Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution

Members of the rDNA multigene family within a species do not evolve independently, rather, they evolve together in a concerted fashion. Between species, however, each multigene family does evolve independently indicating that mechanisms exist which will amplify and fix new mutations both within populations and within species. In order to evaluate the possible mechanisms by which mutation, amplification and fixation occur we have determined the level of linkage disequilibrium between two polymorphic sites in human ribosomal genes in five racial groups and among individuals within two of these groups. The marked linkage disequilibrium we observe within individuals suggests that sister chromatid exchanges are much more important than homologous or nonhomologous recombination events in the concerted evolution of the rDNA family and further that recent models of molecular drive may not apply to the evolution of the rDNA multigene family.     

Ribosomal RNA phylogenetics: the third dimension

With integration of secondary structures, ribosomal genes have once again become very popular for phylogenetic analyses. This additional source of information to the nucleotide sequence provides a massive boost for taxonomic inferences. Herein, we propose that in the near future a further benefit for phylogenetics with such genes will be very likely by inclusion of the third dimension. For the first time, we determined the tertiary structure of the ribosomal internal transcribed spacer 2 for Chlamydomonas rheinhardtii by application of two different in silico prediction algorithms. We compared these methods with focus on phylogenetic usability. Further, we determined the tertiary structures for closely related green algae to provide a small phylogenetic example. The results suggest that the tertiary structure inherits evolutionary information observable neither within the sequence nor in the secondary structure.     

逆转录病毒基因组RNA的二聚作用

逆转录病毒科(Retroviridae)是一成员众多、易变异的RNA病毒科.在逆转录病毒复制周期内,所有逆转录病毒均将两拷贝的单股正链RNA带入病毒粒子[1,2].在此过程中,遗传物质--基因组RNA能顺利包装入病毒粒子是病毒复制与繁衍的关键,而基因组RNA通过二聚作用(Dimer-ization)形成二聚体(Dimer)是包装逆转录病毒的前提.     

Variation in the Complex Carbohydrate Biosynthesis Loci of Acinetobacter baumannii Genomes

Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide) forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones.     

Structural Aspects of Ribosomal RNA Recognition by Ribosomal Proteins

This review is focused on the structural aspects of interaction between ribosomal proteins and ribosomal RNA in bacterial ribosomes and complexes of ribosomal proteins with specific fragments of ribosomal RNA. Special attention is given to the recognition of specific spatial architecture of the double-stranded ribosomal RNA by ribosomal proteins and to the role of unstructured protein regions in stabilization of distant ribosomal RNA segments.     

rrndb: the Ribosomal RNA Operon Copy Number Database

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.     

Epigenetics of Ribosomal RNA Genes

Biochemistry (Moscow) - This review is focused on biology of genes encoding ribosomal RNA (rRNA) in mammals. rRNA is a structural component of the most abundant cellular molecule, the ribosome....     

Dynamics of Ribosomal RNA Structure

Abstract

The structural dynamics of ribosomal 5S RNAs have been investigated by probing single strandedness through enzymatic cleavage and chemical modification. This comparative study includes 5S rRNAs from E. coli, B. stearothermophilus, T. thermophilics, H. cutirubrum, spinach chloroplast, spinach cytomplasm, and Artemia salina. The structural studies support a unique tertiary interaction in eubacterial 5S rRNAs, involving nucleotides around positions 43 and 75. In addition long range structural effects are demonstrated in E. coli 5S rRNA due to the conversion of C to U at position 92.     

Concerted Evolution in the Ribosomal RNA Cistron

Background

Gene conversion is the mechanism proposed to be responsible for the homogenization of multigene families such as the nuclear ribosomal gene clusters. This concerted evolutionary process prevents individual genes in gene clusters from accumulating mutations. The mechanism responsible for concerted evolution is not well understood but recombination during meiosis has been hypothesized to play a significant role in this homogenization. In this study we tested the hypothesis of unequal crossing over playing a significant role in gene conversion events within the ribosomal RNA cistron during meiosis, mitosis or both life stages in the fungal tree pathogen Ceratocystis manginecans.

Methods

Ceratocystis manginecans, a haploid ascomycete, reproduces homothallically and was found to have two distinct sequences within the internally transcribed spacer (ITS) region of the ribosomal RNA cistron. The different ITS types were scored using PCR-RFLP assays and chi-square analyses to determine the level of significance of the changes in the ratios of the ITS types.

Results

The relative ratios of the two ITS sequence types changed when the fungal isolates were cultured vegetatively or allowed to produced sexual structures and spores. These active changes were shown to occur more frequently during meiosis than mitosis.

Conclusion

The evidence presented provides concrete support for homogenization in the rRNA gene clusters found in this fungus and that the most reasonable explanation for this process is unequal crossing over.     

Ribosomal RNA and the major lines of evolution: a perspective

Does the "universal tree" based on small-subunit ribosomal RNA sequences show the phylogenetic relationship of all modern organisms? The answer is "yes" only if all these rRNAs are orthologous. Herein I argue that the major rRNA lineages (e.g. eubacterial, one or more archaebacterial and eukaryotic nucleocytoplasmic) probably arose from a divergent population of rRNAs in the progenote, antedating the universal common ancestral organism. Thus the major lineages of rRNA are probably not orthologous, but paralogous. The extrapolated date for the origin of the common ancestral small-subunit rRNA (3.6-4.7 x 10(9) years ago) is consistent with major rRNA lineages being paralogous. This perspective on the early evolution of genes and organisms rationalizes the presence of unexpected ribosomal characters in microsporidia, and bears on xenogenous and endogenous theories of the origin of the organelles in eukaryotes.     

Persistent Cytoplasmic Synthesis of Ribosomal Proteins during the Selective Inhibition of Ribosomal RNA Synthesis

Synthesis of ribosomal proteins takes place in the cytoplasm and is independent of nuclear synthesis of ribosomal RNA.     

RNA Regulatory Elements in the Genomes of Simple Retroviruses

The RNA genomes of simple retroviruses encode three genes (gag, pol,andenv) which are required for replication. In addition, there are at least three well-definedcis-acting structures which regulate important aspects of the viral life cycle. The packaging signal at the 5′ end of the RNA tags the genomic RNA for specific encapsidation into assembling virus. Since viral Env proteins are translated from spliced mRNAs,cis-acting splicing signals ensure that the proper ratio of spliced and unspliced viral RNAs is present in the infected cell. Finally,cis-acting elements at the 3′ end of the genome promote the export of unspliced RNAs from the nucleus for translation and encapsidation.