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PubMed1986

Sequences of four mouse histone H3 genes: implications for evolution of mouse histone genes.

The sequences of four histone H3 genes coding for the replication variant proteins H3.1 and H3.2 have been determined. Three of these genes, two coding for H3.1 proteins and one for an H3.2 protein, are located on chromosome 13 and expressed at low levels. The fourth gene, encoding an H3.2 protein, is located on chromosome 3 and expressed at a high level. The coding regions of the three genes on chromosome 13 are more similar to each other than to the H3 gene on chromosome 3, and equally divergent from it, suggesting that either gene duplication or gene conversion has occurred since the genes were dispersed onto two chromosomes. A 14-base sequence including the CCAAT sequence and located 5' to the genes on chromosome 13 has been conserved. The histone H3 gene on chromosome 3 has multiple potential binding sites for the Sp1 transcription factor. The coding regions show greater than 95% conservation among the four genes. This is due to the strict pattern of codon usage and the presence of two long (greater than 60 base) regions of completely conserved nucleic acid sequence. These conserved regions in the coding sequence may have an important functional role at the mRNA or DNA level.

Amino Acid Sequence↗
PubMed2005

Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast.

A maximum-likelihood (ML) method is developed to estimate the duration of concerted evolution and the time to the whole-genome duplication (WGD) event in baker's yeast (Saccharomyces cerevisiae). The models with concerted evolution fit the data significantly better than the molecular clock model, indicating a crucial role of concerted evolution via gene conversion after gene duplication in yeast. Our ML estimate of the time to the WGD is nearly identical to the time to the speciation event between S. cerevisiae and Kluyveromyces waltii, suggesting that the WGD occurred in very early stages after speciation or the WGD might have been involved in the speciation event.

Algorithms↗
PubMed2001

The evolution of the MHC-G gene does not support a functional role for the complete protein.

The study of the MHC-G gene evolution during nearly 40 million years does not support a role for the full molecule. The MHC-G-like proteins of New World monkeys are probably classical presenting molecules. Old World Cercopithecinae monkeys do not have a full MHC-G molecule and human individuals homozygous for the HLA-G null allele are healthy and do not show birth pathologies.

Amino Acid Sequence↗
PubMed2006

Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake).

BACKGROUND: The evolution of structurally and functionally similar proteins with highly diverse physiological roles within a single organism is of great interest. Australian elapid snakes offer an excellent opportunity to study the molecular evolution of prothrombin activators. Venom from Pseudonaja textilis contains pseutarin C, a group C prothrombin activator. Its enzymatic subunit is structurally and functionally similar to mammalian factor (F) Xa, whereas its non-enzymatic subunit is similar to FVa. As vertebrates, the snakes also contain a system to activate prothrombin in their own blood during injury. These hemostatic factors are produced in the liver. RESULTS: Here we describe the presence of two molecular forms of FX expressed in the liver of P. textilis. Both isoforms have molecular signatures and domain architecture of FX. However, one isoform shows approximately 94% sequence identity with the snake FX from Tropidechis carinatus, whereas the other is much closer (90% identity) to the catalytic subunit of pseutarin C (PCCS). Real-time polymerase chain reaction reveals that the latter isoform is expressed approximately 56 000 times lower in the liver of P. textilis. However, the isoforms are not expressed in the venom gland. CONCLUSION: A detailed analysis of deletions and insertions along with the sequence indicates that the second isoform is an intermediate caught in the evolution of venom prothrombin activator from the blood coagulation FX. Thus, this isoform represents a 'molecular fossil' and reveals the likely evolutionary path of recruitment of FX in the venom gland.

Amino Acid Sequence↗
PubMed1988

Structure, chromosome location, and expression of the human gamma-actin gene: differential evolution, location, and expression of the cytoskeletal beta- and gamma-actin genes.

The accumulation of the cytoskeletal beta- and gamma-actin mRNAs was determined in a variety of mouse tissues and organs. The beta-isoform is always expressed in excess of the gamma-isoform. However, the molar ratio of beta- to gamma-actin mRNA varies from 1.7 in kidney and testis to 12 in sarcomeric muscle to 114 in liver. We conclude that, whereas the cytoskeletal beta- and gamma-actins are truly coexpressed, their mRNA levels are subject to differential regulation between different cell types. The human gamma-actin gene has been cloned and sequenced, and its chromosome location has been determined. The gene is located on human chromosome 17, unlike beta-actin which is on chromosome 7. Thus, if these genes are also unlinked in the mouse, the coexpression of the beta- and gamma-actin genes in rodent tissues cannot be determined by gene linkage. Comparison of the human beta- and gamma-actin genes reveals that noncoding sequences in the 5'-flanking region and in intron III have been conserved since the duplication that gave rise to these two genes. In contrast, there are sequences in intron III and the 3'-untranslated region which are not present in the beta-actin gene but are conserved between the human gamma-actin and the Xenopus borealis type 1 actin genes. Such conserved noncoding sequences may contribute to the coexpression of beta- and gamma-actin or to the unique regulation and function of the gamma-actin gene. Finally, we demonstrate that the human gamma-actin gene is expressed after introduction into mouse L cells and C2 myoblasts and that, upon fusion of C2 cells to form myotubes, the human gamma-actin gene is appropriately regulated.

Actins↗
PubMed2002

Heterotopic shift of epithelial-mesenchymal interactions in vertebrate jaw evolution.

Genes involved in late specification of the mandibular arch, the source of the vertebrate jaw, are expressed with similar patterns in the oral regions of chick and lamprey embryos. However, morphological comparisons indicate that apparently orthologous homeobox genes were expressed in different subdivisions of the ectomesenchyme in the two species. Therefore, the homology and gene expression of the oral region are uncoupled during the transition from agnathan to gnathostome; we conclude that a heterotopic shift of tissue interaction was involved in the evolution of the jaw.

Animals↗
PubMed1997

Hox genes in evolution: protein surfaces and paralog groups.

The clustered Hox genes, which encode homeodomain transcription factors, control cell fates along the anterior-posterior axis. Differences between Hox proteins cause differences between body parts. Vertebrates have 13 Hox subgroups, called paralog groups, which can be correlated with some of the insect and Amphioxus genes, and have remained distinctive for hundreds of millions of years. We identify characteristic residues that define the different paralog groups. Some paralog groups can be recognized by the homeodomain sequence alone; others only by using characteristic residues outside the homeodomain. Mapping characteristic residues onto the known homeodomain crystal structure reveals that most of the homeodomain amino acids that distinguish paralog groups are oriented away from the DNA, in positions where they might engage in protein-protein interactions.

Amino Acid Sequence↗
PubMed2006

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome.

BACKGROUND: Coordinately regulated genes often physically cluster in eukaryotic genomes, for reasons that remain unclear. RESULTS: Here we provide evidence that many S. cerevisiae genes induced by starvation and other stresses reside in non-random clusters, where transcription of these genes is repressed in the absence of stress. Most genes essential for growth or for rapid, post-transcriptional responses to stress in cycling cells map between these gene clusters. Genes that are transcriptionally induced by stresses include a large fraction of rapidly evolving paralogues of duplicated genes that arose during an ancient whole genome duplication event. Many of these rapidly evolving paralogues have acquired new or more specialized functions that are less essential for growth. The slowly evolving paralogues of these genes are less likely to be transcriptionally repressed in the absence of stress, and are frequently essential for growth or for rapid stress responses that may require constitutive expression of these genes in cycling cells. CONCLUSION: Our findings suggest that a fundamental organizing principle during evolution of the S. cerevisiae genome has been clustering of starvation and other stress-induced genes in chromosome regions that are transcriptionally repressed in the absence of stress, from which most genes essential for growth or rapid stress responses have been excluded. Chromatin-mediated repression of many stress-induced genes may have evolved since the whole genome duplication in parallel with functions for proteins encoded by these genes that are incompatible with growth. These functions likely provide fitness effects that escape detection in assays of reproductive capacity routinely employed to assess evolutionary fitness, or to identify genes that confer stress-resistance in cycling cells.

Evolution, Molecular↗
PubMed1988

Evolution of the IgA heavy chain gene in the genus Mus.

To examine questions of immunoglobulin gene evolution, the IgA alpha heavy chain gene from Mus pahari, an evolutionarily distant relative to Mus musculus domesticus, was cloned and sequenced. The sequence, when compared to the IgA gene of BALB/c or human, demonstrated that the IgA gene is evolving in a mosaic fashion with the hinge region accumulating mutations most rapidly and the third domain at a considerably lower frequency. In spite of this pronounced accumulation of mutations, the hinge region appears to maintain the conformation of a random coil. A marked propensity to accumulate replacement over silent site changes in the coding regions was noted, as was a definite codon bias. The possibility that these two phenomena are interrelated is discussed.

Amino Acid Sequence↗
PubMed1998

Conservation of read-through transcription of the Drosophila serendipity genes during evolution is gratuitous.

The Drosophila melanogaster serendipity (sry) genes sry alpha and sry beta, which code for unrelated proteins and functions, are transcribed both as monocistronic (sry alpha, srv beta) and dicistronic (sry beta-sry alpha) polyadenylated transcripts, the three types of transcripts being differentially expressed throughout development. We show here that, while the sry gene cluster is conserved in two other distantly related Drosophila species, sry beta-sry alpha dicistronic transcription is observed in one of them, Drosophila pseudoobscura but not in the other, Drosophila virilis, indicating that this mode of transcription is not subject to selection during evolution. Sequence comparison of the intergenic sry beta-sry alpha region suggests that sry, beta-sry alpha read-through transcription results from interference between initiation of transcription at the sry alpha promoter and 3' processing of the upstream sry beta transcript. From these and previous analyses, we propose that read-through transcription at the sry locus reflects its clustered gene organisation but is functionally gratuitous. This conclusion is supported by the autonomous rate of evolutionary sequence divergence shown by each individual sry gene.

Animals↗
PubMed1998

Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages.

The specification of floral organ identity in the higher dicots depends on the function of a limited set of homeotic genes, many of them members of the MADS-box gene family. Two such genes, APETALA3 (AP3) and PISTILLATA (PI), are required for petal and stamen identity in Arabidopsis; their orthologs in Antirrhinum exhibit similar functions. To understand how changes in these genes may have influenced the morphological evolution of petals and stamens, we have cloned twenty-six homologs of the AP3 and PI genes from two higher eudicot and eleven lower eudicot and magnolid dicot species. The sequences of these genes reveal the presence of characteristic PI- and AP3-specific motifs. While the PI-specific motif is found in all of the PI genes characterized to date, the lower eudicot and magnolid dicot AP3 homologs contain distinctly different motifs from those seen in the higher eudicots. An analysis of all the available AP3 and PI sequences uncovers multiple duplication events within each of the two gene lineages. A major duplication event in the AP3 lineage coincides with the base of the higher eudicot radiation and may reflect the evolution of a petal-specific AP3 function in the higher eudicot lineage.

Amino Acid Sequence↗
PubMed2001

Maternal effect genes and the evolution of sociality in haplo-diploid organisms.

Maternal care and female-biased sex ratios are considered by many to be essential prerequisites for the evolution of eusocial behaviors among the hymenoptera. Using population genetic models, I investigate the evolution of genes that have positive maternal effects but negative, direct effects on offspring fitness. I find that, under many conditions, such genes evolve more easily in haplo-diploids than in diplo-diploids. In fact, the conditions are less restrictive than those of kin selection theory, which postulate genes with negative direct effects but positive sib-social effects. For example, the conditions permitting the evolution of maternal effect genes are not affected if females mate multiply, whereas multiple mating reduces the efficacy of kin selection by reducing genetic relatedness within colonies. Inbreeding also differentially facilitates evolution of maternal effect genes in haplo-diploids relative to diplo-diploids, although it does not differentially affect the evolution of sib-altruism genes. Furthermore, when the direct, deleterious pleiotropic effect is restricted to sons, a maternal effect gene can evolve when the beneficial maternal effect is less than half (with inbreeding, much less) of the deleterious effect on sons. For kin selection, however, the sib-social benefits must always exceed the direct costs because genetic relatedness is always less than or equal to 1.0. The results suggest that haplo-diploidy facilitates (1) the evolution of maternal care, and (2) the evolution of maternal effect genes with antagonistic pleiotropic effects on sons. The latter effect may help explain the tendency toward female-biased sex ratios in haplo-diploids, especially those with inbreeding. I conclude that haplo-diploidy not only facilitates the evolution of sister-sister altruism by kin selection but also facilitates the evolution of maternal care and female-biased sex ratios, two prerequisites for eusociality.

Alleles↗
PubMed1992

Characterization of two members (CST4 and CST5) of the cystatin gene family and molecular evolution of cystatin genes.

Two members (CST4 and CST5) of the cystatin gene family have been characterized partially by DNA analysis. The CST4 clone contained the gene coding for the precursor form(141 amino acids) of cystatin S, and its exon-intron organization is the same as that of other members (the cystatin SN gene at the CST1 locus, the cystatin SA gene at the CST2 locus, the cystatin C gene at the CST3 locus and a cystatin pseudogene at the CSTP1 locus). The second cystatin pseudogene was elucidated in the clone, CST5, and it was assigned to the CSTP2 locus. Alignment of DNA sequences of cystatin genes with other genes suggested that the genes for cystatins, kininogens, and Bowman-Birk type inhibitors have evolved from an ancient ribonuclease-like gene.

Amino Acid Sequence↗
PubMed2018

Convergent evolution of gene expression in two high-toothed stickleback populations.

Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to gene expression changes accompanying an evolved morphological gain trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we found that trans regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.

Alleles↗
PubMed1984

Relationship between the individual collagenases of Clostridium histolyticum: evidence for evolution by gene duplication.

The relationship between the six collagenases (alpha, beta, gamma, delta, epsilon, and zeta) isolated and characterized in the preceding papers [Bond, M.D., & Van Wart, H.E. (1984) Biochemistry (preceding two papers in this issue)] has been investigated. Chemical modification reactions establish that all six enzymes contain essential carboxyl, tyrosine, and lysine residues. Circular dichroism spectra of the peptide bond region show that the secondary structures of the collagenases are very similar. Ouchterlony double-immunodiffusion experiments carried out with antiserum prepared against beta-collagenase indicate that all six collagenases are cross-reactive. Reverse-phase high-pressure liquid chromatography elution profiles of tryptic digests of these collagenases and sodium dodecyl sulfate electrophoresis gels of the peptides formed on reaction with cyanogen bromide have been obtained. The results indicate that the class I collagenases have extensive sequence homology with each other and that the class II collagenases have extensive sequence homology with each other but that the enzymes in the two classes have substantially different sequences. In addition, the data show that beta-collagenase probably consists of domains that have homologous amino acid sequences, which may have arisen by full or partial intragenic gene duplication. This may account for the unusually high molecular weight of this and the other collagenases. Finally, on the basis of the similarities between the collagenases in the two classes, it is suggested that one class evolved from the other by gene duplication followed by independent evolution by point mutations to yield enzymes with different substrate specificities.

Circular Dichroism↗
PubMed2002

Evolution of gene fusions: horizontal transfer versus independent events.

BACKGROUND: Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution. RESULTS: The evolutionary history of gene fusions was studied by phylogenetic analysis of the domains in the fused proteins and the orthologous domains that form stand-alone proteins. Clustering of fusion components from phylogenetically distant species was construed as evidence of dissemination of the fused genes by horizontal transfer. Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms. On many occasions, the evolutionary scenario also involves one or more secondary fissions of the fusion gene. For approximately half of the fusions, stand-alone forms of the fusion components are encoded by juxtaposed genes, which are known or predicted to belong to the same operon in some of the prokaryotic genomes. This indicates that evolution of gene fusions often, if not always, involves an intermediate stage, during which the future fusion components exist as juxtaposed and co-regulated, but still distinct, genes within operons. CONCLUSION: These findings suggest a major role for horizontal transfer of gene fusions in the evolution of protein-domain architectures, but also indicate that independent fusions of the same pair of domains in distant species is not uncommon, which suggests positive selection for the multidomain architectures.

DNA, Archaeal↗