Pharmacophylogenomics: genes, evolution and drug targets.
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Animals↗
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Results for “gene evolution”
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Immune reconstitution in HIV-1 infected children with discordant response to antiretroviral therapies: patterns of HIV-1 env gene evolution driven by restoration of thymic function.
The evolution of human immunodeficiency virus type 1 (HIV-1) env gp120 region was addressed in HIV-1 infected children showing virological failure to antiretroviral therapy (ART). Sequence analysis of the replicating plasma virus at baseline and after one year of therapy documented evolution of gp120 in all subjects but one. Analysis of the host's selective pressure showed that the values of Ka/Ks ratios were higher in the V3 sequence than in the whole C2-V5 region in 4 of 5 children with improvement of thymic output. Moreover, in 2 of the 4 chidren, the V3 evolution paralleled with a reverse shift of the viral phenotype (from CXCR4-tropic to CCR5-tropic). These results suggest that, under ART, the V3 evolution towards less pathogenic viral variants may be driven by the host's increased selective pressure following restoration of thymic function and immune reconstitution.
Amino Acid Sequence↗
Molecular evolution of class I alcohol dehydrogenases in primates. Models for gene evolution and comparison of 3' untranslated regions of cDNAS.
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Alcohol Dehydrogenase↗
Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication.
It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.
Amino Acid Sequence↗
Gonadotropin-releasing hormone: gene evolution, expression, and regulation.
The gonadotropin-releasing hormone (GnRH) gene is a superb example of the diverse regulation that is required to maintain the function of an evolutionarily conserved and fundamental gene. Because reproductive capacity is critical to the survival of the species, physiological homeostasis dictates optimal conditions for reproductive success, and any perturbation from this balance may affect GnRH expression. These disturbances may include alterations in signals dictated by stress, nutritional imbalance, body weight, and neurological problems; therefore, changes in other neuroendocrine systems may directly influence the hypothalamic-pituitary-gonadal axis through direct regulation of GnRH. Thus, to maintain optimal reproductive capacity, the regulation of the GnRH gene is tightly constrained by a number of diverse signaling pathways and neuromodulators. In this review, we summarize what is currently known of GnRH gene structure, the location and function of the two isoforms of the GnRH gene, some of the many hormones and neuromodulators found to affect GnRH expression, and the molecular mechanisms responsible for the regulation of the GnRH gene. We also discuss the latest models used to study the transcriptional regulation of the GnRH gene, from cell models to evolving in vivo technologies. Although we have come a long way in the last two decades toward uncovering the intricacies behind the control of the GnRH neuron, there remain vast distances to cover before direct therapeutic manipulation of the GnRH gene to control reproductive competence is possible.
Androgens↗
Pack-MULE transposable elements mediate gene evolution in plants.
Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3,000 Pack-MULEs in rice containing fragments derived from more than 1,000 cellular genes. Pack-MULEs frequently contain fragments from multiple chromosomal loci that are fused to form new open reading frames, some of which are expressed as chimaeric transcripts. About 5% of the Pack-MULEs are represented in collections of complementary DNA. Functional analysis of amino acid sequences and proteomic data indicate that some captured gene fragments might be functional. Comparison of the cellular genes and Pack-MULE counterparts indicates that fragments of genomic DNA have been captured, rearranged and amplified over millions of years. Given the abundance of Pack-MULEs in rice and the widespread occurrence of MULEs in all characterized plant genomes, gene fragment acquisition by Pack-MULEs might represent an important new mechanism for the evolution of genes in higher plants.
Base Sequence↗
Evolution of the major histocompatibility complex in vertebrates: a saga of convergent gene evolution?
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Amphibians↗
Structures of two molluscan hemocyanin genes: significance for gene evolution.
We present here the description of genes coding for molluscan hemocyanins. Two distantly related mollusks, Haliotis tuberculata and Octopus dofleini, were studied. The typical architecture of a molluscan hemocyanin subunit, which is a string of seven or eight globular functional units (FUs, designated a to h, about 50 kDa each), is reflected by the gene organization: a series of eight structurally related coding regions in Haliotis, corresponding to FU-a to FU-h, with seven highly variable linker introns of 174 to 3,198 bp length (all in phase 1). In Octopus seven coding regions (FU-a to FU-g) are found, separated by phase 1 introns varying in length from 100 bp to 910 bp. Both genes exhibit typical signal (export) sequences, and in both cases these are interrupted by an additional intron. Each gene also contains an intron between signal peptide and FU-a and in the 3' untranslated region. Of special relevance for evolutionary considerations are introns interrupting those regions that encode a discrete functional unit. We found that five of the eight FUs in Haliotis each are encoded by a single exon, whereas FU-f, FU-g, and FU-a are encoded by two, three and four exons, respectively. Similarly, in Octopus four of the FUs each correspond to an uninterrupted exon, whereas FU-b, FU-e, and FU-f each contain a single intron. Although the positioning of the introns between FUs is highly conserved in the two mollusks, the introns within FUs show no relationship either in location nor phase. It is proposed that the introns between FUs were generated as the eight-unit polypeptide evolved from a monomeric precursor, and that the internal introns have been added later. A hypothesis for evolution of the ring-like quaternary structure of molluscan hemocyanins is presented.
Amino Acid Sequence↗
Rhesus fetal globin genes. Concerted gene evolution in the descent of higher primates.
The comparison of the nucleotide sequences of closely linked duplicated genes of higher eukaryotes has been important in the identification of molecular events that shape the evolution of mammalian genes, most notably recombinational events such as unequal crossovers and gene conversions. Toward this goal we have been comparing the nucleotide sequences of the paired gamma 1- and gamma 2-fetal globin genes from species of catarrhine primates. Previous comparisons document that, within each great ape species as in humans, the paired gamma-genes have been involved in gene conversion events. We now extend our analysis to the catarrhine superfamily Cercopithecoidea by obtaining the nucleotide sequence of the paired gamma 1- and gamma 2-genes of rhesus monkey (Macaca mulatta). The rhesus gamma 1- and gamma 2-genes diverge less from each other than from human, chimpanzee, gorilla, and orangutan gamma 1- or gamma 2-genes. This finding indicates that a species-specific gene conversion occurred between rhesus gamma 1- and gamma 2-genes. This gamma-gene conversion (labeled C14 in our series) involved at least 1898 base pairs, extending across the complete transcriptional region of the rhesus gamma-genes. C14 could have resulted from a single large conversion or several short conversion events which may have involved the (TG)n repetitive sequence element. Parsimony analysis of the enlarged body of gamma-gene sequence data also strengthens the evidence for the 14 previously suggested gamma-gene conversion events: labeled C2, C3, and C4 in Homo; C5, C6, and C7 in Pan; C8, C9, and C10 in Gorilla; C11, C12, C13 in Pongo; C1 in the stem to Homininae (the subfamily of Homo, Pan, and Gorilla) and CO in the stem of Hominidae (the family of Pongo and Homininae).
Amino Acid Sequence↗
Regulatory gene evolution: adaptive differences in expression of alcohol dehydrogenase in Drosophila melanogaster and Drosophila simulans.
In Drosophila melanogaster X D. simulans hybrids, the alcohol dehydrogenase (ADH) electromorphs characteristic of the two parents display tissue- and stage-specific differences in relative level of expression. This implies distinct cis-acting regulatory elements associated with the respective Adh alleles. These cis-acting elements account in part, but not completely, for markedly different overall patterns of ADH expression in the two species. The regulatory patterns seem to be adaptively significant since they correlate with species-specific patterns of ethanol tolerance. The activity differences are accounted for by different levels of enzyme protein, but the underlying mechanisms have not been fully analysed and may be complex. Independent evolution of various aspects of the ADH developmental programme may relate to use of different promoters for transcription of the Adh locus in different developmental contexts. This system illustrates the potential importance of regulatory genes in evolution and provides a model for investigating the molecular basis of evolved regulatory differences.
Alcohol Dehydrogenase↗
Rate constancy of globin gene evolution in placental mammals.
The molecular clock hypothesis is investigated by comparison of the rates of nucleotide substitution in globin genes of mice, cows and goats, humans, and rabbits, using the relative rate test. These comparisons are based on a branching order of genes and species established by cladistic analysis of nucleotide sequences. The species branching order is shown to be mouse, cow/goat, human, and rabbit. Relative rate tests involving paralogous and orthologous genes provide no evidence of heterogeneity, among species, in the rate of evolution of the genes. This result is discrepant with the conclusions of most other recent, similar studies. By comparison with previous studies, the present study is based on a sound phylogeny and involves a larger sample of species, genes, and genic regions. The result provides strong support for the neutral theory of molecular evolution and demonstrates that molecular evolutionary rate does not depend on generation time.
Animals↗
Genomic structure of the human Ig lambda 1 gene suggests that it may be expressed as an Ig lambda 14.1-like protein or as a canonical B cell Ig lambda light chain: implications for Ig lambda gene evolution.
In pre-B cells, immunoglobulin mu (Ig mu) is associated with pre-B cell-specific proteins to form a multimeric complex that is found on the cell surface. One of these proteins is encoded by the three exon Ig lambda-like gene 14.1, whose expression is restricted to pre-B cells and occurs from an unrearranged gene. A comparison of the 14.1 gene structure to the seven-gene human Ig lambda locus revealed that the most 5' gene, Ig lambda 1, is organized in a three-exon structure very similar to the 14.1 gene. Transcription and splicing of these three-exon sequences would lead to an mRNA with an open reading frame which could encode a light (L) chain-like protein with a molecular weight of 23,045. Our analysis suggests that two transcripts may be produced from the Ig lambda 1 gene that share the same Ig lambda 1 constant region-containing third exon. One transcript would include all three 14.1-related exons and be expressed from the germline gene, and the second transcript would be produced after variable-joining (V-J) recombination has occurred to Ig lambda J1 and would encode a classic Ig lambda L chain protein. The conservation of the genomic organization of the human 14.1 and Ig lambda 1 genes and the mouse homolog, lambda 5, relative to the classic Ig lambda L chain genes provides insight into the evolution of Ig genes.
Amino Acid Sequence↗
Nucleotide sequence comparison of five human pepsinogen A (PGA) genes: evolution of the PGA multigene family.
To unravel the genetic basis for the pepsinogen A (PGA) protein polymorphism, we have isolated and characterized a number of PGA genes, distinguishable by polymorphic EcoRI fragments of 12.0, 15.0, and 16.6 kb. Using a HindIII or AvaII polymorphism, we can discriminate between different 15.0 (15.0 and 15.0*) and 12.0 (12.0s and 12.0l) genes, respectively. The coding sequences of a 15.0 and a 16.6 gene were determined, together with considerable stretches of the 5'- and 3'-flanking regions and introns. The genes were demonstrated to encode Pg5 and Pg4, respectively. Because substitutions in codons 43 and 207 appeared to be critical in the determination of the encoded proteins, we sequenced only these regions in the two 12.0 genes and the 15.0* gene. On the basis of these partial sequences, we assume that these genes encode Pg3. In the evolutionary model of the PGA gene cluster presented here, the 12.0 genes arose by an unequal, but homologous crossover. The results of sequence analysis of the second intron of the 12.0s, 12.0l, 15.0, and 16.6 genes suggest that the two 12.0 genes have arisen from two different crossover events.
Amino Acid Sequence↗
Flower development and evolution: gene duplication, diversification and redeployment.
Gene duplication and diversification can provide the raw material for the evolution of new morphologies. In plants, the numbers of MADS-box genes have multiplied considerably, resulting in a plethora of these transcriptional regulators in the angiosperms (flowering plants). MADS-box genes have been implicated in the regulation of a variety of flower developmental processes; therefore, understanding the functional consequences of duplication and diversification in this gene family can shed light on the evolution of different floral forms. Recent functional analyses of MADS-box gene lineages have demonstrated that in various instances these genes have swapped roles, acquired novel roles, or retained ancestral roles. These studies underscore the idea that gene function cannot be extrapolated from structural orthology.
Evolution, Molecular↗
Glutamine synthetase gene evolution in bacteria.
The evolution of the prokaryotic glutamine synthase (GS) genes, namely the GSI and GSII isoforms, has been investigated using the second codon positions, which have previously proven to behave as a good molecular clock. Our data confirm the early divergence between prokaryotic and eukaryotic GSII before the splitting between plants and animals. The phylogenetic tree of the GSI isoforms shows Archaebacteria to be more closely related to Eubacteria than to Eukaryotes. This finding is confirmed by the phylogenetic analysis carried out on both large and small subunits of rRNA. However, differently from the rRNA analyses, Crenarchaeota and Euryarchaeota Archaebacteria, as well as high- and low-GC gram-positive bacteria, appear to be polyphyletic. We provide evidence that the observed polyphyly of Archaebacteria might be only apparent, resulting from a gene duplication event preceding the split between Archaebacteria and Eubacteria and followed by the retention of only one isoform in the extant lineages. Both gram-negative bacteria and high-GC gram-positive bacteria, which appear closely related, have GS activity regulated by an adenylylation/deadenylylation mechanism. A lateral gene transfer from Archaebacteria to low-GC eubacteria is invoked to explain the observed polyphyly of gram-positive bacteria.
Amino Acid Sequence↗
Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution.
To address the evolution of human immunodeficiency virus type 1 (HIV-1) within a single host, we analyzed the HIV-1 C2-V5 env regions of both cell-free genomic-RNA- and proviral-DNA-derived clones. Sequential samples were collected over a period of 3 years from six untreated subjects (three typical progressors [TPs] and three slow progressors [SPs], all with a comparable length of infection except one. The evolutionary analysis of the C2-V5 env sequences performed on 506 molecular clones (253 RNA- and 253 DNA-derived sequences) highlighted a series of differences between TPs and SPs. In particular, (i) clonal sequences from SPs (DNA and RNA) showed lower nucleotide similarity than those from TPs (P = 0. 0001), (ii) DNA clones from SPs showed higher intra- and intersample nucleotide divergence than those from TPs (P < 0.05), (iii) higher host-selective pressure was generally detectable in SPs (DNA and RNA sequences), and (iv) the increase in the genetic distance of DNA and RNA sequences over time was paralleled by an increase in both synonymous (Ks) and nonsynonymous (Ka) substitutions in TPs but only in nonsynonymous substitutions in SPs. Several individual peculiarities of the HIV-1 evolutionary dynamics emerged when the V3, V4, and V5 env regions of both TPs and SPs were evaluated separately. These peculiarities, probably reflecting host-specific features of selective constraints and their continuous modulation, are documented by the dynamics of Ka/Ks ratios of hypervariable env domains.
Base Sequence↗
Microcystin biosynthesis in planktothrix: genes, evolution, and manipulation.
Microcystins represent an extraordinarily large family of cyclic heptapeptide toxins that are nonribosomally synthesized by various cyanobacteria. Microcystins specifically inhibit the eukaryotic protein phosphatases 1 and 2A. Their outstanding variability makes them particularly useful for studies on the evolution of structure-function relationships in peptide synthetases and their genes. Analyses of microcystin synthetase genes provide valuable clues for the potential and limits of combinatorial biosynthesis. We have sequenced and analyzed 55.6 kb of the potential microcystin synthetase gene (mcy) cluster from the filamentous cyanobacterium Planktothrix agardhii CYA 126. The cluster contains genes for peptide synthetases (mcyABC), polyketide synthases (PKSs; mcyD), chimeric enzymes composed of peptide synthetase and PKS modules (mcyEG), a putative thioesterase (mcyT), a putative ABC transporter (mcyH), and a putative peptide-modifying enzyme (mcyJ). The gene content and arrangement and the sequence of specific domains in the gene products differ from those of the mcy cluster in Microcystis, a unicellular cyanobacterium. The data suggest an evolution of mcy clusters from, rather than to, genes for nodularin (a related pentapeptide) biosynthesis. Our data do not support the idea of horizontal gene transfer of complete mcy gene clusters between the genera. We have established a protocol for stable genetic transformation of Planktothrix, a genus that is characterized by multicellular filaments exhibiting continuous motility. Targeted mutation of mcyJ revealed its function as a gene coding for a O-methyltransferase. The mutant cells produce a novel microcystin variant exhibiting reduced inhibitory activity toward protein phosphatases.
Amino Acid Sequence↗
Loss of DNA: a plausible molecular level explanation for crustacean neuropeptide gene evolution.
Alignment of nucleotides of APGWamide, RPCH and AKH genes gives region stretches (common regions) present in all family member variants. Common regions were separated by gap sections in the larger variants of family members. Consensus sequences for single polynucleotides from virtual hybrid molecules of DNA were obtained by joining the common regions of DNA and deleting the extra DNA nucleotides. Conceptual translation of these virtual hybrids resulted in polypeptides similar to APGWamide, RPCH and the AKH pre-pro-peptide. Virtual polypeptides were also similar to LWamide and RFamide along hydras to mammals. DNA loss probably explains the origin of neuropeptides.
Amino Acid Sequence↗