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PubMed1994

A new class of DNA photolyases present in various organisms including aplacental mammals.

DNA photolyase specifically repairs UV light-induced cyclobutane-type pyrimidine dimers in DNA through a light-dependent reaction mechanism. We have obtained photolyase genes from Drosophila melanogaster (fruit fly), Oryzias latipes (killifish) and the marsupial Potorous tridactylis (rat kangaroo), the first photolyase gene cloned from a mammalian species. The deduced amino acid sequences of these higher eukaryote genes show only limited homology with microbial photolyase genes. Together with the previously cloned Carassius auratus (goldfish) gene they form a separate group of photolyase genes. A new classification for photolyases comprising two distantly related groups is proposed. For functional analysis P.tridactylis photolyase was expressed and purified as glutathione S-transferase fusion protein from Escherichia coli cells. The biologically active protein contained FAD as light-absorbing cofactor, a property in common with the microbial class photolyases. Furthermore, we found in the archaebacterium Methanobacterium thermoautotrophicum a gene similar to the higher eukaryote photolyase genes, but we could not obtain evidence for the presence of a homologous gene in the human genome. Our results suggest a divergence of photolyase genes in early evolution.

Amino Acid Sequence↗
PubMed1994

Isolation and characterization of alpha-type HC3 and beta-type HC5 subunit genes of human proteasomes.

Eukaryotic proteasomes from an evolutionarily conserved multi-gene family and are thought to have originated from a common ancestral gene and diverged into alpha-type and beta-type subgroups. To understand the molecular basis of the proteasome genes, we isolated and characterized two human proteasome genes econding the alpha-type HC3 and beta-type HC5 subunit. The functional genes for HC3 and HC5 are similar in being approximately 15 kb in length, but differ in having exon numbers of 9 and 6, respectively. Analyses of about 2.5 to 3.0 kb of the 5'-flanking regions of these two genes revealed the absence of TATA and CAAT promoter elements. However, two or three GC boxes were found. By analysis of the transcriptional regulatory activities in the 5'-flanking regions of the two genes, these GC boxes were found to function coordinately as promoters of the two genes. Interestingly, the HC3 gene possesses an additional silencer element in the 5'-upstream region near the first exon. This element is also able to repress the promoter activities of other genes, such as the HC5 and the type 1 glucose transporter genes, irrespective of whether it has a sense or antisense orientation, indicating that it acts as a general transcriptional silencer. The HC5 gene does not have this silence element, and its promoter activity is five to ten times that of HC3. These results show that the human proteasomal HC3 and HC5 genes differ not only in their genomic structures, such as their numbers of exons and their exon-intron organizations, but also in the mechanisms regulating their transcription, suggesting that they diverged at an early stage of evolution.

Animals↗
PubMed1996

G1/S regulatory mechanisms from yeast to man.

Cyclin-dependent kinases play a key role in promoting and regulating the transition from G1 to S phase in all eukaryotic organisms. The kinase activities involved are distinguished from those participating in other cell cycle phase transitions in that they are driven by a class of specialised G1-specific cyclins. Although the G1 regulatory components have diverged structurally in the course of evolution, the regulatory mechanisms and principles remain highly conserved from yeast to vertebrates. An important issue that remains is that of identifying the principal targets phosphorylated by G1 cyclin-dependent kinases.

Animals↗
PubMed1992

Evolutionary relationships of multiple alpha satellite subfamilies in the centromeres of human chromosomes 13, 14, and 21.

Using Southern and in situ hybridization analyses, we have earlier defined four different subfamilies of alpha satellite DNA (designated pTRA-1, -2, -4, and -7), each of which has a unique higher order structure represented almost identically on human chromosomes 13, 14, and 21. Here we present the complete sequence of single isolates of these four subfamilies, representing approximately 12 kb of sequence information. Sequences of the individual 171-bp monomers that constitute these four subfamilies (and a fifth subfamily, Alpha-R1, that is known to be present on chromosomes 13 and 21) were compared both within and between the different clones. The results indicate that, at the level of their primary sequence, the five alpha subfamilies are characterized by structures that are as unrelated to each other as the different alpha subfamilies from other chromosomes. However, sequence comparisons between monomers of these clones indicate the possibility that pTRA-2, -4, and -1 may have arisen, at least in part, from a common ancestral alphoid sequence. We also provide evidence that exchange of pTRA-1 between nonhomologous centromeres and its homogenization throughout the population, perhaps by unequal exchange mechanisms, could have occurred after the divergence of humans and chimpanzees. The evolution of multiple alphoid subfamilies within a single centromere suggests that unequal exchange mechanisms may be restricted to specific domains. This may in turn contribute to some requirement for subregional pairing of sequences along the length of the centromeres of these chromosomes.

Base Sequence↗
PubMed1991

Genomic organization of the rat aromatic L-amino acid decarboxylase (AADC) locus: partial analysis reveals divergence from the Drosophila dopa decarboxylase (DDC) gene structure.

Aromatic L-amino acid decarboxylase (AADC) is responsible for the conversion of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan to dopamine and serotonin, respectively, which are important neurotransmitters. We characterized genomic clones derived from the rat AADC locus by Southern blot and nucleotide sequencing analyses to explore the exonal organization of the gene. Our results suggest that the rat AADC gene is relatively large, containing at least 12 exons and spanning at least 40 kb in the rat genome. In this study, nine exons corresponding to 71% of the published cDNA sequence were identified, the smallest of which was as short as 20 base pairs (bp). In the Drosophila dopa decarboxylase (DDC) gene, the sequences homologous to these nine exons are all present in the fourth exon. This implies that either multiple intron sequences have been added to the vertebrate AADC gene or alternatively, deleted from the invertebrate gene after the divergence of vertebrates and invertebrates during evolution.

Animals↗
PubMed1996

Organization of the histone H3 genes in soybean, barley and wheat.

Several variants of the replacement histone H3 genes from soybean, barley and wheat have been cloned and sequenced. Analysis of segregating populations in barley and soybean, as well as analysis of clones isolated from a soybean genomic library, suggested that these genes are dispersed throughout the genome. Several genes contains introns located in similar positions, but of different lengths and sequence. Comparison of mRNA levels in different tissues revealed that the intron-containing and intronless genes have different expression patterns. The distribution of the introns in the histone H3 genes across several plant species suggests that some of the introns might have been lost during the evolution of the gene family. Sequence divergence among introns and gene-flanking sequences in cloned gene variants allowed us to use them as specific probes for localizing individual gene copies and analyzing the genomic distribution of these variants across a range of genotypes.

Base Sequence↗
PubMed2006

Ancient divergence of a complex family of immune-type receptor genes.

Multigene families of activating/inhibitory receptors belonging to the immunoglobulin superfamily (IgSF) regulate immunological and other cell-cell interactions. A new family of such genes, termed modular domain immune-type receptors (MDIRs), has been identified in the clearnose skate (Raja eglanteria), a phylogenetically ancient vertebrate. At least five different major forms of predicted MDIR proteins are comprised of four different subfamilies of IgSF ectodomains of the intermediate (I)- or C2-set. The predicted number of individual IgSF ectodomains in MDIRs varies from one to six. MDIR1 contains a positively charged transmembrane residue and MDIR2 and MDIR3 each possesses at least one immunoreceptor tyrosine-based inhibitory motif in their cytoplasmic regions. MDIR4 and MDIR5 lack characteristic activating/inhibitory signalling motifs. MDIRs are encoded in a particularly large and complex multigene family. MDIR domains exhibit distant sequence similarity to mammalian CMRF-35-like molecules, polymeric immunoglobulin receptors, triggering receptors expressed on myeloid cells (TREMs), TREM-like transcripts, NKp44 and FcR homologs, as well as to sequences identified in several different vertebrate genomes. Phylogenetic analyses suggest that MDIRs are representative members of an extended family of IgSF genes that diverged before or very early in evolution of the vertebrates and subsequently came to occupy multiple, fully independent distributions in the present day.

Amino Acid Sequence↗
PubMed2006

Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis.

The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from mungbean (Vigna radiata) genome using degenerate primers, cloned and sequenced. Among these 34% and 65% of respective clones of copia and gypsy RT sequences possessed stop codons or frame-shifts or both. The RT sequences corresponding to both the groups exhibit significant levels of heterogeneity. Presence of mungbean copia and gypsy RT sequences in other papilionoid legumes of the same (Phaseoleae) and different lineages (Loteae, Trifoleae, Cicereae) indicates existence of these elements prior to the radiation of papilionoid legumes and also supports the recent interpretations of close relationship between Phaseoleae and Loteae tribes of Papilionoideae subfamily. On the other hand significant homologies of some mungbean copia as well as gypsy RT sequences with those of unrelated plant species suggest their origin from different plant lineages and also that heterogeneous population of related elements were already existed throughout (even before the divergence of monocot and dicot) the evolution of these genera from their common ancestor.

Amino Acid Sequence↗
PubMed1999

Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization.

The availability of bacterial genome sequences raises an important new problem - how can one move from completely sequenced microorganisms as a reference to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An efficient way to approach this task is the comparison of genomes by subtractive hybridization. Recently we developed a sensitive and reproducible subtraction procedure for comparison of bacterial genomes, based on the method of suppression subtractive hybridization (SSH). In this work we demonstrate the applicability of subtractive hybridization to the comparison of the related but markedly divergent bacterial species Escherichia coli and Salmonella typhimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences were directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and absent from the other. Additional differences in most cases represent sequences that have diverged considerably in the course of evolution. Such an approach to comparative bacterial genomics can be applied both to studies of interspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.

Base Sequence↗
PubMed1997

Comparison of a 20 kb region of human herpesvirus 6B with other human beta herpesviruses reveals conserved replication genes and adjacent divergent open reading frames.

The sequence of a 20.15 kb region from human herpesvirus 6 variant B (HHV-6B) strain Z29 is described (GenBank accession number L14772). Determinations of protein homologies for seventeen predicted gene products revealed HHV-6B homologs of six proteins well-conserved both in genetic context and amino acid sequence throughout the alpha-, beta-, and gammaherpesvirus subfamilies. These include proteins involved in viral DNA replication, packaging and nucleotide metabolism, and conserved proteins of undefined function. The close evolutionary relationship of the human betaherpesviruses, HHV-6B, HHV-6A, HHV-7 and human cytomegalovirus (HCMV) was confirmed by identification of several protein sequences encoded only by these viruses, including homologs of the HCMV early phosphoprotein family and a series of HCMV open reading frames predicted to encode glycoprotein exons. Homologs of essential HSV-1 replication proteins, UL8 and UL9, were also identified. Downstream from the conserved replication locus, each betaherpesvirus contains a region of divergent, small open reading frames. The evolution of this region and its potential use in the development of a viral vector system are discussed.

Conserved Sequence↗
PubMed1990

A calfluxin-related peptide is present in the bag cells and atrial gland of Aplysia.

The caudodorsal cells of Lymnaea and the bag cells of Aplysia are neuroendocrine cells whose peptide products have homologous functions, i.e., regulation of egg deposition. One of the Lymnaea products, calfluxin, increases cytosolic and hence mitochondrial calcium concentrations in secretory cells of the albumen gland, an exocrine organ that secretes perivitellin fluid around the egg cells during packaging; the changes can be visualized at the ultrastructural level for quantification with the pyroantimonate precipitation technique and are correlated with changes in the secretory and biosynthetic activity in the gland. Comparable studies have now been carried out with Aplysia and indicate that the bag cells of A. californica and A. brasiliana also contain a factor with calfluxin-related activity, and that the factor is not the egg-laying hormone (ELH). The bag cell factor does not affect mitochondrial calcium levels in the Lymnaea albumen gland, and synthetic calfluxin does not affect the Aplysia gland. Thus, although the bag cell and caudodorsal cell peptides have the same activity in their respective genera, the sequences have diverged sufficiently during the course of evolution to preclude cross-reactivity. Calfluxin-related activity was also detected in the atrial gland of A. californica and the atrial gland-like epithelium of A. brasiliana, two exocrine organs in the oviduct that express genes structurally related to the bag cell ELH gene. It is postulated that the active atrial gland factors may be peptides A and B.

Animals↗
PubMed1987

Phylogenetic receptor research: implications in studying psychiatric and neurological disease.

Phylogenetic studies will help to evaluate the structure and function of receptors. We were able to show that the regional heterogeneity of the central benzodiazepine receptor previously described in mammals also applies to avians. In addition, a systematic species comparison of the subunit patterns revealed a certain phylogenetic relationship suggesting evolution by gene duplication and subsequent divergence. In analogy to isozyme systems, these results possibly indicate that the GABA/benzodiazepine receptor is an isoreceptor complex. The implications for neuropsychiatric genetics are discussed.

Animals↗
PubMed1986

Isolation and characterization of human blood-coagulation factor X cDNA.

Using synthetic oligodeoxynucleotides as probes, we have isolated factor X cDNA from human liver cDNA library. We sequenced the 1430-bp cDNA which spans the coding region of the mature factor X and contains the polyadenylation signal and poly(A) tail. The amino acid (aa) sequence is in agreement with the published aa sequence. The nucleotide (nt) sequence of cDNA confirmed that factor X is synthesized and secreted as a single-chain precursor, and then converted into dimeric form by proteolytic cleavage of an internal tripeptide. From the nt sequence, it was also predicted that like other secretory proteins, human factor X is synthesized with a leader sequence (prepro-protein). The 5'-coding region of factor X cDNA is 60 and 40% homologous to the corresponding regions of factor IX and prothrombin genes, respectively. This supports the hypothesis of gene evolution by gene duplication followed by divergence.

Amino Acid Sequence↗
PubMed2005

The characterisation of six ADAMTS proteases in the basal chordate Ciona intestinalis provides new insights into the vertebrate ADAMTS family.

ADAMTS, constituting a recently discovered family of secreted zinc-dependent metalloproteases, have been shown to have critical physiological roles through identification of a number of natural animal and human gene mutations. The identification of six ADAMTS genes in the basal chordate Ciona intestinalis provides new insight into how, when and in what order the vertebrate orthologues have evolved. The phylogenetic assignments, based on sequences conserved across all genes, are supported by conserved domain structures within defined sub-families. The phylogeny and the frequent localisation of ADAMTS genes in paralogous regions of the genome are consistent with the vertebrate lineages having arisen by large scale or genome duplication. The high level of conservation in the protease active site of vertebrate orthologues within some sub-families suggests subfunctionalisation, whereas the greater divergence in others would favour the evolution of novel substrate specificities and these observations are borne-out where substrate-specificity is known. The expansion and sub-specialization of the ADAMTS family is a component of the increased complexity of extracellular matrix that is associated with the evolution of vertebrates.

Animals↗
PubMed2005

Frequent allelic loss of 21q11.1 approximately q21.1 region in advanced stage oral squamous cell carcinoma.

A fine mapping of loss of heterozygosity (LOH) was performed in oral squamous cell carcinoma (OSCC), using 12 markers on 21q11.1 approximately q21.1. We studied 43 resected primary invasive tumors and their paired normal tissues, concurrent dysplasia or carcinoma in situ in separate areas from 8 of the specimens, and 6 local recurrent carcinomas. LOH status was compared between lesions of different phases of progression within the same patient. A high frequency of LOH was observed for D21S1410, D21S120, and D21S1433 (60% each) in the primary lesions, constituting two interstitial deleted regions encompassing eight known genes. Cases showing LOH of D21S120 were significantly associated with advanced clinical stages (III and IV; P=0.02). Consistent allelic loss was observed in 64.2% of the informative cases between the precursor lesions and their corresponding invasive tumors, and in 59.5% of those between the primary lesions and their recurrent counterparts. Fewer than half of the different lesions within a given patient showed discordant allelic loss for tested markers. Our results suggest that 21q11.1 approximately q21.1 harbors tumor suppressor genes in OSCC. Genetic divergence may develop during tumor clone evolution.

Carcinoma in Situ↗
PubMed2005

Evolutionary genomics: new genes for new jobs.

Whole genome sequence analyses have confirmed that gene duplication and divergence play major roles in genome evolution. But the details of how young, functionally redundant gene duplicates escape mutational degradation have remained elusive. Several recent studies show that new genes survive because they evolve new, and sometimes essential, functions.

Animals↗
PubMed2006

Mechanisms of gonadal morphogenesis are not conserved between chick and mouse.

To understand mechanisms of sex determination, it is important to know the lineage relationships of cells comprising the gonads. For example, in mice, the Y-linked gene Sry triggers differentiation of Sertoli cells from a cell population originating in the coelomic epithelium overlying the nascent gonad that also gives rise to uncharacterised interstitial cells. In contrast, little is known about origins of somatic cell types in the chick testis, where there is no Sry gene and sex determination depends on a ZZ male/ZW female mechanism. To investigate this, we performed fate mapping experiments in ovo, labelling at indifferent stages the coelomic epithelium by electroporation with a lacZ reporter gene and the underlying nephrogenous (or mesonephric) mesenchyme with chemical dyes. After sex differentiation, LacZ-positive cells were exclusively outside testis cords and were 3betaHSD-negative, indicating that the coelomic epithelium contributes only to non-steroidogenic interstitial cells. However, we detected dye-labelled cells both inside and outside the cords. The former were AMH-positive while some of the latter were 3betaHSD-positive, showing that nephrogenous mesenchyme contributes to both Sertoli cells and steroidogenic cells. This is the first demonstration via lineage analysis that steroidogenic cells originate from nephrogenous mesenchyme, but the revelation that Sertoli cells have different origins between chick and mouse suggests that, during evolution, mechanisms of gonad morphogenesis may diverge alongside those of sex determination.

Animals↗
PubMed2005

Phylogenetic conservation of the regulatory and functional properties of the Vav oncoprotein family.

Vav proteins are phosphorylation-dependent GDP/GTP exchange factors for Rho/Rac GTPases. Despite intense characterization of mammalian Vav proteins both biochemically and genetically, there is little information regarding the conservation of their biological properties in lower organisms. To approach this issue, we have performed a characterization of the regulatory, catalytic, and functional properties of the single Vav family member of Drosophila melanogaster. These analyses have shown that the intramolecular mechanisms controlling the enzyme activity of mammalian Vav proteins are already present in Drosophila, suggesting that such properties have been set up before the divergence between protostomes and deuterostomes during evolution. We also show that Drosophila and mammalian Vav proteins have similar catalytic specificities. As a consequence, Drosophila Vav can trigger oncogenic transformation, morphological change, and enhanced cell motility in mammalian cells. Gain-of-function studies using transgenic flies support the implication of this protein in cytoskeletal-dependent processes such as embryonic dorsal closure, myoblast fusion, tracheal development, and the migration/guidance of different cell types. These results highlight the important roles of Vav proteins in the signal transduction pathways regulating cytoskeletal dynamics. Moreover, they indicate that the foundations for the regulatory and enzymatic activities of this protein family have been set up very early during evolution.

Amino Acid Sequence↗