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PubMed1993

Genetic analysis of the Drosophila cdc2 homolog.

We have identified mutations in the Drosophila cdc2 gene. The recessive lethality of these mutant alleles was rescued after P-element-mediated transformation with a genomic cdc2 fragment. Sequence analysis of amorphic alleles revealed non-conservative exchanges in evolutionary conserved positions. These alleles caused lethality at the larval-pupal interphase due to the absence of imaginal tissues. Embryonic lethality resulted when the maternal Dm cdc2 contribution was reduced through the use of a temperature-sensitive allele. Dm cdc2 function, therefore, is essential for cell proliferation throughout development. Dm cdc2 function is clearly required for mitosis, but no evidence for a requirement in S-phase was obtained. The reversible block of the mitotic proliferation which was observed in the PNS of mutant embryos occurred exclusively in the G2-phase. Moreover, while the mitotic proliferation of imaginal cells was blocked in the amorphic mutant larvae, non-imaginal larval cells continued to grow and endoreplicate their DNA. The Dm cdc2 mutant phenotype could neither be rescued with Dm cdc2c (encoding a cdc2-like kinase) nor enhanced by a reduction of the Dm cdc2c gene dose. These results indicate that the Dm cdc2- and Dm cdc2c-kinases control different processes.

Amino Acid Sequence↗
PubMed2026

Genome-Wide Identification of the R2R3-MYB Gene Family in Solanum americanum and Functional Analysis of Its Role in Fruit Coloration.

Anthocyanins are key secondary metabolites responsible for fruit coloration in plants, and their biosynthesis is largely regulated by R2R3-MYB transcription factors. However, the R2R3-MYB regulators controlling fruit anthocyanin accumulation in wild Solanum species remain poorly understood. Here, Solanum americanum was used to identify candidate R2R3-MYB genes associated with fruit coloration through genome-wide identification, phylogenetic analysis, synteny analysis, expression profiling, and virus-induced gene silencing (VIGS). A total of 122 SaMYB genes were identified, and phylogenetic analysis revealed that SaMYB proteins clustered with Arabidopsis thaliana R2R3-MYB members in conserved subgroups, suggesting evolutionary conservation of this family. Synteny analysis identified 37 syntenic gene pairs among SaMYB genes, and the Ka/Ks values of all analyzable gene pairs were below 1, indicating that these duplicated genes are subject to functional constraint. Integrated analysis of phylogenetic relationships, protein structures, promoter cis-elements, and fruit developmental expression patterns identified SaMYB59 and SaMYB106 as candidate regulators of anthocyanin accumulation. VIGS analysis demonstrated that silencing SaMYB106 reduced purple coloration, decreased anthocyanin content, and downregulated the expression of the structural gene DFR. These results indicate that SaMYB106 functions as a positive regulator of fruit anthocyanin accumulation in S. americanum. This study provides insights into the molecular basis of fruit coloration in wild Solanum species.

Solanum americanum↗
PubMed1993

A gene for cytochrome c oxidase subunit II in duck mitochondrial DNA: structural features and sequence evolution.

The gene encoding cytochrome c oxidase subunit II (COXII) was amplified by polymerase chain reaction (PCR) using mitochondrial DNAs (mtDNAs) isolated from two genera of domesticated ducks, Anas platyrhnchos and Cairina muschata, and their intergeneric and intrageneric hybrids as templates. Comparison of the nucleotide sequences from the two different duck lineages shows that they have approximately 91% homology. The nucleotide substitution pattern in the duck COXII gene reveals a high transition/transversion ratio (8.8:1.0) while 93.2% of the nucleotide substitutions are silent. The duck COXII, which uses GUG as the initiation codon, contains 228 amino acid residues. Comparison of the deduced COXII amino acid sequences in duck, chicken, Xenopus laevis, mouse, bovine and human reveals five highly conserved domains. The evolutionary conservation of the primary structure of COXII implies its functional importance.

Amino Acid Sequence↗
PubMed2001

Integrating genomic homology into gene structure prediction.

TWINSCAN is a new gene-structure prediction system that directly extends the probability model of GENSCAN, allowing it to exploit homology between two related genomes. Separate probability models are used for conservation in exons, introns, splice sites, and UTRs, reflecting the differences among their patterns of evolutionary conservation. TWINSCAN is specifically designed for the analysis of high-throughput genomic sequences containing an unknown number of genes. In experiments on high-throughput mouse sequences, using homologous sequences from the human genome, TWINSCAN shows notable improvement over GENSCAN in exon sensitivity and specificity and dramatic improvement in exact gene sensitivity and specificity. This improvement can be attributed entirely to modeling the patterns of evolutionary conservation in genomic sequence.

Algorithms↗
PubMed2026

Identification and differential regulation of proteasome β family genes by viral infection and cytokines in grass carp (Ctenopharyngodon idella).

Proteasome β (PSMB) subunits are essential components of the proteasome complex and play important roles in antigen processing and immune regulation. In this study, we identified 14 Psmb genes in grass carp (Ctenopharyngodon idella), including seven constitutive Psmbs (Psmb1-7), three immunoproteasome genes (Psmb8-10), two thymoproteasome-related paralogs (Psmb11a and Psmb11b), and two telelost-specific members (Psmb12 and Psmb13). Comparative genomic analyses showed that grass carp Psmb genes are highly conserved in genomic organization, gene synteny, and predicted β-subunit-like protein structures, supporting the evolutionary conservation of the proteasome β-subunit family in fish. Phylogenetic and syntenic analyses further revealed lineage-specific expansion of immunoproteasome-related Psmb genes in teleost fish, with Psmb12 and Psmb13 likely derived from duplications of Psmb9 and Psmb10, respectively. Tissue expression analysis suggested functional divergence among duplicated Psmb members, as constitutive Psmbs were relatively enriched in the brain, whereas immunoproteasome-related and teleost-specific Psmbs were highly expressed in immune- and mucosa-associated tissues. Moreover, GCRV-I infection rapidly induced Psmb8-10 and Psmb11b expression in CIK cells. IFN-γ induced a broader set of Psmb genes than IFNa, whereas IL-10 selectively suppressed several Psmbs. Together, these findings highlight the evolutionary conservation, expansion, and immune-related diversification of the Psmb family in teleost fish.

Animals↗
PubMed2005

Peeling the yeast protein network.

A set of highly connected proteins (or hubs) plays an important role for the integrity of the protein interaction network of Saccharomyces cerevisae by connecting the network's intrinsic modules. The importance of the hubs' central placement is further confirmed by their propensity to be lethal. However, although highly emphasized, little is known about the topological coherence among the hubs. Applying a core decomposition method which allows us to identify the inherent layer structure of the protein interaction network, we find that the probability of nodes both being essential and evolutionary conserved successively increases toward the innermost cores. While connectivity alone is often not a sufficient criterion to assess a protein's functional, evolutionary and topological relevance, we classify nodes as globally and locally central depending on their appearance in the inner or outer cores. The observation that globally central proteins participate in a substantial number of protein complexes which display an elevated degree of evolutionary conservation allows us to hypothesize that globally central proteins serve as the evolutionary backbone of the proteome. Even though protein interaction data are extensively flawed, we find that our results are very robust against inaccurately determined protein interactions.

Databases, Protein↗
PubMed1989

Identification of a conserved sequence in the non-coding regions of many human genes.

We have analyzed a sequence of approximately 70 base pairs (bp) that shows a high degree of similarity to sequences present in the non-coding regions of a number of human and other mammalian genes. The sequence was discovered in a fragment of human genomic DNA adjacent to an integrated hepatitis B virus genome in cells derived from human hepatocellular carcinoma tissue. When one of the viral flanking sequences was compared to nucleotide sequences in GenBank, more than thirty human genes were identified that contained a similar sequence in their non-coding regions. The sequence element was usually found once or twice in a gene, either in an intron or in the 5' or 3' flanking regions. It did not share any similarities with known short interspersed nucleotide elements (SINEs) or presently known gene regulatory elements. This element was highly conserved at the same position within the corresponding human and mouse genes for myoglobin and N-myc, indicating evolutionary conservation and possible functional importance. Preliminary DNase I footprinting data suggested that the element or its adjacent sequences may bind nuclear factors to generate specific DNase I hypersensitive sites. The size, structure, and evolutionary conservation of this sequence indicates that it is distinct from other types of short interspersed repetitive elements. It is possible that the element may have a cis-acting functional role in the genome.

Animals↗
PubMed1996

Developmental expression patterns of CFTR in ferret tracheal surface airway and submucosal gland epithelia.

Submucosal glands are a major site of cystic fibrosis transmembrane conductance regulator (CFTR) expression in the human airway and may play an important role in the pathogenesis of cystic fibrosis. In humans, strategies for gene targeting to submucosal glands will likely be dependent on in utero gene transfer to submucosal gland progenitors because of the inaccessibility of these regions from the fully developed airway. However, little is known about the ontogeny of CFTR gene expression in developing submucosal glands and the potential functional role(s) CFTR may have during gland development. To this end, we describe the partial cloning of the ferret CFTR cDNA which was used for in situ mRNA localization studies in developing ferret trachea. The ferret animal model is attractive for studies pertaining to the development of tracheal submucosal glands because postnatal tracheal development in this species mirrors in utero gland development in humans. Sequence analysis of the first nucleotide binding domain (NBD1) from ferret CFTR revealed a striking homology to the human gene at both the DNA (94.4%) and amino acid level (97%). Interestingly, this high level of amino acid homology extends to a group of mammalian species (ferret, human, sheep, and bovine) which have similar lung morphologies with respect to the presence of surface airway goblet cells and submucosal glands. In contrast, mouse and rat airways which are quite divergent from those of ferret, human, sheep, and bovine species with respect to secretory cell types in the airway and abundance of submucosal glands, demonstrate significantly less homology (80%) with respect to CFTR amino acid sequence in the NBD1 domain. Given that traditional phylogenetic classification of these species does not mirror the evolutionary conservation of CFTR, such findings would suggest that certain aspects of lung morphology may be reflected in the evolutionary conservation of CFTR NBD1 amino acid sequences. CFTR in situ hybridization studies in ferret trachea demonstrate a developmental increase (3-4 fold) in CFTR mRNA expression within the surface airway epithelium between -2 day to 5 wk which mirrors an increase in ciliogenesis over this time frame. Additionally, all stages of gland development including the most primordial gland-forming buds could be seen to contain infrequent cells which highly express CFTR at a level that remained constant throughout development. Such findings suggest that differentiation of gland progenitor cells to CFTR-expressing submucosal gland cells occurs very early within submucosal gland development and morphogenesis.

Amino Acid Sequence↗
PubMed2006

Distal regulatory elements are required for Fshr expression, in vivo.

The gonadotropin follicle-stimulating hormone (FSH) is required for initiation and maintenance of normal gametogenesis and acts through a specific, cell-surface receptor (Fshr) present only on Sertoli and granulosa cells in the gonads. Despite extensive examination of the transcriptional mechanisms regulating Fshr, the sequences directing its expression to these cells remain unidentified. To establish the minimal region necessary for Fshr expression, we generated transgenic mice carrying a yeast artificial chromosome (YAC) that contained 413 kilobases (kb) of the rat Fshr locus (YAC60). Transgene expression, as determined by RT-PCR, was absent from immature testis and Sertoli cells, limited to germ cells of the adult testis, and never observed in the ovary. While the data is limited to only one transgenic line, it suggests that the 413kb region does not specify the normal spatiotemporal expression pattern of Fshr. Comparative genomics was used to identify potential distal regulatory elements, revealing seven regions of high evolutionary conservation (>80% identity over 100bp or more), six of which were absent from the transgene. Functional examination of the evolutionary conserved regions (ECRs) by transient transfection revealed that all of the ECRs had modest transcriptional activity in Sertoli or myoid cells with two, ECR4 and ECR5, showing differential effects in expressing and non-expressing cells. These data reveal that distal regulatory regions (outside the 413kb in YAC60) are required for appropriate temporal and spatial Fshr expression and implicate the identified ECRs in transcriptional regulation of Fshr.

Animals↗
PubMed2005

Conservation versus parallel gains in intron evolution.

Orthologous genes from distant eukaryotic species, e.g. animals and plants, share up to 25-30% intron positions. However, the relative contributions of evolutionary conservation and parallel gain of new introns into this pattern remain unknown. Here, the extent of independent insertion of introns in the same sites (parallel gain) in orthologous genes from phylogenetically distant eukaryotes is assessed within the framework of the protosplice site model. It is shown that protosplice sites are no more conserved during evolution of eukaryotic gene sequences than random sites. Simulation of intron insertion into protosplice sites with the observed protosplice site frequencies and intron densities shows that parallel gain can account but for a small fraction (5-10%) of shared intron positions in distantly related species. Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation.

Animals↗
PubMed2002

Hotspots and the conservation of evolutionary history.

Species diversity is unevenly distributed across the globe, with terrestrial diversity concentrated in a few restricted biodiversity hotspots. These areas are associated with high losses of primary vegetation and increased human population density, resulting in growing numbers of threatened species. We show that conservation of these hotspots is critical because they harbor even greater amounts of evolutionary history than expected by species numbers alone. We used supertrees for carnivores and primates to estimate that nearly 70% of the total amount of evolutionary history represented in these groups is found in 25 biodiversity hotspots.

Animals↗
PubMed2006

A new method for quantifying residue conservation and its applications to the protein folding nucleus.

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.

Amino Acid Sequence↗
PubMed2003

Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa.

By means of computational methods, we identified an uncharacterized human transcript, Chromosome 1 open reading frame 36 (C1orf36), that is expressed in the retina and that maps to 1q32.3. The cDNA contains an open reading frame of 585bp that encodes a 195-aminoacid protein with a predicted mass of 22.7kDa. An alternatively spliced transcript in a retinoblastoma cell line, encoding for a truncated peptide, was also identified. PCR experiments performed using human cDNA from several sources indicate that C1orf36 has a preferential expression in the retina. Accordingly, in situ hybridization experiments, performed using as probe a murine C1orf36 cDNA fragment, detected a hybridization signal on mouse retinal adult sections. The C1orf36 protein shares homology with putative proteins in Mus musculus and Fugu rubripes, suggesting evolutionary conservation of its function. Additional sequence analysis of the C1orf36 gene product predicts its subcellular mitochondrial localization and the presence of both evolutionary conserved phosphorylation sites and regions adopting a coiled-coil conformation. We also defined the genomic structure of the gene. This enabled us to perform a mutational analysis of the C1orf36 coding region of about 300 patients affected by retinitis pigmentosa. No pathological mutations were detected in this analysis.

Amino Acid Sequence↗
PubMed2005

The activity reaction core and plasticity of metabolic networks.

Understanding the system-level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches, such as constraint-based flux-balance analysis, have proved highly successful in analyzing the capabilities of cellular metabolism, including its capacity to predict deletion phenotypes, the ability to calculate the relative flux values of metabolic reactions, and the capability to identify properties of optimal growth states. Here, we use flux-balance analysis to thoroughly assess the activity of Escherichia coli, Helicobacter pylori, and Saccharomyces cerevisiae metabolism in 30,000 diverse simulated environments. We identify a set of metabolic reactions forming a connected metabolic core that carry non-zero fluxes under all growth conditions, and whose flux variations are highly correlated. Furthermore, we find that the enzymes catalyzing the core reactions display a considerably higher fraction of phenotypic essentiality and evolutionary conservation than those catalyzing noncore reactions. Cellular metabolism is characterized by a large number of species-specific conditionally active reactions organized around an evolutionary conserved, but always active, metabolic core. Finally, we find that most current antibiotics interfering with bacterial metabolism target the core enzymes, indicating that our findings may have important implications for antimicrobial drug-target discovery.

Escherichia coli↗
PubMed2003

Evolutionarily conserved ELOVL4 gene expression in the vertebrate retina.

PURPOSE: The gene elongation of very long chain fatty acids-4 (ELOVL4) has been shown to underlie phenotypically heterogeneous forms of autosomal dominant macular degeneration. In this study, the extent of evolutionary conservation and the existence and localization of retinal expression of this gene was investigated across a wide variety of species. METHODS: Southern blot analysis of genomic DNA and bioinformatic analysis using the human ELOVL4 cDNA and protein sequences, respectively, were performed to identify species in which ELOVL4 orthologues and/or homologues are present. Retinal RNA and protein extracts derived from different species were assessed by Northern hybridization and immunoblot techniques to assess evolutionary conservation of gene expression. Immunohistochemical analysis of tissue sections prepared from various mammalian retinas was performed to determine the distribution of ELOVL4 and homologous proteins within specific retinal cell layers. RESULTS: The existence of ELOVL4 sequence orthologues and homologues was confirmed by both Southern blot analysis and in silico searches of protein sequence databases. Phylogenetic analysis places ELOVL4 among a large family of known and putative fatty acid elongase proteins. Northern blot analysis revealed the presence of multiple transcripts corresponding to ELOVL4 homologues expressed in the retina of several different mammalian species. Conserved proteins were also detected among retinal extracts of different mammals and were found to localize predominantly to the photoreceptor cell layer within retinal tissue preparations. CONCLUSIONS: The ELOVL4 gene is highly conserved throughout evolution and is expressed in the photoreceptor cells of the retina in a variety of different species, which suggests that it plays a critical role in retinal cell biology.

Amino Acid Sequence↗
PubMed2001

Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.

MOTIVATION: It is known that the physico-chemical characteristics of proteins underlying specific folding of the polypeptide chain and the protein function are evolutionary conserved. Detection of such characteristics while analyzing homologous sequences would expand essentially the knowledge on protein function, structure, and evolution. These characteristics are maintained constant, in particular, by co-ordinated substitutions. In this process, the destabilizing effect of a substitution may be compensated by another substitution at a different position within the same protein, making the overall change in this protein characteristic insignificant. Consequently, the patterns of co-ordinated substitutions contain important information on conserved physico-chemical properties of proteins, requiring their investigation and development of the corresponding methods and software for correlation analysis of protein sequences available to a wide range of users. RESULTS: A software package for analyzing correlated amino acid substitutions at different positions within aligned protein sequences was developed. The approach implies searching for evolutionary conserved physico-chemical characteristics of proteins based on the information on the pairwise correlations of amino acid substitutions at different protein positions. The software was applied to analyze DNA-binding domains of the homeodomain class. As a result, two conservative physico-chemical characteristics preserved due to the co-ordinated substitutions at certain groups of positions in the protein sequence. Possible functional roles of these characteristics are discussed. AVAILABILITY: The program package is available at http://wwwmgs.bionet.nsc.ru/programs/CRASP/.

Algorithms↗
PubMed2005

Genetic association, post-translational modification, and protein-protein interactions in Type 2 diabetes mellitus.

Type 2 diabetes mellitus is a complex disorder with a strong genetic component. Inherited complex disease susceptibility in humans is most commonly associated with single nucleotide polymorphisms. The mechanisms by which this occurs are still poorly understood. Here we focus on analyzing the effect of a set of disease-causing missense variations of the monogenetic form of Type 2 diabetes mellitus and a set of disease-associated nonsynonymous variations in comparison with that of nonsynonymous variations without any experimental evidence for association with any disease. Analysis of different properties such as evolutionary conservation status, solvent accessibility, secondary structure, etc. suggests that disease-causing variations are associated with extreme changes in the value of the parameters relating to evolutionary conservation and/or protein stability. Disease-associated variations are rather moderately conserved and have a milder effect on protein function and stability. The majority of the genes harboring these variations are clustered in or near the insulin signaling network. Most of these variations are identified as potential sites for post-translational modifications; certain predictions have already reported experimental evidence. Overall our results indicate that Type 2 diabetes mellitus may result from a large number of single nucleotide polymorphisms that impair modular domain function and post-translational modifications involved in signaling. Our emphasis is more on conserved corresponding residues than the variation alone. We believe that the approach of considering a stretch of peptide sequence involving a polymorphism would be a better method of defining the role of the polymorphism in the manifestation of this disease. Because most of the variations associated with the disease are rare, we hypothesize that this disease is a "mosaic model" of interaction between a large number of rare alleles and a small number of common alleles along with the environment, which is little contrary to the existing common disease common variant model.

Diabetes Mellitus, Type 2↗
PubMed2000

Human-mouse differences in the embryonic expression patterns of developmental control genes and disease genes.

Our understanding of early human development has been impeded by the general difficulty in obtaining suitable samples for study. As a result, and because of the extraordinarily high degree of evolutionary conservation of many developmentally important genes and developmental pathways, great reliance has been placed on extrapolation from animal models of development, principally the mouse. However, the strong evolutionary conservation of coding sequence for developmentally important genes does not necessarily mean that their expression patterns are as highly conserved. The very recent availability of human embryonic samples for gene expression studies has now permitted for the first time an assessment of the degree to which we can confidently extrapolate from studies of rodent gene expression patterns. We have found significant human-mouse differences in embryonic expression patterns for a variety of genes. We present detailed data for two illustrative examples. Wnt7a, a very highly conserved gene known to be important in early development, shows significant differences in spatial and temporal expression patterns in the developing brain (midbrain, telencephalon) of man and mice. CAPN3, the locus for LGMD2A limb girdle muscular dystrophy, and its mouse orthologue differ extensively in expression in embryonic heart, lens and smooth muscle. Our study also shows how molecular analyses, while providing explanations for the observed differences, can be important in providing insights into mammalian evolution.

5' Untranslated Regions↗