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PubMed1985

Comparison of human and chimpanzee zeta 1 globin genes.

The DNA base sequences of the entire chimpanzee zeta 1 globin gene and an additional 1 kb of DNA flanking both the human and chimpanzee genes have been determined. Whereas the human zeta 1 gene contains a termination codon in the sixth position, the chimpanzee gene appears to be functional. This finding confirms Proudfoot et al.'s suggestion that the human zeta 1 gene was recently inactivated. Like the corresponding human zeta 1 and zeta 2 genes, the first and second introns of the chimpanzee zeta 1 gene are occupied largely by tandem repeats of short oligonucleotides. These tandem repeats have undergone several rearrangements since the divergence of the human and chimpanzee zeta 1 genes.

Amino Acid Sequence↗

PubMed1996

SOM 1, a small new gene required for mitochondrial inner membrane peptidase function in Saccharomyces cerevisiae.

IMP1 encodes a subunit of the mitochondrial inner membrane peptidase responsible for the proteolytic processing of cytochrome oxidase subunit 2 (Cox2) and cytochrome b2 (Cytb2). The molecular defect in an imp1 mutation and the characterisation of a high-copy-number suppressor is described. A deletion of the suppressor region causes respiration deficiency. The DNA sequence revealed three very small overlapping ORFs. Constructs which carried termination codons within the ORFs or lacked ATG initiation codons still retained complementing activity on a high-copy-number plasmid. Nevertheless, the possibility that the suppressor acts at DNA or RNA level could be excluded. Subcloning of the ORFs, complementation analysis in low-copy-number plasmids and transcript mapping identified the 222 bp ORF as the suppressor gene designated SOM1. The SOM1 gene is transcribed into a 375 bp polyadenylated RNA and the deduced amino acid sequence predicts a small protein of 8.4 kDa with no significant sequence similarity to known proteins. In the som1 deletion mutant, proteolytic processing of the Cox2 precursor is prevented and Cytb2 is strongly reduced. SOM1 represents a new small gene which encodes a novel factor that is essential for the correct function of the Imp1 peptidase and/or the protein sorting machinery.

Amino Acid Sequence↗

PubMed1996

Expression and regulation of the dystrophin Purkinje promoter in human skeletal muscle, heart, and brain.

Dystrophin mRNA transcripts from the P (Purkinje) promoter were shown to be differentially expressed in human skeletal muscle, heart, and brain. The expression pattern was characteristic of tissue type and developmental stage. Polymerase chain reaction (PCR) analysis of the P promoter transcripts in adult skeletal muscle and adult brain identified two alternatively spliced sequences, one that encodes a full-length dystrophin mRNA and a second that transcribes a termination codon 27 nucleotides (8 amino acids) after the ATG initiation site. Alternative splicing of this truncated coding transcript was developmentally regulated, and it was expressed as the major form in adult cortical brain and adult heart. The biological significance of this peptide remains unclear. The full-length transcript was the major form in fetal cortical brain and adult skeletal muscle. Ribonuclease protection assay demonstrated that as much as 20% of dystrophin transcription in normal adult skeletal muscle was derived from the full-length transcript from the P promoter. In contrast, adult heart did not express significant levels of P promoter derived transcripts. Thus, transcripts from the P promoter were found to be developmentally regulated in the brain, and its activity was differentially expressed in skeletal versus cardiac muscle tissues. These data show that the P promoter transcript displays a broader scope of expression, regulation, and complexity than previously appreciated.

Adult↗

PubMed1996

Germinal HPRT splice donor site mutation results in multiple RNA splicing products in T-lymphocyte cultures.

We have used peripheral blood T-lymphocyte cultures to analyze the hprt mutation in two Lesch-Nyhan syndrome males who are cousins and to confirm the carrier status of female members of the family. Both cDNA and genomic DNA sequencing studies show that this patient carries a hitherto undescribed single base deletion in the exon 5 donor splice site sequence (I5: +1, delta G, base number 31635). The largest cDNA product contained all nine hprt exons plus an insertion of 66 bases of intron 5, consistent with the use of a cryptic splice site in intron 5 (aag67/gtaagc). This splicing error would result in a chain terminating codon immediately after exon 5 (I5:2-4, taa) and predicts a polypeptide of 133 amino acids. This loss of the normal splice donor site also results in multiple hprt mRNA species, combining the use of the cryptic splice site in intron 5 and splicing errors involving exons 2-6. In addition to defining a new Lesch-Nyhan mutation (hprtHenryville), these results provide insight into aberrant splicing of hprt mRNA in T-lymphocytes.

Base Sequence↗

PubMed1993

Multiple L1 progenitors in prosimian primates: phylogenetic evidence from ORF1 sequences.

One of the uncertainties regarding the evolution of L1 elements is whether there are numerous progenitor genes. We present phylogenetic evidence from ORF1 sequences of slow loris (Nycticebus coucang) and galago (Galago crassicaudatus) that there were at least two distinct progenitors, active at the same time, in the ancestor of this family of prosimian primates. A maximum parsimony analysis that included representative L1s from human, rabbit, and rodents, along with the prosimian sequences, revealed that one of the galago L1s (Gc11) grouped very strongly with the slow loris sequences. The remaining galago elements formed their own unique and strongly supported clade. An analysis of replacement and silent site changes for each link of the most parsimonious tree indicated that during the descent of the Gc11 sequence approximately two times more synonymous than nonsynonymous substitutions had occurred, implying that the Gc11 founder was functional for some time after the split of galago and slow loris. Strong purifying selection was also evident on the galago branch of the tree. These data indicate that there were two distinct and contemporaneous L1 progenitors in the lorisoid ancestor, evolving under purifying selection, that were retained as functional L1s in the galago lineage (and presumably also in the slow loris). The prosimian ORF1 sequences could be further subdivided into subfamilies. ORF1 sequences from both the galago and slow loris have a premature termination codon near the 3' end, not shared by the other mammalian sequences, that shortens the open reading frame by 288 bp. An analysis of synonymous and nonsynonymous substitutions for the 5' and 3' portions, that included intra- and inter-subfamily comparisons, as well as comparisons among the other mammalian sequences, suggested that this premature stop codon is a prosimian acquisition that has rendered the 3' portion of ORF1 in these primates noncoding.

Animals↗

PubMed1993

Silk moth chorion pseudogenes: hallmarks of genomic evolution by sequence duplication and gene conversion.

The part of the genetic locus of the domesticated silk moth, Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing gene-like sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, psi HcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, psi HcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that psi HcB.15 was generated first from a functional HcB gene and gave rise subsequently to psi HcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversion-mediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction.

Animals↗

PubMed1991

Epitope mapping of two monoclonal antibodies to the central portion of human osteonectin.

In this study preliminary characterization of two monoclonal antibodies against osteonectin was undertaken. One monoclonal originally raised against bovine bone osteonectin cross reacts with human bone and platelet osteonectin. The other monoclonal antibody has been reported to react with osteonectin derived from human bone and bovine bone but not to the same extent with that from platelets. Initial mapping of the antigenic determinants for both monoclonals was done by testing their ability to bind to the expressed forms of osteonectin in two overlapping SaOS-2 lambda gt11 osteonectin cDNA clones. One clone contains a 0.54 kb insert and is comprised of 50 nucleotides of 5' noncoding and a coding segment for a 17 amino acid signal peptide and 146 amino acids of the N-terminal region of the mature protein. The other clone has a 1.9 kb insert, and includes amino acid no. 18 to the C-terminus of the molecule (amino acid no. 286), a single termination codon, and 1115 nucleotides of 3' noncoding sequence. Both monoclonals recognized expressed osteonectin from the two lambda gt11 SaOS-2 cDNA clones. These results localize the epitope to a region between amino acids 18-146 of osteonectin.

Amino Acid Sequence↗

PubMed1997

Mucopolysaccharidosis IVA: a novel splice acceptor site mutation in intron 4 of the N-acetylgalactosamine-6-sulfate sulfatase gene in an Afghanistan girl with classical Morquio disease.

We report here a novel splice site mutation in intron 4 of the gene for N-acetylgalactosamine-6-sulfate sulfatase (GALNS) in an Afghanistan girl with severe mucopolysaccharidosis IVA (classical Morquio disease). Direct sequencing revealed a homozygous G to A transition in the conserved splice acceptor site in intron 4 (cagG-->caaG: designated IVS 4(-I) G-->A) which eliminates 144 nucleotides of exon 5 in her GALNS transcript and introduces an immediate premature termination codon (at Trp 141 of exon 4). The IVS 4(-1) G-->A has not been seen in other populations and this is the first report of the molecular basis of classical Morquio disease in an Afghanistan patient.

Afghanistan↗

PubMed2000

The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization.

We present an overview of the gene content and organization of the mitochondrial genome of Dictyostelium discoideum. The mitochondria genome consists of 55,564 bp with an A + T content of 72.6%. The identified genes include those for two ribosomal RNAs (rn1 and rns), 18 tRNAs, ten subunits of the NADH dehydrogenase complex (nad1, 2, 3, 4, 4L, 5, 6, 7, 9 and 11), apocytochrome b (cytb), three subunits of the cytochrome oxidase (cox1/2 and 3), four subunits of the ATP synthase complex (atp1, 6, 8 and 9), 15 ribosomal proteins, and five other ORFs, excluding intronic ORFs. Notable features of D. discoideum mtDNA include the following. (1) All genes are encoded on the same strand of the DNA and a universal genetic code is used. (2) The cox1 gene has no termination codon and is fused to the downstream cox2 gene. The 13 genes for ribosomal proteins and four ORF genes form a cluster 15.4 kb long with several gene overlaps. (3) The number of tRNAs encoded in the genome is not sufficient to support the synthesis of mitochondrial protein. (4) In total, five group I introns reside in rnl and cox1/2, and three of those in cox1/2 contain four free-standing ORFs. We compare the genome to other sequenced mitochondrial genomes, particularly that of Acanthamoeba castellanii.

Animals↗

PubMed2004

Two point mutations identified in emmer wheat generate null Wx-A1 alleles.

In this report, the Wx-A1 mutations carried by a Triticum dicoccoides line from Israel and a Triticum dicoccum line from Yugoslavia are characterized. A single nucleotide insertion in the T. dicoccoides null allele and a single nucleotide deletion in the T. dicoccum null allele each cause frameshift mutations that induce premature termination codons more than 55 nucleotides upstream of the last exon-exon junction. In both mutants, Wx-A1 transcripts were detectable in 10 day post-anthesis endosperm by relative RT-PCR. However, transcript levels of the T. dicoccoides and T. dicoccum null alleles were reduced to approximately 6.5 and 1.5% of wild-type, respectively. Therefore, the lack of Wx-A1 protein in the mutants appears to be largely due to nonsense-mediated mRNA decay. The two mutations described here arose independently, and are not related to either of the Wx-A1 mutations identified in common wheat.

Alleles↗

PubMed2000

Multiple lineages of the mitochondrial gene NADH dehydrogenase subunit 1 (ND1) in parasitic helminths: implications for molecular evolutionary studies of facultatively anaerobic eukaryotes.

The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed in parasitic helminths and possibly also in other anaerobically adapted eukaryotes.

Animals↗

PubMed2005

Common silent mutations in all types of hereditary complement C1q deficiencies.

Hereditary complete deficiency of complement component C1q is a rare genetic disorder that is associated with severe recurrent infections and a high prevalence of lupus-erythematosus-like symptoms. In the past, several single nucleotide polymorphisms have been identified in all three genes coding for the C1q A, B, and C chains. These point mutations which either lead to termination codons, frameshift, or amino acid exchanges were thought to be responsible for these defects as no other nonsense or missense mutations were found. As a result of the aberrations, either a nonfunctional C1q antigen is present or no C1q protein is detectable in the patients' sera. Screening 46 individuals from seven families with different forms of C1q deficiencies identified a homologous silent mutation at position Gly70 (GGG > GGA) of the C1q A gene of all 11 C1q-deficient patients. A high number of family members that were heterozygous for the coding mutations carried the silent mutation in the homozygous (18%) or heterozygous (36%) state. In addition to the Gly70 mutation in the A gene, another homozygous silent mutation (C gene at position Pro14, CCT >CCC) was detected in all C1q-deficient patients.

Complement C1q↗

PubMed2001

Functional analysis of 5' and 3' regions of the closely related Ly49c and j genes.

The Ly49 multigene family consists of at least 14 closely related genes located in the natural killer (NK) gene complex on mouse Chromosome 6. Reverse transcriptase (RT)-PCR on single NK cells has shown that Ly49c is expressed on approximately 50% of NK cells, whereas the closely related Ly49j gene is expressed on 5-8% of NK cells. In this study, we examined three regions to determine whether they contain cis-acting elements involved in regulating the expression of these two closely related Ly49 genes within NK cells. Luciferase reporter assays in EL-4 cells suggested that the 5' regions of Ly49c and j contain promoter elements and repressor sequences. In addition, luciferase assays suggest that Ly49j also contains an active promoter in the first intron, although the transcripts produced from this promoter appear to be severely truncated. Finally, comparisons of the 3' noncoding regions of Ly49c and j revealed that the sequence of Ly49j diverges completely from Ly49c 130 bp downstream of the termination codon. The polyadenylation signal for Ly49j is located downstream of the Ly49c poly(A) site, which results in a much longer 3' untranslated region (UTR). When the Ly49j 3'UTR was used to provide the polyadenylation signal for the green fluorescent protein (GFP) reporter gene, GFP expression was reduced twofold. These results suggest that both internal promoters, repressors, and 3' regions play a role in regulating Ly49 gene expression.

3' Untranslated Regions↗

PubMed1997

Allelic variants of the human MHC class I chain-related B gene (MICB).

The human major histocompatibility complex (MHC) is located within a 4 megabase segment on chromosome 6p21.3. Recently, a highly divergent MHC class I chain-related gene family, MIC was identified within the class I region. The MICA and MICB genes in this family have unique patterns of tissue expression. The MICA gene is highly polymorphic, with more than 20 alleles identified to date. To elucidate the extent of MICB allelic variations, we sequenced exons 2 (alpha 1), 3 (alpha 2), 4 (alpha 3), and 5 (transmembrane) as well as introns 2 and 4 of this gene in 46 HLA homozygous B-cell lines. We report the identification of eleven alleles based on seven non-synonymous, two synonymous, and four intronic nucleotide variations. Interestingly, one allele has a nonsense mutation resulting in a premature termination codon in the alpha 2 domain. Thus, MICB appears to have fewer alleles than MICA, not unlike the allelic ratio between the HLA-C and -B loci. A preliminary linkage analysis of the MICB alleles with those of the closely located MICA and HLA-B genes revealed no conspicuous linkage disequilibrium between them, implying the presence of a potential recombination hotspot between the MICB and MICA genes.

Alleles↗

PubMed2002

Molecular cloning and phylogenetic analysis of new human endogenous retrovirus HERV-W family in cancer cells.

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences. By using the PCR approach with human genomic DNA derived from cancer cell lines (HepG2, Jurkat, MCF7, UO-31), five env fragments of HERV-W family were newly identified and analyzed. They showed a high degree of nucleotide sequence similarity (94-99%) with that of the HERV-W. Translation of the env fragments showed no frameshift and termination codon by deletion/insertion or point mutation in clones HepG2-1 and JUR-3. The ratio of synonymous to non-synonymous substitutions indicated that negative selective pressure is acting on HepG2-1 and JUR-3 sequences. These env gene sequences could be associated with an active provirus in human cancer cells (HepG2 and Jurkat). The HepG2-1 and JUR-3 showed sister relationship with the HERV-W and W-7-1 derived from human Chromosome (Chr) 7. Phylogenetic analysis from the HERV-W family indicated close relationships of the env gene sequences across human chromosomes.

Amino Acid Substitution↗

PubMed2006

Regulation of the beta-hydroxyacyl ACP dehydratase gene of Picea mariana by alternative splicing.

The gene for beta-hydroxyacyl ACP dehydratase, a de novo fatty acid biosynthetic enzyme, was cloned from Picea mariana (black spruce) and consists of five exons and four introns. The first intron of the beta-hydroxyacyl ACP dehydratase mRNA is alternatively spliced. Retention of intron 1 in splice variants results in truncation of the beta-hydroxyacyl ACP dehydratase ORF at a premature termination codon. In addition, splicing of intron 1 was found to be associated with cold temperature. mRNAs retaining intron 1 increase with seed imbibition at 22 degrees C but not 4 degrees C, whereas, splicing of intron 1 increases in winter weeks with temperatures below freezing. These results provide evidence that alternative splicing may also contribute to regulation of lipid biosynthesis in Picea mariana.

Alternative Splicing↗

PubMed2003

Effects of spontaneous KitlSteel mutations on survival and red blood cells of mice.

Kit ligand (Kitl), which is a member of the helical cytokine superfamily, is encoded by the Steel (Sl) locus of mice and is essential for the development of hematopoietic cells, germ cells, and melanocytes. A large series of Kitl(Sl) alleles has been described, including some that arose spontaneously and others that were induced by either chemical or radiation mutagenesis. Here we describe the nucleotide sequence alterations in two spontaneous Kitl(Sl) alleles. The Kitl(Sl-18R) allele has a point mutation that introduces a premature termination codon, and the encoded protein is expected to be null functionally. The Kitl(Sl-5R) allele has an in-frame deletion that results in deletion of amino acids at position 31 and 32 of Kitl. While both mutations exert severe effects on blood cells and survival of homozygous mice, these effects are slightly milder than those of a previously characterized spontaneous deletion allele, Kitl(Sl-gb). Examination of the survival of compound heterozygotes provided strong genetic evidence that the Kitl(Sl-18R) and Kitl(Sl-5R) mutants are null functionally for mouse survival.

Animals↗

PubMed2006

Deficiency of the tensin2 gene in the ICGN mouse: an animal model for congenital nephrotic syndrome.

The ICGN mouse is a model for nephrotic syndrome (NS) which presents with proteinuria, hyperlipidemia, and edema. In this study we attempted to identify the gene(s) responsible for NS. By analyzing albuminuria in 160 (ICGN x MSM)F(1) x ICGN backcross progenies, we found that NS in the ICGN mouse is caused by more than one gene. We then performed a quantitative trait locus (QTL) analysis and detected a QTL with a very high LOD score peak in the telomeric region of Chr 15. By analyzing the nucleotide sequence of 22 genes located close to the QTL, we found that the tensin2 gene of the ICGN mouse possessed an 8-nucleotide deletion mutation in exon 18, leading to a frameshift and giving rise to a terminal codon at a premature position. Analyses of in situ hybridization and immunohistochemistry revealed that tensin2 was expressed in podocytes and tubular epithelial cells in normal mice but not in the ICGN mouse. These data raise the possibility that a mutation of the tensin2 gene is responsible for NS of the ICGN mouse and tensin2 is a prerequisite for the normal kidney function.

Albuminuria↗