Showing papers on "Exon published in 1982"

Making ends meet: a model for RNA splicing in fungal mitochondria

Abstract: On the basis of available nucleotide sequence and genetic data, we present a model for RNA splicing in fungal mitochondria. Seven intron RNAs of two fungal species can form identical secondary structures, involving four conserved sequences, which bring the ends of each intron together and allow an internal guide RNA sequence to pair with exon bases adjacent to the splice junctions. The splicing sites are thus aligned precisely within a conserved structure, which we suggest could present specific recognition signals to the proteins that catalyse the splicing reaction.

The Human Growth Hormone Gene Family: Nucleotide Sequences Show Recent Divergence and Predict a New Polypeptide Hormone

Abstract: The nucleotide sequences of three nonallelic human genomic DNA fragments which each contain one member of the growth hormone gene family are presented. These genes code for the known polypeptide hormones, growth hormone (hGH), chorionic somatomammotropin (hCS), and a yet unknown protein which differs from hGH in 13 positions. Each gene is structured into five exons, the four introns occurring at identical positions. Reflecting recent gene divergence, 90-95% sequence homology is seen in exons, introns, 5′, and immediate 3′ nontranscribed regions. The regions downstream of the polyadenylation sites in the genes for hGH and its variant, but not for hCS, contain members of an Alu family repeat sequence.

Isolation and characterization of c-myc, a cellular homolog of the oncogene (v-myc) of avian myelocytomatosis virus strain 29.

Abstract: The chicken genome contains nucleotide sequences homologous to transforming genes (oncogenes) of a number of avian retroviruses. We have isolated chicken DNA (c-myc) that is homologous to the oncogene (v-myc) of the avian myelocytomatosis virus MC29 and have compared the structures of the cellular and viral genes. Results from restriction endonuclease mapping of c-myc and from analysis of heteroduplexes between the DNAs of the cellular and viral genes show that c-myc is homologous to 1,500 nucleotides in v-myc DNA. This homologous region is interrupted in c-myc by an intron-like sequence of 1,100 nucleotides which is absent from v-myc. Nuclear RNA from normal chicken cells contains at least five species of transcripts from c-myc ranging from 2.5 to 6.5 kilobases in length. By contrast, cytoplasm contains only the 2.5-kilobase c-myc RNA. These features of the c-myc gene and its nuclear transcripts are characteristic of normal cellular genes and suggest that the myc gene is of cellular rather than viral origin. The exons in c-myc may define two functional domains in the gene and may therefore facilitate the dissection of the different oncogenic potentials of the MC29 virus.

Abnormal RNA processing due to the exon mutation of beta E-globin gene.

Abstract: As is typical of all beta-thalassaemias, the erythroid cells of individuals with the variant haemoglobin E (alpha 2 beta 2(26Glu leads to Lys)) exhibit a quantitative deficiency in their content of beta-globin (in this case beta E-globin) and its messenger RNA2,3. To determine the molecular basis of this phenotype, we have investigated the structure and expression of cloned beta E-globin genes. We report here that the complete nucleotide sequence of a beta E-gene revealed the expected GAG leads to AAG change in codon 26 but no other mutations. Expression of beta E-globin genes introduced into HeLa cells revealed two abnormalities of RNA processing: slow excision of intervening sequence-1 (IVS-1) and alternative splicing into exon-1 at a cryptic donor sequence within which the codon 26 nucleotide substitution resides. These results demonstrate a disturbance in the expression of the beta E-gene attributable solely to the exon mutation-a novel mechanism for gene dysfunction.

Exon/intron organization and complete nucleotide sequence of an HLA gene

Abstract: We have isolated and determined the sequence of a genomic clone containing the gene for a human class I transplantation antigen. The gene contains seven exons. The first five exons code respectively for a signal peptide, for the first, second, and third extracellular domains of the protein molecule, and for the transmembrane region. The cytoplasmic segment is encoded by part of the fifth and the sixth and the seventh exons. The structure of the protein encoded by this unit is closely homologous with known class I transplantation antigens.

The nucleotide sequence, expression, and evolution of one member of a multigene family encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean.

Abstract: We have examined the nuclear genes encoding the small subunit of ribulose-1,5-bisphosphate (RuBP) carboxylase from soybean. One member of this gene family, designated SRS1, has been isolated from a soybean DNA library constructed in the lambda vector Charon 4A. The complete nucleotide sequence and structure of this gene including its two introns and portions of the 5' and 3' flanking sequences were determined. The first exon encodes the entire transit peptide (55 amino acids) and the first 2 amino acids of the mature sequence. Based on analysis of the nucleotide sequence, we concluded that the precursor of the soybean small subunit consists of 178 amino acids. A gene-specific probe for SRS1 was used to show that this gene is transcribed and that steady-state levels of its transcript are strongly light regulated. S1 nuclease mapping was used to locate the potential start of transcription in the sequence and showed that the small subunit gene contains a cap site, TATA box, and -80 sequence, which match the consensus animal sequences. The mature SRS1 small subunit polypeptide of 123 amino acids contains 30 and 34 amino acid replacements relative to the previously determined amino acid sequences from pea and spinach, respectively. Southern blotting of restriction digests of soybean nuclear DNA and data on the complete structure of SRS1 suggest that a multigene family of at least 10 members encodes the RuBP carboxylase small subunit in soybean. Quantitative evolutionary comparison of the soybean small subunit sequence for SRS1 and the pea small subunit sequence suggests that these two genes diverged long before the divergence of pea and soybean.

DNA sequence of a gene encoding a BALB/c mouse Ld transplantation antigen

Abstract: The sequence of a gene, denoted 27.5, encoding a transplantation antigen for the BALB/c mouse has been determined. Gene transfer studies and comparison of the translated sequence with the partial amino acid sequence of the Ld transplantation antigen establish that gene 27.5 encodes an Ld polypeptide. A comparison of the gene 27.5 sequence with several complementary DNA sequences suggests that the BALB/c mouse may contain a number of closely related L-like genes. Gene 27.5 has eight exons that correlate with the structural domains of the transplantation antigen.

The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family.

Abstract: The nucleotide sequence of the chick a-actin gene reveals that the gene is comprised of 7 exons separated by six very short intervening sequences (IVS). The first IVS interrupts the 73 nucleotide 5' untranslated segment between nucleotides 61 and 62. The remaining IVS interrupt the translated region at codons 41/42, 150, 204, 267, and 327/328. The 272 nucleotide 3' untranslated segment is not interrupted by IVS. The amino acid sequence derived from the nucleotide sequence is identical to the published sequence for chick a-actin except for the presence of a met-cys dipeptide at the amino-terminus. The IVS positions in the chick a-actin gene are identical to those of the rat a-actin gene. While there is partial coincidence of the IVS in the a-actin genes with the vertebrate b-actin genes and 2 sea urchin actin genes, there is no coincidence with actin genes from any other source except soybean where one IVS position is shared. This discordance in IVS positions makes the actin gene family unique among the eucaryotic genes analyzed to date.

Structural analysis of the prolactin gene suggests a separate origin for its 5' end.

Abstract: Prolactin, growth hormone (GH) and placental lactogen constitute a family of polypeptide hormones which share certain structural1–7 and functional8 features. The prolactin and GH genes evolved from a gene duplication about 400 million years ago9 and, in humans, segregated onto chromosomes 6 and 17 respectively10,11. We expand here previous reports12,13 on the general organization of the rat prolactin gene, rPRL, assign its haploid gene number and extend its DNA sequence analysis. We postulate that a direct repeat flanking exon I may be the remnant of an insertional event.

Structure of genes for membrane and secreted murine IgD heavy chains

Abstract: We have sequenced secreted and membrane terminal exons of the murine immunoglobulin δ chain. The putative transmembranal exon is strikingly similar to that of the μ chain and the internal cytoplasmic exon codes for exactly the same two amino acids, valine and lysine. A third potential exon was found between S and M exons that could code for yet another hydrophilic carboxyl terminus termed δX.

Intron-exon splice junctions map at protein surfaces.

Abstract: There have been several suggested explanations for the presence of noncoding intervening sequences in many eukaryotic structural genes. They may be examples of ‘selfish DNA’1,2, conferring little phenotypic advantage, or they may have some importance in gene expression and/or evolution. It has been suggested that each exon (coding sequence) may represent a structural or functional unit of the encoded protein3,4, for which there is good evidence in the case of immunoglobulin7 and haemoglobin8,9 genes. Exon modification, duplication and recombination may thus be general mechanisms for the rapid evolution of eukaryotic structural genes. In many cases, however, it is not apparent that an exon corresponds to some specific feature of the encoded protein10,11. We describe here evidence that intron–exon junctions usually map to amino acid residues located at the protein surface, suggesting a restriction on the permitted positions of introns within a gene.

Molecular structure and evolutionary origin of human cardiac muscle actin gene.

Abstract: Two recombinant phages that contain cardiac muscle actin gene were isolated from a human DNA library and their structures were determined. Restriction analysis indicates that both clones carry the same EcoRI 13-kilobase fragment where the coding sequence is mapped. The cloned DNA hybridized with polyadenylylated RNA from human fibroblasts, which directs the synthesis of cytoplasmic beta- and gamma-actin in vitro. However, sequence determination of the cloned DNA showed that the entire coding sequence perfectly matched the amino acid sequence of cardiac muscle actin. The initiation codon is followed by a cysteine codon that is not found at the amino-terminal site of any actin isoform, suggesting the necessity of post-translational processing for in vivo actin synthesis. There are five introns interrupting exons at codons 41/42, 150, 204, 267, and 327/328. Surprisingly, these intron locations are exactly the same as those of the rat skeletal muscle actin gene but different from those of nonmuscle beta-actin gene. Nucleotide sequences of all exon/intron boundaries agree with the G-T/A-G rule (G-T at the 5' and A-G at the 3' termini of each intron). The 3'-untranslated sequence has no homology to that of nonmuscle beta- or gamma-actin gene, but Southern blot hybridization has shown that this region has considerable homology to that of one of the other actin genes. These results indicate that the recombinant phages, which we have isolated, contain cardiac muscle actin gene and that cardiac muscle actin gene and skeletal muscle actin genes are derived from their ancestor gene at a relatively recent time in evolutionary development.

Sequence of an HLA-DR alpha-chain cDNA clone and intron-exon organization of the corresponding gene.

Abstract: The HLA–DR and related antigens are the major cell-surface glycoproteins identified so far as involved in regulation of the immune response in humans1. Here we present and discuss the sequence of cloned cDNA copies of the mRNA for the HLA–DR α-chain2. The sequence is 1,195 nucleotides long, with one open reading frame encoding a 254 amino acid primary translation product. After cleavage of the signal sequence this yields a mature polypeptide of 229 residues. Four introns have been located within the corresponding genomic sequence revealing a correlation between the protein domain structure and the genomic exon organization. Analysis of the HLA–DR α-chain amino acid sequence shows a clear homology with HLA–ABC, β2-microglobulin and immunoglobulin domains.

The amino acid sequence and gene organization of the heavy chain of the HLA-DR antigen: homology to immunoglobulins

Abstract: The amino acid sequence of the heavy chain of HLA-DR antigens has been elucidated from the analysis of a genomic clone coding for this protein A 32-kilobase EcoRI fragment includes four exons containing 227 amino acids out of 229 in the mature HLA-DR heavy chain One exon (alpha 2) encodes a domain of 94 amino acids with strong sequence homology both to Ig constant region domains and to Ig-like domains in HLA-B7, beta 2-microglobulin, and the HLA-DR light chain These results support a structure for the HLA-DR antigen heterodimer consisting of four extracellular domains, two of which are Ig-like [one in the heavy chain (alpha 2) and one in the light chain (beta 2)] The third is the amino-terminal polymorphic domain in the light chain (beta 1), and the fourth is an invariant domain in the heavy chain (alpha 1)

Calcitonin mRNA polymorphism: peptide switching associated with alternative RNA splicing events.

Abstract: Evidence is presented which supports a model proposing that differential RNA splicing events may be used in expression of genes of the endocrine system to generate alternative polypeptide hormones. We previously reported that variation in the expression of the gene encoding the small polypeptide hormone calcitonin is associated with the production of a new calcitonin-like or pseudo-calcitonin (psi Cal) mRNA. A plasmid containing psi Cal cDNA sequences has been constructed, and calcitonin genomic clones have been isolated. Hybridization analysis reveals that calcitonin and psi Cal sequences are chromosomally linked and are present in the same nuclear RNA transcripts. Both calcitonin and psi Cal mRNAs are functional and encode different polypeptide products. These data are compatible with the proposed model that alternative RNA splicing of the transcript(s) of the calcitonin gene ultimately results in the production of different polypeptide products.

Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes

Abstract: We have attempted to ascertain the correlation between the genetic information content in the exons and the surrounding intron sequences with regard to their spatial arrangement within a gene. A comparison is made of the sizes, taken from recent publications, of exons and introns of approximately equal to 80 different protein-coding chromosomal genes, mostly from higher eukaryotes. The exons of these genes do not show very marked variation in size and can be classified into three major discrete and two minor additional size groups, whereas individual introns vary considerably in size within and between genes. Notwithstanding, the overall length of all introns present within a given gene is a function of the total size, mostly corresponding to the total genetic information content, of the exons. Three cases that violate this exon-size dependency of introns are genes coding for (i) histone H1, feather keratin, and interferons, (ii) tubulin and actin, and (iii) silk fibroin. The exons of these genes are larger than 0.7 kilobase pair in total size and the genes show a strong sequence homogeneity among the repetitious family members or internal repeats of coding sequences within the gene. We propose that conservation of sequences, which is required by the family members, internal repeats, or the entire gene, would actually motivate the removal of introns.

The nucleotide sequence of the mouse immunoglobulin epsilon gene: comparison with the human epsilon gene sequence.

Abstract: We have determined the nucleotide sequence of the immunoglobulin epsilon gene cloned from newborn mouse DNA. The epsilon gene sequence allows prediction of the amino acid sequence of the constant region of the epsilon chain and comparison of it with sequences of the human epsilon and other mouse immunoglobulin genes. The epsilon gene was shown to be under the weakest selection pressure at the protein level among the immunoglobulin genes although the divergence at the synonymous position is similar. Our results suggest that the epsilon gene may be dispensable, which is in accord with the fact that IgE has only obscure roles in the immune defense system but has an undesirable role as a mediator of hypersensitivity. The sequence data suggest that the human and murine epsilon genes were derived from different ancestors duplicated a long time ago. The amino acid sequence of the epsilon chain is more homologous to those of the gamma chains than the other mouse heavy chains. Two membrane exons, separated by an 80-base intron, were identified 1.7 kb 3' to the CH4 domain of the epsilon gene and shown to conserve a hydrophobic portion similar to those of other heavy chain genes. RNA blot hybridization showed that the epsilon membrane exons are transcribed into two species of mRNA in an IgE hybridoma.

Deletions in immunoglobulin mu chains.

Abstract: Eight mutant hybridoma lines are described, which synthesize short immunoglobulin mu chains. Four internal deletions were mapped by Southern blot analysis. They are shown to remove DNA from either part or all of the first, and first and second, constant mu exons. The sizes of the deletions range between 0.6 and 5 kb, leaving an equal or unequal number of splice signals. Shorter mu RNA of one size was found irrespective of whether an exon was completely or only partially deleted. These results preclude exclusive 3' (constant region) to 5' (variable region) directional splicing of the mu RNA. No important signals seem to reside in the deleted DNA stretches affecting the transcription or the correct RNA splicing of the remaining exons. The internal mu protein deletions revealed unusual covalent light chain attachment demonstrating functional homology between the first (normally used) and fourth mu constant domain. The other mu protein deletions (10, 11, and 12 kd) involved neither gross DNA nor RNA lesions and are considered to be due to premature chain termination. Since secretion is found in most of the mutant IgM-producing lines, no single one of the four mu constant domains (including the C-terminal one which contains the so-called secretory piece) is necessary for secretion.

Internal structure of a mitochondrial intron of Aspergillus nidulans

Abstract: The intron of the mitochondrial apocytochrome b gene, cobA, of Aspergillus nidulans has been subjected to sequence analysis. It contains an open reading frame of 957 base pairs contiguous with the preceding exon. Regions of the translated open reading frames of cobA and the third intron of the cob gene in yeast show high amino acid homology. Comparison of the cobA intron with this and other yeast introns indicates that cobA codes for a maturase protein that splices out the intron encoding it and possibly other mitochondrial introns. Two very similar decamer peptides are found in the protein sequences of the cobA intron, four mitochondrial yeast introns, and the yeast mitochondrial sequence reading frame 1 (RF-1) and may be diagnostic of one class of maturase-coding introns. Four short DNA sequences, two of which are in the region defined by box9 and box2 mutations in the cob gene of yeast, are conserved in cobA and certain yeast introns. Comparison with three yeast introns strongly suggests that the first 200 base pairs of the open reading frame of the cobA intron do not code for any amino acids present in the putative maturase protein but are required for splicing or the control of splicing, or both.

Molecular cloning of two distinct renin genes from the DBA/2 mouse.

Abstract: We report the molecular cloning of cDNA copies of DBA/2 mouse submaxillary gland (SMG) renin mRNA, which were used to probe Southern transfers of mouse genomic DNA. The results suggested either that there is a single renin gene containing a large intron in that part of the gene corresponding to the probe, or that there are two distinct renin genes. We have shown that the latter is the case by cloning and isolating two similar but distinct renin genes from DBA/2 mouse DNA. Restriction maps of the regions containing the two renin genes are presented, together with nucleotide sequence data locating a complete exon coding for amino acids 268-315 of mouse SMG renin.

DNA sequence of the gene encoding the E alpha Ia polypeptide of the BALB/c mouse

Abstract: A 3.4-kilobase DNA fragment containing the gene coding for the E alpha chain of an Ia (I region-associated) antigen from the BALB/c mouse has been sequenced. It contains at least three exons, which correlate with the major structural domains of the E alpha chain-the two external domains alpha 1 and alpha 2, and the transmembrane-cytoplasmic domain. The coding sequence of the mouse E alpha gene shows striking homology to its counterpart at the DNA and protein levels. The translated alpha 2 exon demonstrates significant similarity to beta 2-microglobulin, to immunoglobulin constant region domains, and to certain domains of transplantation antigens. These observations and those of others suggest that the Ia antigen, transplantation antigen, and immunoglobulin gene families share a common ancestor.