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PubMed1992

G+C-rich tract in 5' end of human introns.

Analysis of an artificial neural network trained to classify DNA as coding or non-coding revealed compositional differences between sequence parts translated into protein and those that were not. The 5' end of human introns was found to have a base composition that was non-random to an extent matching the non-randomness in the 3' end that contains the polypyrimidine tract. The prevailing nucleotides in the initial 50 nucleotides of human introns are guanine and cytosine, the trinucleotide GGG was found to occur almost four times as frequently as it would in sequences with a uniform distribution of the nucleotides. The initial part of terminal exons and their associated terminal introns were shown to have a very special base composition deviating strongly from the normal picture in other exons and introns.

Base Composition↗
PubMed1994

Peptide antibiotics of the tuberactinomycin family as inhibitors of group I intron RNA splicing.

The tuberactinomycins are a group of cyclic peptide antibiotics, which are potent inhibitors of prokaryotic protein synthesis. We report the inhibitory effect of viomycin, di-beta-lysyl-capreomycin IIA and tuberactinomycin A on group I intron self-splicing. They compete with the guanosine cofactor for the G-binding site located in the conserved core of the intron. They are 100-fold more active than all other competitive inhibitors described so far (dGTP, arginine or streptomycin), inhibiting splicing at concentrations between 10 and 50 microM. Mutation of the G-binding site leads to partial resistance, and the inhibitory effect of these drugs is dependent on Mg2+ concentration. This suggests that the tuberactinomycins have more than one contact site with the intron RNA: via the G-binding site and via additional contacts with the RNA backbone. Positioning the tuberactinomycins in the three-dimensional model of the td intron core suggests that the charged lysyl side-chain (R1) is in contact with the backbone of the P1 helix. Structure/function analyses with various tuberactinomycin analogues with different activities confirm the involvement of this sidechain in inhibition of group I self-splicing. The demonstration of a new class of splicing inhibitors, the peptide antibiotics, illustrates how antibiotics may interact with catalytic RNA.

Bacteriophage T4↗
PubMed1986

Multiple self-splicing introns in bacteriophage T4: evidence from autocatalytic GTP labeling of RNA in vitro.

RNA from T4-infected cells yielded multiple end-labeled species when incubated with alpha-32P-GTP under self-splicing conditions. One of these corresponds to the previously identified intron from the td gene of T4, while others appear to represent additional group I introns in T4. Two loci distinct from the td gene were found to hybridize to a mixed alpha-32P-GTP-labeled T4 RNA probe. These mapped in or near the unlinked genes nrdB and nrdC. A fragment from the nrdB region that contains the intron has been cloned and shown to generate characteristic group I splice products with RNA synthesized in vivo and in vitro. Multiple introns, and the prospect that these occur within several genes in the same metabolic pathway, suggest a possible regulatory role for splicing in T4.

Genes, Viral↗
PubMed1987

A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof.

The nuclear cyt-18 mutants of Neurospora crassa are defective in splicing a number of group I introns in mitochondria. Here, cloning and sequencing of the cyt-18 gene show that it contains an open reading frame having significant homology to bacterial tyrosyl-tRNA synthetases. Biochemical and genetic experiments lead to the conclusions that the cyt-18 gene encodes mitochondrial tyrosyl-tRNA synthetase, that mutations in this gene inhibit splicing directly, and that mitochondrial tyrosyl-tRNA synthetase or a derivative of this protein is related to the soluble activity that functions in splicing the mitochondrial large rRNA intron and possibly other group I introns. Analysis of partial revertants provides direct evidence that the cyt-18 gene encodes a protein or proteins with two activities, splicing and aminoacylation, that can be partially separated by mutation. Our findings may be relevant to the evolution of introns and splicing mechanisms in eukaryotes.

Amino Acid Sequence↗
PubMed1989

Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria.

Two introns of the mitochondrial genome 777-3A of S. cerevisiae, bl4 in cob and al4 in coxl genes, contain ORFs that can be translated into two homologous proteins. We changed the UGA, AUA, and CUN codons of these ORFs to the universal genetic code, in order to study the functions of their translated products in E. coli and in yeast, by retargeting the nuclear encoded protein into mitochondria. The p27bl4 protein has been shown to be required for the splicing of both introns bl4 and al4. The homologous p28al4 protein is highly toxic to E. coli. It can specifically cleave double-stranded DNA at a sequence representing the junction of the two fused flanking exons. We present evidence that this system is a good model for studying the role of mitochondrial intron-encoded proteins in the rearrangement of genetic information at both the RNA (RNA splicing-bl4 maturase) and DNA levels (intron transposition-al4 transposase).

Base Sequence↗
PubMed1992

New reactions catalyzed by a group II intron ribozyme with RNA and DNA substrates.

Here we describe three novel reactions of the self-splicing group II intron bI1 (the first intron of the COB gene of yeast mitochondria) demonstrating its catalytic versatility: reversal of the first step of the self-splicing reaction catalyzed by a linear form of the intron utilizing the energy of a phosphoanhydride bond for transesterification, ligation of a single-stranded DNA to an RNA, and cleavage of a single-stranded DNA substrate. These results have the following evolutionary implications: use of the alpha-beta bond of a terminal triphosphate for transesterification suggests that an RNA RNA replicase could use mononucleotide triphosphates as precursors, and cleavage of single-stranded DNA and DNA-RNA ligation suggests that excised group II introns might integrate directly into DNA without prior reverse transcription.

Amino Acid Sequence↗
PubMed1993

RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency.

A functionally critical position (Q/R site) of the AMPA receptor subunit GluR-B is controlled by RNA editing that operates in the nucleus, since in brain and clonal cell lines of neural origin, unspliced GluR-B transcripts occur edited in the Q/R site CAG codon and, additionally, in intronic adenosines. Transfection of GluR-B gene constructs into PC12 cells revealed that the proximal part of the intron downstream of the unedited exonic site is required for Q/R site editing. This intron portion contains an imperfect inverted repeat preceding a 10 nt sequence with exact complementarity to the exon centered on the unedited codon. Single nucleotide substitutions in this short intronic sequence or its exonic complement curtailed Q/R site editing, which was recovered by restoring complementarity in the respective partner strand. Base conversion in the channel-coding region of GluR-B directed by base paired sequences may be executed by a ubiquitous nuclear adenosine deaminase specific for double-stranded RNA.

Adenosine Deaminase↗
PubMed1993

Sequence diversity in the intron of the calmodulin gene from Plasmodium falciparum.

Sequence variation in the single intron of the calmodulin gene of Plasmodium falciparum has been examined following amplification using the polymerase chain reaction (PCR). The intron has 4 repeating motifs varying in length: 3 of these contain a dinunucleotide repeat, dA-dT, the fourth is a pentameric repeating unit, dA-dT-dA-dT-dT. These DNA polymorphisms can be applied to the study of parasite populations in mixed infections and in strain identification. The function of these repeating motifs is unknown. Computer modelling of the possible intron structures demonstrates that each of these repeating motifs forms individual stem loops such that any changes in repeat number are self-compensatory and do not change the overall intron structure. The implications of this sequence variation are discussed.

Animals↗
PubMed1992

The unique structure of the Paramecium caudatum hemoglobin gene: the presence of one intron in the middle of the coding region.

The gene encoding hemoglobin (Hb) in the ciliated protist, Paramecium caudatum, has been cloned and sequenced. A single Hb locus was detected on an isolated genomic fragment with a size of approx. 15 kbp. This gene contained 443 bp. The 5' transcriptional regulatory region contained TATA box- and CAAT box-like sequences which resemble the structure of the promoter region in higher eukaryotic genes. The amino acid sequence deduced from the gene agreed precisely with that of the major Hb component. It was an unusual structure, much smaller than Hbs from many other organisms. Furthermore, all of the untranslated regions in this gene were also small. Particularly, one intervening sequence (intron) being only 23 bp was shorter than any other introns reported for eukaryotic genes encoding protein. The position of the intron in the P. caudatum Hb gene corresponded closely to that of the second intron which had been reported only for plant Hb genes. Possible routes for the evolution of Hb genes were discussed.

Amino Acid Sequence↗
PubMed1995

Upstream and intron regulatory regions for expression of the rat neuron-specific enolase gene.

Neuron-specific enolase (NSE) occurs in mature neurons and paraneurons. We have isolated the genomic clone coding for rat NSE and clarified its gene structure. In order to analyze the regulatory sequence in the 5'-upstream region and introns, we carried out transient expression experiments of NSE genomic DNA fragments fused to chloramphenicol acetyltransferase (CAT) gene which were transfected into several cultured cells. The used cells were primary cultured rat neurons, PC12, neuroblastoma 35, neuroblastoma 103, C6, primary cultured rat glial cells and HeLa cells. The promoter sequence (190 bp) upstream to the transcription initiation site was important in the expression of CAT gene in these cells. From the experiments with external and internal deletion mutants of the fusion gene, the cis-acting regulatory region responsible for the enhanced expression of the CAT activity in the primary cultured neuron and PC12 cells was found to be localized at upstream 500 bp sequence of the intron 1 and 1.5 kbp upstream sequence of the transcription initiation site. In the upstream important sequences, there were the nearest sequences for AP-1 binding motif, AP-2 binding element, SP-1 binding sequence, cAMP response element, half site of glucocorticoid receptor (GRE) binding sequence, half site of thyroid hormor receptor (TR) or retinoic acid receptor (RAR) binding sequence and MTF-1 binding sequence. Furthermore, Octamer-6 binding motifs also were found. In the intron 1, 5' end upstream 50 bp and downstream 100 bp were the most important sequences. We found the nearest sequences for cAMP response element, E2F binding sequence, early growth response (EGR)-1 binding motif, half site of TCF-1 binding sequence and a neuron-specific element-like sequence in the intron 1.

Animals↗
PubMed1988

A class-I intron in a cyanelle tRNA gene from Cyanophora paradoxa: phylogenetic relationship between cyanelles and plant chloroplasts.

Cyanelles are photosynthetic organelles which are considered as intermediates between cyanobacteria and chloroplasts, and which have been found in unicellular eukaryotes such as Cyanophora paradoxa. The nucleotide sequence of a 667-bp region of the cyanelle genome from Cyanophora paradoxa containing genes coding for tRNA(UUCGlu) and tRNA(UAALeu) has been determined. The gene coding for tRNA(UAALeu) is split by a 232-bp intron which has a secondary structure typical for class-I structured introns and which is closely related to the intron located in the corresponding gene from liverwort and higher plant chloroplasts. It appears therefore that these tRNA(UAALeu) genes are all derived from one common ancestral gene which already contained a class-I intron.

Ascomycota↗
PubMed1989

Distribution of introns in frameshift-suppressor proline-tRNA genes of Saccharomyces cerevisiae.

Mutations in the suf9, suf10, and suf11 genes of yeast suppress + 1 nucleotide (nt) insertions in proline codons. Nucleotide sequence analysis indicates that the suf9 and suf11 genes are members of the proline tRNA(UGG) gene family, which also includes three other previously identified genes, suf7, suf8, and trn1. All five members of this gene family contain introns. The suf9 and suf11 introns are 31 and 30 nt in length, respectively, and are similar but not identical in sequence to other introns within the family. The suf10 gene is identical in sequence to suf2, which was shown previously to encode proline tRNA(IGG). Both members of this gene family lack introns. Alleles of suf9, suf10, and suf11 that confer frameshift suppression were also analyzed. The SUF9-1 allele results in a G----U substitution at nt position 39 in the anticodon stem. The recessive suf11-1 allele is a double mutant containing the same nt position 39 alteration as in SUF9-1 plus a second U----A substitution at nt position 38 in the anticodon loop. The SUF10-1 suppressor mutation corresponds to a +1G insertion in the anticodon loop. Since the nt substitutions in suf11-1 alter the sequence of the 3' exon/intron boundary, the double mutant pre-tRNA was tested for its ability to be cleaved in vitro by tRNA-splicing endonuclease. It was found that suf11-1 pre-tRNA is cleaved with reduced efficiency at the 3' splice junction.

Base Sequence↗
PubMed1990

Nucleolin gene organization in rodents: highly conserved sequences within three of the 13 introns.

The complete nucleotide (nt) sequence of the rat nuc gene encoding nucleolin, the major nucleolar-specific protein in eukaryotic exponentially growing cells, is compared with the corresponding locus recently characterized in mouse. [Bourbon et al., J. Mol. Biol. 200 (1988) 627-638]. In both murine species the genomic organization has been strikingly conserved during evolution, i.e., the coding region extends over 9 kb and is split into 14 exons, encoding a 712-amino acid protein. Moreover, all the exon-intron junction positions were strictly maintained during evolution. More unexpectedly, this analysis revealed that several introns contain highly conserved sequence elements of about 120 nt. The nt sequence of the homologous locus isolated from a Chinese hamster genomic clone established that these regions were under unusually high selective constraints (84-96% identity between the hamster and murine nuc genes) and, although they do not contain open reading frames, they surprisingly appear to be more conserved than most of the exons, suggesting that they play an important role. Such an element of 130 nt presents features of known genes transcribed by RNA polymerase III. Furthermore, in the rat nuc pre-mRNA the 5'- and 3'-end regions of the last intron are fully complementary over 16 nt, and so are predicted to be included in a prominent stem structure. Moreover, an homologous RNA stem structure can be derived from the mouse sequence, including two compensatory nt changes. As the secondary structure would occlude the canonical sequences required for the proper excision of this intron in both murine species, this remarkable finding could be relevant to the regulation of the nuc gene expression at the RNA processing level.

Amino Acid Sequence↗
PubMed1991

Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos.

The fifth group-I intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos (CeLSU.5) is mobile during interspecific crosses between C. eugametos and Chlamydomonas moewusii. Like the six other mobile introns that have been well characterized so far, CeLSU.5 contains a long open reading frame (ceuIR) coding for a site-specific endonuclease (I-CeuI) that cleaves the C. moewusii intronless gene in the vicinity of the intron-insertion site. This stimulates gap repair and mediates efficient transfer of the intron at its cognate site. By expressing the ceuIR gene in the Escherichia coli vectors pKK233-2 and pTRC-99A, we recently demonstrated that the endonuclease is highly toxic to E. coli [Gauthier et al., Curr. Genet. 19 (1991) 43-47]. To eliminate this problem and characterize the cleavage pattern and recognition sequence of the I-CeuI endonuclease, we have expressed the ceuIR gene in E. coli under the control of a bacteriophage T7 promoter in a tightly regulated M13 system, and developed an in vitro system to assay partially purified I-CeuI activity. This allowed us to determine that I-CeuI recognizes a sequence of less than 26 bp centered around the insertion site and produces a staggered cut 5 bp downstream from this site, yielding 4-nucleotide (CTAA), 3'-OH overhangs.

Animals↗
PubMed1992

The mosaic organization of the mitochondrial introns of Saccharomyces cerevisiae: features and evolutionary origins.

The introns of three genes (oxi3, cob and 21S) from the mitochondrial (mt) genome of Saccharomyces cerevisiae contain closed reading frames (CRFs). In the present work, we have analyzed these sequences in their oligodeoxyribonucleotide (oligo; isostich) patterns. We have shown that the relative amounts of di- to hexanucleotides, when compared to random sequences having the same sizes and compositions, exhibit the same deviations as the intergenic noncoding sequences of the mt genome (except for the CRFs from 21S intron). In contrast, intronic open reading frames (ORFs) showed oligo patterns which were generally quite distinct from those of CRFs, although some similarities could be detected in some cases (especially for aI5 alpha). The mt introns of yeast, therefore, are endowed with a mosaic structure, in which CRFs derive from mt intergenic sequences, whereas ORFs have a different origin (indicated as exogenous by other evidences) yet show, in some cases, the effects of 'sequence assimilation' with CRFs.

Base Composition↗
PubMed1995

The rhodopsin-encoding gene of bony fish lacks introns.

A study of the sequences of the rhodopsin-encoding genes (Rh) in eight fish species from two of the major subdivisions of the teleosts reveals that no introns are present in the coding region. This contrasts with the opsin-encoding genes of all other vertebrates where either four or five introns are invariably found. Phylogenetic analysis shows that this intronless teleost Rh is homologous to the intron-containing Rh of amphibia, birds and mammals. Possible mechanisms for intron loss are discussed, including replacement by homologous conversion of Rh with a processed cDNA.

Amphibians↗
PubMed1996

Analysis of intron 4 of the p53 gene in human cutaneous melanoma.

DNA sequencing of intron 4 of the p53 gene from seven cutaneous melanoma cell lines showed an absence of mutations. However, both control and melanoma cell lines sequences were different from the reference source obtained from GenBank databank (accession No. X54156). Base pairs 101 and 689 were determined to be T (instead of A) and C (instead of G). Also, an additional C was not detected at position 371. Comparative analysis with p53 DNA-binding sequences, a sequence recognized by a p53 intron 4-binding protein and consensus sequences recognized by transcription factors demonstrated that intron 4 contains putative sequences for NF-kappa B, SP1, AP1 and TFIID binding. Binding of transcription factors could be one of the mechanisms by which intron 4 modulates human p53 expression.

Base Sequence↗
PubMed1991

The exon-intron organization of the human erythrocyte alpha-spectrin gene.

The human erythrocyte alpha-spectrin gene which spans 80 kbp has been cloned from human genomic DNA as overlapping lambda recombinants. The exon-intron junctions were identified and the exons mapped. The gene is encoded by 52 exons whose sizes range from 684 bp to the smallest of 18 bp. The donor and acceptor splice site sequences match the splice site consensus sequences, with the exception of one splice site where a donor sequence begins with -GC. The size and location of exons do not correlate with the 106-amino-acid repeat, except in three locations where the surrounding codons are conserved as well. The lack of correspondence between exons and 106-amino-acid repeat is interpreted to reflect the appearance of a spectrin-like gene from a minigene early in the evolution of eukaryotes. Since current evidence indicates that introns were present in genes before the divergence of prokaryotes and eukaryotes, it is possible that the original distribution of introns within the minigene has been lost by the random deletion of introns from the spectrin gene.

Amino Acid Sequence↗