Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials, 37 placentals), including 11 new sequences, were employed to establish a ``core' secondary structure model for mammalian 12S rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence for base-pairing in the form of compensatory mutations. In cases where compensatory evidence was not available among mammalian sequences, we evaluated evidence among other vertebrate 12S rRNAs. Our results suggest a core model for secondary structure in mammalian 12S rRNAs with deletions as well as additions to the Gutell (1994: Nucleic Acids Res. 22) models for Bos and Homo. In all, we recognize 40 stems, 34 of which are supported by at least some compensatory evidence within Mammalia. We also investigated the occurrence and conservation in mammalian 12S rRNAs of nucleotide positions that are known to participate in the decoding site in E. coli. Twenty-four nucleotide positions known to participate in the decoding site in E. coli also occur among mammalian 12S rRNAs and 17 are invariant for the same base as in E. coli. Patterns of nucleotide substitution were assessed based on our secondary structure model. Transitions in loops become saturated by approximately 10–20 million years. Transitions in stems, in turn, show partial saturation at 20 million years but divergence continues to increase beyond 100 million years. Transversions accumulate linearly beyond 100 million years in both stems and loops although the rate of accumulation of transversions is three- to fourfold higher in loops. Presumably, this difference results from constraints to maintain pairing in stems. Received: 21 June 1995 / Accepted: 25 March 1996     

POLYPHASIC CHARACTERIZATION OF DOLICHOSPERMUM SPP. AND SPHAEROSPERMOPSIS SPP. (NOSTOCALES,CYANOBACTERIA): MORPHOLOGY, 16S rRNA GENE SEQUENCES AND FATTY ACID AND SECONDARY METABOLITE PROFILES1

The genera Dolichospermum (Ralfs ex Bornet et Flahault) Wacklin, L. Hoffm. et Komárek and Sphaerospermopsis Zapomělová, Jezberová, Hrouzek, Hisem, K. ?eháková et Komárk.‐Legn. represent a highly diversified group of planktonic cyanobacteria that have been recently separated from the traditional genus Anabaena Bory ex Bornet et Flahault. In this study, morphological diversity, phylogeny of the 16S rRNA gene, production of fatty acids, and secondary metabolite profiles were evaluated in 33 strains of 14 morphospecies isolated from the Czech Republic. Clustering of the strains based on 16S rRNA gene sequences corresponded to wider groups of species in terms of morphology. The overall secondary metabolite and fatty acid profiles, however, were not correlated to each other and neither were they correlated to the 16S rRNA phylogeny nor the morphology of the strains. Nevertheless, a minor part of the detected secondary metabolites (19% of all compounds) was present only in close relatives and can be thus considered as autapomorphic features.     

The nucleotide sequence of the cytoplasmic 5S rRNA from the horsetail, Equisetum arvense

Using 3'- and 5'-end labelling sequencing techniques, the following sequence for the cytoplasmic 5S rRNA of the horsetail Equisetum arvense could be determined: (sequence in text). This sequence exhibits all features expected for higher plant cytoplasmic 5S rRNAs, and can be fitted to the secondary structure model for 5S rRNA proposed by De Wachter et al. (15).     

The nucleotide sequence of ribosomal 5S RNA from Rhizobium meliloti: comparison with 5S rRNA of Agrobacterium

The complete nucleotide sequence of R. meliloti 5S ribosomal RNA has been determined and compared with the already known sequence of A. tumefaciens 5S rRNA (Vandenberghe et al., 1985, Eur. J. Biochem., 149, 537-542) and of other 5S rRNAs from Rodobacteria Alpha-2 (Wolters et al., 1988, Nucleic Acids Res., 16, rl-r70). The differences found at eight positions (23, 73, 83, 72 in helical fragments; 16, 40, 88 in loops; 54 in bulge), which might affect secondary structures of 5S rRNA, are small. Moreover, the sequence analysis specifies both variable and common positions in 5S rRNA secondary structure of Rodobacteria Alpha-2.     

Cytogenetic characterization of three Hypericum species by in situ hybridization

The chromosomal positions of the 5S/25S rRNA genes of Hypericum perforatum (2n=32), H. maculatum (2n=16) and H. attenuatum (2n=32) were comparatively determined by FISH, and six, three and seven chromosome pairs of the respective karyotypes were subsequently distinguished. The rDNA loci between H. perforatum and H. maculatum seem to be identical (with respect to the ploidy difference), indicating that H. perforatum probably arose by autotetraploidization from an ancestor closely related to H. maculatum. The positional differences between the 5S rRNA gene loci of H. perforatum and H. maculatum on the one hand and H. attenuatum on the other argue against a previous hypothesis according to which H. perforatum originated from a remote interspecific hybridization between H. maculatum and H. attenuatum. Received: 7 October 1999 / Accepted: 23 November 1999     

Species-specific expression of sialosyl-Lex on polymorphonuclear leukocytes (PMN), in relation to selectin-dependent PMN responses

Sialosyl-Le^x (SLe^x) and its positional isomer sialosyl-Le^a are the epitopes recognized by the lectin domain of E- and P-selectins. Expression of SLe^x in polymorphonuclear leukocytes (PMN) plays an important role in recruitment of these cells at sites of inflammation through activation of selectins. We studied expression of SLe^x in PMN of seven mammalian species in comparison with that in humans. Only PMN of humans (no other species) expressed SLe^x or other lacto-series epitopes such as Le^x or Le^y. The observed absence of these epitopes in rat PMN seems inconsistent with recent reports that the lung inflammation process in a rat model is inhibited by perfusion of SLe^x oligosaccharide (Mulligan MS,et al. (1993a)Nature 364:149; (1993b)J Exp Med 178:623). Rat selectins may be able to recognize SLe^x, even though this epitope is absent in rat PMN.Abbreviations FITC fluorescein isothiocyanate - mAb monoclonal antibody - PMN polymorphonuclear leukocytes - SLe^a sialosyl-Le^a antigen - SLe^x sialosyl-Le^x antigen     

Chemical modification studies and the secondary structure of HeLa cell 5.8S rRNA.

Various secondary structure models have been proposed for 5.8 S rRNA. In this paper HeLa cell 5.8 S rRNA is shown to possess several sites that are reactive to carbodiimide at 25 degrees, and other regions that are unreactive. Previous work has established the distribution of reactive and unreactive cytidine residues along the primary structure (11). The secondary structure model of Nazar et al. (7) is fully compatible with the chemical reactivity data whereas other models are partly incompatible. We conclude that the model of Nazar et al. provides the best approximation so far available to the conformation of isolated 5.8 S rRNA. Findings on the effect temperature on the chemical reactivity of different parts of the structure are summarized. The findings described in this paper should provide a basis for examining the specific interaction of 5.8 S rRNA with 28 s rRNA.     

Research on polychaete annelid osmoregulatory peptide(s) by immunocytochemical and physiological approaches. Computer reconstruction of the brain and evidence for a role of angiotensin-like molecules in Nereis (Hediste) diversicolor OF Müller

Summary— Immunohistochemical and physiological studies were carried out on Nereis (Hediste) diversicolor OF Müller in order to obtain evidence concerning the neuroendocrine control of polychaete osmoregulation. The occurrence in this animal of peptides immunologically related to mammalian angiotensin II and I (AII and AI) and oxytocin (OT) was demonstrated in the brain and the ventral nerve cord (VNC) perikarya and nerve fibres as well as in a few peripheral structures (peripheral nerves, epithelial cells, nuchal organ, intestine and nephridia). The exact localization of immunoreactive cells was achieved by serial sections of brain and ventral nerve cord followed by a three-dimensional reconstruction of brain ganglionic nuclei using the CATIA (‘Conception Assistée Tridimensionnelle Inter Active’) Dassault system program. Injections of polyclonal antisera against AII or OT provoked a partial inhibition of the increase in body weight in Nereis exposed to hypo-osmotic medium. The effect of a-AII seemed more pronounced than that of a-OT. In a subsequent test, injections of synthetic AII and AII-amide (peptide recently isolated from an achaete (Salzet et al (1995) J Biol Chem 270, 1575–1582) enhanced the increase in body weight and, therefore, strenghthened the hypothesis of the neuroendocrine control of Nereis osmoregulation. The antidiuretic effect of both synthetic peptides in this study was indicative of the exact role of Nereis endogenous melecule(s). AII was less potent than its amidated form. If AI-like can easily be struck off the list of putative endogenous osmoregulaory factors, the role of OT-like substance in Nereis osmoregulation, which is partially demonstrated in this study, needs to be clarified by further physiological experiments using injection of synthetic peptide(s) or endogenous substance(s). All these results are discussed and compared to those recently obtained in an achaete annelid (Salzet et al (1993) Brain Res 631, 247–255; Salzet et al (1993) Brain Res 601, 173–184; Salzet et al (1995) J Biol Chem 270, 1575–1582.     

Diversity of Microorganisms Isolated from Amber

Abstract Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25–40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice. Received: 14 December 1998; Accepted: 16 March 1999     

Mutations Stabilize Small Subunit Ribosomal RNA in Desiccation-Tolerant Cyanobacteria <Emphasis Type="Italic">Nostoc</Emphasis>

The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 16S rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.     

Two accurate sequence,structure, and phylogenetic template-based RNA alignment systems

Background

The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data.

Methods

Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment.

Results

The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed.

Conclusions

Both CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.

     

Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)

We inferred secondary structure models of the internal transcribed spacers (ITS) 1 and 2 of bush crickets using a combined comparative and thermodynamic approach. The inferred secondary structure models were used to account for interdependency of interacting nucleotides in a phylogenetic analysis of the bush cricket genus Poecilimon. Our analysis indicates that the two previously reported conformational structures (i.e., hairpin and ring) of ITS2 are likely to fold in bush crickets as well and that both predicted structures are similar to those proposed for other eukaryotes. Comparing predicted ITS1 secondary structure models proved to be difficult because of substantial variation in their nucleotide sequence length. Our study revealed that the phylogenetic signal of ITS1 and ITS2 is largely congruent with that preserved in the mitochondrial genes 16S rRNA, tRNA‐Val and 12S rRNA. The phylogenetic signal in both the nuclear and the mitochondrial genome question the monophyly of the genus Poecilimon: species of the genera Poecilimonella, Parapoecilimon, Polysarcus and Phonochorion consistently cluster within Poecilimon.     

Speciation and chromosomal evolution of the Palearctic species of chironomids of the genus Sergentia Kieffer (Diptera, Chironomidae): Divergence of the Karyotypes of S. baueri Wülker et al., 1999, S. prima Proviz et al., 1997, S. electa Proviz et al., 1999 and their relationship with the endemic species from Baikal lake

The banding structures of chromosomes of three Palearctic species of chironomids of the genus Sergentia Kieffer, 1922 from the Irkutsk reservoir were comparatively analyzed: S. baueri Wülker et al., 1999 (2n = 8), S. prima Proviz et al., 1997 (2n = 8), and S. electa Proviz et al., 1999 (2n = 6). The S. baueri karyotype was taken as a standard in chromosome mapping. It was established that in contrast to S. baueri and S. prima the S. electa karyotype was formed due to a complex translocation: transfer of chromosome IV in the median part of chromosome III. The sequences of chromosome I bands were found to be completely homologous in all Palearctic species and in S. rara Proviz et al., 1999 (2n = 8) taken as the original species in the group of Baikalian endemics. In both groups, seven homozygous inversions were detected, of which the common one is the inversion in chromosome III. It was assumed on the basis of the results of the karyological analysis that among the Palearctic species S. baueri is most similar to the Baikalian endemics and S. electa is phylogenetically closer to S. prima. Specific features of the chromosome and morphological evolutions of the Sergentia genus species are considered.     

Phylogeny of Ultra-Rapidly Evolving Dinoflagellate Chloroplast Genes: A Possible Common Origin for Sporozoan and Dinoflagellate Plastids

Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements. Received: 27 December 1999 / Accepted: 24 March 2000     

Molecular ecology ofFrankia: Advantages and disadvantages of the use of DNA probes

Ecological studies on the actinomyceteFrankia are often influenced by the difficulty to isolate and identify this microorganism. The application of molecular biological techniques offers possibilities to detect microbes without isolation and cultivation.Nif genes or whole plasmids can serve as targets for the design of specific probes. Alternatively, ribosomal RNA (rRNA), commonly used in modern phylogenetic studies, can be used as a target molecule in ecological studies. This paper gives an overview of new developments on the use of 16S rRNA as a target molecule for oligonucleotide probes. Group-specific sequences in the 16S rRNA ofFrankia can be used as targets for oligonucleotide probes that a) recognize ineffectiveFrankia strains onAlnus, b) recognize effective strains onAlnus, c) recognize allFrankia strains tested so far. The present paper summarizes the essential steps needed for the use of these probes for the detection ofFrankia strains in soil without isolation and cultivation.     

An interfacial equilibria model for the electrokinetic properties of a fat emulsion. Part III: A predictive computer model

Abstract

The semi-empirical thermodynamic model for the binding of metal ions to an emulsion (intralipid 20%) reported previously (Hall et al., 1991 ; Gaskin et al., 1993) is incorporated into a thermodynamic computer model. This permits the zeta potential and emulsion stability together with precipitate formation to be estimated for any intravenous nutrition regimen. A regimen frequently used in the intravenous nutrition of patients is considered in this modeling study. The effect of solution pH and calcium on the zeta potential of the emulsion is predicted. Calcium and magnesium are the only metal cations which are predicted to be of importance when considering stability of this emulsion.     

Species diversity and ecosystem response to carbon dioxide fertilization: conclusions from a temperate forest model

This paper explores how the response of a temperate forest ecosystem to climate change might depend on species diversity and community change. In particular, we look at the dynamics of a model of temperate forest growth under doubled CO₂. We combine a detailed, field-calibrated model of forest dynamics (Pacala et al 1993) with greenhouse data on the range of seedling biomass growth response to doubled CO₂ concentrations (Bazzaz et al. 1990; Bazzaz & Miao 1993). Because total ecosystem response to climate change depends delicately on many environmental variables other than CO₂, we isolate the effects of community change by comparing runs of the regular model, allowing dynamic community change, with runs of a reduced model that holds species composition static by using a single tree species with average parameters. Simulations that allowed community change instead of holding species composition constant showed a roughly 30% additional increase in total basal area over time scales of 50-150 years. Although the model omits many possible feedbacks and mechanisms associated with climate change, it suggests the large potential effects that species differences and feedbacks can have in ecosystem models and reinforces the possible importance of diversity to ecosystem function (Naeem et ai 1994; Tilman & Downing 1994) over time scales within the planning horizon for global change policy.     

How to avoid undesirable interactions during ribosome assembly?

Ribosome subunit assembly in bacteria is assisted by several non‐ribosomal proteins, the absence of which leads to assembly defects. The two DEAD‐box RNA helicases SrmB and DeaD/CsdA are required for efficient assembly of the ribosome large subunit, in particular at low temperature, but their sites of action on rRNA were not known until now. In this issue of Molecular Microbiology, Proux et al. show that SrmB acts far away from its tethering site on the assembly intermediate particle. A genetic screen identified mutations in complementary sequences of 23S and 5S rRNA that help to bypass SrmB deficiency, partially correcting the large subunit assembly defect. The results suggest that 5S rRNA and 23S rRNA can interact via base‐pairing, forming a non‐native structure that needs to be corrected. The authors discuss attractive hypotheses on SrmB acts during large subunit assembly.