Internal ribosomal entry site lacks secondary structure

The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the observation that, in the natural _vpu-env_ bicistronic mRNA in HIV-1, the mRNA segment (60 nt) immediately upstream of the initiation AUG of _env_ has the weakest secondary structure among all dominant HIV-1 mRNA species. These results suggest a unified model of alternative translation initiation

Mating System Of Natural Populations Of The White-footed Mouse, Peromyscus Leucopus

The mating system of the white-footed mouse, Peromyscus leucopus has caused much confusion among evolutionary biologists interested in the social biology of the species. Some studies documented well-developed paternal behaviour (Horner 1947; McCarty and Southwick 1977; Hartung and Dewsburry 1979) and pair-activity (Mineau and Madison 1977). These results favour a monogamous mating system. Other studies proposed polyandry based on spatial association between adult males and females (Myton 1974). Still others argued for polygyny (Cicirello and Wolff, in press). All these studies are speculative.;I studied the mating system of the species with four different approaches. I first tested whether oestrous females would reject strange males and accept familiar males as mates, then examined whether paternal behaviour documented in previous studies might be unnatural behaviour caused by confined caging conditions. Meanwhile, I investigated association patterns of adult males and females in their natural habitats, and collected genetic information on mothers and their young to test the presence of multiple paternity within single litters.;Oestrous females readily accepted multiple-male insemination, with no indication of discriminating between familiar and strange males. Males did not provide paternal care of any sort in a large enclosure with 4 nest boxes and stopped interacting with the females once the copulation was over. The majority of experimental females showed aggression towards males except during their oestrus. In their natural habitats, females close to oestrus have more adult males nearby than females far from oestrus, indicating that adult males adjusted their position in relation to breeding status of females. Genetic analysis revealed that 25-100% of field-conceived litters were sired by multiple males. I conclude that promiscuity is a prevailing feature of the mating system of P. leucopus, with males exhibiting serial polygyny and females simultaneous polyandry. Adaptive significance of this mating system is discussed in relation to physiology, ecology and life history characters of the species

The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses

<p>Abstract</p> <p>Background</p> <p>Fungal and animal mitochondrial genomes typically have one tRNA for each synonymous codon family. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of a tRNA anticodon should evolve towards maximizing Watson-Crick base pairing with the most frequently used codon within each synonymous codon family, whereas the wobble versatility hypothesis argues that the nucleotide at the wobble site should be occupied by a nucleotide most versatile in wobble pairing, i.e., the tRNA wobble nucleotide should be G for NNY codon families, and U for NNR and NNN codon families (where Y stands for C or U, R for A or G and N for any nucleotide).</p> <p>Results</p> <p>We here integrate these two traditional hypotheses on tRNA anticodons into a unified model based on an analysis of the wobble costs associated with different wobble base pairs. This novel approach allows the relative cost of wobble pairing to be qualitatively evaluated. A comprehensive study of 36 fungal genomes suggests very different costs between two kinds of U:G wobble pairs, i.e., (1) between a G at the wobble site of a tRNA anticodon and a U at the third codon position (designated M_U3:G) and (2) between a U at the wobble site of a tRNA anticodon and a G at the third codon position (designated M_G3:U).</p> <p>Conclusion</p> <p>In general, M_U3:Gis much smaller than M_G3:U, suggesting no selection against U-ending codons in NNY codon families with a wobble G in the tRNA anticodon but strong selection against G-ending codons in NNR codon families with a wobble U at the tRNA anticodon. This finding resolves several puzzling observations in fungal genomics and corroborates previous studies showing that U3:G wobble is energetically more favorable than G3:U wobble.</p

An Improved Implementation of Codon Adaptation Index

Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular. Current computational implementations have a number of problems leading to various systematic biases. I illustrate these problems and provide a better computer implementation to solve these problems. The improved CAI can predict protein production better than CAI from other commonly used implementations

Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances

I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a cherry is a pair of adjacent leaves descending from the most recent common ancestor), and the other with two. When genetic distances are underestimated, the 3-cherry tree shape is favored with either the ME or FM criterion. When the genetic distances are overestimated, the ME criterion favors the 2-cherry tree, but the direction of bias with the FM criterion depends on whether negative branches are allowed, i.e. allowing negative branches favors the 3-cherry tree shape but disallowing negative branches favors the 2-cherry tree shape. The extent of the bias is explored by computer simulation of sequence evolution

Factors Affecting Splicing Strength of Yeast Genes

Accurate and efficient splicing is of crucial importance for highly-transcribed intron-containing genes (ICGs) in rapidly replicating unicellular eukaryotes such as the budding yeast Saccharomyces cerevisiae. We characterize the 5′ and 3′ splice sites (ss) by position weight matrix scores (PWMSs), which is the highest for the consensus sequence and the lowest for splice sites differing most from the consensus sequence and used PWMS as a proxy for splicing strength. HAC1, which is known to be spliced by a nonspliceosomal mechanism, has the most negative PWMS for both its 5′ ss and 3′ ss. Several genes under strong splicing regulation and requiring additional splicing factors for their splicing also have small or negative PWMS values. Splicing strength is higher for highly transcribed ICGs than for lowly transcribed ICGs and higher for transcripts that bind strongly to spliceosomes than those that bind weakly. The 3′ splice site features a prominent poly-U tract before the 3′AG. Our results suggest the potential of using PWMS as a screening tool for ICGs that are either spliced by a nonspliceosome mechanism or under strong splicing regulation in yeast and other fungal species

DNA methylation and Mycoplasma genomes

Abstract. DNA methylation is one of the many hypotheses proposed to explain the observed deficiency in CpG dinucleotides in a variety of genomes covering a wide taxonomic distribution. Recent studies challenged the methylation hypothesis on empirical grounds. First, it cannot explain why the Mycoplasma genitalium genome exhibits strong CpG deficiency without DNA methylation. Second, it cannot explain the great variation in CpG deficiency between M. genitalium and M. pneumoniae that also does not have CpG-specific methyltransferase genes. I analyzed the genomic sequences of these Mycoplasma species together with the recently sequenced genomes of M. pulmonis, Ureaplasma urealyticum, and Staphylococcus aureus, and found the results fully compatible with the methylation hypothesis. In particular, I present compelling empirical evidence to support the following scenario. The common ancestor of the three Mycoplasma species has CpG-specific methyltransferases, and has evolved strong CpG deficiency as a result of the specific DNA methylation. Subsequently, this ancestral genome diverged into M. pulmonis and the common ancestor of M. pneumoniae and M. genitalium. M. pulmonis has retained methyltransferases and exhibits the strongest CpG deficiency. The common ancestor lost the methyltransferase gene and then diverged into M. genitalium and M. pneumoniae. M. genitalium and M. pneumoniae, after losing methylation activities, began to regain CpG dinucleotides through random mutation. M. genitalium evolved more slowly than M. pneumoniae, gained relatively fewer CpG dinucleotides, and is more CpGdeficient

Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes.

Abstract The H-strand of vertebrate mitochondrial DNA is left single-stranded for hours during the slow DNA replication. This facilitates CYU mutations on the H-strand (and consequently GYA mutations on the L-strand) via spontaneous deamination which occurs much more frequently on single-stranded than on double-stranded DNA. For the 12 coding sequences (CDS) collinear with the L-strand, NNY synonymous codon families (where N stands for any of the four nucleotides and Y stands for either C or U) end mostly with C, and NNR and NNN codon families (where R stands for either A or G) end mostly with A. For the lone ND6 gene on the other strand, the codon bias is the opposite, with NNY codon families ending mostly with U and NNR and NNN codon families ending mostly with G. These patterns are consistent with the strand-specific mutation bias. The codon usage biased towards C-ending and A-ending in the 12 CDS sequences affects the codon-anticodon adaptation. The wobble site of the anticodon is always G for NNY codon families dominated by C-ending codons and U for NNR and NNN codon families dominated by A-ending codons. The only, but consistent, exception is the anticodon of tRNA-Met which consistently has a 5V-CAU-3V anticodon base-pairing with the AUG codon (the translation initiation codon) instead of the more frequent AUA. The observed CAU anticodon (matching AUG) would increase the rate of translation initiation but would reduce the rate of peptide elongation because most methionine codons are AUA, whereas the unobserved UAU anticodon (matching AUA) would increase the elongation rate at the cost of translation initiation rate. The consistent CAU anticodon in tRNA-Met suggests the importance of maximizing the rate of translation initiation.

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesian methods are under heavy development, as they offer the possibility to solve a number of long-standing issues and to integrate several steps of the phylogenetic analyses into a single framework. Specific topics include not only phylogenetic reconstruction, but also the comparison of phylogenies, the detection of adaptive evolution, and the estimation of divergence times between species

A General Model of Codon Bias Due to GC Mutational Bias

Background - In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a measure of third position GC content. For individual amino acids as well, G/C ending codons usage generally increases with increasing GC bias and decreases with increasing AT bias. Arginine and leucine, amino acids that allow GC-changing synonymous substitutions in the first and third codon positions, have codons which may be expected to show different usage patterns. // Principal Findings - In analyzing codon usage bias in hundreds of prokaryotic and plant genomes and in human genes, we find that two G-ending codons, AGG (arginine) and TTG (leucine), unlike all other G/C-ending codons, show overall usage that decreases with increasing GC bias, contrary to the usual expectation that G/C-ending codon usage should increase with increasing genomic GC bias. Moreover, the usage of some codons appears nonlinear, even nonmonotone, as a function of GC bias. To explain these observations, we propose a continuous-time Markov chain model of GC-biased synonymous substitution. This model correctly predicts the qualitative usage patterns of all codons, including nonlinear codon usage in isoleucine, arginine and leucine. The model accounts for 72%, 64% and 52% of the observed variability of codon usage in prokaryotes, plants and human respectively. When codons are grouped based on common GC content, 87%, 80% and 68% of the variation in usage is explained for prokaryotes, plants and human respectively. // Conclusions - The model clarifies the sometimes-counterintuitive effects that GC mutational bias can have on codon usage, quantifies the influence of GC mutational bias and provides a natural null model relative to which other influences on codon bias may be measured