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Missense mutations and evolutionary conserved amino acids at the human hypoxanthine phosphoribosyl-transferase locus.

Molecular characterization of in vivo mutation at the human hypoxanthine phosphoribosyltransferase (hprt) locus has revealed a broad spectrum of mutation, both with regard to germ-line mutation in Lesch-Nyhan and gout patients, and somatic mutation in 6-thioguanine resistant T-lymphocytes from healthy individuals. The pattern of missense mutation shows a non-random distribution with a preferential location to codons for amino acids which are identical in human and the two parasites Schistosoma mansoni and Plasmodium falciparum. Although these 'evolutionary conserved' amino acids account for only 32% of the amino acids in the human hprt protein, they are involved in 76% of the missense mutations at the hprt locus in human T-lymphocytes, 67% in Lesch-Nyhan patients (with severe hprt-deficiency), but only 43% in gout patients (with partial hprt deficiency). This observation supports the notion that evolutionary conserved amino acids constitute functionally important sites in the hprt enzyme, and missense mutations affecting these amino acids will often lead to complete loss of enzyme activity. Substitutions of 'non-conserved' amino acids cause less severe hprt-deficiency (as seen in the gout patients), or may even escape clinical diagnosis. These considerations are important for the understanding of structure-activity relationships in the hprt protein, possible differences between hprt mutational spectra in germ-line and somatic cells, and the mutational spectra induced by specific exogeneous mutagens.

Amino Acid Sequence↗

Evolutionary conservation of brain Thy-1 glycoprotein in vertebrates and invertebrates.

The evolutionary conservation of brain Thy-1 glycoprotein in 24 vertebrate and invertebrate species has been investigated by means of a soluble phase radioimmunoassay (RIA) and by the "Western blot" technique. The brain glycoproteins from virtually all the vertebrate species inhibited the precipitation of mouse Thy-1.1 by a rabbit anti-rat Thy-1 antiserum. Most reagents also inhibited the binding of a mouse anti-rat Thy-1 monoclonal antibody to rat Thy-1. Whole tissue glycoproteins from earthworm, snail and oyster and ganglia glycoproteins of a locust species were also found to be inhibitory. Western blotting analysis on NaDod SO4 polyacrylamide gel electrophoresis under reducing conditions revealed a Thy-1 homologous molecule (22-25 KD) in mammals, birds, fish, reptiles and invertebrate species. The snail Thy-1-like molecule was eluted from the gel and was shown to specifically inhibit the serological reaction. The rabbit anti-rat Thy-1 antiserum also detected a doublet molecule of approximately 85,000 KD, which is conserved in all species, including yeast and bacteria. The origin and nature of the presumed glycoproteins is unknown. Our results suggest that the Thy-1 molecule has been conserved throughout metazoan evolution and that the Thy-1 gene is the most conserved among the immune related genes (immunoglobulins, beta 2-microglobulin and major histocompatibility) which share extensive amino acid homology.

Animals↗

Expression analysis and evolutionary conservation of the mouse germ cell-specific D6Mm5e gene.

During our search for genes required for gonadal development and function in the mouse, we identified D6Mm5e (DNA segment, Chr 6. Miriam Meisler 5, expressed), a gene with an expression pattern highly restricted to the embryonic ovary and the postnatal testis. Based on RT-PCR, Northern blot, and in situ hybridization analyses, we show that D6Mm5e is expressed in the germ cells of the female embryo upon their initial entry into meiosis, and in male germ cells during the last stages of spermatogenesis. Two transcripts are detected in the gonads resulting from the alternative splicing of exon 8. This splicing event does not introduce a frame shift, and creates an mRNA product that uses the same stop codon as the longer transcript. Although D6Mm5e does not belong to any known protein family and does not contain any known protein signature motifs, the high level of evolutionary conservation and the cellular and temporal expression suggest that D6Mm5e may have a role in male and female gametogenesis. Here we report the gonad-restricted mRNA expression profile of D6Mm5e in the mouse, and the evolutionary conservation of its amino acid sequence.

Alternative Splicing↗

Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms.

INTRODUCTION: Aberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge. METHODS: As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants. RESULTS: Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral. CONCLUSION: In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic.

Breast Neoplasms↗

Evidence for evolutionary conservation of a physical linkage between the human BAF60b, a subunit of SWI/SNF complex, and thyroid hormone receptor interacting protein-1 genes on chromosome 17.

The ubiquitously expressed rat BAF60b gene, which codes for a subunit of the multiprotein SWI/SNF complex, was recently identified between the pituitary growth hormone (GH-N) and thyroid hormone receptor interacting protein-1 (TRIP-1) genes. In primates, duplication of the GH-N gene has resulted in the addition of four placenta-specific (GH-V, CS-A, CS-B, and CS-L) genes downstream of the GH-N gene. As part of our study of the effect of remote sequences on the transcriptional regulation of the GH/CS gene family, we showed recently that these genes lie 40 kb upstream of the human TRIP-1 gene. We have now investigated the presence of the human BAF60b gene upstream of the TRIP-1 gene for evidence of evolutionary conservation of this arrangement or its disruption by the recent duplication of the nearby GH-N gene in primates. We report that, as in the rat genome, the human BAF60b gene is in the reverse transcriptional direction relative to the TRIP-1 gene, such that their polyadenylation sites are separated by 93 bp which compares with 92 bp in the rat. Reexamination of reported porcine TRIP-1 sequences also revealed the presence of the BAF60b gene separated by 93 bp, supporting an evolutionary conservation of this arrangement.

ATPases Associated with Diverse Cellular Activitie↗

Localization and characterization of mouse-human alignments within the human genome. Does evolutionary conservation suggest functional importance?

In an attempt to validate the use of evolutionary conservation as a method to identify putative regulatory elements, we have quantified the frequency of Single Nucleotide Polymorphisms (SNPs) within the most tightly conserved regions across the entire Human Genome. Our results show that conserved non-coding sequences have a significantly lower SNP frequency than their exonic counterparts, which suggests that these regions are functionally important.

Animals↗

Evolutionary conservation of DNA coding for maternal RNA in sea urchins.

The extent of evolutionary conservation of DNA complimentary to RNA stored in the mature oocyte of the sea urchin S. purpuratus has been assessed. To do this, such DNA was hybridized with total genomic DNA of S. purpuratus and S. franciscanus and the thermal stability of the resultant duplexes was measured by two methods. In the first method, the duplexes were bound to hydroxylapatite and thermally eluted; the difference in thermal stability between homologous and heterologous duplexes averaged 6.9 degrees C in duplicate determinations. In the second experiment, the same hybrids were thermally melted in 2.4M tetraethylammonium chloride, then assayed with S1 nuclease; the difference in thermal stability of homologous and heterologous duplexes was 4.8 degrees C. Either value is significantly lower than the divergence of total single-copy DNA among these species as measured by the same techniques. This demonstrates that DNA sequences complimentary to maternal RNA are conserved during evolution, and thus that a high fraction of them are likely to be physiologically functional.

Animals↗

Comparison of the Drosophila melanogaster, human and murine Sm B cDNAs: evolutionary conservation.

To analyze the evolutionary stability of the Sm B polypeptides, the cDNA nucleotide (nt) sequence was derived for the Drosophila melanogaster Sm B polypeptide and compared to the cDNAs encoding human and murine Sm B. The three cDNAs were transcribed and translated in reticulocyte lysates followed by analysis of the synthesized proteins by SDS-PAGE. D. melanogaster B migrated at approximately 25 kDa, in comparison to 28 kDa for the murine and human B proteins, although all three proteins were immunoprecipitated by human anti-Sm autoantibodies and by the Y12 anti-Sm murine monoclonal antibody (Y12 mAb). Immunoblots and immunoprecipitations of [35S]methionine-labeled D. melanogaster S2/M3 cells confirmed the smaller size of the D. melanogaster protein, and revealed that B' was absent in this cell line, as in murine cells. In comparison to the 231 amino acids (aa) of human and murine B, the deduced sequence for the D. melanogaster clone was 199 aa (predicted M(r) of 24,598) with two 5-aa deletions and a 19-aa truncation at the 3' end, compared to the other two clones. D. melanogaster protein B shared 65% aa sequence identity with the human and mouse clones, and 80% similarity when conservative aa substitutions were noted. The C-terminal portion of the D. melanogaster protein was the most evolutionarily variable in comparison to the deduced aa sequences for the other two proteins; however, autoantigenic epitopes bound by human anti-Sm antibodies and the Y12 mAb in this region of the protein were conserved across species lines.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

[Detection and analysis of Tetrahymena pyriformis 26S ribosomal DNA domain sequences, differing in degree of evolutionary conservation].

Domains of different evolutionary conservatism were defined in the 26S rDNA sequence of T. pyriformis. The fragment of studied DNA (1212 bp) showing high evolutionary conservatism was cloned. It was shown this fragment of DNA may be used to a probe for blot-hybridization analysis of the structure of rDNA from various taxa, protists to mammals. Superconservative and hypervariable domains were defined. The first are good for the primers for PCR analysis of rDNA from various taxa, the second--for species specific primers.

Animals↗

Cloning of the alphaA-crystallin genes of a blind cave form and the epigean form of Astyanax fasciatus: a comparative analysis of structure, expression and evolutionary conservation.

In the present study we have analyzed the integrity and expression of the alphaA-crystallin gene, that codes for a major structural component of the lens, in a blind cave form of the teleostean fish, Astyanax fasciatus. This is the first alphaA-crystallin gene cloned from a teleostean fish. Sequence comparison of this cave-form gene with its epigean conspecific and with homologs of distantly related taxa has illustrated conservation of regulatory and coding regions. Although no crystallin proteins are produced in the lens of the cave form, and the mRNA of this gene could not be detected by in situ hybridization of different developmental stages, the promoter region of cave-fish alphaA-crystallin is functionally intact. The deduced amino-acid sequence of the alphaA-crystallin gene of the cave form differs from that of its epigean conspecific at only one position (139). This is within an important, small heat-shock protein-related region, HCR2. A comparison of the 5'-flanking regions of the A. fasciatus alphaA-crystallin gene with the chicken homolog revealed the high conservation of lens-specific regulatory sequences and further demonstrates the evolutionary conservation of this gene. 1988 Elsevier Science B.V.

Amino Acid Sequence↗

Similarities and differences in tRNA identity between Escherichia coli and Saccharomyces cerevisiae: evolutionary conservation and divergence.

Identity elements, which allow correct recognition of tRNAs by their cognate aminoacyl-tRNA synthetase, have been well elucidated in Escherichia coli to begin to see a pattern for tRNA recognition. We examined the identity elements of several tRNA species from Saccharomyces cerevisiae and Thermus thermophilus using in vitro transcripts. Comparison of identity elements among different organisms indicates not only conservation but also evolutionary divergence of tRNA recognition.

Amino Acyl-tRNA Synthetases↗

Characterization and expression of the gene encoding membralin, an evolutionary conserved protein expressed in the central nervous system.

We have identified a novel gene that encodes an evolutionary conserved protein that we name membralin since it contains multiple transmembrane regions. The human gene C19orf6 localizes to chromosome 19p13.3. Splice variant membralin-1 is encoded by 11 exons, translating into 620 amino acids. In addition, we found evidence for two additional splice variants in the human. The mouse gene ORF61 localizes to chromosome 10. We cloned two splice variants in mouse: membralin-1, which is encoded by 12 exons, translating into 574 amino acids, and membralin-2, which translates into 598 amino acids. The existence of rat membralin-1 (574 amino acids long) is, so far, only supported by in situ hybridization result, whereas the existence of rat membralin-2 (598 amino acids long) is strongly supported by overlapping ESTs. Gene homologues were also identified in fruit-fly (CG8405, chromosome 2R 52; two splice variants), nematode (chromosome III), and Arabidopsis thaliana (chromosome 1). Sequence analysis revealed no closely related genes, suggesting that membralin represents the sole member of a unique protein family.

Alternative Splicing↗

Cloning of mouse type VII collagen reveals evolutionary conservation of functional protein domains and genomic organization.

Type VII collagen is the major component of anchoring fibrils, attachment structures necessary for stable association of the dermal-epidermal basement membrane to the underlying dermis. The critical role of the anchoring fibrils in providing integrity to the cutaneous basement membrane zone is attested to by demonstration of mutations in the type VII collagen gene (COL7A1) in patients with dystrophic epidermolysis bullosa. To gain insight into the evolutionary conservation of the type VII collagen gene, in this study we have cloned the entire mouse type VII collagen cDNA and elucidated the intron-exon organization of the corresponding gene, Col7a1. The coding region of the cDNA consists of 8832 nucleotides encoding a polypeptide of 2944 amino acids with a calculated molecular mass of approximately 295 kDa. Computer analysis predicted the presence of an 18-amino acid signal peptide. Comparison of the deduced mouse alpha1(VII) collagen polypeptide with the corresponding human sequence indicated 84.7% identity and 90.4% homology at the amino acid level. In addition, the domain organization, including imperfections and interruptions within the collagenous domain consisting of Gly-X-Y repeat sequences, was highly conserved. The unit of evolutionary period between the full-length human and mouse polypeptides was calculated to be 6.5 million years, however, suggesting relatively rapid evolutionary divergence in comparison to other collagen genes. Elucidation of the intron-exon organization of the mouse Col7a1 gene revealed 118 distinct exons, the same number as present in the human gene. These data indicate a high degree of structural conservation between the human and mouse type VII collagen, supporting the critical role of this collagen as the major component of the anchoring fibrils.

Amino Acid Sequence↗

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

The HSSP (Homology-Derived Secondary Structure of Proteins) database provides multiple sequence alignments (MSAs) for proteins of known three-dimensional (3D) structure in the Protein Data Bank (PDB). The database also contains an estimate of the degree of evolutionary conservation at each amino acid position. This estimate, which is based on the relative entropy, correlates with the functional importance of the position; evolutionarily conserved positions (i.e., positions with limited variability and low entropy) are occasionally important to maintain the 3D structure and biological function(s) of the protein. We recently developed the Rate4Site algorithm for scoring amino acid conservation based on their calculated evolutionary rate. This algorithm takes into account the phylogenetic relationships between the homologs and the stochastic nature of the evolutionary process. Here we present the ConSurf-HSSP database of Rate4Site estimates of the evolutionary rates of the amino acid positions, calculated using HSSP's MSAs. The database provides precalculated evolutionary rates for nearly all of the PDB. These rates are projected, using a color code, onto the protein structure, and can be viewed online using the ConSurf server interface. To exemplify the database, we analyzed in detail the conservation pattern obtained for pyruvate kinase and compared the results with those observed using the relative entropy scores of the HSSP database. It is reassuring to know that the main functional region of the enzyme is detectable using both conservation scores. Interestingly, the ConSurf-HSSP calculations mapped additional functionally important regions, which are moderately conserved and were overlooked by the original HSSP estimate. The ConSurf-HSSP database is available online (http://consurf-hssp.tau.ac.il).

Algorithms↗

Evolutionary conservation of the dystrophin central rod domain.

Dystrophin cDNA fragments encoding the C-terminal repeats of the central rod region have been expressed as fusion proteins. The polyclonal antisera raised to the purified fusion proteins have been characterized and neither antiserum cross-reacted with dystrophin-related protein. Antisera detected dystrophin with molecular mass close to that of the human in all terrestrial vertebrates and amphibia studied. Experiments with antisera to the N-terminal region of the dystrophin rod confirmed that epitopes to the rod region were conserved during this evolutionary period and the length of this domain remained unaltered.

Animals↗

Evolutionary conservation of prion-forming abilities of the yeast Sup35 protein.

Saccharomyces cerevisiae prion [PSI ] is a self-propagating isoform of the eukaryotic release factor eRF3 (Sup35p). Sup35p consists of the evolutionary conserved release factor domain (Sup35C) and two evolutionary variable regions - Sup35N, which serves as a prion-forming domain in S. cerevisiae, and Sup35M. Here, we demonstrate that the prion form of Sup35p is not observed among industrial and natural strains of yeast. Moreover, the prion ([PSI + ]) state of the endogenous S. cerevisiae Sup35p cannot be transmitted to the next generations via heterologous Sup35p or Sup35NM, originating from the distantly related yeast species Pichia methanolica. This suggests the existence of a 'species barrier' in yeast prion conversion. However, the chimeric Sup35p, containing the Sup35NM region of Pichia, can be turned into a prion in S. cerevisiae by overproduction of the identical Pichia Sup35NM. Therefore, the prion-forming potential of Sup35NM is conserved in evolution. In the heterologous system, overproduction of Pichia Sup35p or Sup35NM induced formation of the prion form of S. cerevisiae Sup35p, albeit less efficiently than overproduction of the endogenous Sup35p. This implies that prion induction by protein overproduction does not require strict correspondence of the 'inducer' and 'inducee' sequences, and can overcome the 'species barrier'.

Amino Acid Sequence↗

Evolutionary conservation of chymotrypsinogen gene: genomic analysis and protein modeling.

Chymotrypsinogen is widely present in various animal pancreases. To study evolutionary relationship of chymotrypsinogen gene in species, we used a cDNA probe of human prechymotrypsinogen to investigate the species distribution of chymotrypsinogen gene, and designed oligodeoxynucleotide primers to investigate the genomic organization in the three domains of active sites. The genomic analyses showed that chymotrypsinogen gene is evolutionary conserved in species. On the basis of the deduced amino acid residues, a three-dimensional model for human chymotrypsinogen was further built by computer graphics. The model showed high similarity to the X-ray crystal structure of bovine chymotrypsinogen A, thus, demonstrated that the three-dimensional structure is more conserved in evolution than protein sequences.

Animals↗

The -175T----C mutation increases promoter strength in erythroid cells: correlation with evolutionary conservation of binding sites for two trans-acting factors.

A point mutation at position -175 has been detected in Agamma as well as Ggamma globin genes in individuals with hereditary persistence of fetal hemoglobin (HPFH). To prove that this single point mutation results in increased promoter strength, we transfected erythroid and nonerythroid cell lines with constructs containing normal and mutant promoters linked to the bacterial chloramphenicol acetyl transferase (CAT) gene. Differences in transfection efficiency were controlled by cotransfection of pRSVgpt. In K562 erythroleukemia cells, the -175 HPFH promoter directed three- to fourfold more CAT activity than its wild type counterpart. However, in HeLa cells the two promoters were similar in strength. The -195 to -165 region of the gamma-globin promoter contains binding sites for two proteins: a ubiquitously distributed octamer binding protein, OBP, and the erythroid-specific protein, GF-1. We find that while the GF-1 binding site is highly conserved among related primate gamma-globin genes, the octamer binding site is not. The evolutionary conservation of GF-1 as well as its erythroid-specific distribution suggest that this protein is important in gamma-globin gene expression. A role for OBP in the regulation of gamma-globin, if any, must have arisen recently in primate evolution.

Animals↗