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Results for “Genetic code evolution”

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PubMed2003

In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.

MOTIVATION: Motif-prediction algorithm capabilities for the analysis of bacterial regulatory networks and the prediction of new regulatory sites can be greatly enhanced by the use of comparative genomics approaches. In this study, we make use of a consensus-building algorithm and comparative genomics to conduct an in-depth analysis of the LexA-regulon of gamma proteobacteria, and we use the inferred results to study the evolution of this regulatory network and to examine the usefulness of the control sequences and gene contents of regulons in phylogenetic analysis. RESULTS: We show, for the first time, the substantial heterogeneity that the LexA-regulon of gamma proteobacteria displays in terms of gene content and we analyze possible branching points in its evolution. We also demonstrate the feasibility of using regulon-related information to derive sound phylogenetic inferences. AVAILABILITY: Complementary analysis data and both the source code and the Windows-executable files of the consensus-building software are available at http://www.cnm.es/~ivan/RCGScanner/

Algorithms↗

PubMed1998

The molecular evolution of sperm bindin in six species of sea urchins (Echinoida: Strongylocentrotidae).

The acrosomal protein bindin attaches sperm to eggs during sea urchin fertilization. Complementary to ongoing functional biochemical studies, I take a comparative approach to explore the molecular evolution of bindin in a group of closely related free-spawning echinoid species. Two alleles of the mature bindin gene were sequenced for each of six species in the sea urchin family Strongylocentrotidae. The nucleotide sequences diverged by at least 1% per Myr at both silent and replacement sites. Two short sections flanking the conserved block show an excess of nonsynonymous substitutions. Each is homologous to a region that had been identified as a target of selection in other sea urchin comparisons. A large proportion of the bindin-coding sequence consists of a highly variable repeat region. Bindin sequences, even including the large intron, could not resolve the branching order among five of the species.

Alleles↗

PubMed2005

Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii.

Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites - Rickettsia prowazekii and Rickettsia conorii - were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.

Biological Evolution↗

PubMed1984

Species-specific rDNA transcription is due to promoter-specific binding factors.

RNA polymerase I transcription factors were purified from HeLa and mouse L cell extracts by phosphocellulose chromatography. Three fractions from each species were found to be required for transcription. One of these fractions, virtually devoid of RNA polymerase I activity, was found to form a stable preinitiation complex with small DNA fragments containing promoter sequences from the homologous but not the heterologous species. These species-specific DNA-binding factors can explain nucleolar dominance in vivo in mouse-human hybrid somatic cells and species specificity in cell-free, RNA polymerase I-dependent transcription systems. The evolution of species-specific transcriptional control signals may be the natural outcome of a special relationship that exists between the RNA polymerase I transcription machinery and the multigene family coding for rRNA.

Animals↗

PubMed1994

[Single-primer variant of PCR-amplifications of segments of the main noncoding region of human mitochondrial DNA].

A method for amplifying segments of the main non-coding region of human mitochondrial DNA using a single-primer PCR is proposed. The method employs oligonucleotides that are homologous to this region of the human mitochondrial genome. Possible reaction mechanisms and the perspectives for using the method in evolutionary and population genetic studies are discussed.

Base Sequence↗

PubMed2004

Can fat explain the human brain's big bang evolution?-Horrobin's leads for comparative and functional genomics.

When David Horrobin suggested that phospholipid and fatty acid metabolism played a major role in human evolution, his 'fat utilization hypothesis' unified intriguing work from paleoanthropology, evolutionary biology, genetic and nervous system research in a novel and coherent lipid-related context. Interestingly, unlike most other evolutionary concepts, the hypothesis allows specific predictions which can be empirically tested in the near future. This paper summarizes some of Horrobin's intriguing propositions and suggests as to how approaches of comparative genomics published in Cell, Nature, Science and elsewhere since 1997 may be used to examine his evolutionary hypothesis. Indeed, systematic investigations of the genomic clock in the species' mitochondrial DNA, the Y and autosomal chromosomes as evidence of evolutionary relationships and distinctions can help to scrutinize associated predictions for their validity, namely that key mutations which differentiate us from Neanderthals and from great apes are in the genes coding for proteins which regulate fat metabolism, and particularly the phospholipid metabolism of the synapses of the brain. It is concluded that beyond clues to humans' relationships with living primates and to the Neanderthals' cognitive performance and their disappearance, the suggested molecular clock analyses may provide crucial insights into the biochemical evolution-and means of possible manipulation-of our brain.

Animals↗

PubMed2005

Escherichia coli K1 polysialic acid O-acetyltransferase gene, neuO, and the mechanism of capsule form variation involving a mobile contingency locus.

Potential O-acetylation of the sialic acid residues of Escherichia coli K1, groups W-135, Y, and C meningococci, and group B Streptococcus capsular polysaccharides modifies their immunogenicity and susceptibility to glycosidases. Despite the biological importance of O-acetylation, no sialic or polysialic acid O-acetyltransferase has been identified in any system. Here we show that the E. coli K1 O-acetyltransferase encoded by neuO is genetically linked to the endo-neuraminidase tail protein gene of a chromosomal accretion element, designated CUS-3, with homology to lambdoid bacteriophage. Molecular epidemiological analysis established concordance between O-acetyltransferase and CUS-3 in a set of E. coli K1 strains. Deleting neuO eliminated enzymatic activity, which was restored by complementation in trans, and confirmed by (13)C-NMR analysis of the acetylated product. Analysis of mutants that accumulate intracellular polysialic acid because of export defects (kpsM and kpsS) or an inability to synthesize the sialic acid precursor, N-acetylmannosamine (neuC), indicated that NeuO does not require constant association with its substrate for activity. DNA sequencing and PCR analysis of neuO from strains that had undergone random capsule form variation showed that slip strand DNA mispairing or unequal recombination resulted in gain or loss of (5'-AAGACTC-3')(n) heptanucleotide repeats (where n approximately equals 14-39) located in the neuO 5' region. These repeats code for a previously undescribed structure designated the poly(Psi) motif. The unexpected discovery of the neuO contingency locus (hypervariable gene controlling expression of a surface epitope) in E. coli, and of a potential phage for redistributing variant neuO alleles, provides a robust system for investigating the functions of localized hypermutability in pathogen evolution.

Acetylation↗

PubMed1990

Comma-free and synchronizable codes.

Shepherd (1981. Proc. natn. Acad. Sci. U.S.A. 78, 1596-1600), Clarke (1982. J. theor. Biol. 99, 397-403), Crick et al. (1976. Origins of Life 7, 389) have put forward the possibility that there was a code, ancestral to the existing genetic code, which was non-degenerate and comma-free. The point of a comma-free code, as first proposed in Crick et al. (1957), is that it provides immunity from frameshift reading errors. In this paper it is argued that if frameshift error immunity is to be used as a selection factor in guiding the search for a hypothetical ancestral code, then the appropriate mathematical formulation of this characteristic is not comma-freeness but synchronizability. The calling card of the comma-free notion is that it results in a limit of 20 on the number of sense codons when applied to the genetic coding system. But so does synchronizability, which includes comma-freeness as a special case. Further, using synchronizability as a constraint instead of comma-freeness yields roughly 3000 times as many potential models for an ancestral code. In particular, the RNY model becomes more compatible with immunity from frameshift error as an evolutionary constraint.

Base Sequence↗

PubMed1999

DNA sequence variation in a non-coding region of low recombination on the human X chromosome.

DNA sequence variation has become a major source of insight regarding the origin and history of our species as well as an important tool for the identification of allelic variants associated with disease. Comparative sequencing of DNA has to date focused mainly on mitochondrial (mt) DNA, which due to its apparent lack of recombination and high evolutionary rate lends itself well to the study of human evolution. These advantages also entail limitations. For example, the high mutation rate of mtDNA results in multiple substitutions that make phylogenetic analysis difficult and, because mtDNA is maternally inherited, it reflects only the history of females. For the history of males, the non-recombining part of the paternally inherited Y chromosome can be studied. The extent of variation on the Y chromosome is so low that variation at particular sites known to be polymorphic rather than entire sequences are typically determined. It is currently unclear how some forms of analysis (such as the coalescent) should be applied to such data. Furthermore, the lack of recombination means that selection at any locus affects all 59 Mb of DNA. To gauge the extent and pattern of point substitutional variation in non-coding parts of the human genome, we have sequenced 10 kb of non-coding DNA in a region of low recombination at Xq13.3. Analysis of this sequence in 69 individuals representing all major linguistic groups reveals the highest overall diversity in Africa, whereas deep divergences also exist in Asia. The time elapsed since the most recent common ancestor (MRCA) is 535,000+/-119,000 years. We expect this type of nuclear locus to provide more answers about the genetic origin and history of humans.

Africa↗

PubMed2000

Clinical and molecular advances in autosomal dominant cerebellar ataxias: from genotype to phenotype and physiopathology.

Major advances have been made in the understanding of autosomal dominant cerebellar ataxias since genetic markers came into use in the 1980s. The subsequent mapping of nine genes, six of which have been identified, involved in this clinically diverse group of disorders highlighted their great genetic heterogeneity. Evidence is now accumulating that, except for SCA8, the same molecular and physiopathological processes underlie these diseases and other neurodegenerative disorders sharing the same mutational basis, the expansion of a (CAG)n-polyglutamine coding sequence. The clinical overlap among the different genetic entities makes prediction of the molecular origin impossible in a single patient so that molecular characterisation is necessary. However, extended clinical and neuropathological comparisons have shown that each genetic entity has a characteristic constellation of signs and symptoms that are related to CAG repeat size and disease duration. The combined genetic and clinical information form the basis of a new classification that will aid better understanding of disease evolution, assure follow up and permit genetic counselling by the clinician.

Anticipation, Genetic↗

PubMed2000

Modulation of RNA function by aminoglycoside antibiotics.

One of the most important families of antibiotics are the aminoglycosides, including drugs such as neomycin B, paromomycin, gentamicin and streptomycin. With the discovery of the catalytic potential of RNA, these antibiotics became very popular due to their RNA-binding capacity. They serve for the analysis of RNA function as well as for the study of RNA as a potential therapeutic target. Improvements in RNA structure determination recently provided first insights into the decoding site of the ribosome at high resolution and how aminoglycosides might induce misreading of the genetic code. In addition to inhibiting prokaryotic translation, aminoglycosides inhibit several catalytic RNAs such as self-splicing group I introns, RNase P and small ribozymes in vitro. Furthermore, these antibiotics interfere with human immunodeficiency virus (HIV) replication by disrupting essential RNA-protein contacts. Most exciting is the potential of many RNA-binding antibiotics to stimulate RNA activities, conceiving small-molecule partners for the hypothesis of an ancient RNA world. SELEX (systematic evolution of ligands by exponential enrichment) has been used in this evolutionary game leading to small synthetic RNAs, whose NMR structures gave valuable information on how aminoglycosides interact with RNA, which could possibly be used in applied science.

Aminoglycosides↗

PubMedDate not supplied

[Role of stabilizing and splitting selection in evolution of of viruses from the Parvoviridae and Astroviridae families].

We had previously collected and analyzed, by phylogenetic methods, all genetic data available now for the Parvoviridae and Astroviridae families, which made it possible to define the evolutionary relations between the viruses as well as to depict a variety of events in the evolutionary history of the two families. The offered case study is dedicated to investigating the stabilizing and splitting selection types in the evolution of the discussed viral families. We analyzed the number of synonymous and non-synonymous nucleotide substitutions in the coding genomes' regions of the viruses. Finally, the stabilizing selection was shown to be a key factor in the evolution of parvoviruses and astroviruses.

Animals↗

PubMed2004

Natural selection and molecular evolution in PTC, a bitter-taste receptor gene.

The ability to taste phenylthiocarbamide (PTC) is a classic phenotype that has long been known to vary in human populations. This phenotype is of genetic, epidemiologic, and evolutionary interest because the ability to taste PTC is correlated with the ability to taste other bitter substances, many of which are toxic. Thus, variation in PTC perception may reflect variation in dietary preferences throughout human history and could correlate with susceptibility to diet-related diseases in modern populations. To test R. A. Fisher's long-standing hypothesis that variability in PTC perception has been maintained by balancing natural selection, we examined patterns of DNA sequence variation in the recently identified PTC gene, which accounts for up to 85% of phenotypic variance in the trait. We analyzed the entire coding region of PTC (1,002 bp) in a sample of 330 chromosomes collected from African (n=62), Asian (n=138), European (n=110), and North American (n=20) populations by use of new statistical tests for natural selection that take into account the potentially confounding effects of human population growth. Two intermediate-frequency haplotypes corresponding to "taster" and "nontaster" phenotypes were found. These haplotypes had similar frequencies across Africa, Asia, and Europe. Genetic differentiation between the continental population samples was low (FST=0.056) in comparison with estimates based on other genes. In addition, Tajima's D and Fu and Li's D and F statistics demonstrated a significant deviation from neutrality because of an excess of intermediate-frequency variants when human population growth was taken into account (P<.01). These results combine to suggest that balancing natural selection has acted to maintain "taster" and "nontaster" alleles at the PTC locus in humans.

Alleles↗

PubMed2001

The genetic organization and evolution of the broad host range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa.

Employing the biparental exogenous plasmid isolation method, conjugative plasmids conferring mercury resistance were isolated from the microbial community of the rhizosphere of field grown alfalfa plants. Five different plasmids were identified, designated pSB101-pSB105. One of the plasmids, pSB102, displayed broad host range (bhr) properties for plasmid replication and transfer unrelated to the known incompatibility (Inc) groups of bhr plasmids IncP-1, IncW, IncN and IncA/C. Nucleotide sequence analysis of plasmid pSB102 revealed a size of 55 578 bp. The transfer region of pSB102 was predicted on the basis of sequence similarity to those of other plasmids and included a putative mating pair formation apparatus most closely related to the type IV secretion system encoded on the chromosome of the mammalian pathogen Brucella sp. The region encoding replication and maintenance functions comprised genes exhibiting different degrees of similarity to RepA, KorA, IncC and KorB of bhr plasmids pSa (IncW), pM3 (IncP-9), R751 (IncP-1beta) and RK2 (IncP-1alpha), respectively. The mercury resistance determinants were located on a transposable element of the Tn5053 family designated Tn5718. No putative functions could be assigned to a quarter of the coding capacity of pSB102 on the basis of comparisons with database entries. The genetic organization of the pSB102 transfer region revealed striking similarities to plasmid pXF51 of the plant pathogen Xylella fastidiosa.

Bacteria↗

PubMed2006

Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb.

We have reported previously that introgression by Zizania latifolia resulted in extensive DNA methylation changes in the recipient rice genome, as detected by a set of pre-selected DNA segments. In this study, using the methylation-sensitive amplified polymorphism (MSAP) method, we globally assessed the extent and pattern of cytosine methylation alterations in three typical introgression lines relative to their rice parent at approximately 2,700 unbiased genomic loci each representing a recognition site cleaved by one or both of the isoschizomers, HpaII/MspI. Based on differential digestion by the isoschizomers, it is estimated that 15.9% of CCGG sites are either fully methylated at the internal Cs and/or hemi-methylated at the external Cs in the rice parental cultivar Matsumae. In comparison, a statistically significant increase in the overall level of both methylation types was detected in all three studied introgression lines (19.2, 18.6, 19.6%, respectively). Based on comparisons of MSAP profiles between the isoschizomers within the rice parent and between parent and the introgression lines, four major groups of MSAP banding patterns are recognized, which can be further divided into various subgroups as a result of inheritance of, or variation in, parental methylation patterns. The altered methylation patterns include hyper- and hypomethylation changes, as well as inter-conversion of hemi- to full-methylation, or vice versa, at the relevant CCGG site(s). Most alterations revealed by MSAP in low-copy loci can be validated by DNA gel blot analysis. The changed methylation patterns are uniform among randomly selected individuals for a given introgression line within or among selfed generations. Sequencing on 31 isolated fragments that showed different changing patterns in the introgression line(s) allowed their mapping onto variable regions on one or more of the 12 rice chromosomes. These segments include protein-coding genes, transposon/retrotransposons and sequences with no homology. Possible causes for the introgression-induced methylation changes and their implications for genome evolution and crop breeding are discussed.

Cytosine↗

PubMed2006

Potential regulatory elements in the Trypanosoma cruzi rRNA gene promoter.

The Trypanosoma cruzi rRNA gene promoter was characterized by deletion and point mutation analyses. A core of 89 bp was identified as the minimal region with full promoter activity. This core region is flanked upstream by a control element that stimulates its activity, and downstream by a novel down regulating region of about 200 bp. A point mutation analysis of the transcription start region evidenced 7 contiguous nucleotides where individual substitutions produced in all cases a defective promoter. It is generally accepted that the anciently speciated trypanosomatids lack strict promoters for protein coding genes transcribed by RNA polymerase II. The occurrence of a well structured rRNA gene promoter in these species suggests an early appearance of the RNA polymerase I promoters in the evolution of eukaryotic cells.

Animals↗

PubMed2004

Recombination signal sequence variations and the mechanism of patterned T-cell receptor-beta locus rearrangement.

Rearrangement of antigen receptor genes is controlled at multiple levels. One important regulation is achieved through variation in the recombination signals (RS) that flank the rearranging variable (V), diversity (D), and joining (J) gene segments. Several functional and biochemical studies have confirmed the importance of RS variations in gene rearrangement but very few molecular analyses has been reported with known, endogenous RS motifs. We have shown previously that rearrangement of the murine T-cell receptor (TCR)-B, D, and J genes follows a stereotypical pattern determined largely by the BJ genes and their flanking RS. Therefore, we studied the mechanism by which the endogenous BJ RS determine patterned gene rearrangement. We have compared the activity of three representative RS in transfection and in vitro DNA cleavage assays. Mutagenesis studies identified residues in various components of the RS and flanking coding ends that cooperate to determine the ultimate efficiency of recombination. Surprisingly, we find that changes in one component of the RS can be compensated by other elements to restore functional activity. DNA electrophoretic mobility shift assays (EMSA) show that a combinatorial effect of various higher order protein/RS complexes can, in part, control the efficiency of recombination. We propose that evolution of a patterned primary antigen receptor repertoire reflects the delicate interplay between various components of the RS and flanking coding end motifs resulting from the highly flexible interactions of the recombinase with its target DNA.

Animals↗

PubMed1992

At least three promoters direct expression of the mouse glucocorticoid receptor gene.

We have characterized the gene for the mouse glucocorticoid receptor. The gene spans approximately 110 kilobases, and glucocorticoid receptor transcripts are assembled from nine exons. Expression of the gene is controlled by at least three promoters, resulting in glucocorticoid receptor transcripts with different 5' nontranslated exons. One promoter is cell-specific, found to be active only in T lymphocytes. The other two promoters are active to various degrees in all cell lines and tissues so far analyzed and are located in a CpG island. The promoter activities are accompanied by DNase I hypersensitivity sites in chromatin. In contrast to a conservation of exon-intron structure, differences in promoter organization suggest a divergence between the evolution of regulatory and coding regions among members of the steroid receptor super-family.

Animals↗