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PubMed2001

[Molecular characteristics of the new evolutionary-conserved nuclear protein e(y)2].

Molecular structural and function analyses of the Drosophila melanogaster enhancer of yellow 2 (e(y)2) gene showed that its product acts as a transcription factor and is one of the basic elements of the eukaryotic transcription system. The gene is expressed at all stages of D. melanogaster development and consists of a single intron coding for the protein of 101 amino acid residues. The e(y)2 protein does not contain regions homologous to known proteins. The protein binds with chromatin but not with DNA. On evidence of immune staining, e(y)2 occurs in the nuclei of all D. melanogaster cells. Each nucleus contains approximately 1.2 x 10(4) molecules of the protein. Immune staining revealed approximately 200 sites of e(y)2 location on polytene chromosomes. The protein is evolutionarily conserved: its homologs were found in evolutionary distant organisms, such as plants, mammals, and protozoans. Amino acid sequences of human, rabbit, and mouse e(y)2 are identical to each other.

Amino Acid Sequence↗
PubMed1993

Evolutionary conservation of the mouse apolipoprotein e-c1-c2 gene cluster: structure and genetic variability in inbred mice.

The human apolipoprotein E (APOE), APOC1, pseudo APOC1 (APOC1'), and APOC2 genes are clustered within 48 kb on the long arm of chromosome 19. A mouse Apoe cDNA probe was used to isolate overlapping cosmid clones from a cosmid library of the C57BL/Rij inbred mouse strain. These clones were investigated for the presence of the Apoc1 and Apoc2 genes by heterologous hybridization. Our results show that the Apoe-c1-c2 gene cluster is conserved in the mouse. In line with evolutionary data, the mouse lacks the equivalent of APOC1'. These data were confirmed using a mouse Apoc2 cDNA clone, and surprisingly the cDNA clone isolated here was 965 bp in size, which is on average 450 bp longer than other APOC2 cDNAs described so far. Correspondingly, the Apoc2 gene occupies an unusually large genomic region, due to an extended 5' end. Interestingly, a variable number of tandem repeat (VNTR) in the third intron of the human APOC2 gene shows a high sequence homology and is located at the identical position in the mouse gene. Despite the high copy number of this VNTR (27 or 34 copies) only two variants were found among 11 different inbred strains. With the aid of six restriction fragment length variations in this gene cluster only two different haplotypes could be deduced, indicating that the Apoe-c1-c2 gene cluster is highly conserved in the inbred strains that were studied.

Animals↗
PubMed2004

The evolutionary conservation of the human chitotriosidase gene in rodents and primates.

Chitinases have been identified in a variety of organisms ranging from prokaryotes to eukaryotes, known to specifically degrade chitin, an abundant polymer of N-acetylglucosamine. Recently a human chitinolytic enzyme called CHIT1 was discovered. CHIT1 is expressed by activated macrophages and hydrolyzes artificial chitotrioside substrates, but its specific function in humans is unknown, since it is generally believed that man completely lacks endogenous chitin and endogenous substrates for chitinases. An intriguing question is whether the chitotriosidase activity is just an evolutionary remnant or it has a physiological function in man. To test these hypotheses we utilized a "phylogenomic" approach performing accurate sequence analyses of this gene, coding for CHIT1, in rodents and primates. Inspecting the sequences available in public databases, we determined that this gene is conserved in rodents (mouse and rat) and primates (chimpanzee, gorilla, orangutan, gibbon, baboon, a common marmoset and black macaque). Moreover we found that a 24-base pair duplication that determines an enzymatically inactive human protein is not present in primates, suggesting that this polymorphism was created during human evolution. These results indicate that chitotriosidase is conserved across the evolutionary scale. Such conservation of the CHIT1 gene argues in favour of an important biological role.

Amino Acid Sequence↗
PubMed1993

Evolutionary conservation of possible functional domains of the human and murine XIST genes.

The human XIST gene, a candidate for a role in X chromosome inactivation, has recently been cloned and sequenced, yielding a 17 kb cDNA with no apparent significant, conserved open reading frame. In addition, the XIST transcript has been localized within the nucleus to the Barr body by RNA in situ hybridization. This subnuclear localization and lack of any significant protein-coding potential suggest that XIST may act as a functional RNA within the nucleus. In the absence of a conserved open reading frame, we have turned to evolutionary studies as a first step toward elucidating a function for XIST in the process of X inactivation. While probes for XIST detect homologues in numerous eutherians, sequence comparisons require significant gapping and reveal identity levels intermediate between those seen for coding and non-coding regions in other genes. Further, sequence comparison of the most likely candidate open reading frame among several primate species reveals sequence changes not normally associated with protein-coding regions. Other features of XIST are conserved in different species, however, including the position of a major transcription start site and active X chromosome-specific DNA methylation patterns at the gene's 5' end. Finally, a possible molecular basis for differing propensity toward X inactivation between Xce alleles in mouse is investigated by comparing the sequence of the Xist conserved 5' repeats in mouse strains carrying different Xce alleles.

Alleles↗
PubMed1992

Cloning of the human activin receptor cDNA reveals high evolutionary conservation.

The entire coding region of the human activin receptor was obtained from a human testis cDNA library. Analysis of the 1539 nucleotide (513 amino acid) sequence of the receptor reveals that there are only 83 nucleotide differences compared to the coding sequence of the mouse activin receptor. Similar to its ligands, the amino acid sequence of the activin receptor is highly conserved with only two conservative amino acid differences (Lys-39 and Val-92 in human versus Arg-39 and Ile-92 in the mouse). This high degree of conservation of the activin receptor illustrates a strong evolutionary selection and confirms that activin and its receptor play an important role in development.

Activin Receptors↗
PubMed1996

Evolutionary conservation of sequences directing chromosome breakage and rDNA palindrome formation in tetrahymenine ciliates.

Extensive, programmed chromosome breakage occurs during formation of the somatic macronucleus of ciliated protozoa. The cis-acting signal directing breakage has been most rigorously defined in Tetrahymena thermophila, where it consists of a 15-bp DNA sequence known as Cbs, for chromosome breakage sequence. We have identified sequences identical or nearly identical to the T. thermophila Cbs at sites of breakage flanking the germline micronuclear rDNA locus of six additional species of Tetrahymena as well as members of two related genera. Other general features of the breakage site are also conserved, but surprisingly, the orientation and number of copies of Cbs are not always conserved, suggesting the occurrence of germline rearrangement events over evolutionary time. At one end of the T. thermophila micronuclear rDNA locus, a pair of short inverted repeats adjacent to Cbs directs the formation of a giant palindromic molecule. We have examined the corresponding sequences from two other Tetrahymena species. We find the sequence to be partially conserved, as previously implied from analysis of macronuclear rDNA, but of variable length and organization.

Animals↗
PubMed1991

Mammalian hexokinase 1: evolutionary conservation and structure to function analysis.

We have amplified and sequenced the complete coding region of bovine hexokinase isoenzyme 1 (HK1) from brain RNA with PCR primers selected for sequence conservation. The sequence information was analyzed to evaluate the evolutionary and structure-function relationships among the mammalian and yeast HK isoenzymes. Structure to function analysis identified an unduplicated, invariant N-terminal domain involved in HK1 outer mitochondrial membrane targeting, as well as putative carbohydrate and nucleotide-binding sites in the regulatory and catalytic halves of HK1 essential to enzyme function. The ATP-binding site in the catalytic half of the HK1 protein resembles nucleotide-binding regions from protein kinases, with the single amino acid replacement (lysine to glutamate) in the ATP-binding site of the amino half explaining the loss of HK1 catalytic function in the regulatory domain. Sequence comparisons suggest that the 50-kDa mammalian and yeast glucokinases arose separately in evolution. In addition to providing valuable phylogenetic and structure-function insights, this work provides an efficient strategy for rapid cloning and sequencing of the coding regions for other HKs and related proteins.

Amino Acid Sequence↗
PubMed2006

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins.

Alternative splicing is an important mechanism for fine tuning of gene expression at the post-transcriptional level. SR proteins govern splice site selection and spliceosome assembly. The Arabidopsis genome encodes 19 SR proteins, several of which have no orthologues in metazoan. Three of the plant specific subfamilies are characterized by the presence of a relatively long alternatively spliced intron located in their first RNA recognition motif, which potentially results in an extremely truncated protein. In atRSZ33, a member of the RS2Z subfamily, this alternative splicing event was shown to be autoregulated. Here we show that atRSp31, a member of the RS subfamily, does not autoregulate alternative splicing of its similarly positioned intron. Interestingly, this alternative splicing event is regulated by atRSZ33. We demonstrate that the positions of these long introns and their capability for alternative splicing are conserved from green algae to flowering plants. Moreover, in particular alternative splicing events the splicing signals are embedded into highly conserved sequences. In different taxa, these conserved sequences occur in at least one gene within a subfamily. The evolutionary preservation of alternative splice forms together with highly conserved intron features argues for additional functions hidden in the genes of these plant-specific SR proteins.

Alternative Splicing↗
PubMed1994

An Ig heavy chain enhancer of the channel catfish Ictalurus punctatus: evolutionary conservation of function but not structure.

The teleost fishes are among the earliest evolutionary lineages to have an Ig heavy chain (IgH) locus whose organization approximates that of mammals. To understand transcriptional control of the IgH locus in a teleost fish and to gain insight into the evolution of the control elements, the enhancer activity in the IgH locus of the channel catfish, Ictalurus punctatus, was investigated. Segments of the locus extending from upstream of the proximal JH gene to 2.5 kb downstream of the second transmembrane (TM2) exon of the mu gene were tested in transient transfection expression assays in murine myeloma and T cell lines, and in catfish B lymphoblastoid, monocyte-like, and putative T cell lines. In marked contrast to mammals, no enhancer activity was observed in the catfish JH to C mu intron, but strong enhancer activity (approaching that of the murine IgH intronic enhancer) was identified in a 1.8-kb segment that included the TM2 exon. This catfish enhancer was active in a B lineage-specific manner in both catfish and murine cells. It was not localized in a small core region, but appeared to contain multiple, dispersed cooperative elements rich in octamer- and mu E5-related motifs. Although the catfish IgH enhancer shares functional characteristics with the mammalian IgH intronic and 3' enhancers, its unusual organization does not permit any obvious inferences concerning evolutionary relationships between the catfish enhancer and any one of the murine IgH enhancers.

Animals↗
PubMed2001

Evolutionary conservation of the folding nucleus.

Here, we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: (i) grouping of amino acid residues into classes according to their physical-chemical properties and (ii) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological "signals" from conservation profiles disappear.

Conserved Sequence↗
PubMed1998

Evolutionary conserved rigid module-domain interactions can be detected at the sequence level: the examples of complement and blood coagulation proteases.

Several extracellular modular proteins, including proteases of the complement and blood coagulation cascades, are shown here to exhibit conserved sequence patterns specific for a particular module-domain association. This was detected by comparative analysis of sequence variability in different multiple sequence alignments, which provides a new tool to investigate the evolution of modular proteins. A first example deals with the proteins featuring a common complement control protein (CCP) module-serine protease (SP) domain pattern at their C-terminal end, defined here as the CCP-SP sub-family. These proteins include the complement proteases C1r, C1s and MASPs, the Limulus clotting factor C, and the proteins of the haptoglobin family. A second example deals with blood coagulation factors VII, IX and X and protein C, all featuring a common epidermal growth factor (EGF)-SP C-terminal assembly. Highly specific motifs are found at the connection between the CCP or EGF module and the activation peptide of the SP domain: [P/A]-x-C-x-[P/A]-[I/V]-C-G-x-[P/S/K] in the case of the CCP-SP proteins, and C-x-[P/S]-x-x-x-[Y/F]-P-C-G in the case of the EGF-SP proteins. Each motif is strictly conserved in the whole sub-family and it is detected in no more than one other known protein sequence. Strikingly, most of the conserved residues specific to each sub-family appear to be clustered at the interface between the SP domain and the CCP or EGF module. We propose that a rigid module-domain interaction occurs in these proteins and has been conserved through evolution. The functional implications of these assemblies, underlined by such evolutionary constraints, are discussed.

Amino Acid Sequence↗
PubMed1993

Nucleotide sequence of a cDNA for canine beta-spectrin reveals high evolutionary conservation.

A cDNA coding for the carboxy-terminus of canine beta-spectrin was isolated from a canine tracheal cDNA library. Analysis of the 3267 nucleotide sequence revealed a single open reading frame coding for 707 amino acids. Comparison of the deduced amino acid sequence to that of the recently reported general isoform of human beta-spectrin (beta G) revealed 98% identity. This high degree of conservation of the general isoform of beta-spectrin illustrates a strong evolutionary selection and should help in identification of sites that are candidates to mediate specialized functions of this general isoform. This is the first report of a cDNA encoding canine beta-spectrin.

Amino Acid Sequence↗
PubMed2001

Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences.

Hox transcription factors have been implicated in playing a central role in the evolution of animal morphology. Many studies indicate the evolutionary importance of regulatory changes in Hox genes, but little is known about the role of functional changes in Hox proteins. In the nematodes Pristionchus pacificus and Caenorhabditis elegans, developmental processes can be compared at the cellular, genetic, and molecular levels and differences in gene function can be identified. The Hox gene lin-39 is involved in the regulation of nematode vulva development. Comparison of known lin-39 mutations in P. pacificus and C. elegans revealed both conservation and changes of gene function. Here, we study evolutionary changes of lin-39 function using hybrid transgenes and site-directed mutagenesis in an in vivo assay using C. elegans lin-39 mutants. Our data show that despite the functional differences of LIN-39 between the two species, Ppa-LIN-39, when driven by Cel-lin-39 regulatory elements, can functionally replace Cel-lin-39. Furthermore, we show that the MAPK docking and phosphorylation motifs unique for Cel-LIN-39 are dispensable for Cel-lin-39 function. Therefore, the evolution of lin-39 function is driven by changes in regulatory elements rather than changes in the protein itself.

Amino Acid Sequence↗
PubMed1995

Evolutionary conservation of both the hydrophilic and hydrophobic nature of transmembrane residues.

An algorithm (HRG), developed to allow the pairwise comparisons of the aligned residues of several members of large gene families of polytopic integral membrane proteins is described. Using hydrophobicity scales, application of this algorithm allows the number and size of the membrane-spanning domains of bacteriorhodopsin, a polytopic protein whose structure has been partially determined, to be predicted with a high degree of accuracy (sensitivity 94%, specificity 82% for predicting the membrane embedded or extramembranous location of residues). As opposed to previously reported structure-prediction algorithms, delineation of putative transmembrane segments from connecting loops is also more clearly evident with the application of the HRG algorithm, even with proteins from widely divergent species. This indicates strong evolutionary pressure for the conservation of both the hydrophobic and hydrophilic character of residues in membrane-embedded regions of polytopic proteins, such as those of the G-protein-coupled receptor superfamily. These and other structural and functional implications evident from the application of the HRG algorithm are considered.

Algorithms↗
PubMed1991

Evolutionary conservation of a microbody targeting signal that targets proteins to peroxisomes, glyoxysomes, and glycosomes.

Peroxisomes, glyoxysomes, glycosomes, and hydrogenosomes have each been classified as microbodies, i.e., subcellular organelles with an electron-dense matrix that is bound by a single membrane. We investigated whether these organelles might share a common evolutionary origin by asking if targeting signals used for translocation of proteins into these microbodies are related. A peroxisomal targeting signal (PTS) consisting of the COOH-terminal tripeptide serine-lysine-leucine-COOH has been identified in a number of peroxisomal proteins (Gould, S.J., G.-A. Keller, N. Hosken, J. Wilkinson, and S. Subramani. 1989. J. Cell Biol. 108:1657-1664). Antibodies raised to a peptide ending in this sequence (SKL-COOH) recognize a number of peroxisomal proteins. Immunocryoelectron microscopy experiments using this anti-SKL antibody revealed the presence of proteins containing the PTS within glyoxysomes of cells from Pichia pastoris, germinating castor bean seeds, and Neurospora crassa, as well as within the glycosomes of Trypanosoma brucei. Western blot analysis of purified organelle fractions revealed the presence of many proteins containing this PTS in both glyoxysomes and glycosomes. These results indicate that at least one of the signals, and therefore the mechanism, for protein translocation into peroxisomes, glyoxysomes, and glycosomes has been conserved, lending support to a common evolutionary origin for these microbodies. Hydrogenosomes, the fourth type of microbody, did not contain proteins that cross-reacted with the anti-PTS antibody, suggesting that this organelle is unrelated to microbodies.

Amino Acid Sequence↗
PubMed1979

Evolutionary conservation of large chromosomal segments reflected in mammalian gene maps.

Conservation of genetic linkage over long periods of time is exemplifted. Comparisons are made between chromosomal regions in different species as well as within two species, man and the house mouse. Homologous regions are defined and the phenomenon of differential silencing of genes is described. The importance of conservation of particular sequences of genes is discussed in relation to medical genetics, animal breeding, evolutionary theory and genetic regulation.

Animals↗
PubMed2006

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases.

MOTIVATION: According to the models of divergent molecular evolution, the evolvability of new protein function may depend on the induction of new phenotypic traits by a small number of mutations of the binding site residues. Evolutionary relationships between protein kinases are often employed to infer inhibitor binding profiles from sequence analysis. However, protein kinases binding profiles may display inhibitor selectivity within a given kinase subfamily, while exhibiting cross-activity between kinases that are phylogenetically remote from the prime target. The emerging insights into kinase function and evolution combined with a rapidly growing number of publically available crystal structures of protein kinases complexes have motivated structural bioinformatics analysis of sequence-structure relationships in determining the binding function of protein tyrosine kinases. RESULTS: In silico profiling of Imatinib mesylate and PD-173955 kinase inhibitors with protein tyrosine kinases is conducted on kinome scale by using evolutionary analysis and fingerprinting inhibitor-protein interactions with the panel of all publically available protein tyrosine kinases crystal structures. We have found that sequence plasticity of the binding site residues alone may not be sufficient to enable protein tyrosine kinases to readily evolve novel binding activities with inhibitors. While evolutionary signal derived solely from the tyrosine kinase sequence conservation can not be readily translated into the ligand binding phenotype, the proposed structural bioinformatics analysis can discriminate a functionally relevant kinase binding signal from a simple phylogenetic relationship. The results of this work reveal that protein conformational diversity is intimately linked with sequence plasticity of the binding site residues in achieving functional adaptability of protein kinases towards specific drug binding. This study offers a plausible molecular rationale to the experimental binding profiles of the studied kinase inhibitors and provides a theoretical basis for constructing functionally relevant kinase binding trees.

Amino Acid Sequence↗
PubMed2006

Chromaffin cells in the adrenal homolog of Aphanius fasciatus (teleost fish) express piecemeal degranulation in response to osmotic stress: a hint for a conservative evolutionary process.

The effect of severe osmotic stress on the ultrastructural morphology of chromaffin cells in the adrenal homolog of Aphanius fasciatus, a small eurhyaline teleost living in saltpans, was evaluated by electron microscopy quantitative analysis. Fishes were transferred from salt water, whose salinity was 3.7%, to dechlorinated tap water and chromaffin cells were studied at resting condition and after 2 and 48 hr from the beginning of the experiment. Ultrastructural examination revealed a series of granule and cytoplasmic changes highly specific for piecemeal degranulation (PMD), a secretory process based on vesicular transport of cargoes from within granules for extracellular release, which was previously described in chromaffin cells of the mouse, rat, and human adrenal medulla. There was indeed a significant trend toward loss of content material from chromaffin granules accompanied by enlargement of granule size. Remarkably, chromaffin granules maintained their individual close structure during the whole releasing process and eventually transformed into large empty containers. A dramatic increase in the density of small, membrane-bound, variably electron-dense vesicles free in the cytoplasm or attached to granules was recognized during the first 2 hr of stress response. These features fell to control levels after 48 hr. A similar time-course pattern was observed concerning the formation of budding projections from the surface of chromaffin granules. This study provides new insight into PMD physiology and suggests that PMD is part of an adaptive secretory response to severe osmotic stress in fishes. From an evolutionary point of view, this study lends support to the concept that PMD is a secretory mechanism highly conserved throughout vertebrate classes.

Adrenal Medulla↗