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PubMed1991

Characterization of the human beta-thromboglobulin gene. Comparison with the gene for platelet factor 4.

beta-Thromboglobulin (beta TG) is a platelet alpha-granule protein that is released in large amounts following platelet activation. This protein has approximately 70% amino acid identity with another platelet alpha granule protein, platelet factor 4 (PF4), and approximately 30% identity with other members of a family of proteins encoded by the small inducible genes (SIG) that are involved in the overlapping processes of inflammation, wound repair, and coagulation. Thus, the isolated beta TG gene is of interest in that it may further increase our understanding of beta TG's biological role, the regulation of its megakaryocytic-specific nature of expression, and the evolution and divergence of the SIG family. Using a beta TG cDNA isolated from a DAMI cell cDNA library, we cloned the corresponding beta TG gene. The gene is 1,139 base pairs (bp) long, and, like other members of the SIG family, the beta TG gene is divided into 3 exons. Two major transcriptional start sites were defined by primer extension analysis of platelet RNA, and, based on the more commonly used start site, the 5'-untranslated region is 87 bp. A TATA box is present beginning 32 bp upstream to this site. The first exon contains the 5'-untranslated region as well as the signal peptide. The second exon begins 6 bp 3' to the homologous site in PF4, and the third exon begins at a position homologous to that in PF4. Interestingly, the beta TG and PF4 genes have little detectable homology in the flanking or intronic sequences. In particular, a pyrimidine tract 5' to both the rat and human PF4 genes is not present in the upstream region of the beta TG gene. Genomic Southern blot analysis suggests that, as with the PF4 gene, there are multiple copies of the beta TG gene in the human genome. Chromosomal localization using polymerase chain reaction analysis of human/hamster somatic cell hybrids demonstrated that the beta TG gene, like the PF4 gene, is located on chromosome 4. It is, therefore, possible that the beta TG and PF4 gene form a single genomic locus on chromosome 4 whose members become coordinately activated during megakaryocyte differentiation.

Amino Acid Sequence↗

PubMed1990

Regulation and role of phospholipases in host-bacteria interaction.

Deacylating phospholipases play essential roles in numerous biological events, requiring tight control of hydrolytic activity. Most cells, unless stimulated or perturbed, exhibit little phospholipid turnover. Activation of phospholipases A (PLA) is usually triggered by membrane perturbing conditions or agents. Some activators indiscriminately activate any PLA, others are highly specific. Our studies concern an activator that is a potent bactericidal protein with membrane-perturbing properties, isolated from polymorphonuclear leukocytes (PMN), that is only cytotoxic for gram-negative bacteria and primarily responsible for the fate of several gram-negative bacterial species, ingested and killed by the PMN. It is this protein that activates the hydrolysis of the phospholipids of the killed bacteria (E. coli) by three PLA: 1) an E. coli PLA, the pldA gene product; 2) a PLA2 of PMN; 3) a soluble PLA2 in the extracellular fluid of an inflammatory exudate. However, this activator protein does not trigger the action of many other PLA2, all members of a highly conserved class of PLA. Our structural studies (including genetic engineering) of both responsive and non-responsive PLA2 have revealed that the amino acid composition and sequence of the NH2-terminal alpha-helix of the PLA2 molecule are major determinants of the ability of the PMN protein to activate a given PLA2. Our results provide another demonstration that these important enzymes have diverged during evolution to perform different biological functions.

Animals↗

PubMed1981

Cytogenetic observations in chronic myeloid leukemia (CML) correlations of the cytogenetic findings with morphological cytochemical features of blast cells in various types of blastic phase.

Forty-nine cases of chronic myeloid leukemia have been investigated using cytogenic methods. Twenty-six patients were studied in chronic phase, twenty-three during the transformation of the disease. Out of the second group of the patients, nine were myeloid, five myelomonocytic, two promyelocytic, two megakaryoblastic and five lymphoid in their morphological and cytochemical appearance. Some correlation could be observed between the clinical, morphological, cytological and cytogenetic findings of different subgroups of the blastic phase in CML. The results demonstrate the divergent clonal evolution of transformed blast cells, and emphasize the importance of chromosome investigations -- in addition to the early diagnosis of metamorphosis -- in distinguishing the different subgroups of the terminal stage of CML.

Adult↗

PubMed2006

Estimating the genomewide rate of adaptive protein evolution in Drosophila.

When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution--a statistic denoted alpha. But such tests are subject to many biases. Most serious is the possibility that high estimates of alpha reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in alpha is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of alpha from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely used estimators and assessing the power of the methods. As part of this process, a new maximum-likelihood estimator is introduced. This estimator is applied to a newly compiled data set of 115 genes from Drosophila simulans, each with each orthologs from D. melanogaster and D. yakuba. In this way, it is estimated that alpha approximately 0.4+/-0.1, a value that does not vary substantially between different loci or over different periods of divergence. The implications of these results are discussed.

Adaptation, Physiological↗

PubMed2003

Evolution of energy metabolism and its compartmentation in Kinetoplastida.

Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties.In this review, we describe the unique compartmentation of metabolism in Kinetoplastida and the metabolic properties resulting from this compartmentation. We discuss the evidence for our recently proposed hypothesis that a common ancestor of Kinetoplastida and Euglenida acquired a photosynthetic alga as an endosymbiont, contrary to the earlier notion that this event occurred at a later stage of evolution, in the Euglenida lineage alone. The endosymbiont was subsequently lost from the kinetoplastid lineage but, during that process, some of its pathways of energy and carbohydrate metabolism were sequestered in the kinetoplastid peroxisomes, which consequently became glycosomes. The evolution of the kinetoplastid glycosomes and the possible selective advantages of these organelles for Kinetoplastida are discussed. We propose that the possession of glycosomes provided metabolic flexibility that has been important for the organisms to adapt easily to changing environmental conditions. It is likely that metabolic flexibility has been an important selective advantage for many kinetoplastid species during their evolution into the highly successful parasites today found in many divergent taxonomic groups.Also addressed is the evolution of the kinetoplastid mitochondrion, from a supposedly pluripotent organelle, attributed to a single endosymbiotic event that resulted in all mitochondria and hydrogenosomes of extant eukaryotes. Furthermore, indications are presented that Kinetoplastida may have acquired other enzymes of energy and carbohydrate metabolism by various lateral gene transfer events different from those that involved the algal- and alpha-proteobacterial-like endosymbionts responsible for the respective formation of the glycosomes and mitochondria.

Journal Article↗

PubMed1984

Plasma cortisol transport and primate evolution.

Primates have diverged into three major evolutionary groups: prosimians, Old World primates, and New World primates; the last group is distinguished by high circulating cortisol concentrations and resistance to the action of glucocorticoids. We have studied a large spectrum of primate species within these groups to characterize the phylogenetic relationships of cortisol-binding globulin (CBG) among them. The CBG in each species was found to be glycosylated, as judged from lectin interactions, and to exhibit an electrophoretic mobility similar to that of human CBG. Although the CBG affinity for cortisol differed among species, the effects of changes in temperature on the CBG affinity were similar. Strikingly, the CBG-binding capacity of plasma in the New World primates was 1/10th to 1/100th those in the Old World primates and prosimians, while the CBG-binding affinity for cortisol was lower. The reduced capacity and affinity of CBG result in a markedly higher fraction of unbound plasma cortisol in the New World primates than in the Old World primates or the prosimian species examined. This evolutionary pattern of CBG may be a compensatory mechanism for the target organ resistance to glucocorticoids that characterizes the New World monkeys.

Animals↗

PubMed2005

[Divergence patterns of banding sequences in different polytene chromosome arms reflect relatively independent evolution of different genome components].

Divergence patterns of the banding sequences from the chromosomal arms A, C, D, E, and F were compared in 63 species of the genus Chironomus. Evaluation of the number of breakpoints between the pairs of inverted banding sequences and the analysis of the lengths of the conserved segments in the chromosomal arms in the chironomid species examined showed that different arms evolved relatively independently and at different rates. No direct correlation between the arm length and the breakpoints number was observed. The length of the conservative segment was not fixed, but was arm-specific. Robustness and fidelity of the estimates of phylogenetic relationships between the species examined increased with the arm number, i.e., with the genome proportion included in the analysis.

Animals↗

PubMed2005

Microsatellite diversity within Oryza sativa with emphasis on indica-japonica divergence.

The molecular evolution of cultivated rice Oryza sativa L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the indica rice (H=0.678) was 1.18 times larger than in the japonica rice (H=0.574). Taking the sampling effect into consideration, average allele number in the indica rice was 1.40 times higher than that in the japonica rice (14.6 vs 10.4 per variety). Chromosome-based comparisons revealed that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the indica rice than the japonica rice. An overall estimate of F(ST) was 0.084-0.158, indicating that the differentiation is moderate and 8.4-15.8% of the total genetic variation resided between the indica and japonica groups. Our chromosome-based comparisons further suggested that the extent of the indica-japonica differentiation varied substantially, ranging from 7.62% in chromosome 3 to 28.72% in chromosome 1. Cluster analyses found that most varieties formed merely two clusters for the indica and japonica varieties, in which two japonica varieties and five indica varieties were included in the counterpart clusters, respectively. The 12 chromosome-based trees further showed that 57 rice varieties cannot be clearly clustered together into either the indica or japonica groups, but displayed relatively different clustering patterns. The results suggest that the process of indica japonica differentiation may have proceeded through an extensive contribution by the alleles of the majority in the rice genome.

Chromosome Mapping↗

PubMed1999

A structural view of evolutionary divergence.

Two directed evolution experiments on p-nitrobenzyl esterase yielded one enzyme with a 100-fold increased activity in aqueous-organic solvents and another with a 17 degrees C increase in thermostability. Structures of the wild type and its organophilic and thermophilic counterparts are presented at resolutions of 1.5 A, 1.6 A, and 2.0 A, respectively. These structures identify groups of interacting mutations and demonstrate how directed evolution can traverse complex fitness landscapes. Early-generation mutations stabilize flexible loops not visible in the wild-type structure and set the stage for further beneficial mutations in later generations. The mutations exert their influence on the esterase structure over large distances, in a manner that would be difficult to predict. The loops with the largest structural changes generally are not the sites of mutations. Similarly, none of the seven amino acid substitutions in the organophile are in the active site, even though the enzyme experiences significant changes in the organization of this site. In addition to reduction of surface loop flexibility, thermostability in the evolved esterase results from altered core packing, helix stabilization, and the acquisition of surface salt bridges, in agreement with other comparative studies of mesophilic and thermophilic enzymes. Crystallographic analysis of the wild type and its evolved counterparts reveals networks of mutations that collectively reorganize the active site. Interestingly, the changes that led to diversity within the alpha/beta hydrolase enzyme family and the reorganization seen in this study result from main-chain movements.

Biological Evolution↗

PubMed2005

Factors that shape seed mass evolution.

We used correlated divergence analysis to determine which factors have been most closely associated with changes in seed mass during seed plant evolution. We found that divergences in seed mass have been more consistently associated with divergences in growth form than with divergences in any other variable. This finding is consistent with the strong relationship between seed mass and growth form across present-day species and with the available data from the paleobotanical literature. Divergences in seed mass have also been associated with divergences in latitude, net primary productivity, temperature, precipitation, and leaf area index. However, these environmental variables had much less explanatory power than did plant traits such as seed dispersal syndrome and plant growth form.

Biological Evolution↗

PubMed2004

Human endogenous retroviral elements belonging to the HERV-S family from human tissues, cancer cells, and primates: expression, structure, phylogeny and evolution.

A new human endogenous retrovirus family (HERV-S) was recently identified from the human chromosome X. The HERV-S was 6.7 kb in length with typical retroviral structure (LTR-gag-pol-env-LTR). We investigated pol fragments of HERV-S family in various human tissues and cancer cells. The pol gene was expressed in only brain and thymus among human tissues (brain, prostate, testis, heart, kidney, liver, lung, placenta, skeletal muscle, spleen, thymus, uterus), whereas the pol gene was detected in various cancer cell lines (RT4, PFSK-1, BT-474, HCT-116, Jurkat, HepG2, MCF7, OVCAR-3, MIA-PaCa-2, PC3, LOX-IMVI, AZ521, 2F7, and C-33A) except for TE-1, UO-31, A549, and U-937 by RT-PCR analysis. Expression and sequencing data of the 33 clones imply that the pol gene of HERV-S family is more active in cancer cells than in human tissues, which may have transcriptional potential role related to various human cancers. Phylogenetic analysis of HERV-S pol family distinctively divided into three groups (group I, II, and III) through evolutionary divergence in primate evolution. Evolutionary divergence of the HERV-S family by PCR amplification and sequence analysis indicated that they were integrated into the primate genomes approximately 43 Myr ago and have been evolved rate of 0.3% nucleotide differences per Myr during primate evolution.

Amino Acid Sequence↗

PubMed2006

Niche evolution and adaptive radiation: testing the order of trait divergence.

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (alpha niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (beta niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This alpha niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (beta niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the beta niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of alpha niche traits might be a common feature of niche evolution in many adaptive radiations.

Adaptation, Biological↗

PubMed1988

The secondary structure of large-subunit rRNA divergent domains, a marker for protist evolution.

The secondary structure of the large-subunit ribosomal RNA (24-26S rRNA) has been studied with emphasis on comparative analysis of the folding patterns of the divergent domains in the available protist sequences, that is Prorocentrum micans (dinoflagellate), Saccharomyces carlsbergensis (yeast), Tetrahymena thermophila (ciliate), Physarum polycephalum and Dictyostelium discoideum (slime moulds), Crithidia fasciculata and Giardia lamblia (parasitic flagellates). The folding for the D3, D7a and D10 divergent domains has been refined and a consensus model for the protist 24-26S rRNA structure is proposed. Two hundred seventy-seven nucleotide-long aligned sequences representing all or part of the D3, H32-33, D8, D9 and D10 divergent domains are used for the construction of unrooted phylogenetic trees either calculated from a nucleotide difference matrix, or determined with the PAUP programme based on the parsimony method. Both phylogenies suggest three major branchings, the first leading to the dinoflagellate (which branches off first), ciliate and yeast, the second to the slime moulds, and the last to the parasitic flagellates.

Animals↗

PubMed2006

Tandem repetitive D domains of the sperm ligand zonadhesin evolve faster in the paralogue than in the orthologue comparison.

Gene duplication is regarded as an important evolutionary mechanism creating genetic and phenotypic novelty. At the same time, the evolutionary mechanisms following gene duplication have been a subject of much debate. Here we analyze the sequence evolution of zonadhesin, a mammalian sperm ligand that binds to the oocyte zona pellucida in a species-specific manner. In pig, rabbit, and primates, precursor zonadhesin comprises, among others, one partial and four complete tandem repetitive D domains. The mouse precursor is distinguished by 20 additional partial D3 domains consisting of 120 amino acids each. This gene structure allows sequence comparison in both paralogues and orthologues. Detailed sequence analysis reveals that D domains evolve faster across paralogues than orthologues. Moreover, at the codon level, partial D3 paralogues of mouse show evidence of positive selection, whereas the corresponding orthologues do not. Individual posttranslational motif patterns and positive selection point to neofunctionalization of partial D3 paralogues of mouse, rather than subfunctionalization. However, as we found additional evidence for homogenization by partial gene conversion, sequence evolution of partial D3 paralogues of mouse might be better described as a combination of divergent and convergent evolution. So far, the divergence at the codon level has outbalanced the convergence at the level of smaller fragments. The probable driving force behind the evolutionary patterns observed is sexual selection. We finally discuss whether the functional determination influences the evolutionary regime acting on sperm ligands and egg receptors, respectively.

Amino Acid Motifs↗

PubMed2005

Structural divergence and distant relationships in proteins: evolution of the globins.

The globin family has long been known from studies of approximately 150-residue proteins such as vertebrate myoglobins and haemoglobins. Recently, this family has been enriched by the investigation of the sequences and structures of truncated globins, which have the same basic topology but are approximately 30 residues shorter and exhibit functions other than the familiar one of binding diatomic ligands. The divergence of protein sequences, structures and functions reveals Nature's exploration of the potential inherent in a folding pattern, that is, the topology of the native structure. The observation of what remains constant and what varies during the evolution of a protein family reveals essential features of structure and function. Study of proteins with a wide range of divergence can therefore sharpen our understanding of how different amino acid sequences can determine similar three-dimensional structures. Globins have provided, and continue to provide, interesting material for such studies.

Amino Acid Sequence↗

PubMed1993

A soluble multimeric recombinant CD2 protein identifies CD48 as a low affinity ligand for human CD2: divergence of CD2 ligands during the evolution of humans and mice.

To search for possible ligands of CD2 distinct from CD58 (lymphocyte function-associated antigen 3), we have produced a soluble pentameric CD2-immunoglobulin (Ig) fusion protein (spCD2) linking the 182-amino acid human CD2 extracellular segment with CH2-CH3-CH4 domains of human IgM heavy chain, thus enhancing the micromolar affinity of the CD2 monomer through multimeric interaction. Using quantitative immunofluorescence and standard stringency wash conditions, we observed that the binding of spCD2 to human B lymphoblastoid JY cells and red blood cells is virtually inhibited by anti-CD58 TS2/9 monoclonal antibody, even though these cells express levels of CD48 and CD59 comparable to CD58. Consistent with these results, spCD2 did not show any binding to Chinese hamster ovary (CHO) cells transfected with human CD48 or CD59. However, binding studies on CD48-, CD58-, or CD59-transfected CHO cells with spCD2 under low stringency wash conditions revealed that human CD48 is a low affinity ligand of human CD2 compared with CD58 (Kd approximately 10(-4) vs. approximately 10(-6) M, respectively). The findings are noteworthy given that in the murine system CD48 is the major ligand for CD2. No detectable binding was observed to CD59-transfected CHO cells despite a report suggesting that CD59 may bind to the human CD2 adhesion domain. Importantly, in cell-cell adhesion assays between CD2+ Jurkat T cells and CD48- or CD59-transfected CHO cells, there was no conjugate formation, whereas binding of Jurkat T cells to CD58-transfected CHO cells was readily detected. Collectively, our findings provide evidence for a conservation of the CD2-CD48 interaction in the human species that may be of limited, if any, functional significance. Given the importance of the CD2-CD48 interaction in the murine system and CD2-CD58 interaction in humans, it would appear that there has been a divergence of functional CD2 ligands during the evolution of humans and mice.

Animals↗

PubMed1991

Avoidance of inter-repeat recombination by sequence divergence and a mechanism of neutral evolution.

Eucaryotic genomes are loaded with diverse repeated sequences and are therefore threatened by rearrangements via inter-repeat crossovers and by gene-inactivating conversions between genes and their inactive pseudogenes. Such repeated DNA sequences are usually diverged and polymorphic. Sequence divergence by well-spread point mutations is a potent inhibitor of homologous recombination due to the loss of recombination initiation sites and to the editing of recombinational intermediates by the mismatch repair system. Evidence is reviewed suggesting that a germ line process can identify duplicated sequences by homologous pairing, modify them by methylation and mutate by C----T transitions. Since this process requires a minimum contiguous homology that is larger than the average exon size, it is proposed that fragmentation by intron inserts protects the coding sequences from inactivation by homologous interactions with their pseudogene sequences.

Animals↗

PubMed2006

Divergent selection on opsins drives incipient speciation in Lake Victoria cichlids.

Divergent natural selection acting on ecological traits, which also affect mate choice, is a key element of ecological speciation theory, but has not previously been demonstrated at the molecular gene level to our knowledge. Here we demonstrate parallel evolution in two cichlid genera under strong divergent selection in a gene that affects both. Strong divergent natural selection fixed opsin proteins with different predicted light absorbance properties at opposite ends of an environmental gradient. By expressing them and measuring absorbance, we show that the reciprocal fixation adapts populations to divergent light environments. The divergent evolution of the visual system coincides with divergence in male breeding coloration, consistent with incipient ecological by-product speciation.

Africa, Eastern↗