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PubMed2002

Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.

Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.

Acetyltransferases↗
PubMed2005

Dispersal, philopatry, and infidelity: dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus).

Dispersal influences evolution, demography, and social characteristics but is generally difficult to study. Here we combine long-term demographic data from an intensively studied population of superb fairy-wrens (Malurus cyaneus) and multivariate spatial autocorrelation analyses of microsatellite genotypes to describe dispersal behavior in this species. The demographic data revealed: (1) sex-biased dispersal: almost all individuals that dispersed into the study area over an eight-year period were female (93%; n = 153); (2) high rates of extragroup infidelity (66% of offspring), which also facilitated local gene dispersal; and (3) skewed lifetime reproductive success in both males and females. These data led to three expectations concerning the patterns of fine-scale genetic structure: (1) little or no spatial genetic autocorrelation among females, (2) positive spatial genetic autocorrelation among males, and (3) a heterogeneous genetic landscape. Global autocorrelation analysis of the genotypes present in the study population confirmed the first two expectations. A novel two-dimensional local autocorrelation analysis confirmed the third and provided new insight into the patterns of genetic structure across the two-dimensional landscape. We highlight the potential of autocorrelation analysis to infer evolutionary processes but also emphasize that genetic patterns in space cannot be fully understood without an appropriate and intensive sampling regime and detailed knowledge of the individuals genotyped.

Animals↗
PubMed1999

Historical and biomechanical analysis of integration and dissociation in molluscan feeding, with special emphasis on the true limpets (Patellogastropoda: Gastropoda).

Modifications of the molluscan feeding apparatus have long been recognized as a crucial feature in molluscan diversification, related to the important process of gathering energy from the environment. An ecologically and evolutionarily significant dichotomy in molluscan feeding kinematics is whether radular teeth flex laterally (flexoglossate) or do not (stereoglossate). In this study, we use a combination of phylogenetic inference and biomechanical modeling to understand the transformational and causal basis for flexure or lack thereof. We also determine whether structural subsystems making up the feeding system are structurally, functionally, and evolutionarily integrated or dissociated. Regarding evolutionary dissociation, statistical analysis of state changes revealed by the phylogenetic analysis shows that radular and cartilage subsystems evolved independently. Regarding kinematics, the phylogenetic analysis shows that flexure arose at the base of the Mollusca and lack of flexure is a derived condition in one gastropod clade, the Patellogastropoda. Significantly, radular morphology shows no change at the node where kinematics become stereoglossate. However, acquisition of stereoglossy in the Patellogastropoda is correlated with the structural dissociation of the subradular membrane and underlying cartilages. Correlation is not causality, so we present a biomechanical model explaining the structural conditions necessary for the plesiomorphic kinematic state (flexoglossy). Our model suggests that plesiomorphically the radular teeth must flex laterally as they pass over the bending plane as a result of the mechanical restrictions in the flexible but inelastic subradular membrane and close association between subradular membrane and cartilages. Relating this model to the specific character states of the clades, we conclude that lack of flexure in patellogastropods is caused by the dissociation of the subradular membrane and cartilage supports.

Animals↗
PubMed2004

Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins.

Absence of any regular structure is increasingly being observed in structural studies of proteins. These disordered regions or random coils, which have been observed under physiological conditions, are indicators of protein plasticity. The wide variety of interactions possible due to the flexibility of these 'natively disordered' regions confers functional advantage to the protein and the organism in general. This concept is underscored by the increasing proportion of intrinsically unstructured proteins seen with the ascension in the complexity of the organisms. The 'natively unfolded/disordered' state of the protein can be predicted utilizing Uversky's or Dunker's algorithm. We utilized Uversky's prediction scheme and based on the unique position of a protein in the charge-hydrophobicity plot, a derived net score was used to predict the overall disorder of the human housekeeping and non-housekeeping proteins. Substantial numbers of proteins in both the classes were predicted to be unfolded. However, comparative genomic analysis of predicted unfolded Homo sapiens proteins with homologues in Caenorhabditis elegans, Drosophila melanogaster and Mus musculus revealed significant increase in unfoldedness in non-housekeeping proteins in comparison with housekeeping proteins. Our analysis in the evolutionary context suggests addition or substitution of amino acid residues which favour unfoldedness in non-housekeeping proteins compared to housekeeping proteins.

Algorithms↗
PubMed1991

A comparison of three computer models for prediction of dose in acute amitriptyline overdose.

The pharmacokinetics of amitriptyline in overdose have been reported not to fit conventional compartmental models. In this study, the dose-concentration-time relationships of amitriptyline in overdose were modeled with discriminant analysis, with an evolutionary heuristic search program, and with a decision-tree model based on the entropy of uncertainty of classification. The computer models all used the same data from dogs administered treatment (80 mg/kg), toxic (250 mg/kg), or fatal (500 mg/kg) doses directly into the surgically isolated duodenum. All the models achieved a high degree of success (77 to 93%) in assigning records to the high-, low-, or middle-dose groups. Two of the models gave a probability of the assignment. Results of this analysis suggest that blood amitriptyline and nortriptyline concentrations are most useful in estimating dose in acute amitriptyline overdose.

Amitriptyline↗
PubMed2000

Unique epitopes in RNA helicase II/Gu protein recognized by serum from a watermelon stomach patient.

RNA helicase II/Gu (RH II/Gu) is a nucleolar antigen originally identified using an autoimmune serum from a patient with watermelon stomach. A later report showed that anti-RH II/Gu autoantibodies were also present at low frequency in connective tissue disease (CTD) patients who did not show any symptoms suggestive of a watermelon stomach lesion. In an attempt to understand the relationship between watermelon stomach, also called gastric antral vascular ectasia (GAVE), and autoimmune disorder, we identified the antigenic sites recognized by these autoantibodies. Serum Gu uniquely recognized epitopes at amino acids 646-748 of RH II/Gu and all four CTD patient sera recognized antigenic sites within amino acids 1-173. Anti-RH II/Gu serum produced by immunizing rabbit with recombinant human RH II/Gu protein bound to the same antigenic sites recognized by the CTD patient sera, but it did not recognize the serum Gu epitopes. Results are also presented showing the use of these anti-RH II/Gu antibodies in the analysis of the evolutionary conservation of RH II/Gu in human, monkey and mouse.

Amino Acid Sequence↗
PubMed2002

Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela).

The golden-striped salamander, Chioglossa lusitanica, is a streamside species distributed in the northwest of the Iberian Peninsula. We gathered cytochrome b mitochondrial DNA sequence data from samples across the species range and used nested clade distance analysis to assess evolutionary processes explaining the geographical distribution of mtDNA diversity in Chioglossa lusitanica. A significant association was observed between genetic structure and geography. The geographical patterns were explained by past fragmentation and restricted gene flow. Inferences were concordant with previous hypotheses (from allozyme data) involving an old fragmentation event and secondary contact near the Mondego River in central Portugal. A range expansion to the north from a southern refuge was supported by descriptive interpretations of mtDNA data and by complementary analyses suggesting population expansions, but not by formal nested clade analysis. The power of nested clade analysis to detect the genetic signature of range expansion deserves further testing.

Animals↗
PubMed1992

Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family.

Sequences of 47 members of the Zn-containing alcohol dehydrogenase (ADH) family were aligned progressively, and an evolutionary tree with detailed branch order and branch lengths was produced. The alignment shows that only 9 amino acid residues (of 374 in the horse liver ADH sequence) are conserved in this family; these include eight Gly and one Val with structural roles. Three residues that bind the catalytic Zn and modulate its electrostatic environment are conserved in 45 members. Asp 223, which determines specificity for NAD, is found in all but the two NADP-dependent enzymes, which have Gly or Ala. Ser or Thr 48, which makes a hydrogen bond to the substrate, is present in 46 members. The four Cys ligands for the structural zinc are conserved except in zeta-crystallin, the sorbitol dehydrogenases, and two bacterial enzymes. Analysis of the evolutionary tree gives estimates of the times of divergence for different animal ADHs. The human class II (pi) and class III (chi) ADHs probably diverged about 630 million years ago, and the newly identified human ADH6 appeared about 520 million years ago, implying that these classes of enzymes may exist or have existed in all vertebrates. The human class I ADH isoenzymes (alpha, beta, and gamma) diverged about 80 million years ago, suggesting that these isoenzymes may exist or have existed in all primates. Analysis of branch lengths shows that these plant ADHs are more conserved than the animal ones and that class III ADHs are more conserved than class I ADHs. The rate of acceptance of point mutations (PAM units) shows that selection pressure has existed for ADHs, implying that these enzymes play definite metabolic roles.

Alcohol Dehydrogenase↗
PubMed1994

Molecular characterization of the Rh-like locus and gene transcripts from the rhesus monkey (Macaca mulatta).

The human Rh blood group locus consists of two structurally related genes (D and CcEe) in Rh-positive haplotypes but a single gene (CcEe) in Rh-negative haplotypes. The genome of rhesus monkeys (Macaca mulatta), while not expressing any of the human Rh D, C, c, E, or e specificities, carries a Rh-like locus strongly related to the human Rh locus. Southern blot analysis suggested the presence of only one Rh-like gene with an additional truncated fragment corresponding to the 5' region. RNA preparations from M. mulatta bone marrow cells contained Rh-like species of 1.7 kb. Two allelic Rh-like transcripts were amplified by PCR and sequenced. The predicted translation product of the first transcript was a 417-amino-acid protein closely similar to the human Rh counterpart. The predicted product of the second transcript consisted of a 361-amino-acid polypeptide truncated in the NH2 terminal region and differing from the former by a few substitutions. The macaque Rh-like protein sequences differed from those of human D and Cc/Ee polypeptides by 22-25%, whereas the degree of identity between the human proteins was 91.5%. Implications of these results in the analysis of the evolutionary pathway of the Rh locus are discussed.

Alleles↗
PubMed2005

Evolution of subspecies of Francisella tularensis.

Analysis of unidirectional genomic deletion events and single nucleotide variations suggested that the four subspecies of Francisella tularensis have evolved by vertical descent. The analysis indicated an evolutionary scenario where the highly virulent F. tularensis subsp. tularensis (type A) appeared before the less virulent F. tularensis subsp. holarctica (type B). Compared to their virulent progenitors, attenuated strains of F. tularensis exhibited specific unidirectional gene losses.

Evolution, Molecular↗
PubMedDate not supplied

Evolution of male sexual characters in the oriental Drosophila melanogaster species group.

Understanding the genetic and molecular mechanisms of morphological evolution is one of the greatest challenges in evolutionary biology. Sexually dimorphic traits, which often evolve at a high rate due to their involvement in mate choice and sexual selection, present unique opportunities for investigating changes in development over short evolutionary distances. Phylogenetic analysis is essential to provide a historical framework for comparative studies of development by establishing the order and polarity of morphological changes. In this report, we apply a new molecular phylogeny to reconstruct the evolution of male sexual characters in a group of species closely related to the model species Drosophila melanogaster. These highly variable traits include wing melanin patterns, the sex comb, and the structure of external genitalia and analia. We show that sexually dimorphic characters can diverge very rapidly among closely related species. More surprisingly, we also find a pervasive pattern of independent origin and secondary loss of male sexual traits in different evolutionary lineages.

Animals↗
PubMed2005

Progressive proximal expansion of the primate X chromosome centromere.

Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the functional centromere. We analyzed the finished sequence of this human genomic region to investigate its evolutionary history. Phylogenetic analysis of >1,500 alpha-satellite monomers from the region revealed the presence of five physical domains, each containing monomers from a distinct phylogenetic clade. The most distal domain contains long interspersed nucleotide element repeats that were active >35 million years ago, whereas the four proximal domains contain more recently active long interspersed nucleotide element repeats. An out-of-register, unequal recombination (i.e., crossover) detected at the edge of the X chromosome-specific alpha-satellite array (DXZ1) may reflect the most recent of a series of punctuating events during evolution that resulted in a proximal physical expansion of the X centromere. The first 18 kb of this array has 97-99% pairwise identity among all 2-kb repeat units. To perform more detailed evolutionary comparisons, we sequenced the junction between the ancient DNA of Xp and the primate-specific alpha satellite in chimpanzee, gorilla, orangutan, vervet, macaque, and baboon. The striking conservation found in all cases supports the ancestral nature of the alpha satellite at this location. These studies demonstrate that the primate X centromere appears to have evolved through repeated expansion events occurring within the central, active region of centromeric DNA, with the newly added sequences then conferring centromere function.

Animals↗
PubMed2002

Feast and famine in plant genomes.

Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a 'one-way ticket to genomic obesity', as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.

Chromosomes↗
PubMed2001

Purification, characterization and gene expression of a glycine and proline-rich antibacterial protein family from larvae of a beetle, Allomyrina dichotoma.

Two structurally related antibacterial proteins were isolated from larvae of a beetle, Allomyrina dichotoma, immunized with Escherichia coli. The two proteins were designated A. dichotoma (A. d.) coleoptericin A and B. The mature portion of A. d. coleoptericins deduced from nucleotide sequences of the cDNAs consists of seventy-two amino acids without cysteine residues and is rich in glycine (11.1%) and proline (11.1%). Comparison of the amino acid sequences of the A. d. coleoptericins revealed that these antibacterial proteins have 94%, 75%, 50% and 43% similarity to rhinocerosin, holotricin 2, coleoptericin and acaloleptin A1. Recombinant A. d. coleoptericin A and B showed strong antibacterial activity against Staphylococcus aureus, methicillin resistant S. aureus (MRSA) and Bacillus subtilis. Recombinant A. d. coleoptericin A and B were shown to not form pores through bacterial membranes of E. coli, but to hamper cell division. Results of Northern blotting showed that A. d. coleoptericin genes are inducible by bacteria and are expressed strongly in the fat bodies and haemocytes, and weakly in the Malpighian tubules. Analysis of the evolutionary relationship of amino acid sequences among A. d. coleoptericins and other antibacterial proteins suggests that A. d. coleoptericins, rhinocerosin and holotricin 2 are closely related and form a gene family.

Amino Acid Sequence↗
PubMed2006

Molecular, biochemical and structural characterization of osmotin-like protein from black nightshade (Solanum nigrum).

A full-length 910bp cDNA encoding osmotin-like protein with an open reading frame of 744bp encoding a protein of 247 amino acids with a calculated molecular mass of 26.8kDa was cloned from Solanum nigrum (SniOLP). Phylogenetic analysis revealed the evolutionary conservation of this protein among diverse taxa. The genomic DNA gel blot showed that SniOLP belongs to a small multigene family and it showed organ-specific expression. Time-course studies revealed that the expression of SniOLP was upregulated by treatment with various signaling molecules, osmotic and oxidative stress inducers. Recombinant protein purified from overexpressed Escherichia coli cells showed hyphal growth inhibition in Rhizoctonia batiticola and Sclerotinia sclerotiorum but without any endo-beta-1,3-glucanase activity. Model built by homology modeling showed that the protein consists of an acidic cleft region that is capable of interacting with the carbohydrate components of the fungal cell walls. Analysis of the structure and functional relationship was carried out by docking of the beta-(1,3)-glucan onto the acidic cleft region on the surface of the protein (SniOLP).

Adaptation, Physiological↗
PubMed2004

False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.

Sexually induced gene 1 (Sig1) in the centric diatom Thalassiosira weissflogii is considered to encode a gamete recognition protein. Sorhannus (2003) analyzed nucleotide sequences of Sig1 using parsimony analysis and the maximum-likelihood (ML)-based Bayesian method for inferring positive selection at single amino acid sites and reported that positively selected sites were detected by the latter method but not by the former. He then concluded that for this type of study, the ML-based method is more reliable than parsimony analysis. Here we show that his results apparently represent false-positive cases of the ML-based method and that there is no solid evidence that this gene contains positively selected sites. We further demonstrate that in the tax gene of human T-cell lymphotropic virus type I (HTLV-I), all codon sites, including invariable sites, can be inferred as positively selected sites by the ML-based method. These observations indicate that the ML-based method may produce many false-positive sites. One of the main reasons for the occurrence of false positives is that in the ML-based method, codon sites are grouped into several categories, with different nonsynonymous/synonymous rate ratios (omegas), on a purely statistical basis, and positive selection is inferred indirectly by examining whether the average omega for each category is greater than 1. In parsimony analysis, however, the evolutionary change of nucleotides at each codon site is examined. For this reason, parsimony-based methods rarely produce false positives and are safer than ML-based methods for detecting positive selection at individual codon sites, although a large number of sequences are necessary.

Bayes Theorem↗
PubMed1984

Analysis of a major human chorionic somatomammotropin gene. Evidence for two functional promoter elements.

The sequence of one of the two major expressed human chorionic somatomammotropin genes (hCS-1) was determined. The hCS-1 gene and the human growth hormone gene (hGH-1) share 92% nucleotide sequence homology in their 5'- and 3'-flanking regions, introns and exons. This finding, in addition to the existence of multiple closely linked hGH and hCS genes, suggests that these genes are evolving by concerted mechanisms. S1 nuclease, hybridization, and primer extension analysis of placental poly(A+) RNA demonstrated the presence of two functional initiation sites within the hCS-1 and/or the hCS-2 gene(s). The majority (about 95%) of the transcripts initiate 30 nucleotides downstream from the TATAAA sequence, and about 5% of the transcripts initiate 30 nucleotides downstream from a CATAAA sequence located 55 nucleotides 5' to the TATAAA sequence. The presence of two functional promoter elements as well as direct repeated sequences flanking the TATAAA sequence and exon I of the hCS genes are consistent with the hypothesis (Cooke, N. E., and Baxter, J. D. (1982) Nature (Lond.) 297, 603-606) that an important regulatory element may have been inserted into the gene in a separate evolutionary event. An analysis of other direct repeats, internal homology, and homology between other growth hormone and chorionic somatomammotropin genes offers a more extensive conceptualization of how this gene family evolved.

Amino Acid Sequence↗
PubMed1985

Eubacteria, halobacteria, and the origin of photosynthesis: the photocytes.

The halobacteria and the photosynthetic members of the eubacteria have previously been classified in two separate urkingdoms--the archaebacteria and the eubacteria, respectively. They were thought to be no more closely related to each other than they each were to the eukaryotes. In accord with this earlier classification, photosynthesis was thought to have originated twice by independent events--once within the eubacteria and once within the archaebacteria. In this paper, however, using three-dimensional ribosome structure as a probe of evolutionary divergences, we show that the eubacteria and the halobacteria are more closely related to each other than they are to any other known organisms. The simplest interpretation of our data is that all extant photosynthetic cells are descended from a single common ancestor that possessed a primeval photosynthetic mechanism. Numerous data on the occurrence of related biochemical processes in halobacteria and eubacteria support this theory. Essential components of the photosynthetic apparatus, such as carotenoids, are present in both halobacteria and in eubacteria, including the nonphotosynthetic eubacteria, suggesting that photosynthesis could be a primitive property of both groups. Our data indicate that together the eubacteria and the halobacteria form a monophyletic group for which we propose the name "photocytes." If other techniques of phylogenetic analysis confirm this evolutionary tree, we propose that the photocytes be given urkingdom status.

Biological Evolution↗