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At least 235 records · Page 13Linked to original sources
PubMed1983

The structure of the vimentin gene.

The structure of the chromosomal gene encoding the intermediate filament protein vimentin is described. This gene, which is present as a single copy in the hamster genome, comprises about 10 kb of DNA and contains more than 80% of intron sequences. S1 mapping and sequence analysis reveal nine exons with a total length of 1848 nucleotides. For the complete primary structure of hamster vimentin, 464 amino acids are predicted, giving a molecular weight of 53,500 daltons. The intron positions are at codons 186, 206/207, 238/239, 292/293, 334/335, 408, 423, and 451/452. The overall homology with chicken desmin is 60% and is even higher in the central (alpha-helical) regions of both molecules. Cross-hybridization at the DNA level, however, is low. Comparison of the amino acid sequence of vimentin with prekeratin sequences shows that there is lesser homology of primary structure, but both the position and size of alpha-helical regions are strongly conserved. At the 5' end of the gene there is a consensus promoter sequence. The first AUG start codon is found 132 nucleotides downstream of the estimated cap site. The 3' nontranslated sequence shows homologies with the chicken vimentin gene. An interesting feature of the vimentin gene is a stretch of 44 nucleotides of alternating dC and dA within intron 2 that may form left-handed Z-DNA.

Amino Acid Sequence↗
PubMed1986

Three tightly linked genes encoding human type I keratins: conservation of sequence in the 5'-untranslated leader and 5'-upstream regions of coexpressed keratin genes.

We have isolated and subcloned three separate segments of human DNA which share strong sequence homology with a previously sequenced gene encoding a type I keratin, K14 (50 kilodaltons). Restriction endonuclease mapping has demonstrated that these three genes are tightly linked chromosomally, whereas the K14 gene appears to be separate. As judged by positive hybridization-translation and Northern blot analyses, the central linked gene encodes a keratin, K17, which is expressed in abundance with K14 and two other type I keratins in cultured human epidermal cells. None of these other epidermal keratin mRNAs appears to be generated from the K17 gene through differential splicing of its transcript. The sequence of the K17 gene reveals striking homologies not only with the coding portions and intron positions of the K14 gene, but also with its 5'-noncoding and 5'-upstream sequences. These similarities may provide an important clue in elucidating the molecular mechanisms underlying the coexpression of the two genes.

Base Sequence↗
PubMed2003

Arabidopsis genes encoding mitochondrial type II NAD(P)H dehydrogenases have different evolutionary origin and show distinct responses to light.

In addition to proton-pumping complex I, plant mitochondria contain several type II NAD(P)H dehydrogenases in the electron transport chain. The extra enzymes allow the nonenergy-conserving electron transfer from cytoplasmic and matrix NAD(P)H to ubiquinone. We have investigated the type II NAD(P)H dehydrogenase gene families in Arabidopsis. This model plant contains two and four genes closely related to potato (Solanum tuberosum) genes nda1 and ndb1, respectively. A novel homolog, termed ndc1, with a lower but significant similarity to potato nda1 and ndb1, is also present. All genes are expressed in several organs of the plant. Among the nda genes, expression of nda1, but not nda2, is dependent on light and circadian regulation, suggesting separate roles in photosynthesis-associated and other respiratory NADH oxidation. Genes from all three gene families encode proteins exclusively targeted to mitochondria, as revealed by expression of green fluorescent fusion proteins and by western blotting of fractionated cells. Phylogenetic analysis indicates that ndc1 affiliates with cyanobacterial type II NADH dehydrogenase genes, suggesting that this gene entered the eukaryotic cell via the chloroplast progenitor. The ndc1 should then have been transferred to the nucleus and acquired a signal for mitochondrial targeting of the protein product. Although they are of different origin, the nda, ndb, and ndc genes carry an identical intron position.

Amino Acid Sequence↗
PubMed2005

Structure and expression of the zebrafish mest gene, an ortholog of mammalian imprinted gene PEG1/MEST.

PEG1/MEST is a paternally expressed gene in placental mammals. Here, we report identification of zebrafish (Danio rerio) gene mest, an ortholog of mammalian PEG1/MEST. Zebrafish mest encodes a polypeptide of 344 amino acids and shows a significant similarity to mammalian orthologs. Zebrafish mest is present as a single copy in the zebrafish genome and is closely linked to copg2 as in mammals. It is notable that 10 of 11 intron positions in mest are conserved among mammalian PEG1/MEST genes, indicating that the genomic organization and linkage between mest and copg2 loci was established in ancient vertebrates. Zebrafish mest is expressed in blastula, segmentation, and larval stages, exhibiting gradually increased expression as the development proceeds. Allelic expression analysis in hybrid larvae shows that both parental alleles are transcribed. We also observed one-codon alternative splicing involving an alternative usage of the two consecutive splice acceptors of intron 1, generating two protein isoforms with different lengths of a single amino acid.

Alternative Splicing↗
PubMed1993

Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1.

We have developed a new reporter gene fusion to monitor mRNA splicing in yeast. An intron-containing fragment from the Saccharomyces cerevisiae ACT1 gene has been fused to CUP1, the yeast metallothionein homolog. CUP1 is a nonessential gene that allows cells to grow in the presence of copper in a dosage-dependent manner. By inserting previously characterized intron mutations into the fusion construct, we have established that the efficiency of splicing correlates with the level of copper resistance of these strains. A highly sensitive assay for 5' splice site usage was designed by engineering an ACT1-CUP1 construct with duplicated 5' splice sites; mutations were introduced into the upstream splice site in order to evaluate the roles of these highly conserved nucleotides in intron recognition. Almost all mutations in the intron portion of the 5' consensus sequence abolish recognition of the mutated site, while mutations in the exon portion of the consensus sequence have variable affects on cleavage at the mutated site. Interestingly, mutations at intron position 4 demonstrate that this nucleotide plays a role in 5' splice site recognition other than by base pairing with U1 snRNA. The use of CUP1 as a reporter gene may be generally applicable for monitoring cellular processes in yeast.

Base Sequence↗
PubMed2000

Genomic typing of minor histocompatibility antigen HA-1 by reference strand mediated conformation analysis (RSCA).

Disparities in minor histocompatibility antigen (mHAg) HA-1 are involved in the development of acute graft-versus-host disease (GvHD) in adult recipient after HLA-identical sibling donor hematopoietic stem cell transplantation. The mHAg HA-1 is an HLA-A*0201-restricted nonapeptide, which derives from the cleavage of a protein encoded at chromosome 19. The sequence analysis of HA-1 cDNA identified two alleles, termed HA-1H and HA-1R, which differ in only two nucleotides at 3' end of exon A, at positions 500 and 504. DNA-based methods for HA-1 typing were developed in 1998, using polymerase chain reaction with sequence-specific primers (PCR-SSP) and restriction fragment length polymorphism (PCR-RFLP). Here, we report the usefulness of reference strand mediated conformation analysis (RSCA), which was developed for mutation detection and typing of polymorphic loci, to discriminate between the two HA-1 alleles. We performed genomic typing of HA-1 locus in 203 HLA-A*0201-positive samples using RSCA and we confirmed these results by PCR-SSP. The results demonstrate the high reproducibility of this method and their strong correlation with the results obtained by PCR-SSP (99%). Only two samples showed disparity between the RSCA typing and the PCR-SSP. Direct sequencing of these samples confirmed that the correct allele assignment was that obtained by the RSCA typing. Furthermore, HA-1- RSCA-based typing provides additional information about the intronic structure of both alleles. With this approach, we describe the almost constant presence (99.2%) of a 5-bp deletion at intronic position 214-218 associated to the HA-1H allele, previously unidentified. We conclude that HA-1 genomic typing by RSCA is easy to perform and that could be used as a routine typing method.

Alleles↗
PubMed2000

Organization of the human interleukin-1 receptor antagonist gene IL1HY1.

The interleukin (IL)-1 family of proteins plays an important role in inflammatory and defense mechanisms. The recently characterized IL1HY1 cDNA encodes a new member of the IL-1 receptor antagonist family (IL-1ra). In this report, we describe the complete nucleotide sequence of the human IL1HY1 gene. We sequenced approximately 7,600 nucleotides and found four coding exons ranging in size from 55 to 2,288 nucleotides. The 5' untranslated region is formed by one of two alternatively used exons and one invariably present exon which also contains the region encoding the first nine amino acids of the protein. IL1HY1 and IL-1ra intron positions are well conserved within the protein-coding region, providing evidence that these genes arose from a duplication of a primordial IL-1 receptor antagonist gene.

5' Untranslated Regions↗
PubMed1993

Structural organization of the genes encoding human and murine FK506-binding protein (FKBP) 13 and comparison to FKBP1.

FK506-binding protein (FKBP)12 and FKBP13 are members of a family of proteins which bind the immunosuppressant drugs, FK506 and rapamycin. FKBP12 and FKBP13 are encoded by distinct genes, designated FKBP1 and FKBP2, respectively. The structure of human FKBP1 was previously characterized. We now report the genomic structure of the human and murine FKBP2 genes. Comparison of FKBP1 and FKBP2 reveals significant homology and correlation of intron positions in the C-terminal region, suggesting that these genes may have evolved from a common ancestral gene.

Amino Acid Sequence↗
PubMed1996

The organization of the human gene NCX1 encoding the sodium-calcium exchanger.

The intron-exon organization of the human Na/Ca-exchanger gene NCX1 and of the N-terminal half of the related gene NCX2 has been determined. The NCX1 gene consists of 12 exons spread over 200 kb on chromosome 2 close to STS D2S2328 and encodes a 6.2-kb transcript. Both NCX1 and NCX2 feature an unusual 1.8-kb exon, containing two-thirds of the protein coding sequence and a similar area of the coding sequences split into several small exons, displaying tissue-specific alternative splicing. The similar intron positions in the "cardiac" (NCX1) and "brain" (NCX2) mammalian exchanger genes suggest their origin from the recent duplication and translocation of a common ancestral gene, a putative precursor of which has been identified in the nematode Caenorhabditis elegans.

Amino Acid Sequence↗
PubMed2000

Phylogenetic analysis of teneurin genes and comparison to the rearrangement hot spot elements of E. coli.

Teneurins are a novel family of transmembrane proteins conserved between invertebrates and vertebrates. There are two members in Drosophila, one in C. elegans and four members in mouse. Here, we describe the analysis of the genomic structure of the human teneurin-1 gene. The entire human teneurin-1 (TEN1) gene is contained in eight PAC clones representing part of the chromosomal locus Xq25. Interestingly, many X-linked mental retardation syndromes (XLMR) and non-specific mental retardation (MRX) are mapped to this region. The location of the human TEN1 together with the neuronal expression makes TEN1 a candidate gene for XLMR and MRX. We also identified large parts of the human teneurin-2 sequence on chromosome 5 and sections of human teneurin-4 at chromosomal position 11q14. Database searches resulted in the identification of ESTs encoding parts of all four human members of the teneurin family. Analysis of the genomic organization of the Drosophila ten-a gene revealed the presence of exons encoding a long form of ten-a, which can be aligned with all other teneurins known. Sequence comparison and phylogenetic trees of teneurins show that insects and vertebrates diverged before the teneurin ancestor was duplicated independently in the two phyla. This is supported by the presence of conserved intron positions between teneurin genes of man, Drosophila and C. elegans. It is therefore not possible to class any of the vertebrate teneurins with either Drosophila Ten-a or Ten-m. The C-terminal part of all teneurins harbours 26 repetitive sequence motifs termed YD-repeats. YD-repeats are most similar to the repeats encoded by the core of the rearrangement hot spot (rhs) elements of Escherichia coli. This makes the teneurin ancestor a candidate gene for the source of the rhs core acquired by horizontal gene transfer.

Amino Acid Sequence↗
PubMed1992

Molecular structure of the human alcohol dehydrogenase 3 gene.

The structure and nucleotide sequence of an ADH3(1) allele, which encodes the ADH gamma 1 subunit, have been determined. The intron positions of the ADH3 gene are identical to those of the other class I and class II ADH genes. The level of nucleotide variation at the ADH3 locus is somewhat higher than those at the ADH1 and ADH2 loci.

Alcohol Dehydrogenase↗
PubMed2006

Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont.

Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Opisthokonta (metazoan animals and fungi). Here we investigate the phylogenetic distribution of mtTFB homologs throughout the domain Eucarya, documenting the first examples of this protein outside of the opisthokonts. Surprisingly, we identified putative mtTFB homologs only in amoebozoan protists and trypanosomatids. Phylogenetic analysis together with conservation of intron positions in amoebozoan and human genes supports the grouping of the putative mtTFB homologs as a distinct clade. Phylogenetic analysis further demonstrates that the mtTFB is most likely derived from the DMT of the mitochondrial endosymbiont.

Acanthamoeba castellanii↗
PubMed1995

The nitrate reductase gene from a shoyu koji mold, Aspergillus oryzae KBN616.

A niaD gene encoding nitrate reductase was isolated from Aspergillus oryzae KBN616 and sequenced. The structural gene comprises 2973 bp and 868 amino acids, which showed a high degree of similarity to nitrate reductases from other filamentous fungi. The coding sequence is interrupted by six introns varying in size from 48 to 98 bp. The intron positions are all conserved among the niaD genes from A. oryzae, Aspergillus nidulans, and Aspergillus niger. A homologous transformation system was developed for an industrial shoyu koji mold, A. oryzae KBN616, based on the nitrate reductase (niaD) of the nitrate assimilation pathway.

Amino Acid Sequence↗
PubMed1988

Intron sequence and structure requirements for tRNA splicing in Saccharomyces cerevisiae.

Predicted single-stranded structure at the 3' splice site is a conserved feature among intervening sequences (IVSs) in eukaryotic nuclear tRNA precursors. The role of 3' splice site structure in splicing was examined through hexanucleotide insertions at a central intron position in the Saccharomyces cerevisiae tRNA gene. These insertions were designed to alter the structure at the splice site without changing its sequence. Endonuclease cleavage of pre-tRNA substrates was then measured in vitro, and suppressor activity was examined in vivo. A precursor with fully double-stranded structure at the 3' splice site was not cleaved by endonuclease. The introduction of one unpaired nucleotide at the 3' splice site was sufficient to restore cleavage, although at a reduced rate. We have also observed that guanosine at the antepenultimate position provides a second consensus feature among IVSs in tRNA precursors. Point mutations at this position were found to affect splicing although there was no specific requirement for guanosine. These and previous results suggest that elements of secondary and/or tertiary structure at the 3' end of IVSs are primary determinants in pre-tRNA splice site utilization whereas specific sequence requirements are limited.

Base Sequence↗
PubMed2005

Splicing abnormalities in congenital myasthenic syndromes.

A total of 173 mutations has been reported to date in eight genes in congenital myasthenic syndromes. Sixteen intronic and five exonic mutations in three genes affect pre-mRNA splicing. Eight of these are of particular interest, and are reviewed in this article. An A-to-G mutation at intron position +3 results in exon skipping only when there are mismatched nucleotides to U1 snRNA at positions +4 to +6. Similarly, a mutation at the last nucleotide of an exon causes exon skipping when a nucleotide at position +6 is not complementary to U1 snRNA. We observe the similar compensation mechanisms for mismatches to U1 snRNA at 179,917 native human splice donor sites. A 7-bp deletion in CHRNE exon 7 causes skipping of the preceding 101-bp exon 6. We found in general that the nonsense-mediated altered splicing of a remote exon (NASRE) is mediated by inherent weak splicing signals flanking the skipped exon and degradation of a normally spliced transcript by the nonsense-mediated mRNA decay (NMD). A 16-bp duplication spanning the CHRNE intron 10/exon 11 boundary generates two copies of 3' splice sites, and the downstream copy is exclusively silenced. Analysis of a series of artificial mutants conforms to the scanning model of recognition of the 3' splice site that predicts that the first 'ag' more than 13 nucleotides downstream of the branch point is selected for splicing. Splicing mutations may be more frequent than suspected, and one must always be aware of possible splicing abnormalities when analyzing human mutations.

DNA Mutational Analysis↗
PubMed2001

MACF1 gene structure: a hybrid of plectin and dystrophin.

Mammalian MACF1 (Macrophin1; previously named ACF7) is a giant cytoskeletal linker protein with three known isoforms that arise by alternative splicing. We isolated a 19.1-kb cDNA encoding a fourth isoform (MACF1-4) with a unique N-terminus. Instead of an N-terminal actin-binding domain found in the other three isoforms, MACF1-4 has eight plectin repeats. The MACF1 gene is located on human Chr 1p32, contains at least 102 exons, spans over 270 kb, and gives rise to four major isoforms with different N-termini. The genomic organization of the actin-binding domain is highly conserved in mammalian genes for both plectin and BPAG1. All eight plectin repeats are encoded by one large exon; this feature is similar to the genomic structure of plectin. The intron positions within spectrin repeats in MACF1 are very similar to those in the dystrophin gene. This demonstrates that MACF1 has characteristic features of genes for two classes of cytoskeletal proteins, i.e., plectin and dystrophin.

Alternative Splicing↗
PubMed1990

Gene structures of three vertebrate adenylate kinase isozymes.

Adenylate kinase is an ubiquitous enzyme which contributes to homeostasis of adenine nucleotide composition in the cell. In vertebrates, three isozymes (AK1, AK2, and AK3) are characterized which have distinct distribution in tissues as well as subcellular compartments. The genetic backgrounds of these adenylate kinase isozymes were analyzed. cDNA clones for AK1 were isolated from poly(A)+RNA of chicken skeletal muscle. The results of mRNA analysis in various tissues using the AK1 cDNA indicated that the AK1 gene expression is regulated both tissue-specifically and developmentally at the transcriptional level. The AK1 gene was cloned from chicken and human DNA and characterized. Both genes were split into seven exons. The intron positions in both genes coincided. cDNA clones for AK2 isolated from bovine liver poly(A)+RNA contained two types. One type (AK2A) encoded the same amino acid sequence as that reported for bovine heart AK2. The other type (AK2B) encoded the same sequence as AK2 except for the COOH terminus. The mRNA species corresponding to the two cDNA clones were identified in bovine liver and heart. Both the cDNA sequences were found to direct the active adenylate kinase synthesis in E. coli. The AK2 gene was cloned and characterized. It consisted of seven exons and six introns. From genomic structure analysis, the two cDNA species were shown to be derived from a single gene by the alternative splicing mechanism. Three types of cDNA clones for AK3 were isolated from bovine liver poly(A)+RNA, which contained the common AK3-coding region and different 3' portions. No NH2-terminal presequence of mitochondrial targeting was identified in AK3 from the sequencing and expression analyses of the cDNA. Upon expression of the cDNA sequence in E. coli, AK3 protein was recovered in the periplasmic space of the bacteria, indicating that AK3 without presequence was exported through the inner bacterial membrane as it is imported through the mitochondrial membranes. Internal targeting signals may be responsible for the translocation process. The AK3 gene was cloned and partially characterized. It is split into at least five exons. The comparisons of amino acid sequences and genomic structure of three isozymes revealed that a segment corresponding to either exon 5 of the AK2 gene or a part of exon 3 of the AK3 gene is missing in the AK1 gene. Phylogenetic analysis suggested that AK1, a shorter molecule, would have been separated from a longer molecule very early in evolution of adenylate kinase.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenylate Kinase↗
PubMed2004

Neuroglobin, cytoglobin, and a novel, eye-specific globin from chicken.

Neuroglobin and cytoglobin are two recently discovered respiratory proteins of vertebrates. Here we report the first identification and expression analyses of these proteins in bird species. Neuroglobin from the domestic chicken Gallus gallus differs in approximately 30% from the mammalian proteins, but its genome structure shows the conservation of the B12.2, E11.0, and G7.0 intron positions. The chicken cytoglobin protein is shorter than the mammalian orthologs, from which it differs overall by approximately 25%, due to the absence of the C-terminal exon in the gene. Comparison of chicken and mammalian gene order shows that neuroglobin and cytoglobin are located on conserved syntenic chromosomal segments. While neuroglobin is expressed in the chicken's brain and eye, cytoglobin RNA was detected in all investigated tissues. In addition, a novel globin-type has been identified that is only expressed in the chicken's eye. The gene of this eye-globin contains the typical globin introns at B12.2 and G7.0. Phylogenetic analyses suggest that this globin is most closely related to the cytoglobin lineage. Although the function of this eye-globin remains presently uncertain, it adds an additional diversity to the vertebrate globin family.

Amino Acid Sequence↗