Nucleotide sequence of Clostridium pasteurianum 5S rRNA

On comparing two structured RNA multiple alignments

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server.

Use of statistical measures for analyzing RNA secondary structures

With more and more RNA secondary structures accumulated, the need for comparing different RNA secondary structures often arises in function prediction and evolutionary analysis. Numerous efficient algorithms were developed for comparing different RNA secondary structures, but challenges remain. In this article, a new statistical measure extending the notion of relative entropy based on the proposed stochastic model is evaluated for RNA secondary structures. The results obtained from several experiments on real datasets have shown the effectiveness of the proposed approach. Moreover, the time complexity of our method is favorable by comparing with that of the existing methods which solve the similar problem.

Sequence, proposed secondary structure, and phylogenetic analysis of the chloroplast 5S rRNA gene of the brown alga Pylaiella littoralis (L.) Kjellm

The chloroplast 5S rRNA gene of the brown alga Pylaiella littoralis (L.) Kjellm has been cloned and sequenced. The gene is located 23 bp downstream from the 3' end of the 23S rRNA gene. The sequence of the gene is as follows: GGTCTTG GTGTTTAAAGGATAGTGGAACCACATTGAT CCATATCGAACTCAATGGTGAAACATTATT ACAGTAACAATACTTAAGGAGGAGTCCTTTGGGAAGATAGCTTATGCCTAAGAC. A secondary structure model is proposed, and compared to those for the chloroplast 5S rRNAs of spinach and the red alga Porphyra umbilicalis. Cladograms based on chloroplast and bacterial 5S rRNA and rRNA gene sequences were constructed using the MacClade program with a user-defined character transformation in which transitions and transversions were assigned unequal step values. The topology of the resulting cladogram indicates a polyphyletic origin for photosynthetic organelles.

Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences

Nucleotide sequences of 5S rRNAs from 11 coryneform bacteria were determined. These were the type strains of Corynebacterium glutamicum, Corynebacterium xerosis, Brevibacterium linens, Arthrobacter globiformis, Cellulomonas biazotea, Aureobacterium testaceum, Curtobacterium citreum, Pimelobacter simplex, and Caseobacter polymorphus and representative strains of "Corynebacterium aquaticum" and Corynebacterium xerosis. A phylogenetic tree constructed from the sequences of these bacteria and published sequences indicated that the coryneform bacteria consist of a distinct eubacterial branch together with Streptomyces and Micrococcus spp. These bacteria could be further divided into four subgroups.

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data

The 5S rRNA sequences of eubacteria and mycoplasmas have been analyzed and a phylogenetic tree constructed. We determined the sequences of 5S rRNA from Clostridium innocuum, Acholeplasma laidlawii, Acholeplasma modicum, Anaeroplasma bactoclasticum, Anaeroplasma abactoclasticum, Ureaplasma urealyticum, Mycoplasma mycoides mycoides, Mycoplasma pneumoniae, and Mycoplasma gallisepticum. Analysis of these and published sequences shows that mycoplasmas form a coherent phylogenetic group that, with C. innocuum, arose as a branch of the low G+C Gram-positive tree, near the lactobacilli and streptococci. The initial event in mycoplasma phylogeny was formation of the Acholeplasma branch; hence, loss of cell wall probably occurred at the time of genome reduction to approximately to 1000 MDa. A subsequent branch produced the Spiroplasma. This branch appears to have been the origin of sterol-requiring mycoplasmas. During development of the Spiroplasma branch there were several independent genome reductions, each to approximately 500 MDa, resulting in Mycoplasma and Ureaplasma species. Mycoplasmas, particularly species with the smallest genomes, have high mutation rates, suggesting that they are in a state of rapid evolution.

The 5S ribosomal RNAs of Paracoccus denitrificans and Prochloron

The nucleotide sequences of the 5S rRNAs of Paracoccus denitrificans and Prochloron sp. are (formula: see text), respectively. Specific phylogenetic relationships of P. denitrificans with purple non-sulphur bacteria, and of Prochloron with cyanobacteria are demonstrated, and unique features of potential secondary structure are described.

Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable

The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.

Evolution of membrane bioenergetics

One of the first problems encountered by primitive cells was that of volume regulation; the continuous entry of ions, (eg, NaCl) and water in response to the internal colloid osmotic pressure threatening to destroy the cell by lysis. We propose that to meet this environmental challenge cells evolved an ATP-driven proton extrusion system plus a membrane carrier that would exchange external protons with internal Na+. With the appearance of the ability to generate proton gradients, additional mechanisms to harness this source of energy emerged. These would include proton-nutrient cotransport, K+ accumulation, nucleic acid entry, and motility. A more efficient system for the uptake of certain carbohydrates by vectorial phosphorylation via the PEP-phosphotransferase system probably appeared rather early in the evolution of anaerobic bacteria. The reversal of the proton-ATPase reaction to give net ATP synthesis became possible with the development of other types of efficient proton transporting machinery. Either light-driven bacterial rhodopsin or a redox system coupled to proton translocation would have served this function. Oxidation of one substrate coupled to the reduction of another substrate by membrane-bound enzymes evolved in such a manner that protons were extruded from the cell during the reaction. The progressive elaboration of this type of redox proton pump permitted the use of exogenous electron acceptors, such as fumarate, sulfate, and nitrate. The stepwise growth of these electron transport chains required the accretion of several flavoproteins, iron-sulfur proteins, quinones, and cytochromes. With modifications of these four basic components a chlorophyll-dependent photosynthetic system was subsequently evolved. The oxygen that was generated by this photosynthetic system from water would eventually accumulate in the atmosphere of the earth. With molecular oxygen present, the emergence of cytochrome oxidase would complete the respiratory chain. The proton economy of membrane energetics has been retained by most present-day microorganisms, mitochondria, chloroplasts, and cells of higher plants. A secondary use of the energy stored as an electrochemical difference of Na+ for powering membrane events probably also evolved in microorganisms. The exclusive age of the Na+ economy is distinctive of the plasma membrane of animal cells; the Na+-K+ ATPase sets up an electrochemical Na+ gradient that provides the energy for osmoregulation, Na+-nutrient co-transport, and the action potential of excitable cells.

Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes

The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis and Streptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided for B. cereus and Sporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.