleotide polymorphism, localized in the V4 region of the 18S rRNA, allowed the identification of three genotypes. The rap-1c haplotypes allowed defining four genotypes. Parental and original strains were defined by multiple haplotypes identified in both genes. The rap-1c gene, analyzed by high-resolution melting (HRM), allowed discrimination between two genotypes according to their phenotype, and both were different from JG-29. B. bigemina biological clones made it possible to define the population structure of isolates and strains. The polymorphic regions of the 18S rRNA and rap-1c genes allowed the identification of different subpopulations within original B. bigemina isolates by the definition of several haplotypes and the differentiation of fully virulent from low virulence clones.

Random mutagenesis of yeast 25S rRNA identify bases critical for 60S subunit structural integrity and function

In yeast Saccharomyces cerevisiae, 25S rRNA makes up the major mass and shape of the 60S ribosomal subunit. During translation initiation, the 60S subunit joins the 40S initiation complex, producing the 80S initiation complex. During elongation, the 60S subunit binds the CCA-ends of aminoacyl- and peptidyl-tRNAs at the A-loop and P-loop, respectively, transferring the peptide onto the α-amino group of the aminoacyl-tRNA. To study the role of 25S rRNA in translation in vivo, we randomly mutated 25S rRNA and isolated and characterized seven point mutations that affected yeast cell growth and polysome profiles. Four of these mutations, G651A, A1435U, A1446G and A1587G, change a base involved in base triples crucial for structural integrity. Three other mutations change bases near the ribosomal surface: C2879U and U2408C alter the A-loop and P-loop, respectively, and G1735A maps near a Eukarya-specific bridge to the 40S subunit. By polysome profiling in mmslΔ mutants defective in nonfunctional 25S rRNA decay, we show that some of these mutations are defective in both the initiation and elongation phases of translation. Of the mutants characterized, C2879U displays the strongest defect in translation initiation. The ribosome transit-time assay directly shows that this mutation is also defective in peptide elongation/termination. Thus, our genetic analysis not only identifies bases critical for structural integrity of the 60S subunit, but also suggests a role for bases near the peptidyl transferase center in translation initiation.

Caloramator quimbayensis sp. nov., an anaerobic, moderately thermophilic bacterium isolated from a terrestrial hot spring

An anaerobic, moderately thermophilic, terminal-spore-forming bacterium, designated strain USBA AT, was isolated from a terrestrial hot spring located at an altitude of 2683 m in the Andean region of Colombia (04° 50′ 14.0″ N 75° 32′ 53.4″ W). Cells of strain USBA AT were Gram-stain-positive, straight to slightly curved rods (0.9×2.5 µm), that were arranged singly or in pairs, and were motile by means of flagella. Growth occurred at 37–55 °C and pH 6.0–8.0, with a doubling time of 2 h under the optimal conditions (50 °C and pH 7.0). Glucose fermentation in strain USBA AT required yeast extract or peptone (each at 0.2 %, w/v). The novel strain fermented sugars, amino acids, Casamino acids, propanol, propionate, starch and dextrin, but no growth was observed on galactose, lactose, xylose, histidine, serine, threonine, benzoate, butyrate, lactate, pyruvate, succinate, methanol, ethanol, glycerol, casein, gelatin or xylan. The end products of glucose fermentation were formate, acetate, ethanol and lactate. Strain USBA AT did not grow autotrophically (with CO2 as carbon source and H2 as electron donor) and did not reduce thiosulfate, sulfate, elemental sulfur, sulfite, vanadium (V) or Fe (III) citrate. Growth of strain USBA AT was inhibited by ampicillin, chloramphenicol, kanamycin, penicillin and streptomycin (each at 10 µg ml−1). The predominant fatty acids were iso-C15 : 0, C16 : 0 and iso-C17 : 0 and the genomic DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis indicated that strain USBA AT belonged in the phylum Firmicutes and that its closest relative was Caloramator viterbiensis JW/MS-VS5T (95.0 % sequence similarity). A DNA–DNA relatedness value of only 30 % was recorded in hybridization experiments between strain USBA AT and Caloramator viterbiensis DSM 13723T. Based on the phenotypic, chemotaxonomic and phylogenetic evidence and the results of the DNA–DNA hybridization experiments, strain USBA AT represents a novel species of the genus Caloramator , for which the name Caloramator quimbayensis sp. nov. is proposed. The type strain is USBA AT ( = CMPUJ U833T  = DSM 22093T).

Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation

In eukaryotes, the 40 S ribosomal subunit serves as the platform of initiation factor assembly, to place itself precisely on the AUG start codon. Structural arrangement of the 18 S rRNA determines the overall shape of the 40 S subunit. Here, we present genetic evaluation of yeast 18 S rRNA function using 10 point mutations altering the polysome profile. All the mutants reduce the abundance of the mutant 40 S, making it limiting for translation initiation. Two of the isolated mutations, G875A, altering the core of the platform domain that binds eIF1 and eIF2, and A1193U, changing the h31 loop located below the P-site tRNA(i)(Met), show phenotypes indicating defective regulation of AUG selection. Evidence is provided that these mutations reduce the interaction with the components of the preinitiation complex, thereby inhibiting its function at different steps. These results indicate that the 18 S rRNA mutations impair the integrity of scanning-competent preinitiation complex, thereby altering the 40 S subunit response to stringent AUG selection. Interestingly, nine of the mutations alter the body/platform domains of 18 S rRNA, potentially affecting the bridges to the 60 S subunit, but they do not change the level of 18 S rRNA intermediates. Based on these results, we also discuss the mechanism of the selective degradation of the mutant 40 S subunits.

Peptidolytic Microbial Community of Methanogenic Reactors from two Modified Uasbs of Brewery Industries

We studied the peptide-degrading anaerobic communities of methanogenic reactors from two mesophilic full-scale modified upflow anaerobic sludge blanket (UASB) reactors treating brewery wastewater in Colombia. Most probable number (MPN) counts varied between 7.1 x 10(8) and 6.6 × 10(9) bacteria/g volatile suspended solids VSS (Methanogenic Reactor 1) and 7.2 × 10(6) and 6.4 × 10(7) bacteria/g (VSS) (Methanogenic Reactor 2). Metabolites detected in the highest positive MPN dilutions in both reactors were mostly acetate, propionate, isovalerate and, in some cases, negligible concentrations of butyrate. Using the highest positive dilutions of MPN counts, 50 dominant strains were isolated from both reactors, and 12 strains were selected for sequencing their 16S rRNA gene based on their phenotypic characteristics. The small-subunit rRNA gene sequences indicated that these strains were affiliated to the families Propionibacteriaceae, Clostridiaceae and Syntrophomonadaceae in the low G + C gram-positive group and Desulfovibrio spp. in the class δ-Proteobacteria. The main metabolites detected in the highest positive dilutions of MPN and the presence of Syntrophomonadaceae indicate the effect of the syntrophic associations on the bioconversion of these substrates in methanogenic reactors. Additionally, the potential utilization of external electron acceptors for the complete degradation of amino acids by Clostridium strains confirms the relevance of these acceptors in the transformation of peptides and amino acids in these systems.

Tistlia consotensis gen. nov., sp. nov., an aerobic, chemoheterotrophic, free-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring

A Gram-negative, aerobic, mesophilic, non-spore-forming, chemotrophic, chlorophyll-lacking, nitrogen-fixing bacterium, designated strain USBA 355T, was isolated from the saline spring ‘Salado de Consotá’ situated in the Colombian Andes. The non-flagellated cells of strain USBA 355T were straight to slightly curved rods (0.6–0.7 × 3.0–3.5 μm). Growth occurred optimally at 30 °C (growth temperature range between 20 and 40 °C), at pH 6.5–6.7 (pH growth range between 5.0 and 8.0) and at 0.5 % NaCl (w/v) (range between 0 and 4 %). The major quinone present was Q-10 and the predominant fatty acids identified were C19 : 0 cyclo ω8c, C18 : 1 ω7c and C18 : 0. The G+C content of the chromosomal DNA was 71±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA 355T formed a distant phylogenetic line of descent with members of the genus Thalassobaculum, family Rhodospirillaceae, class Alphaproteobacteria (90 % gene sequence similarity). Comparison of the phylogenetic, chemotaxonomic and physiological features of strain USBA 355T with all other members of the family Rhodospirillaceae suggested that it represents a novel genus and species for which the name Tistlia consotensis gen. nov., sp. nov. is proposed. The type strain of the type species is USBA 355T (=JCM 15529T=KCTC 22406T).

Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring

A thermophilic, sulfate-reducing bacterium, designated strain USBA-053(T), was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45' 33.29″ N 73° 6' 49.89″ W), Colombia. Cells of strain USBA-053(T) were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H(2) as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO(2) and H(2)S. Strain USBA-053(T) fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l(-1), with an optimum at 25 g l(-1) NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053(T) was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96(T) as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053(T) represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053(T) ( = KCTC 5670(T) = DSM 22027(T)).

A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces

The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

Ribosomal DNA (rDNA) plays a key role in ribosome biogenesis, encoding genes for the structural RNA components of this important cellular organelle. These genes are vital for efficient functioning of the cellular protein synthesis machinery and as such are highly conserved and normally present in high copy numbers. In the baker's yeast Saccharomyces cerevisiae, there are more than 100 rDNA repeats located at a single locus on chromosome XII. Stability and sequence homogeneity of the rDNA array is essential for function, and this is achieved primarily by the mechanism of gene conversion. Detecting variation within these arrays is extremely problematic due to their large size and repetitive structure. In an attempt to address this, we have analyzed over 35 Mbp of rDNA sequence obtained from whole-genome shotgun sequencing (WGSS) of 34 strains of S. cerevisiae. Contrary to expectation, we find significant rDNA sequence variation exists within individual genomes. Many of the detected polymorphisms are not fully resolved. For this type of sequence variation, we introduce the term partial single nucleotide polymorphism, or pSNP. Comparative analysis of the complete data set reveals that different S. cerevisiae genomes possess different patterns of rDNA polymorphism, with much of the variation located within the rapidly evolving nontranscribed intergenic spacer (IGS) region. Furthermore, we find that strains known to have either structured or mosaic/hybrid genomes can be distinguished from one another based on rDNA pSNP number, indicating that pSNP dynamics may provide a reliable new measure of genome origin and stability.

A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters

The root lesion nematodes of the genus Pratylenchus Filipjev, 1936 are migratory endoparasites of plant roots, considered among the most widespread and important nematode parasites in a variety of crops. We obtained gene sequences from the D2 and D3 expansion segments of 28S rRNA partial and 18S rRNA from 31 populations belonging to 11 valid and two unidentified species of root lesion nematodes and five outgroup taxa. These datasets were analyzed using maximum parsimony and Bayesian inference. The alignments were generated using the secondary structure models for these molecules and analyzed with Bayesian inference under the standard models and the complex model, considering helices under the doublet model and loops and bulges under the general time reversible model. The phylogenetic informativeness of morphological characters is tested by reconstruction of their histories on rRNA based trees using parallel parsimony and Bayesian approaches. Phylogenetic and sequence analyses of the 28S D2-D3 dataset with 145 accessions for 28 species and 18S dataset with 68 accessions for 15 species confirmed among large numbers of geographical diverse isolates that most classical morphospecies are monophyletic. Phylogenetic analyses revealed at least six distinct major clades of examined Pratylenchus species and these clades are generally congruent with those defined by characters derived from lip patterns, numbers of lip annules, and spermatheca shape. Morphological results suggest the need for sophisticated character discovery and analysis for morphology based phylogenetics in nematodes.

Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest

An aerobic bacterium, designated strain E1HC-02T, was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02T were short irregular rods (0.5–1.0×0.2–0.4 μm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 °C and at a pH of 9.1. Strain E1HC-02T metabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02T showed that it was a member of the family Microbacteriaceae, phylum Actinobacteria. The cell wall contained a type B2β peptidoglycan, the dominant cellular fatty acid was 18 : 1ω7c and the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02T were distinctly different to all of the 17 genera of the family Microbacteriaceae and hence strain E1HC-02T is designated as representing a novel species of a new genus, Frondicola australicus gen. nov., sp. nov. The type strain of the type species is E1HC-02T (=JCM 13598T=DSM 17894T).

Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage

An aerobic bacterium, designated strain E5HC-32T, was isolated from soil underlying the decaying leaf litter of a slash pine forest located in south east Queensland, Australia. The strictly aerobic, motile rod-shaped cells (0.8–1.6×2.6–4.8 μm) produced subterminal spherical spores which distended the cells. Strain E5HC-32T grew optimally in 1 % trypticase soy broth (TSB) at 30 °C (temperature range for growth, 25–40 °C) and a pH of 8.4 (pH growth range, pH 7.1–9.1). Electron microscopic examination of negatively stained cells revealed the presence of peritrichous flagella and thin sections showed the presence of a typical Gram-positive type cell-wall ultrastructure. The strain was catalase-positive and oxidase-negative and metabolized pyruvic acid methyl ester, d-galactonic acid lactone, α-ketobutyric acid, α-ketovaleric acid, l-proline, l-alanine, urocanic acid, inosine, uridine, thymidine, glycerol, α-cyclodextrin, α-d-lactose, d-psicose, d-raffinose, l-rhamnose, d-sorbitol, turanose, cis-aconitic acid, α-hydroxybutyric acid, l-alaninamide and 2-aminoethanol. The G+C content of DNA was 41±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis revealed that strain E5HC-32T was placed equidistantly as a member of the class Bacilli, phylum Firmicutes, with Bacillus sphaericus DSM 28T and Bacillus odysseyi ATCC PTA-4993T (similarity of 93 %). In addition to its significant phylogenetic separation from its nearest relatives, strain E5HC-32T possessed phenotypic traits that also suggested that it represented a novel species, for which the name Bacillus decisifrondis sp. nov. is proposed. The type strain is E5HC-32T (=JCM 13601T=DSM 17725T).

Evolutionary rates vary among rRNA structural elements

Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.

Exploration of pairing constraints identifies a 9 base-pair core within box C/D snoRNA-rRNA duplexes

2'-O-ribose methylation of eukaryotic ribosomal RNAs is guided by RNA duplexes consisting of rRNA and box C/D small nucleolar (sno)RNA sequences, the methylated sites invariably mapping five positions apart from the D box. Here we have analyzed the RNA duplex pairing constraints by investigating the features of 415 duplexes from the fungus, plant and animal kingdoms, and the evolution of those duplexes within the 124 sets they group into. The D-box upstream 1st and >or=15th positions consist of Watson-Crick base-pairs, G:U base-pairs and mismatched bases with ratios close to random assortments; these positions display single base differences in >60% of the RNA duplex sets. The D-box upstream 2nd to 11th positions have >90% Watson-Crick base-pairs; they display single base mutations with a U-shaped distribution of lower values of 0% and 1.6% at the methylated site 5th and 4th positions, and double compensatory mutations leading to new Watson-Crick base-pairs with an inverted U-shaped distribution of higher values at the 8th to 11th positions. Half of the single mutations at the 3rd to 11th positions resulted in G:U base-pairing, mainly through A-->G mutations in the rRNA strands and C-->T mutations in the snoRNA strands. Double compensatory mutations at the 3rd to 11th positions are extremely frequent, representing 36% of all mutations; they frequently arose from an A-->G mutation in the rRNA strands followed by a T-->C mutation in the snoRNA strands. Differences in the mutational pathways through which the rRNA and snoRNA strand evolved must be related to differences in the rRNA and snoRNA copy number and gene organization. Altogether these data identify the D-box upstream 3rd to 11th positions as box C/D snoRNA-rRNA duplex cores. The impact of the pairing constraints on the evolution of the 9 base-pair RNA duplex cores is discussed.

Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data

Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

Identification of rDNA-specific non-LTR retrotransposons in Cnidaria

Ribosomal RNA genes are abundant repetitive sequences in most eukaryotes. Ribosomal DNA (rDNA) contains many insertions derived from mobile elements including non-long terminal repeat (non-LTR) retrotransposons. R2 is the well-characterized 28S rDNA-specific non-LTR retrotransposon family that is distributed over at least 4 bilaterian phyla. R2 is a large family sharing the same insertion specificity and classified into 4 clades (R2-A, -B, -C, and -D) based on the N-terminal domain structure and the phylogeny. There is no observation of horizontal transfer of R2; therefore, the origin of R2 dates back to before the split between protostomes and deuterostomes. Here, we in silico identified 1 R2 element from the sea anemone Nematostella vectensis and 2 R2-like retrotransposons from the hydrozoan Hydra magnipapillata. R2 from N. vectensis was inserted into the 28S rDNA like other R2, but the R2-like elements from H. magnipapillata were inserted into the specific sequence in the highly conserved region of the 18S rDNA. We designated the Hydra R2-like elements R8. R8 is inserted at 37 bp upstream from R7, another 18S rDNA-specific retrotransposon family. There is no obvious sequence similarity between targets of R2 and R8, probably because they recognize long DNA sequences. Domain structure and phylogeny indicate that R2 from N. vectensis is the member of the R2-D clade, and R8 from H. magnipapillata belongs to the R2-A clade despite its different sequence specificity. These results suggest that R2 had been generated before the split between cnidarians and bilaterians and that R8 is a retrotransposon family that changed its target from the 28S rDNA to the 18S rDNA.

Molecular Mechanisms for the Variation of Mitochondrial Gene Content and Gene Arrangement Among Chigger Mites of the Genus Leptotrombidium (Acari: Acariformes)

The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene arrangement among chigger mites of the genus Leptotrombidium. We found previously that the mt genome of Leptotrombidium pallidum has an extra gene for large-subunit rRNA (rrnL), a pseudo-gene for small-subunit rRNA (PrrnS), and three extra LNRs, additional to the 37 genes and an LNR typical of Metazoa. Further, the arrangement of mt genes of L. pallidum differs drastically from that of the hypothetical ancestor of the arthropods. To find to what extent the novel gene content and gene arrangement occurred in Leptotrombidium, we sequenced the entire or partial mt genomes of three other species, L. akamushi, L. deliense, and L. fletcheri. These three species share the arrangement of all genes with L. pallidum, except trnQ (for tRNA-glutamine). Unlike L. pallidum, however, these three species do not have extra rrnL or PrrnS and have only one extra LNR. By comparison between Leptotrombidium species and the ancestor of the arthropods, we propose that (1) the type of mt genome present in L. pallidum evolved from the type present in the other three Leptotrombidium species, and (2) three molecular mechanisms were involved in the evolution of mt gene content and gene arrangement in Leptotrombidium species.

Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models

A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide strong support at key nodes that were equivocal based on other molecular markers. Combining LSU sequences with those of the small subunit of the nuclear ribosome (SSU or 18S), we present a detailed working hypothesis of medusozoan relationships and discuss character evolution within this diverse clade. Stauromedusae, comprising the benthic, so-called stalked jellyfish, appears to be the sister group of all other medusozoans, implying that the free-swimming medusa stage, the motor nerve net, and statocysts of ecto-endodermal origin are features derived within Medusozoa. Cubozoans, which have had uncertain phylogenetic affinities since the elucidation of their life cycles, form a clade-named Acraspeda-with the scyphozoan groups Coronatae, Rhizostomeae, and Semaeostomeae. The polyps of both cubozoans and hydrozoans appear to be secondarily simplified. Hydrozoa is comprised by two well-supported clades, Trachylina and Hydroidolina. The position of Limnomedusae within Trachylina indicates that the ancestral hydrozoan had a biphasic life cycle and that the medusa was formed via an entocodon. Recently hypothesized homologies between the entocodon and bilaterian mesoderm are therefore suspect. Laingiomedusae, which has often been viewed as a close ally of the trachyline group Narcomedusae, is instead shown to be unambiguously a member of Hydroidolina. The important model organisms of the Hydra species complex are part of a clade, Aplanulata, with other hydrozoans possessing direct development not involving a ciliated planula stage. Finally, applying phylogenetic mixture models to our data proved to be of little additional value over a more traditional phylogenetic approach involving explicit hypothesis testing and bootstrap analyses under multiple optimality criteria. [18S; 28S; Cubozoa; Hydrozoa; medusa; molecular systematics; polyp; Scyphozoa; Staurozoa.].

Ultrastructural and molecular delineation of the Chytridiaceae (Chytridiales)

The Chytridiomycota is in need of taxonomic revision, especially the largest order, the Chytridiales. We analyzed 25 isolates in, or allied to, the Chytridium clade of this order. Isolates were selected based on one or more of the following criteria: (i) having a large subunit molecular sequence similar to that of the type of the genus Chytriomyces, (ii) having specific zoospore morphology, and (iii) currently classified as a species in the genus Chytriomyces . We examined ultrastructural characters and partial sequences of large subunit and small subunit rDNA and generated a phylogenetic hypothesis using maximum parsimony and Bayesian analyses. The sequence analyses strongly supported the Chytridiaceae, Phlyctochytrium, and Chytriomyces angularis clades, and each clade had a specific zoospore type. Developmental morphology of the thallus did not mirror the DNA-based phylogeny. Based on the results of phylogenetic analyses of sequences and ultrastructural characters, we emend the Chytridiaceae by including exogenous and polycentric development and define the family on the basis of a single zoospore type. Species identified as being in the genus Chytriomyces occur in several separate, well-supported clades along with species currently classified in seven other genera ( Asterophlyctis , Entophlyctis , Obelidium , Physocladia , Podochytrium , Rhizoclosmatium , and Siphonaria ), indicating that Chytriomyces as currently defined is polyphyletic.

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.

Molecular microbial biodiversity assessment: a biological indicator of soil health

The soil performs a variety of key functions: (i) provides the food, fuel, and fiber needs of the world's population, (ii) regulates the quality of the air and water, (iii) decomposes organic wastes, (iv) recycles nutrients, and (v) acts as a sink for pollutants (including global gases). Soil degradation is increasingly recognized as an urgent environmental issue and a crucial need exists for the capacity to evaluate soil health. After all, soil health is a key component in sustaining the different world's ecosystems and the myriad of natural and socioeconomic systems they support. In this respect, soil health has been defined as the "continued capacity of a specific kind of soil to function as a vital living system, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, to maintain or enhance the quality of air and water environments, and to support human health and habitation". A biological indicator is an organism, a part of an organism, or a community of organisms, used to obtain information about environmental quality. The assessment of microbial biodiversity has the potential to provide useful insight into the health and functioning of soil. Our inability to culture most microorganisms that are present in soils has, until recently, impaired studying the relationships between the structure and the function of soil microbial communities. This shortcoming has been recently overcome by using several molecular techniques that allow the detection, enumeration, and characterization of soil microorganisms without cultivation.

The symbiont Capsaspora owczarzaki, nov. gen. nov. sp., isolated from three strains of the pulmonate snail Biomphalaria glabrata is related to members of the Mesomycetozoea

While investigating the resistance of some strains of Biomphalaria glabrata to infection with Schistosoma mansoni, a unicellular eukaryotic symbiont was noted in the snail haemolymph. It was similar in appearance to Nuclearia sp. reported from B. glabrata. Sequences comprising the 18S, ITS1, 5.8S, ITS2 and the beginning of the 28S rDNA gene regions were obtained from symbionts isolated from three strains of B. glabrata, and compared with the same sequences obtained from a culture of Nuclearia sp. 18S rDNA sequences were identical for all four isolates. 18S rDNA sequences were used in a phylogenetic analysis to produce minimum evolution, maximum parsimony, maximum likelihood and Bayesian trees. All four analyses indicated that the B. glabrata symbiont is not closely related to Nuclearia but instead to the Mesomycetozoea, a recently recognised clade of symbiotic eukaryotes. Based on phylogenetic analysis, life history and morphological differences, the symbiont is described as a new genus and species, Capsaspora owczarzaki. Distinguishing characters are the presence of life cycle stage(s) that occur within snail haemolymph; ability to kill and ingest digenetic trematode larvae; ability to undergo asexual fission to produce daughter cells; absence of flagella, a mucous sheath and membranes containing chitin, elastin, or collagen; and presence of long unbranching pseudopodia and a penetration process. Using both polymerase chain reaction (PCR) and culturing techniques, the S. mansoni-resistant Salvador and 13-16-R1 strains were found to be significantly more likely to harbour the symbiont than the susceptible M line strain. Small but consistent sequence differences were noted among symbiont isolates from different snail strains, raising the possibility that the symbiont has diverged in different snail lineages. This suggests further that the symbiont is not restricted to albino lab-reared snails. A role, if any, of the symbiont in resistance awaits further study.

On the origin of the Hirudinea and the demise of the Oligochaeta

The phylogenetic relationships of the Clitellata were investigated with a data set of published and new complete 18S rRNA gene sequences of 51 species representing 41 families. Sequences were aligned on the basis of a secondary structure model and analysed with maximum parsimony and maximum likelihood. In contrast to the latter method, parsimony did not recover the monophyly of Clitellata. However, a close scrutiny of the data suggested a spurious attraction between some polychaetes and clitellates. As a rule, molecular trees are closely aligned with morphology-based phylogenies. Acanthobdellida and Euhirudinea were reconciled in their traditional Hirudinea clade and were included in the Oligochaeta with the Branchiobdellida via the Lumbriculidae as a possible link between the two assemblages. While the 18S gene yielded a meaningful historical signal for determining relationships within clitellates, the exact position of Hirudinea and Branchiobdellida within oligochaetes remained unresolved. The lack of phylogenetic signal is interpreted as evidence for a rapid radiation of these taxa. The placement of Clitellata within the Polychaeta remained unresolved. The biological reality of polytomies within annelids is suggested and supports the hypothesis of an extremely ancient radiation of polychaetes and emergence of clitellates.

Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity

Picoplankton--cells with a diameter of less than 3 microm--are the dominant contributors to both primary production and biomass in open oceanic regions. However, compared with the prokaryotes, the eukaryotic component of picoplankton is still poorly known. Recent discoveries of new eukaryotic algal taxa based on picoplankton cultures suggest the existence of many undiscovered taxa. Conventional approaches based on phenotypic criteria have limitations in depicting picoplankton composition due to their tiny size and lack of distinctive taxonomic characters. Here we analyse, using an approach that has been very successful for prokaryotes but has so far seldom been applied to eukaryotes, 35 full sequences of the small-subunit (18S) ribosomal RNA gene derived from a picoplanktonic assemblage collected at a depth of 75 m in the equatorial Pacific Ocean, and show that there is a high diversity of picoeukaryotes. Most of the sequences were previously unknown but could still be assigned to important marine phyla including prasinophytes, haptophytes, dinoflagellates, stramenopiles, choanoflagellates and acantharians. We also found a novel lineage, closely related to dinoflagellates and not previously described.

Temperature-based variation of rRNA secondary structure models: a case study in the insect Drosophila simulans, the land snail Isabellaria adriani, and the crustacean Daphnia pulex

The influence of a temperature default on ribosomal RNA (rRNA) secondary structure models was studied with the "Mfold" energy-optimization program. Folding models of the internal transcribed spacer (ITS) 1 rRNA for both Drosophila simulans (Insecta) and Isabellaria adriani (Gastropoda) were generated at two different temperatures. The folding models are compared with the models previously shown for the ITS-1 of D. melanogaster Oregon R strain and I. adriani. A search for phylogenetically informative ITS-1 folding motifs was conducted for D. simulans. In I. adriani, a new approach for ITS-1 secondary structure analyses is suggested. The paper also elucidates results inferred from three energy-optimizing programs (Mfold, GeneBee, and STAR). These three folding programs give different information on the structure and free energy of a ITS-1 rRNA molecule. Furthermore, secondary-structure models of the small subunit (ssu) rRNA of Daphnia pulex (Crustacea: Cladocera) were investigated. The ssu rRNA molecule is usually folded according to alignment information. Here, ssu folding patterns are computed with Mfold using two temperature conditions. The two Mfold models are compared with the alignment model previously suggested for D. pulex. Three cladoceran-specific motifs and a short stem motif within the ssu rRNA of eukaryotes are discussed with respect to structure and phylogenetic information.

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA

The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.