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PubMed2025

Evolution of primate T-cell leukemia virus type 1 accessory genes and functional divergence of its antisense proteins.

Human T-cell leukemia virus type 1 (HTLV-1) is derived from simian T-cell leukemia virus type 1 (STLV-1), and together they form a broader category known as primate T-cell leukemia virus type 1 (PTLV-1). PTLV-1 encodes multiple proteins from overlapping open reading frames (ORFs) in the pX region. This study aims to characterize the conservation of these proteins in different PTLV-1 subtypes and their role in pathogenesis. For the first time, we report the full-length proviral sequence of an STLV-1 strain isolated from chimpanzee and African green monkey. Phylogenetic analysis reveals high conservation of the accessory proteins p12, p30, and p13 in the HTLV-1a subtype. Conversely, some African PTLV-1 subtypes exhibit loss of ORFs for p12 or p13. For Asian subtypes, simian strains often lack p12, p13, or p30 proteins, whereas human strains retain the ORFs of p30 and p13 but not p12. To assess the infectivity of a simian strain of PTLV-1 lacking ORFs for p12, p13, and p30, we constructed a molecular clone from a naturally infected Japanese macaque (Mfu: Macaca fuscata) and compared it with HTLV-1a. Using a reporter assay and ELISA, we found similar infectivity to Jurkat T cells; however, STLV-1 Mfu exhibited impaired infectivity in the monocytic cell line THP-1. Additionally, despite the conservation of the HTLV-1/STLV-1 bZIP factor (HBZ/SBZ) ORFs, HBZ/SBZ proteins derived from HTLV-1a and African PTLV-1 subtypes induce significantly higher activation of the TGF-β/Smad signaling pathway than those from Asian subtypes. Collectively, our findings suggest that the acquisition of the accessory proteins by PTLV-1 subtypes potentially confers an advantageous adaptation of PTLV-1 during infection in apes, including humans. Moreover, among PTLV-1 strains, HBZ/SBZ had varying degrees of activity on the TGF-β/Smad pathway; this fact underscores the complex interplay between viral proteins and host signaling pathways, possibly influencing the viral pathogenicity in different species.

Animals↗
PubMed2005

Maximal sequence length of exact match between members from a gene family during early evolution.

Mutation (substitution, deletion, insertion, etc.) in nucleotide acid causes the maximal sequence lengths of exact match (MALE) between paralogous members from a duplicate event to become shorter during evolution. In this work, MALE changes between members of 26 gene families from four representative species (Arabidopsis thaliana, Oryza sativa, Mus musculus and Homo sapiens) were investigated. Comparative study of paralogous' MALE and amino acid substitution rate (d(A)<0.5) indicated that a close relationship existed between them. The results suggested that MALE could be a sound evolutionary scale for the divergent time for paralogous genes during their early evolution. A reference table between MALE and divergent time for the four species was set up, which would be useful widely, for large-scale genome alignment and comparison. As an example, detection of large-scale duplication events of rice genome based on the table was illustrated.

Amino Acid Sequence↗
PubMed1986

Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock.

The discovery that the rate of evolution of vertebrate mitochondrial DNA is rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its widespread use in evolutionary studies. Comparison of mitochondrial and nuclear DNA divergences among echinoid and vertebrate taxa of similar ages indicates that the rapid rate of vertebrate mitochondrial DNA evolution is, in part, an artifact of a widely divergent rate of nuclear DNA evolution. This disparity in relative rates of mitochondrial and nuclear DNA divergence suggests that the controls and constraints under which the mitochondrial and nuclear genomes operate are evolving independently, and provides evidence that is independent of fossil dating for a robust rejection of a generalized molecular clock hypothesis of DNA evolution.

Animals↗
PubMed2005

Matters of scale: positive allometry and the evolution of male dimorphisms.

The developmental independence of alternative phenotypes is key to evolutionary theories of phenotypic plasticity and the origins of diversity. Male dimorphisms associated with alternative reproductive tactics are widely cited examples of such facultative expression of divergent fitness optima. Current models for the evolution of male dimorphisms invoke a size-dependent threshold at which the phenotype is reprogrammed. We use predictions derived from allometric modeling to test for the existence of reprogramming thresholds in two species of beetle, Onthophagus taurus and Onthophagus binodis, and the European earwig Forficula auricularia. We also compare the allometry of a number of morphological traits to determine whether minor males suppress their secondary sexual traits. The intercept of the horn allometry was suppressed, but there was no evidence of reprogramming of horn growth in either beetle species. There was reprogramming in the earwig. In the beetles, the horn length in all males can be explained largely in terms of exponential horn growth following an extraordinarily steep power function. The asymptote in O. taurus can be explained by exponential growth meeting the constraint of resource exhaustion. These findings question the currently held view that beetle horn dimorphisms showcase the importance of developmental independence in the evolution of diversity.

Animals↗
PubMedDate not supplied

[Relationship between the study of DNA reassociation kinetics of various chromosomal forms of Ellobius and questions concerning the pathways of chromosome rearrangement during evolution].

Fifteen chromosome forms of Ellobius talpinus (from 2n = 31 to 2n = 54) were found in the small area in the Pamirs. Low-chromosome karyotypes evolved from 54-chromosomal ancestral form by Robertsonia centric fusions. The DNA reassociation kinetics of 34- and 54-chromosome forms of E. talpinus have been studied. For comparison DNA of E. lutescens (2n = 17) the karyotype of which seems to have arisen from 54-chromosome ancestor by Robertsonian and other types rearrangements was examined. Reassociation profiles of Ellobius DNA suggest the existence of several repeated sequences families with different frequences of repetitions. The reassociation curves of DNA from 34- and 54-chromosome forms were identical. These data indicate absence of changes in DNA molecular organization during the evolution of E. talpinus karyotypes by Robertsonian fusions. Comparative analysis of DNA reassociation kinetics of E. talpinus and E. lutescens showed identical characteristics of highly repeated sequences and of one from the three intermediate fractions, however Cot 1/2, complexity and repetitive frequencies of two intermediate fractions of E. talpinus and E. lutescens were different. It is possible that non-robertsonian rearrangements of E. lutescens karyotype affected only intermediate repetitions. The alternative explanation of these data is a simple divergence of repeated sequences during the evolution of E. lutescens DNA.

Animals↗
PubMed1981

[Intercellular serine proteinases from spore-forming bacilli].

Some physico-chemical properties, immunological reactions, structural, functional and evolutionary features of intracellular serine proteinases from spore-forming bacilli were studied. These enzymes belong to an individual subfamily of serine proteinases and in terms of their structure and evolution are most closely related to secretory subtilisins. Intracellular serine proteinases are found in a wide variety of microorganisms--from the spore-forming bacilli to Escherichia coli and are characterized by a higher (as compared to secretory subtilisins) rate of evolution due to a more rigid selective control of the structure and function of intracellular enzymes. Active intracellular proteinases have a unique dimeric structure, which allows to exclude random proteolysis of native proteins in vivo. Secretory subtilisins and intracellular bacillary serine proteinases are coded by separate closely related structural genes, whose presence in the bacillary genome can be explained by duplication of the precursor gene. The existence of duplicated genes of serine proteinases provides sufficient evidence for the marked structural divergence and a high rate of evolution of secretory subtilisins.

Amino Acid Sequence↗
PubMed2003

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes.

One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.

Evolution, Molecular↗
PubMed2000

Retroviruses and primate evolution.

Human endogenous retroviruses (HERVs), probably representing footprints of ancient germ-cell retroviral infections, occupy about 1% of the human genome. HERVs can influence genome regulation through expression of retroviral genes, either via genomic rearrangements following HERV integrations or through the involvement of HERV LTRs in the regulation of gene expression. Some HERVs emerged in the genome over 30 MYr ago, while others have appeared rather recently, at about the time of hominid and ape lineages divergence. HERVs might have conferred antiviral resistance on early human ancestors, thus helping them to survive. Furthermore, newly integrated HERVs could have changed the pattern of gene expression and therefore played a significant role in the evolution and divergence of Hominoidea superfamily. Comparative analysis of HERVs, HERV LTRs, neighboring genes, and their regulatory interplay in the human and ape genomes will help us to understand the possible impact of HERVs on evolution and genome regulation in the primates. BioEssays 22:161-171, 2000.

Animals↗
PubMed1998

Adaptive radiation in a heterogeneous environment.

Successive adaptive radiations have played a pivotal role in the evolution of biological diversity. The effects of adaptive radiation are often seen, but the underlying causes are difficult to disentangle and remain unclear. Here we examine directly the role of ecological opportunity and competition in driving genetic diversification. We use the common aerobic bacterium Pseudomonas fluorescens, which evolves rapidly under novel environmental conditions to generate a large repertoire of mutants. When provided with ecological opportunity (afforded by spatial structure), identical populations diversify morphologically, but when ecological opportunity is restricted there is no such divergence. In spatially structured environments, the evolution of variant morphs follows a predictable sequence and we show that competition among the newly evolved niche-specialists maintains this variation. These results demonstrate that the elementary processes of mutation and selection alone are sufficient to promote rapid proliferation of new designs and support the theory that trade-offs in competitive ability drive adaptive radiation.

Adaptation, Physiological↗
PubMed2002

Evaluating mental health outcomes in an inpatient setting: convergent and divergent validity of the OQ-45 and BASIS-32.

The evolution of managed behavioral health care has led to an increased emphasis on reliable and valid assessment of outcomes in clinical practice. The present study evaluated the convergent, divergent, and concurrent validity and sensitivity to change of two widely used measures: Behavior and Symptom Identification Scale (BASIS-32) and Outcome Questionnaire (OQ-45). Comparisons of the two measures revealed that both were sensitive to change over a relatively short inpatient stay. Both measures also showed evidence of convergent and divergent validity of specific subscales, although the total scores of each measure also were highly correlated. Evidence of concurrent validity was suggested by differences between diagnostic groups on specific subscale scores. Together with previous research, these results suggest that the BASIS-32 and OQ-45 can be useful measures for tracking patient functioning over a range of treatment contexts.

Adult↗
PubMed1986

Recent evolutionary divergence of plasma prekallikrein and factor XI.

The evolution in mammals of the zymogens of the contact activation system of coagulation (factor XII, prekallikrein and factor XI) has been investigated. The NH2-terminal sequences of human plasma prekallikrein and the heavy and light chains of kallikrein have been determined and compared with those of bovine prekallikrein and of human and bovine factors XII and XI. The human and bovine NH2-terminal sequences of the light chains (catalytic polypeptide) show striking similarities both among themselves and with those of the catalytic polypeptide chains of other coagulation and digestive proteases, indicating a common origin. Comparison of the NH2-terminal sequences of human prekallikrein with those of the bovine prekallikrein and human bovine factors XIa and XIIa indicates a common origin of the heavy chain of kallikrein and factor XIa, different from that of either factor XIIa or other known amino acid sequences. Ancestral sequences for human and bovine prekallikrein and factor XI, deduced by genetic analysis of the minimum number of base changes indicate that the NH2-terminus of prekallikrein and factor XI have evolved at about the same rate. The estimated time for the gene duplication was about 124 million years ago, a value consistent with the age of the mammals.

Amino Acid Sequence↗
PubMed2005

Rapid evolution of the MH class I locus results in different allelic compositions in recently diverged populations of Atlantic salmon.

We compared major histocompatibility class I allelic diversity in two currently reproductively isolated Atlantic salmon (Salmo salar) populations (Irish and Norwegian) with a common postglacial origin in order to test for among-population differences in allelic composition and patterns of recombination and point mutation. We also examined the evidence for adaptive molecular divergence at this locus by analyzing the rate of amino acid replacement in relation to a neutral expectation. Contrary to our prediction, and in contrast to the situation for other genetic markers, the two populations have almost nonoverlapping sets of major histocompatibility class I alleles. Although there is a strong signal of point mutation that predates population divergence, recent recombination, acting in similar, but not identical, ways in both populations appears to be a significant force in creating new alleles. Moreover, selection acting on peptide-binding residues seems to favor new recombinant alleles and is likely to be responsible for the rapid divergence between populations.

Alleles↗
PubMed2000

Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi.

The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two different molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named 'Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more influenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous-Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous.

Animals↗
PubMed2006

Lachesis muta (Viperidae) cDNAs reveal diverging pit viper molecules and scaffolds typical of cobra (Elapidae) venoms: implications for snake toxin repertoire evolution.

Efforts to describe toxins from the two major families of venomous snakes (Viperidae and Elapidae) usually reveal proteins belonging to few structural types, particular of each family. Here we carried on an effort to determine uncommon cDNAs that represent possible new toxins from Lachesis muta (Viperidae). In addition to nine classes of typical toxins, atypical molecules never observed in the hundreds of Viperidae snakes studied so far are highly expressed: a diverging C-type lectin that is related to Viperidae toxins but appears to be independently originated; an ohanin-like toxin, which would be the third member of the most recently described class of Elapidae toxins, related to human butyrophilin and B30.2 proteins; and a 3FTx-like toxin, a new member of the widely studied three-finger family of proteins, which includes major Elapidae neurotoxins and CD59 antigen. The presence of these common and uncommon molecules suggests that the repertoire of toxins could be more conserved between families than has been considered, and their features indicate a dynamic process of venom evolution through molecular mechanisms, such as multiple recruitments of important scaffolds and domain exchange between paralogs, always keeping a minimalist nature in most toxin structures in opposition to their nontoxin counterparts.

Amino Acid Sequence↗
PubMed2005

Variation in positive selection in termite GNBPs and Relish.

Social insects are model organisms for investigating molecular evolution in the innate immune system. Their diversity affords comparative analysis among closely related species, and group living is likely to contribute to the pathogen stress imposed on the immune system. We used different models of nucleotide substitution at nonsynonymous (amino acid altering) and synonymous (silent) sites to compare the different levels and type of selection among three immunity genes in 13 Australian termite species (Nasutitermes). The immunity genes include two encoding pathogen recognition proteins (gram-negative bacterial-binding proteins) that duplicated and diverged before or soon after the evolution of the termites and a transcription factor (Relish), which induces the production of antimicrobial peptides. A comparison of evolutionary models that assign four unrestricted classes of dN/dS (the ratio of the nonsynonymous to synonymous substitution rate) to different Nasutitermes lineages revealed that the occurrence of positive selection (dN/dS > 1) varies among lineages and the three genes. Positive selection appears to have driven the evolution of all three genes in an ancestral lineage of three subterranean termites. It had previously been suggested that there was a transition along this ancestral lineage to termite morphology and ecology associated with a diet of decayed wood, a diet that may expose termites to elevated levels of fungal and bacterial pathogens. Relish appears to have experienced the highest levels of selective pressure for change among all three genes. Positively selected sites in the molecule are located in regions that are important for its activation, which suggests that amino acid substitutions at these sites are a counter response to pathogen mechanisms that disrupt the activation of Relish.

Amino Acid Substitution↗
PubMed1988

Organization of human homeobox genes.

The chromosomal localization of 17 human homeoboxes and the predicted primary sequence of the encoded homeodomains is reported. These homeoboxes are clustered in four complex HOX loci on chromosomes 2, 7, 12 and 17. Although the identification of human homeoboxes has not been completed, existing data permit preliminary conclusions on the origin and evolution of these complex loci to be drawn. The homeo-domains of one HOX locus can be unambiguously aligned to the homeodomains of the other HOX loci, so that corresponding homeodomains in all loci can share the maximal peptide sequence identity. This one-to-one correspondence of individual homeodomains in different chromosomal loci suggests the hypothesis of large-scale duplications of a single complex locus and subsequent spreading in different chromosomes. The existence of an ancestral complex locus might have predated the divergence of the arthropod/annelid and vertebrate evolutive lineages.

Amino Acid Sequence↗
PubMed1999

Evolution of bHLH transcription factors: modular evolution by domain shuffling?

Multidomain proteins usually contain several conserved and apparently independently evolved domains. As a result, classifications based on only a single small domain may obscure the true evolutionary relationships of the proteins. The current classification of basic helix-loop-helix (bHLH) domain-containing proteins is based on the conserved bHLH domain alone. Herein, we explore whether sequence homology and, therefore, evolutionary relationships can be detected among the flanking or non-bHLH components of the amino acid sequences of 122 bHLH proteins. These 122 proteins were the same proteins previously used to construct the existing classification of the bHLH-domain-containing proteins. Several possible scenarios are examined in order to explain the observed patterns of sequence divergence, including (1) monophyly, (2) convergent evolution, (3) addition of functional components to the bHLH domain, and (4) modular evolution with domain shuffling. Drawing on several lines of evidence, we suggest that modular evolution by domain shuffling may have played an important role in the evolution of this large group of transcriptional regulators.

DNA-Binding Proteins↗
PubMed1994

Evolution of base composition in the insulin and insulin-like growth factor genes.

The genomes of homeothermic (warm-blooded) vertebrates are mosaic interspersions of homogeneously GC-rich and GC-poor regions (isochores). Evolution of genome compartmentalization and GC-rich isochores is hypothesized to reflect either selective advantages of an elevated GC content or chromosome location and mutational pressure associated with the timing of DNA replication in germ cells. To address the present controversy regarding the origins and maintenance of isochores in homeothermic vertebrates, newly obtained as well as published nucleotide sequences of the insulin and insulin-like growth factor (IGF) genes, members of a well-characterized gene family believed to have evolved by repeated duplication and divergence, were utilized to examine the evolution of base composition in nonconstrained (flanking) and weakly constrained (introns and fourfold degenerate sites) regions. A phylogeny derived from amino acid sequences supports a common evolutionary history for the insulin/IGF family genes. In cold-blooded vertebrates, insulin and the IGFs were similar in base composition. In contrast, insulin and IGF-II demonstrate dramatic increases in GC richness in mammals, but no such trend occurred in IGF-I. Base composition of the coding portions of the insulin and IGF genes across vertebrates correlated (r = 0.90) with that of the introns and flanking regions. The GC content of homologous introns differed dramatically between insulin/IGF-II and IGF-I genes in mammals but was similar to the GC level of noncoding regions in neighboring genes. Our findings suggest that the base composition of introns and flanking regions is determined by chromosomal location and the mutational pressure of the isochore in which the sequences are embedded. An elevated GC content at codon third positions in the insulin and the IGF genes may reflect selective constraints on the usage of synonymous codons.

Animals↗