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PubMed1996

Cloning and sequencing of cDNAs encoding ribonucleotide reductase from zebrafish Danio rerio.

We have cloned and sequenced cDNAs coding for the R1 and R2 proteins of ribonucleotide reductase from zebrafish (Danio rerio). This ribonucleotide reductase shows high amino acid sequence identity to those of other vertebrates. The R1 cDNA has a coding sequence of 2382 bp, yielding a 794 amino acid protein, and the R2 cDNA has a coding sequence of 1158 bp, yielding a 386 amino acid protein. The zebrafish R1 shows 94% similarity and R2 shows 91% similarity to the human R1 and R2, respectively. The similarity extends to intron positions, of which the equivalent of mouse R2 intron 3 has been studied.

Amino Acid Sequence↗
PubMed2002

On biased distribution of introns in various eukaryotes.

We conducted comprehensive analyses on intron positions in the Mus musculus genome by comparing genomic sequences in the GenBank database and cDNA sequences in the mouse cDNA library recently developed by Riken Genomic Sciences Center. Our results confirm that introns have a tendency to be located toward the 5' end of the gene. The same type of analysis was conducted in the coding region of seven eukaryotes (Saccharomyces cerevisiae, Plasmodium falciparum, Caenorhabditis elegans, Drosophila melanogaster, M. musculus, Homo sapiens, Arabidopsis thaliana). Introns in genes with a single intron have a locational bias toward the 5' end in all species except A. thaliana. We also measured the distance from the start codon to the position of the intron, and found that single introns prefer the location immediately after the start codon in S. cerevisiae and P. falciparum. We discuss three possible explanations for these findings: (1) they are the consequence of intron loss by reverse-transcriptase; (2) they are necessary to accommodate the function; and (3) they are concerned with the mechanism of pre-mRNA splicing.

Animals↗
PubMed1997

Intron distribution in ancient paralogs supports random insertion and not random loss.

The intron positions of ten different protein families were examined to determine (the statistical likelihood of) whether spliceosomal introns are the result of random insertion events into previously intronless genes, on the one hand, or the result of random loss from common ancestral introns, on the other. The number of expected matches for the alternative scenarios was calculated for a binomial distribution by considering currently observed introns relative to all possible locations for insertion or loss. Introns occurring at approximately the same location (hereafter called a "match") were tallied for each of the paired proteins. Matches were identified by their positions in the multiple alignment and were defined as any two introns occurring within a window of 11 possible nucleotide positions, thereby allowing for possible alignment errors and "intron sliding." Matches were tallied from the raw data and compared with the expected number of matches for the two different scenarios. The results suggest that the distribution of introns in genes encoding proteins is due to random insertion and not random loss.

Animals↗
PubMed1984

Characterization of bovine keratin genes: similarities of exon patterns in genes coding for different keratins.

Four different genomic clones which contain the genes coding for epidermal keratins Ia (mol. wt. approximately 68 000), Ib (68 000), III (60 000) and VIb (54 500) have been selected using cDNA probes and identified by hybrid-selection translation. The genes vary considerably in length, primarily due to differences in intron sizes: keratin Ia, 9.3 kb (approximately 2.55 kb total exons); keratin Ib, 6.0 kb (2.25 kb exons); keratin III, 6.0 kb (2.2 kb exons); keratin VIb, 4.4 kb (1.85 kb exons). The genes for all three representatives of the basic (type II) cytokeratin subfamily, i.e., keratins Ia, Ib and III, contain eight introns of variable sizes (0.1-1.8 kb) and their exon patterns are very similar. The gene coding for keratin VIb, a representative of the acidic (type I) subfamily, contains seven introns, and the size pattern of its five innermost exons closely resembles that of the genes of the type II keratins. Most of the introns are located in regions coding for the alpha-helical cores of these proteins. Mapping of the intron positions by the S1 nuclease technique and sequencing of some exon-intron boundaries has revealed that some of the introns of all four keratin genes have similar positions to each other and to those of the hamster vimentin gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14.

The protocadherins are a subfamily of the calcium-dependent cell-cell adhesion and recognition proteins of the cadherin superfamily. In this study we describe the isolation and characterization of two novel protocadherins, PCDH8 and PCDH9, that constitute a new linkage group on human chromosome 13 and mouse chromosome 14. Like other protocadherins both genes are predominantly expressed in brain, but PCDH9 is also expressed in a broader variety of tissues, and the expression patterns appear to be developmentally regulated. We have determined the genomic organization of PCDH8, which differs significantly from that of the other cadherin subfamilies. In contrast to the classical and desmosomal cadherins, which in general consist of 15-17 exons and share a remarkable degree of conservation in intron position, PCDH8 consists of only three exons and lacks introns in the extracellular domain. The first exon encodes the extracellular domain, the transmembrane region, and part of the cytoplasmic tail. The second exon encodes the remainder of the cytoplasmic region and is partially untranslated. The differences in the genomic structure of cadherin subfamilies will be discussed in the context of the evolution of the cadherin superfamily.

Amino Acid Sequence↗
PubMed1997

The correlation between introns and the three-dimensional structure of proteins.

We test the hypothesis that introns were used to construct the first genes from small exons, whose protein products represent compact elements of structure. For any three-dimensional structure, a computer program analyzes the structure into a set of modules, segments of the polypeptide chain bounded in space by a maximum diameter, separated by a set of 'boundary regions'. The 'boundary regions' are such that if the gene were divided by an intron in each 'boundary region', the protein would be divided into modules less than the specified diameter. Using a set of 32 ancient proteins, which have no introns in prokaryotes, we examine the intron positions in their eukaryotic homologs and show that the introns are correlated with modules of diameter 21, 28 and 33 A, with P values below 0.001.

Exons↗
PubMed1993

Dinucleotides and G+C content in human genes: opposite behavior of GpG, GpC, and TpC at II-III codon positions and in introns.

We have studied the behavior of the dinucleotide preferences under G+C content variation in human genes. The doublet preferences for each dinucleotide were compared between two functionally distinct zones in genes, the II-III codon positions, and the introns. The 16 dinucleotides have been tentatively classified in three groups: AA, AC, CC, CT, and GA, doublets showing no difference between introns and II-III codon positions in the full range of G+C variation TG and TA, which differ in the full range of G+C variation AT, AG, GT, TC, TT, GG, GC, CG, and CA, which show differences in regions over 50% G+C A remarkable pattern observed concerns the behavior of GG, GC, and TC, which showed opposite trends in II-III codon positions and in introns. If codon positions and introns are under the same structural requirements and the same mutational bias, our results indicate that the differences observed could be related to post-transcriptional constraints acting on mRNA.

Base Composition↗
PubMed1990

Structure, exon pattern, and chromosome mapping of the gene for cytosolic copper-zinc superoxide dismutase (sod-1) from Neurospora crassa.

A 4.8-kilobase BamHI-HindIII fragment encoding the entire Neurospora crassa CuZn superoxide dismutase gene (herein designated sod-1) was isolated from a genomic library using two 60-base deoxyoligonucleotide probes corresponding to the published N. crassa amino acid sequence. The nucleotide sequence of the gene encodes an amino acid sequence matching the published protein sequence at 152 of 153 positions. Codon preference shows an unusually strong bias such that only 32 of the possible 61 codons are used, with no codons ending in A. Codon usage is that of highly expressed N. crassa genes. The gene contains three introns, none of which corresponds to any of the introns previously identified in the human gene. Analysis of the intron positions provides support for the hypothesis that CuZn superoxide dismutases evolved by gene duplication and fusion followed by the addition of exons encoding an N-terminal beta-hairpin and a zinc-binding subdomain. The N. crassa gene has an intron mapping to amino acid residue 114 in a sequence-conserved region of the protein whereas the human gene has an intron mapping to a similar but not identical position at residue 118. The discordant position of these introns suggests that one of them was inserted relatively recently. The first N. crassa intron contains a sequence that is similar to the transcriptional regulatory site, UAS1, of the yeast CYC1 (iso-1-cytochrome c) gene and to a putative UAS from the yeast manganese superoxide dismutase gene. A 10-nucleotide portion of this region also matches exactly a sequence in intron 2 of the con-10 gene of N. crassa. sod-1 was mapped to the left arm of chromosome I by following the segregation of a restriction fragment length polymorphism in a sexual cross. Although results indicate that there is a single gene for cytosolic CuZn superoxide dismutase, two additional, perhaps distantly related, sequences were identified that hybridized weakly to both oligonucleotide probes.

Amino Acid Sequence↗
PubMed2006

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

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

Alternative Splicing↗
PubMed1988

Sequence and structure of the mouse gene coding for the largest neurofilament subunit.

We have determined the complete nucleotide sequence of the mouse gene encoding the neurofilament NF-H protein. The C-terminal domain of NF-H is very rich in charged amino acids (aa) and contains a 3-aa sequence, Lys-Ser-Pro, that is repeated 51 times within a stretch of 368 aa. The location of this serine-rich repeat in the phosphorylated domain of NF-H indicates that it represents the major protein kinase recognition site. The nfh gene shares two common intron positions with the nfl and nfm genes, but has an additional intron that occurs at a location equivalent to one of the introns in non-neuronal intermediate filament-coding genes. This additional nfh intron may have been acquired via duplication of a primordial intermediate filament gene.

Amino Acid Sequence↗
PubMed2006

Intron-rich ancestors.

Eukaryotic genes are interrupted by spliceosomal introns, which are removed from gene transcripts. The number of introns per gene varies by more than two orders of magnitude between species, implying that there has been extensive intron loss and/or gain throughout eukaryotic evolution. A recent study of intron positions in animals confirms that the ancestral bilaterian was rich in introns, and that differences in intron number between animals largely reflect different levels of intron loss. These results refocus our attention on the evolutionary history and importance of introns in early eukaryotic evolution.

Alternative Splicing↗
PubMed1998

Cathepsin L gene organization in crustaceans.

The gene structure of a cathepsin L of the shrimp Penaeus vannamei has been determined by the polymerase chain reaction. It comprises six exons of various lengths spanning a total of 1792bp. This architecture is homologous to that of rat cathepsin L, three conserved sites of intron position have been effectively identified, with the exception of the third intron break-point located immediately after the cysteinyl active site. In contrast, no similarity is observed with Drosophila or Plasmodium cathepsin L-like gene organizations. This gene expresses a major cathepsin L enzyme in the hepatopancreas. The last intron is polymorphic, suggesting the presence of at least three different genes.

Amino Acid Sequence↗
PubMed1995

A cdc2 homologue and closely related processed retropseudogenes from Norway spruce.

The p34cdc2 protein kinase is a key component in the regulation of the eukaryotic cell cycle and has been conserved during evolution. We have isolated cDNA clones corresponding to a cdc2 gene (cdc2Pa) from the conifer Norway spruce, Picea abies (L.) Karst. The deduced amino acid sequence is 85-90% identical to p34cdc2 homologues from other plants, contains eleven subdomains characteristic for the protein kinase family, and three sequence motifs specific for the cdc2 protein kinases. A partial genomic clone of cdc2Pa reveals two introns at positions identical to intron positions in Arabidopsis thaliana cdc2a. A Southern blot analysis shows that cdc2Pa is a single-copy gene belonging to a family of about 10 related genes. Partial genomic sequences of six of the genes in this family (86-92% identical to cdc2Pa) show distinct features of processed retropseudogenes. These lack introns and contain deletions, insertions and/or non-silent point mutations. This result is consistent with the hypothesis that processed retropseudogenes in plants may be common among genes expressed in the apical meristem, that is, in cells which have the potential to take part in the formation of reproductive organs. Although cdc2Pa transcripts were abundant in the epicotyl and thus likely in the apical meristem, we observed no strict coupling of expression to cell division in embryos and seedlings.

Amino Acid Sequence↗
PubMed1993

Characterization of an ethylene-responsive glutathione S-transferase gene cluster in carnation.

In this paper we present the structural analysis of two tightly linked genes from the glutathione S-transferase (GST) gene family in carnation (Dianthus caryophyllus). Southern blot analysis and restriction endonuclease mapping revealed a single cloned region of the carnation genome was highly homologous to the previously characterized ethylene-responsive GST mRNA expressed in flower petals during senescence. Nucleotide sequencing of this region revealed the presence of two tandemly arranged genes designated GST1 and GST2. Comparison of the nucleotide sequences of the cloned genomic region with the previously characterized GST cDNA clone pSR8 revealed that GST1 contains the entire transcription unit in 10 exons interrupted by 9 introns. The transcription unit of GST2 was found to be very similar to GST1 with complete conservation of intron position. In addition, the length and nucleotide sequences of the two genes' introns were highly conserved. GST2 was not completely represented by the cloned genomic region, missing the 3' portion of the transcription unit. Primer extension analysis indicated a single transcriptional start site for transcripts which accumulate in senescing carnation petals. The 5'-flanking sequences of GST1 and GST2 were compared and regions of homology and divergence identified. These upstream sequences were compared with other plant ethylene-responsive genes and GST genes and several sequence motifs of potential importance in the regulation of GST expression were identified. A chimeric gene constructed between -1457 bp of the 5'-flanking DNA of GST1 and the coding region of beta-glucuronidase was found to confer ethylene-inducible expression in flower petals following delivery of the construct into tissue by particle bombardment.

Amino Acid Sequence↗
PubMed1999

Cloning the neuropeptide Y exon 2 from sea bass (Dicentrarchus labrax).

A partial genomic library of sea bass DNA was constructed and screened with a goldfish NPY cDNA probe. Two identical clones were isolated and sequenced. The clones contain a segment with high identity to exon 2 of the NPY gene in tetrapods. This segment encodes a 62-amino acid peptide consisting of a signal peptide of 28 amino acids and the main portion of the mature NPY (34 amino acids). In the latter extension, sea bass NPY shows high identity with the human and deduced ancestral gnathostome sequences (88 and 91%, respectively). The open reading frame is followed by a consensus splice donor site. Northern blot hybridization to examine tissue distribution detected a 1-kb RNA transcript restricted to brain tissue. These data show that the NPY gene of this teleost fish has the same intron positions as tetrapods for at least two of the gene's three introns. In addition, the high evolutionary conservation of NPY is corroborated since sea bass NPY exhibits the same identity to both goldfish and human NPY.

Amino Acid Sequence↗
PubMed2002

Cyp6a8 of Drosophila melanogaster: gene structure, and sequence and functional analysis of the upstream DNA.

In Drosophila, the insecticide resistant 91-R strain is an overproducer and susceptible 91-C and ry(506) strains are the underproducers of CYP6A8 mRNA encoded by a cytochrome P450 gene, Cyp6a8. Low expression of Cyp6a8 in the underproducer strains is due to a downregulatory effect of a putative repressor locus, which is thought to be mutant in the overproducer strain. In the present investigation, organization of Cyp6a8 and promoter activity of its upstream DNA were analyzed. Cyp6a8 has two introns of which intron II is similar to the introns of other insect CYP genes with respect to its length and position. Intron I is only 36 bp long and lacks consensus splice sites. It is also in-frame with the CYP6A8 open reading frame. Therefore, inefficient splicing of intron I may produce two isoforms of CYP6A8. Analysis of Cyp6a8 upstream DNA of the overproducer 91-R strain showed that DNA sequences between -199 and -761 bp are required for the highest constitutive and barbital-induced expression of Cyp6a8. This region has six barbie boxes and binding sites for various transcription factors. Promoter activity of the -11/-761 DNA of the overproducer 91-R strain was found to be 4-fold lower in the genome of underproducer ry(506) strain, which is wild type for the putative repressor gene, than in the genome of F1 hybrids of 91-R and ry(506) strains. These results suggest that -11/-761 Cyp6a8 DNA of the 91-R strain can respond to the active repressor present in the hybrid genome and further support our previous findings that overexpression of Cyp6a8 is a result of mutation of a repressor gene rather than mutation of the cis-regulatory sequences.

Alleles↗
PubMed1994

Two genes encoding GF14 (14-3-3) proteins in Zea mays. Structure, expression, and potential regulation by the G-box binding complex.

Two maize (Zea mays) genes, designated GRF1 and GRF2, have been isolated and characterized. The proteins encoded by these genes, called GF14 proteins, participate in protein/DNA complexes and show more than 60% identity with a highly conserved, widely distributed protein family, collectively referred to as 14-3-3 proteins. Members of the 14-3-3 protein family have been reported to activate Tyr and Trp hydroxylases, modulate protein kinase C activity, and activate ADP-ribosyltransferase. The mRNAs of the GRF genes are encoded by six exons interrupted by five introns. The transcriptional units of the GRF genes were found to be very similar, with complete conservation of the intron positions. In addition, the length and nucleotide sequences of the two genes' introns were highly conserved. The 5' flanking sequences of the two GRF genes were compared and regions of homology and divergence identified. This comparison revealed the presence of a conserved G-box element in the 5' flanking region of both genes. Electrophoretic mobility shift assays of maize protein extract with the GRF G-box indicates that GBF binds to this G-box site in the 5' up stream region of GRF. Antibody supershifts indicate that GF14 protein is associated with the G-box-binding complex that interacts with the GRF upstream region.

14-3-3 Proteins↗
PubMed1986

Homology between cellulase genes of Trichoderma reesei: complete nucleotide sequence of the endoglucanase I gene.

The filamentous fungus Trichoderma reesei produces several endoglucanases (EG) and cellobiohydrolases (CBH) which are involved in cellulose hydrolysis in a complex synergistic manner. We have cloned and sequenced the gene and the full-length cDNA coding for the major endoglucanase EG-I, and compared this to the cbh1 gene sequence to clarify the relationship between the EG and CBH classes of cellulases. The deduced 437-amino acids (aa) long EG-I protein with a 22-aa long signal peptide is 45% identical in aa sequence with CBH-I. The best conserved region is found at the C terminus and shows about 70% homology. The data suggest that the two enzymes have arisen from a common ancestor by gene duplication. Despite this, the intron positions have not been conserved in these genes which both contain two short introns. The deduced EG-I sequence contains six putative N-glycosylation sites, and a putative O-glycosylated region is found near the C terminus, closely resembling a similar region at the C terminus of CBH-I. Comparison of the aa sequences suggests that the evolutionary divergence of EG-I from CBH-I has involved four separate 10-20 aa "deletions" from the ancestral protein.

Amino Acid Sequence↗