Search

All chordates share a basic body plan and many common features of early development. Anteroposterior (AP) regions of the vertebrate neural tube are specified by a combinatorial pattern of Hox gene expression that is conserved in urochordates and cephalochordates. Another primitive feature of Hox gene regulation in all chordates is a sensitivity to retinoic acid during embryogenesis, and recent developmental genetic studies have demonstrated the essential role for retinoid signalling in vertebrates. Two AP regions develop within the chordate neural tube during gastrulation: an anterior 'forebrain-midbrain' region specified by Otx genes and a posterior 'hindbrain-spinal cord' region specified by Hox genes. A third, intermediate region corresponding to the midbrain or midbrain-hindbrain boundary develops at around the same time in vertebrates, and comparative data suggest that this was also present in the chordate ancestor. Within the anterior part of the Hox-expressing domain, however, vertebrates appear to have evolved unique roles for segmentation genes, such as Krox-20, in patterning the hindbrain. Genetic approaches in mammals and zebrafish, coupled with molecular phylogenetic studies in ascidians, amphioxus and lampreys, promise to reveal how the complex mechanisms that specify the vertebrate body plan may have arisen from a relatively simple set of ancestral developmental components.

Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaning spanning the history of this organelle. Because most known coding changes are mitochondrial, such data bear on the general mechanism of codon reassignment. Coding changes have been attributed variously to loss of codons due to changes in directional mutation affecting the genome GC content (Osawa and Jukes 1988), to pressure to reduce the number of mitochondrial tRNAs to minimize the genome size (Anderson and Kurland 1991), and to the existence of transitional coding mechanisms in which translation is ambiguous (Schultz and Yarus 1994a). We find that a succession of such steps explains existing reassignments well. In particular, (1) Genomic variation in the prevalence of a codon's third-position nucleotide predicts relative mitochondrial codon usage well, though GC content does not. This is because A and T, and G and C, are uncorrelated in mitochondrial genomes. (2) Codons predicted to reach zero usage (disappear) do so more often than expected by chance, and codons that do disappear are disproportionately likely to be reassigned. However, codons predicted to disappear are not significantly more likely to be reassigned. Therefore, low codon frequencies can be related to codon reassignment, but appear to be neither necessary nor sufficient for reassignment. (3) Changes in the genetic code are not more likely to accompany smaller numbers of tRNA genes and are not more frequent in smaller genomes. Thus, mitochondrial codons are not reassigned during demonstrable selection for decreased genome size. Instead, the data suggest that both codon disappearance and codon reassignment depend on at least one other event. This mitochondrial event (leading to reassignment) occurs more frequently when a codon has disappeared, and produces only a small subset of possible reassignments. We suggest that coding ambiguity, the extension of a tRNA's decoding capacity beyond its original set of codons, is the second event. Ambiguity can act alone but often acts in concert with codon disappearance, which promotes codon reassignment.

Human intermodulation distortion product otoacoustic emissions (DPOAE) can be a mixture of low and high latency components. They have different level, phase, and suppression characteristics, which indicate that emissions arise both from the frequency region of the primary tones directly and indirectly via the DP frequency place. Which component dominates the measured DPOAE in the ear canal depends on the stimulus parameters, especially the frequency ratio, f2/f1. Interference between the two emissions adds complexity to measurements of DPOAE. The behavior and even existence of whichever emission route is lower in level often cannot directly be deduced from the raw DPOAE data because the other emission covers it. It is therefore not known whether both emissions are present for all stimulus parameters or whether the trends seen in each emission when they are the dominant emission route continue under stimulus conditions when they are not dominant. In this study, the two DPOAE components are separated by a post-processing method. Previously, maps of raw DPOAE data against f2/f1 and DP frequency have been obtained. To separate the components, sets of data consisting of f2/f1 sweeps were transformed by an inverse Fourier transform into the time domain. The low and high latency components appeared as two distinct peaks because of their different phase gradients. These peaks were separated by windowing in the time domain and two frequency domain maps were reconstructed, representing the low and high latency DPOAEs. It was found that the low latency component of the 2 f1-f2 DP was only emitted strongly with f2/f1 between approximately 1.1 and 1.3. The removal of the high latency component revealed the low ratio edge of this region, at which the level falls sharply. However, the low latency emission has been traced at reduced amplitude over a wide range of stimulus parameters. Although previously only observed at small frequency ratios, the high latency component was found to be present widely in the lower sideband, its level reducing slowly at larger f2/f1. Its phase behavior changes in the lower sideband, being approximately constant with DP frequency at small ratios of f2/f1, but deviating from this at wider ratios. These results support the hypothesis that a DPOAE component which propagates to and is re-emitted from the DP frequency place (place fixed emission) is present across a wide parameter range. However, for all but the close primary condition the lower sideband DPOAE is dominated by direct emission from the region of f2 and f1 wave interaction (wave fixed emission). A simple transmission line model is presented to illustrate how the observed DPOAE maps can arise on the basis of this hypothesis.

Background: The nuclear genetic code has changed in several lineages of ciliates. These changes, UAR to glutamine and UGA to cysteine, imply that eukaryotic release factor 1 (eRF1), the protein that recognizes stop codons and terminates translation, changes specificity. Here we test whether changes in eRF1 drive genetic code evolution., Results: Database sequence analysis reveals numerous genetic code alterations in ciliates, including UGA --> tryptophan in Blepharisma americanum and the distantly related Colpoda. We sequenced eRF1 from four ciliates: B. americanum, a heterotrich that independently derived the same eRF1 specificity as Euplotes, and three spirotrichs, Stylonychia lemnae, S. mytilus, and Oxytricha trifallax, that independently derived the same genetic code as Tetrahymena (UAR --> glutamine). Distantly related ciliates with similar codes show characteristic changes in eRF1. We used a sliding window analysis to test associations between changes in specific eRF1 residues and changes in the genetic code. The regions of eRF1 that display convergent substitutions are identical to those identified in a recently reported nonsense suppression mutant screen in yeast., Conclusions: Genetic code change by stop codon reassignment is surprisingly frequent in ciliates, with UGA --> tryptophan occurring twice independently. This is the first description of this code, previously found only in bacteria and mitochondria, in a eukaryotic nuclear genome. eRF1 has evolved strikingly convergently in lineages with variant genetic codes. The strong concordance with biochemical data indicates that our methodology may be generally useful for detecting molecular determinants of biochemical changes in evolution.

Background: Identification of orthologous relationships between genes from widely divergent taxa allows partial reconstruction of the gene complement of ancestral genomes. C2H2 zinc-finger genes are one of the largest and most complex gene superfamilies in metazoan genomes, with hundreds of members in the human genome. Here we analyze C2H2 zinc-finger genes from three taxa - Drosophila, Caenorhabditis elegans and human - from which near-complete genome sequence data are available., Results: Our analyses conclusively identify 39 families of genes, of which 38 can be defined as orthology groups in that they are descended from single ancestral genes in the common ancestor of Drosophila, C. elegans and humans., Conclusions: On the basis of current metazoan phylogeny, these 39 groups represent the minimum complement of C2H2 zinc-finger genes present in the genome of the bilaterian common ancestor.

Background: Correlations between genome composition (in terms of GC content) and usage of particular codons and amino acids have been widely reported, but poorly explained. We show here that a simple model of processes acting at the nucleotide level explains codon usage across a large sample of species (311 bacteria, 28 archaea and 257 eukaryotes). The model quantitatively predicts responses (slope and intercept of the regression line on genome GC content) of individual codons and amino acids to genome composition., Results: Codons respond to genome composition on the basis of their GC content relative to their synonyms (explaining 71-87% of the variance in response among the different codons, depending on measure). Amino-acid responses are determined by the mean GC content of their codons (explaining 71-79% of the variance). Similar trends hold for genes within a genome. Position-dependent selection for error minimization explains why individual bases respond differently to directional mutation pressure., Conclusions: Our model suggests that GC content drives codon usage (rather than the converse). It unifies a large body of empirical evidence concerning relationships between GC content and amino-acid or codon usage in disparate systems. The relationship between GC content and codon and amino-acid usage is ahistorical; it is replicated independently in the three domains of living organisms, reinforcing the idea that genes and genomes at mutation/selection equilibrium reproduce a unique relationship between nucleic acid and protein composition. Thus, the model may be useful in predicting amino-acid or nucleotide sequences in poorly characterized taxa.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible. Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space. This result is robust to variation in the methods and assumptions of the analysis. Although significantly better codes do exist under some assumptions, they are extremely rare and thus consistent with reports of an adaptive code: previous analyses which suggest otherwise derive from a misleading metric. However, all extant, naturally occurring, secondarily derived, nonstandard genetic codes do appear less adaptive. The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error. Potential criticisms of previous analyses appear to be without substance. That known variants of the standard genetic code appear less adaptive suggests that different evolutionary factors predominated before and after fixation of the canonical code. While the evidence for an adaptive code is clear, the process by which the code achieved this optimization requires further attention.

If the genetic code arose in an RNA world, present codon assignments may reflect primordial RNA-amino acid affinities. Whether aptamers selected from random pools to bind free amino acids do so using the cognate codons at their binding sites has been controversial. Here we defend and extend our previous analysis of arginine binding sites, and propose a model for the maintenance of codon-amino acid interactions through the evolution of amino acids from ribozyme cofactors into the building blocks of proteins.

The primary site of generation on the basilar membrane for the 2f1-f2 distortion product (DP) is generally considered to be near where the higher-frequency stimulus tone peaks. This site has also been shown to be a source of DP otoacoustic emission (DPOAE) in the ear canal, but a second source of emission is known to exist in the region of the DP frequency place. The DPOAE phase versus frequency gradient provides a means of investigating the emission mechanisms. "Wave-fixed" and "place-fixed" mechanisms have been proposed to account for the very different phase gradients found depending on whether the 2f1-f2 DPOAE is evoked by a small or large stimulus-frequency ratio. DPOAE phase versus frequency gradients can be investigated either by sweeping f1,f2 or by sweeping both frequencies maintaining a constant frequency ratio. Each manipulation gives only a partial description of DP behavior. In this study, the place-fixed/ wave-fixed dichotomy is analyzed using extensive 2f1-f2 and 2f2-f1 DP stimulus-frequency sweep data presented on matrices of f1 vs f2 and f2/f1 ratio versus DP frequency. These show how the DPs are related and provide a more complete picture of 2 f1-f2 and 2f2-f1 DPOAE phase and amplitude versus frequency behavior. The phase data contain evidence for a systematic variation in the proportions of wave- and place-fixed emission. The results suggest that 2f1-f2 DPOAEs with a wide stimulus frequency ratio are wave fixed, while all other DPOAEs are place fixed. A transition occurs within the 2 f1-f2 DP data region at a frequency ratio of about f2/f1 = 1.1. The 2f1-f2 DP and 2 f2-f1 DP phase behavior is continuous across the f2/f1 = 1 boundary. As the 2 f2-f1 DP generation region must be strongly influenced by the DP frequency place, the results imply that the place-fixed component of the 2 f1-f2 DP is also linked to its frequency place. A similar pattern was obtained with the 3f1-2f2 and 3f2-2f1 DPs. The results support the following model: For the limited set of stimulus conditions that gives rise to 2 f1-f2 wave-fixed emissions, DP energy is largely generated in the f2 region and is emitted directly. All other DPOAEs are place-fixed emissions, and while nonlinearity within the f2 stimulus envelope remains the generator, the DP is not directly emitted but travels apically until it is re-emitted basally via a separate reflection mechanism in the region of the DP place.

Theories about the origin of the genetic code require specific recognition between nucleic acids and amino acids at some stage of the code's evolution. A statistical analysis of arginine-binding RNA aptamers now offers the opportunity to test such interactions and provides the strongest support for an intrinsic affinity between any amino acid and its codons.

In previous studies of purine ribonucleotide metabolism in the human myeloid leukemia cell line HL-60, we observed that there is a down-regulation of guanine ribonucleotide biosynthesis from the central intermediate, inosine monophosphate (IMP) and a depletion of intracellular guanosine triphosphate (GTP) and guanosine diphosphate (GDP) pools that occur during the induced maturation of these cells. We also found that inhibitors of IMP dehydrogenase, the enzyme that catalyzes the first step of guanylate synthesis from IMP, are potent inducers of HL-60 maturation. Because of these observations we specifically investigated the activity of IMP dehydrogenase in HL-60 cells and in a new inducible human myeloid leukemia cell line, RDFD2-25, both during maintenance culture and during induced maturation of the cells. Enzyme activity was examined directly in cell extracts with a radiometric assay that measures free 3H2O formed from [2-3H] IMP during the conversion of IMP to XMP. Uninduced HL-60 and RDFD2 cells in maintenance culture were found to have high levels of IMPD activity (5.2 to 5.7 pmol IMP metabolized/10(7) cells/min) compared with normal neutrophils and monocytes that had been purified from blood (less than 1.5 pmol IMP metabolized/10(7) cells/min). However, when HL-60 and RDFD2-25 cells were induced to mature with retinoic acid (10(-6) mol/L), dimethylformamide (6 X 10(-2) mol/L), or a known IMPD inhibitor, tiazofurin (10(-6) mol/L), IMPD activity in the cells fell by 51% to 80% within three to six hours. These changes in IMPD activity preceded detectable functional and antigenic maturation of the cells by at least 12 hours and were not temporally related to changes in cellular proliferation. These findings are consistent with the concept that the regulation of myeloid cell maturation may be influenced by intracellular concentrations of guanine ribonucleotides because IMP dehydrogenase activity is known to be rate limiting for the production of these nucleotides.