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PubMed2005

Rapid evolution of expression and regulatory divergences after yeast gene duplication.

Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an approximately 20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9 x 10(-9) per year, whereas the baseline rate for very ancient gene duplication is 0.14 x 10(-9) per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network.

Evolution, Molecular↗
PubMed2006

Divergence of duplicated genes in maize: evolution of contrasting targeting information for enzymes in the porphyrin pathway.

The divergence of sequence and expression pattern of duplicated genes provides a means for genetic innovation to occur without sacrificing an essential function. The cpx1 and cpx2 genes of maize are a singular example of duplicated genes that have diverged by deletion and creation of protein targeting information. The cpx genes encode coproporphyrinogen III oxidase ('coprogen oxidase'), which catalyzes a step in the synthesis of chlorophyll and heme. In plants, this enzyme has been found exclusively in the plastids. The cpx1 and cpx2 genes encode almost identical, catalytically active enzymes with distinctive N-terminal peptide sequences. The cpx1 gene encodes the expected plastid transit peptide, but this region is deleted from the cpx2 gene. While the 5' regions of both messenger RNAs are highly similar, the cpx2 gene has an open-reading frame that could encode a new targeting signal. GFP fused with CPX1 localized to the plastids. In contrast, the GFP fusion with CPX2 did not target plastids and appeared to localize to mitochondria. Both cpx genes are expressed ubiquitously but, based on mutant phenotype, they seem to have discrete biological roles. Seedlings homozygous for a null mutation in the cpx1 gene completely lack chlorophyll and develop necrotic lesions in the light. However, the mutant seedlings and callus cultures will grow in tissue culture in the dark, implying that they retain a capacity to produce heme. We discuss models for the evolution of the cpx genes and possible roles of mitochondrion-localized coprogen oxidase activity in maize.

Amino Acid Sequence↗
PubMed2003

Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella.

Homologues of the protein constituents of the Klebsiella pneumoniae (Klebsiella oxytoca) type II secreton (T2S), the Pseudomonas aeruginosa type IV pilus/fimbrium biogenesis machinery (T4P) and the Methanococcus voltae flagellum biogenesis machinery (Fla) have been identified. Known constituents of these systems include (1). a major prepilin (preflagellin), (2). several minor prepilins (preflagellins), (3). a prepilin (preflagellin) peptidase/methylase, (4). an ATPase, (5). a multispanning transmembrane (TM) protein, (6). an outer-membrane secretin (lacking in Fla) and (7). several functionally uncharacterized envelope proteins. Sequence and phylogenetic analyses led to the conclusion that, although many of the protein constituents are probably homologous, extensive sequence divergence during evolution clouds this homology so that a common ancestry can be established for all three types of systems for only two constituents, the ATPase and the TM protein. Sequence divergence of the individual T2S constituents has occurred at characteristic rates, apparently without shuffling of constituents between systems. The same is probably also true for the T4P and Fla systems. The family of ATPases is much larger than the family of TM proteins, and many ATPase homologues function in capacities unrelated to those considered here. Many phylogenetic clusters of the ATPases probably exhibit uniform function. Some of these have a corresponding TM protein homologue although others probably function without one. It is further shown that proteins that compose the different phylogenetic clusters in both the ATPase and the TM protein families exhibit unique structural characteristics that are of probable functional significance. The TM proteins are shown to have arisen by at least two dissimilar intragenic duplication events, one in the bacterial kingdom and one in the archaeal kingdom. The archaeal TM proteins are twice as large as the bacterial TM proteins, suggesting an oligomeric structure for the latter.

Adenosine Triphosphatases↗
PubMed2005

Pain, immunity, opiate and opioid compounds and health.

We surmise that opioid peptides, i.e., methionine enkephalin, first arose during evolution as modulators of cellular immune function given their immune actions and the presence of enkelytin, a potent antibacterial peptide, and its precursor proenkephalin in animals 500 million years divergent in evolution. Pain probably emerged from this perspective because of its association with proinflammatory events. Endogenous morphine appears to exert positive effects on homeostasis by limiting the degree of excitation. Supporting this view is the fact that the mu3 opiate receptor subtype, which is opioid peptide insensitive and morphine selective, is coupled to constitutive nitric oxide release, which also has this down regulating action in neural, immune, vascular and gastrointestinal tissues. Thus, morphine down regulates immune processes in addiction, an action/function that it appears to normally perform when the situation calls for this action and by so doing in this natural setting, sustains life.

Amino Acid Sequence↗
PubMed1999

Mammalian Y chromosome evolution and the male-specific functions of Y chromosome-borne genes.

All mammals have an XY chromosomal sex determining system, in which a small Y chromosome triggers male development, and contains genes required for spermatogenesis. The X and Y chromosomes were originally homologous, but diverged during evolution as the Y chromosome was degraded progressively. Comparisons among the sex chromosomes of different mammal groups indicate that the X and Y chromosomes received additions of material from other chromosomes. Genes on the Y chromosome originated from the ancient X-Y pair, or from these additions, or were copies of genes on one of the autosomes. Only genes with important male-specific functions, such as sex determination and spermatogenesis, are selected for and retained on the differential region of the Y chromosome. The mammalian sex determining gene, SRY, controls the testis determination pathway, which includes at least one related gene. Several candidate spermatogenesis genes have been identified, but so far the only one that is conserved on the Y chromosome of all therian mammals is RBM (RNA-binding motif gene, Y chromosome).

Animals↗
PubMed1993

Evolution of rodent lysozymes: isolation and sequence of the rat lysozyme genes.

Mice have two lysozyme c genes that are the products of a gene duplication. The rat genome also possesses two lysozyme genes, which implies that the duplication of the lysozyme gene preceded the mouse-rat divergence. Concerted evolution has homogenized the 3' half (middle of exon 2 through 3' flanking) of the genes in each species. A mosaic pattern of concerted evolution is found for the 5' half of the gene, with both the 5' and 3' ends, but not the middle, of exon 1 evolving in a concerted fashion. Differences exist in the homogenization pattern in the rat and mouse, suggesting the existence of species-specific patterns of concerted evolution. Exon 1 contains most of the amino acid substitutions that distinguish mouse M from mouse P lysozyme or rat 1 from rat 2 lysozyme. Some of the amino acid differences found between mouse lysozyme genes are found also in the rat, and they suggest that rat 1 and 2 are homologous to mouse M and P, respectively. Nuclease S1 mapping indicated that only the rat 1 gene is expressed at detectable levels, and, specifically, that this gene is expressed by cells in the lung, small intestine, and spleen. The mouse expresses different lysozyme genes in the intestinal (P) and macrophage (M) cells, while the rat expresses only one gene in both of these tissues. The absence of detectable expression and the accumulation of a large number of amino acid substitutions in the parts of exons 1 and 2 of the rat 2 gene not participating in concerted evolution suggest that the rat 2 gene is a pseudogene.

Amino Acid Sequence↗
PubMed1999

Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika.

The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly.

Animals↗
PubMedDate not supplied

[Application of the serological method for evaluation of relations between gymnosperms and dicotyledonous plants].

An attempt has been undertaken to evaluate interrelations of gymnospermous and dicotyledonous plants on the basis of immunochemical studies of seed proteins. For this purpose, 12 antisera were raised to proteins of taxa representing four gymnosperm classes: Ginkgoopsida, Cycadopsida, Coniferopsida, and Gnetopsida. Seed proteins of eight dicotyledonous subclasses (after Takhtadzhyan, 1987) were used. The representatives of all dicotyledonous subclasses gave immunochemical reactions with those of all gymnospermous classes. The data obtained suggest the presence of sufficiently close immunochemical relations between gymnosperms and dicotyledons. Samples were found among the representatives of subclasses Dilleniidae, Hamamelididae, and Rosidae, which gave satisfactory reactions with eight to ten antisera to proteins of dicotyledonous seeds. Analysis of the data we obtained suggests that gymnospermous and dicotyledonous plants took their origin from a common pragymnospermous ancestor and later evolved independently or that dicotyledons separated from gymnosperms at an early stage of their evolution before divergence of the latter into several phyletic lineages.

Biological Evolution↗
PubMed1987

Primary structure of human pancreatic alpha-amylase gene: its comparison with human salivary alpha-amylase gene.

We have determined the entire structure of the human pancreatic alpha-amylase (Amy2) gene. It is approx. 9 kb long and is separated into ten exons. This gene (amy2) has a structure very similar to that of human salivary alpha-amylase (Amy1) gene [Nishide et al. Gene 41 (1986a) 299-304] in the nucleotide sequence and the size and location of the exons. The major difference lies in the fact that amy1 has one extra exon on the 5' side. Other differences are at the 5' border of exon 1 and the 3' border of exon 10. The close similarity of these two genes, as compared with mouse pancreatic and salivary amylase genes, suggests that during evolution, the divergence into the two amylase genes may have occurred after the divergence of mice and man.

Amino Acid Sequence↗
PubMed1995

Evolution of neuroblast identity: seven-up and prospero expression reveal homologous and divergent neuroblast fates in Drosophila and Schistocerca.

In the Drosophila CNS, early neuroblast formation and fate are controlled by the pair-rule class of segmentation genes. The distantly related Schistocerca (grasshopper) embryo has a similar arrangement of neuroblasts, despite lack of known pair-rule gene function. Does divergent pair-rule gene function lead to different neuroblast identities, or can different patterning mechanisms produce homologous neuroblasts? We use four molecular markers to compare Drosophila and Schistocerca neuroblast identity: seven-up, prospero, engrailed, and fushi-tarazu/Dax. In both insects some early-forming neuroblasts share key features of neuroblast identity (position, time of formation, and temporally accurate gene expression); thus, different patterning mechanisms can generate similar neuroblast fates. In contrast, several later-forming neuroblasts show species-specific differences in position and/or gene expression; these neuroblast identities seem to have diverged, suggesting that evolution of the insect central nervous system can occur through changes in embryonic neuroblast identity.

Amino Acid Sequence↗
PubMed1989

Sequence and secondary structure of the central domain of Drosophila 26S rRNA: a universal model for the central domain of the large rRNA containing the region in which the central break may happen.

An 890-bp sequence from the central region of Drosophila melanogaster 26S ribosomal DNA (rDNA) has been determined and used in an extensive comparative analysis of the central domain of the large subunit ribosomal RNA (lrRNA) from prokaryotes, organelles, and eukaryotes. An alignment of these different sequences has allowed us to precisely map the regions of the central domain that have highly diverged during evolution. Using this sequence comparison, we have derived a secondary structure model of the central domain of Drosophila 26S ribosomal RNA (rRNA). We show that a large part of this model can be applied to the central domain of lrRNA from prokaryotes, eukaryotes, and organelles, therefore defining a universal common structural core. Likewise, a comparative study of the secondary structure of the divergent regions has been performed in several organisms. The results show that, despite a nearly complete divergence in their length and sequence, a common structural core is also present in divergent regions. In some organisms, one or two of the divergent regions of the central domain are removed by processing events. The sequence and structure of these regions (fragmentation spacers) have been compared to those of the corresponding divergent regions that remain part of the mature rRNA in other species.

Animals↗
PubMed1996

Evolution of disintegrin cysteine-rich and mammalian matrix-degrading metalloproteinases: gene duplication and divergence of a common ancestor rather than convergent evolution.

The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.

Amino Acid Sequence↗
PubMed2003

Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida.

Sea urchins of the family Strongylocentrotidae have been important model systems in many fields of basic biology, yet knowledge of their evolutionary identities such as the phylogenetic relationships and divergence times remains limited. Here, I inferred molecular phylogenies of seven Strongylocentrotid species (Strongylocentrotus franciscanus, S. nudus, S. purpuratus, S. intermedius, S. droebachiensis, S. pallidus, and Hemicentrotus pulcherrimus) from the analyses of mitochondrial DNA sequences of 12SrDNA (349 nt), 12SrDNA-tRNA(gln) region (862 nt), and a combined sequence of cytochrome oxidase subunit I (COI, 1080 nt) and NADH dehydrogenase subunit I (NDI, 742 nt). The rate of sequence evolution and divergence times for each species were then estimated from the trees with reference to the time of separation between Strongylocentrotidae and Parechinidae, 35 to 50 MYA. The three trees agree well with each other, and the phylogeny is summarized by ((S. franciscanus, S. nudus), (H. pulcherrimus (S. purpuratus, S. intermedius (S. droebachiensis, S. pallidus)))). It is notable that the genus Strongylocentrotus consists of two distinct clades and that H. pulcherrimus branches off within Strongylocentrotus, implying assignment of a separate, monospecific genus to this species inappropriate. The rate of sequence evolution is calibrated to be 0.24%-0.34%/Myr in 12SrDNA, 0.25%-0.36%/Myr in 12SrDNA-tRNA(gln), and 0.65%-0.93%/Myr in COI-NDI combined sequences. S. purpuratus, in particular, shows the significantly higher rate of evolution in the 12SrDNA and 12SrDNA-tRNA(gln) regions compared to other species, suggesting careful use of its sequences in comparative studies. The two clades of Strongylocentrotidae seem to have split 13-19 MYA, and H. pulcherrimus branched off 7.2-14 MYA. In the former clade, S. franciscanus and S. nudus separated 5.7-8.1 MYA. In the latter clade, S. purpuratus, S. intermedius, and the clade of S. droebachiensis and S. pallidus diverged approximately 4.6-12 MYA, and the last two closest species separated 2.1-3.1 MYA.

Animals↗
PubMed2004

Loss of heterozygosity in clonal evolution with genetic progression and divergence in spindle cell carcinoma of the gallbladder.

Spindle cell carcinoma (SpCC) of the gallbladder is a rare neoplasm that shows carcinoma with a variable component of sarcomatoid spindle cells. The clinical and pathological features of this neoplasm have been well documented, but the histogenesis has long been a matter of speculation. In an attempt to clarify the clonality and genetic relationships involved in the evolution of this neoplasm, we microdissected a total of 18 carcinomatous and sarcomatous foci from 2 gallbladder SpCCs and analyzed the allelic status with 42 microsatellite markers on chromosomal arms 1p, 1q, 3p, 4q, 5q, 6q, 8p, 9p, 10q, 11p, 11q, 13q, 16q, 17p, 17q, 18q, and 22q. The 2 cases examined had a polypoid tumor in the gallbladder, in which both adenocarcinomatous and sarcomatoid spindle cell components were identified histologically. In both SpCCs, homogenous allelic losses were identified in both the carcinomatous and sarcomatous components; 17p, 18q, and 5q in case 1 and 17p and 11q in case 2. These indicated that both SpCCs had a single clonal origin. In case 1, additional loss of heterozygosity (LOH; 6q) consisting of genetic progression occurred in both the carcinomatous and sarcomatoid components. In case 2, there was additional LOH (9p) in the carcinomatous components and additional microsatellite instability at D5S644 in both the carcinomatous and sarcomatoid components, indicating a monoclonal neoplasm with genetic progression and divergence. In the 2 cases, the genetic changes indicated that an original clone of a pure adenocarcinoma apparently acquired sarcomatoid spindle cell phenotype by successive genetic changes. On the other hand, we saw no evidence of tumors in which a sarcomatoid spindle cell appeared to give rise to a carcinomatous subclone in the examined cases. In conclusion, the current study includes the first LOH analyses of SpCC of the gallbladder. Our data support the concept that gallbladder SpCC is derived from a single clone originating from a carcinoma. Furthermore, we showed genetic heterogeneity accompanying the phenotypic divergence, with patterns of genetic alterations that are consistent with both the progression and divergence within the individual tumors.

Aged↗
PubMed1999

Evolutionary changes reflected by the cellular amino acid composition.

Comparison of the amino acid composition of cell-proteins using 17 amino acids has been used to investigate the biological evolution of organisms such as bacteria, blue-green alga, green alga, fungi, slime mold, protozoa and vertebrates. The degree of difference in the amino acid ratios between any two groups reflects the degree of divergency in biological evolution. The amino acid composition of the Gram-negative bacteria (Escherichia coli, Klebsiella, Proteus, and Vibrio alginolyticus) was identical. However, the amino acid composition of Staphylococcus aureus and Bacillus subtilis, which are Gram-positive bacteria, differed from each other and from the Gram-negative bacteria. The amino acid composition of the blue-green alga (Cyanobacterium, Chroococidiopsis) was quite similar to that of E. coli. A marked difference in the amino acid composition was observed between E. coli and green alga (Chlorella), and significant differences were observed between E. coli and other organisms, such as fungi, protozoa (Tetrahymena), slime mold (Dictyostelium discoideum) and vertebrates. In conclusion, the change in cellular amino acid composition reflects the divergence which has occurred during biological evolution, whereas a basic pattern of amino acid composition is maintained in spite of a long period of evolutional divergence among the various organisms. Thus, it is proposed that the primitive life forms established at the end of prebiotic evolution had a similar amino acid composition.

Amino Acids↗
PubMed2003

Endocannabinoids as autoregulatory signaling molecules: coupling to nitric oxide and a possible association with the relaxation response.

Endocannabinoid signaling processes are present in diverse organisms and in organisms 500 million years divergent in evolution. Cannabinoid receptor-1 expression (CB1), anandamide, and anandamide amidase have been found in invertebrates. Furthermore, this signaling system is coupled to constitutive nitric oxide synthase (cNOS)-derived nitric oxide (NO) release in both vertebrates and invertebrates, thereby regulating neural, immune, and vascular-like functions in these divergent organisms. In human endothelial cells from various blood vessels, CB1 immunoreactive components are present as is its coupling to anandamide-stimulated cNOS-derived NO production, which exerts an autoregulatory role on cNOS release. The modulation of vascular diameter and vascular tone represents a crucial point of interest in these pathways, and interactions between NO and the sympathetic nerve system are of importance, i.e, norepinephrine. Here, a possible association of NO and endocannabinoid signaling with the relaxation response, a physiological counterpart of the stress response, may exist.

Animals↗
PubMed2004

Intermedin, a novel calcitonin family peptide that exists in teleosts as well as in mammals: a comparison with other calcitonin/intermedin family peptides in vertebrates.

Endocrine regulation in vertebrates is critical for the adaptation and regulation of homeostasis. The G protein-coupled receptor (GPCR) signaling transduction system represents one of the most ancient forms of cell surface signaling. Recently, comparative sequence analysis has aided in the identification and pairing of a variety of ligand/GPCR signaling systems. Among the ligands of type II GPCRs, the calcitonin family peptides including calcitonin, alpha-calcitonin gene-related peptide (alphaCGRP), betaCGRP, adrenomedullin, and amylin are among the best studied hormones, and the founding member, calcitonin, was originally identified and isolated from teleosts. This unique group of peptides shares a conserved tertiary structure with an N-terminal disulfide-bridged ring. In mammals, these peptides signal through two closely related type II GPCRs and three unique receptor activity-modifying proteins. Recently, based on the analysis of multiple vertebrate genomes, we identified a novel calcitonin/CGRP family peptide named intermedin. Here we show that in humans the five paralogous family genes, calcitonin, CGRP, amylin, adrenomedullin, and intermedin, evolved before the emergence of modern vertebrates, and that teleost genomes carry multiple copies of these co-evolved hormone genes. Sequence comparison showed that each of these genes is highly conserved in different vertebrates and that multiple copies of these peptides in teleosts could be derived from ancient genome duplication and/or lineage-specific intragenic duplications. The present article provides an overview of the calcitonin/intermedin family peptides found in teleost and mammalian genomes, and describes their putative functions. In addition, we demonstrate that one of the intermedin orthologs deduced from the pufferfish (Fugu rubripes) genome shares a conserved signaling activity with mammalian intermedin. The combined results indicate that the physiology associated with each of these family peptides likely evolved during early vertebrate evolution and diverged to serve select physiological functions in different vertebrates.

Adrenomedullin↗
PubMed2006

Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock.

The circadian clock of the honey bee is implicated in ecologically relevant complex behaviors. These include time sensing, time-compensated sun-compass navigation, and social behaviors such as coordination of activity, dance language communication, and division of labor. The molecular underpinnings of the bee circadian clock are largely unknown. We show that clock gene structure and expression pattern in the honey bee are more similar to the mouse than to Drosophila. The honey bee genome does not encode an ortholog of Drosophila Timeless (Tim1), has only the mammalian type Cryptochrome (Cry-m), and has a single ortholog for each of the other canonical "clock genes." In foragers that typically have strong circadian rhythms, brain mRNA levels of amCry, but not amTim as in Drosophila, consistently oscillate with strong amplitude and a phase similar to amPeriod (amPer) under both light-dark and constant darkness illumination regimes. In contrast to Drosophila, the honey bee amCYC protein contains a transactivation domain and its brain transcript levels oscillate at virtually an anti-phase to amPer, as it does in the mouse. Phylogenetic analyses indicate that the basal insect lineage had both the mammalian and Drosophila types of Cry and Tim. Our results suggest that during evolution, Drosophila diverged from the ancestral insect clock and specialized in using a set of clock gene orthologs that was lost by both mammals and bees, which in turn converged and specialized in the other set. These findings illustrate a previously unappreciated diversity of insect clockwork and raise critical questions concerning the evolution and functional significance of species-specific variation in molecular clockwork.

Amino Acid Motifs↗