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At least 145 records · Page 8Linked to original sources
PubMed1990

Transcriptional and translational cis-regulatory sequences of the spermatocyte-specific Drosophila janusB gene are located in the 3' exonic region of the overlapping janusA gene.

The janus locus of Drosophila melanogaster displays a very unusual organization. It comprises two partially overlapping genes, janA and janB, which are transcribed in the same orientation; the start of transcription of janB, the downstream gene, is located in the 3' exonic region of janA. Both genes are expressed during spermatogenesis. Transcription of janB is restricted to this developmental process, whereas janA is ubiquitously transcribed in both the somatic and germinal tissues of males and females. In order to delimit the cis-acting sequences regulating the transcription of janB, the expression of four chimeric janB-lacZ genes was examined in transgenic lines by Northern blot analysis, in situ hybridization and in situ histochemical staining for beta-galactosidase activity. Results showed that the testis-specific expression of the janB gene is mediated by a short DNA sequence (positions -174 to +107) which is located entirely within the last exon of the upstream janA gene. The tissue specificity of the expression of the janB gene is maintained when most of the janA coding and upstream sequences are deleted. Yet the presence in cis of an active janA gene leads to reduced accumulation of the janB-lacZ hybrid mRNA. This supports the hypothesis that janA transcription interferes with the function of the janB cis-regulatory elements. Our results also demonstrate that the 5' untranslated leader of the janB mRNA contains translational cis-acting elements, which completely block the translation of the janB-lacZ transcripts during the premeiotic stages of sperm development. A janB-lacZ construct was used to examine the sexual phenotype of the germline cells of masculinized XX transformer-2 (tra-2) flies. This has enabled us to confirm at the molecular level previous observations that the germline cells of these flies can enter the spermatogenic pathway of differentiation.

Animals↗
PubMed1992

Mechanism of post-segregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene.

The hok/sok locus of plasmid R1, which mediates plasmid stabilization by killing of plasmid-free segregants, codes for two RNAs, Hok mRNA and Sok antisense RNA. Hok mRNA encodes the Hok killer protein of 52 amino acid residues. Expression of hok is regulated post-transcriptionally by Sok antisense RNA. Killing of plasmid-free daughter-cells by the hok/sok system is accomplished through differential decay of the Hok and Sok-RNAs: Hok mRNA is very stable while Sok-RNA decays rapidly, thus leading to derepression of Hok mRNA translation in plasmid-free segregants, ensuring a rapid and selective killing of these cells. Sok antisense RNA is complementary to the leader region of the Hok mRNA. However, the region of complementarity does not overlap with the hok Shine-Dalgarno sequence. Thus, Sok-RNA regulates hok translation indirectly by an as yet unknown mechanism. We show here that Sok antisense RNA regulates the translation of another reading frame located in the hok/sok locus. This new reading frame, which overlaps with almost the entire hok gene, was denoted mok (mediation of killing). Point-mutations that prevent mok translation through the hok translational initiation region abolish efficient expression of hok. Furthermore, these mutations abolish the Sok-RNA-mediated control of hok gene expression. Hence, the antisense-RNA-mediated regulation of the hok gene seems to occur via translational coupling between the hok and mok reading-frames.

Base Sequence↗
PubMed1987

Regulation of the Escherichia coli excision repair gene uvrC. Overlap between the uvrC structural gene and the region coding for a 24 kD protein.

The UvrA, UvrB and UvrC proteins of E. coli are subunits of a DNA repair enzyme, the ABC exonuclease. In this paper we study the uvrC regulatory region. The uvrC structural gene is preceded by an open reading frame encoding a 24 kD protein. A uvrC promoter has been mapped within this gene. The transcription start of a second promoter located 5' of the 24 kD gene is mapped in vivo. We show that transcription from both promoters on the chromosome is not inducible by UV damage. The possible translation start codons of the UvrC and of the 24 kD protein are determined. Sequences encoding the N-terminal part of the UvrC protein overlap with sequences encoding the C-terminal part of the 24 kD protein. To examine a possible function of the 24 kD gene in repair, a 24 kD insertion mutant was created in the chromosome. The mutant however only slightly affects the UV sensitivity of the cell. Transcription of P3 alone provides sufficient UvrC protein for the normal repair of UV lesions.

Amino Acid Sequence↗
PubMed2006

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans.

We have systematically examined the correlation between transcriptional expression pattern and the physical layout of gene pairs in the genome of Caenorhabditis elegans using a public tissue-specific SAGE library data set. We find a strong positive correlation in the expression patterns of neighboring gene pairs that are close together and transcribed in the same direction as well as for neighboring pairs that are located on opposing strands and transcribed in divergent directions. Coupling between members of nonoverlapping neighboring gene pairs is independent of operons and decreases to background levels as the distance increases beyond 10 kb. These findings suggest the existence of regional transcriptional domains in the C. elegans genome. In contrast, genes that are on opposing strands and transcribed in convergent directions are less transcriptionally coupled than the genome-wide background, suggesting a mutual inhibition mechanism. We have also examined the conservation and functional consequences of extreme cases of topological entanglement in the C. elegans genome, in which two or more genes physically overlap in their UTRs or coding regions. We have found that overlapping gene pairs are more conserved and are enriched in essential genes and genes that cause various defined phenotypes revealed by RNAi trials. SAGE analysis indicates that genes that are on the same strand, physically overlap, and transcript at the same directions are very highly correlated in gene expression, while overlapping gene pairs in which one member of the pair resides within an intron of the other are weakly, if at all, coupled, similar to convergent overlapping genes.

Amino Acid Sequence↗
PubMed1995

The products of gene I and the overlapping in-frame gene XI are required for filamentous phage assembly.

The class I filamentous bacteriophage are non-lytic single-stranded DNA phage, which are assembled at the cell envelope as they are extruded from the Gram-negative bacteria, Escherichia coli. The process requires the products of the phage genes I and IV, which reside in the inner and outer membrane, respectively, and are not present in the mature phage particle. Gene I encodes two proteins, the full length 348-residue pI and a smaller pI*, which this report shows is the result of an internal translation initiation event at methionine codon 241. Both pI and pI* are shown to be required for phage assembly. Therefore, pI* can be considered the product of an additional phage gene, XI, which is a separate in-frame gene that overlaps gene I. Both proteins contain a 13-residue region adjacent to the cytoplasmic face of the inner membrane that probably exists as a positively charged amphiphilic helix. Although this region is not required for membrane insertion of pI and pI*, it is shown to be required for phage assembly. Oligonucleotide-directed mutagenesis of this region, which removes positive charges or alters the hydrophobic face of the putative helix, renders pI and pI* unable to function in phage assembly. This region of pI and pI* is highly homologous in structure to the carboxyl-terminal 11 amino acids of pVIII, the main coat protein, which also reside adjacent to the cytoplasmic face of the inner membrane.

Amino Acid Sequence↗
PubMed2001

Conserved and non-conserved regions in the Sendai virus genome: evolution of a gene possessing overlapping reading frames.

We have sequenced the entire genome of a virulent field isolate of Sendai virus, the Hamamatsu strain, and compared the sequence with that of a distant related strain, the Z strain. Calculation of synonymous and non-synonymous (amino acid changing) nucleotide substitutions revealed regions where changes were permissive and non-permissive, and the experimentally determined functional region were found to be conserved, showing that important regions for function were conserved during evolution. In the cistron-overlapping regions in the P gene, one reading frame was conserved, whereas the other overlapping frame was flexible. The priority of one frame could be a strategy for evolution of an overlapping gene of RNA viruses. We found that the carboxyl two thirds of the C protein was conserved over the amino-terminal one third, possessing priority to the overlapping P polypeptide. This suggests that the carboxyl two thirds of the C protein have a functional importance. We also found a highly variable region between the L coding frame and the 5' trailer sequence. The relevance of these findings to actual viral replication should be clarified in the future.

Base Sequence↗
PubMed1994

The insulin and cAMP response elements of the prolactin gene are overlapping sequences.

Prolactin gene expression is affected by numerous signals, but many of the promoter elements required for these responses have not been clearly identified. This report identifies sequences within the prolactin gene promoter that are required for the responses to cAMP and insulin. The cAMP response element, -101 to -92 shares a 6 of 8 base pair homology with previously identified cAMP response elements. Mutation of this element also results in a > 100-fold decrease in basal prolactin gene expression. This is characteristic of cAMP response elements, but the importance of this element to basal prolactin gene transcription was previously unrecognized. The insulin response element, -97 to -67, is not homologous to previously reported insulin response elements and mediates the 10-fold increases in prolactin gene expression due to insulin observed in GH cells. These elements also function to mediate insulin and cAMP responses from the heterologous delta MTV-CAT reporter plasmid. Together, insulin and cAMP increase prolactin gene expression additively. The clustering of these elements may provide clues to the independent and possible coordinate regulation by these effectors.

Animals↗
PubMed1993

Three overlapping lct genes involved in L-lactate utilization by Escherichia coli.

In Escherichia coli, the lct locus at min 80 on the chromosome map is associated with ability to grow on L-lactate and to synthesize a substrate-inducible flavin-linked dehydrogenase. Similar to that of the glpD-encoded aerobic glycerol-3-phosphate dehydrogenase, the level of induced enzyme activity is elevated by aerobiosis. Both of these controls are mediated by the two-component signal transduction system ArcB/ArcA, although sensitivity to the control is much more striking for L-lactate dehydrogenase. This study disclosed that the lct locus contained three overlapping genes in the clockwise order of lctD (encoding a flavin mononucleotide-dependent dehydrogenase), lctR (encoding a putative regulator), and lctP (encoding a permease) on the chromosomal map. These genes, however, are transcribed in the counterclockwise direction. No homology in amino acid sequence was found between aerobic glycerol-3-phosphate dehydrogenase and L-lactate dehydrogenase. A phi (lctD-lac) mutant was inducible by L-lactate but not D-lactate. Although the mutant lost the ability to grow on L-lactate, growth on D-lactate, known to depend on a different enzyme, remained normal.

Amino Acid Sequence↗
PubMed2001

Characterization of the mouse matrilin-4 gene: a 5' antiparallel overlap with the gene encoding the transcription factor RBP-l.

We have isolated and characterized the gene encoding mouse matrilin-4 (Matn4), an extracellular matrix protein present in a broad spectrum of tissues. The gene spanned 16 kb, consisted of 12 exons, and localized to chromosome 2. As in all known matrilin genes, the last intron, separating the exons coding for the coiled-coil domain, did not follow the GT-AG rule and belonged to the subgroup of introns having AT-AC at the ends. Matn4 contained two exons in the 5' UTR that could be alternatively spliced. We localized a major and a minor transcription start site to two different untranslated exons: exon 0a and exon 0b. Matn4 divergently overlapped 5' with the gene encoding RBP-L (for recombining binding protein suppressor of hairless-like; Rbpsuhl), a transcription factor with homology to RBP-JK. Exon 1 of Rbpsuhl was located in the second intron of Matn4, whereas exon 0a, the first exon of Matn4, was located in the second intron of Rbpsuhl. The second exons of the respective genes overlapped in an antisense orientation. We mapped the major transcription start of Rbpsuhl to a position approximately 150 nt upstream of the splice acceptor site of the first intron, leading to the synthesis of a truncated variant of RBP-L probably missing the amino-terminal 121 amino acid residues. We analyzed the expression of the different Matn4 and Rbpsuhl transcripts by quantitative RT-PCR; this showed the highest expression for both genes in lung and brain. In situ hybridization of brain sections showed a partially overlapping expression pattern for the two genes.

5' Untranslated Regions↗
PubMed1987

Structure and expression of the overlapping ND4L and ND5 genes of Neurospora crassa mitochondria.

Genes homologous to the mammalian mitochondrial NADH dehydrogenase subunit genes ND4L and ND5 were identified in the mitochondrial genome of the filamentous fungus Neurospora crassa, and the structure and expression of these genes was examined. The ND4L gene (interrupted by one intervening sequence) potentially encodes an 89 residue long hydrophobic protein that shares about 26% homology (or 41% homology if conservative amino acid substitutions are allowed) with the analogous human mitochondrial protein. The ND5 gene (which contains two introns) encodes a 715 residue polypeptide that shares 23% homology with the human analogue; a 300 amino acid long region is highly conserved (50% homology) in the two ND5 proteins. The stop codon of the ND4L gene overlaps the initiation codon of the downstream ND5 gene, and the two genes are cotranscribed and probably cotranslated. A presumed mature dicistronic (ND4L plus ND5) RNA was detected. The postulated mRNA (about 3.2 kb) contains 5' and 3' non-coding regions of about 86 and 730 nucleotides, respectively; this species is generated from very large precursor RNAs by a complex processing pathway. The ND4L and ND5 introns are all stable after their excision from the precursor species.

Amino Acid Sequence↗
PubMed1988

Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon.

The Ty (transposon yeast) family of retroviral-like transposons include two genes, TYA and TYB, analogous to the gag and pol genes of metazoan retroviruses. TYB lies downstream of TYA, the two genes overlapping by 38 base pairs. The primary translation product of TYB is a TYA/TYB fusion protein whose expression has been inferred to occur by translational frameshifting within the overlap region. We show that the event leading to expression of TYB is very efficient, resulting in 20% read-through into TYB from TYA. We demonstrate that the Ty mRNA is colinear with the DNA sequence of the element, eliminating any pretranslational model for TYB expression. Frameshifting requires no particular sequence of the upstream TYA gene, nor any global RNA structure. Surprisingly, it can be promoted by a 14-base-pair oligonucleotide of the overlap region. The ability of this oligonucleotide to function is inhibited when it is positioned immediately downstream of an initiator AUG. We conclude that the TYB gene is expressed by an efficient ribosomal frameshifting event requiring a small oligonucleotide sequence derived from the TYA/TYB overlap region.

Amino Acid Sequence↗
PubMed1989

Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension.

Gene splicing by overlap extension is a new approach for recombining DNA molecules at precise junctions irrespective of nucleotide sequences at the recombination site and without the use of restriction endonucleases or ligase. Fragments from the genes that are to be recombined are generated in separate polymerase chain reactions (PCRs). The primers are designed so that the ends of the products contain complementary sequences. When these PCR products are mixed, denatured, and reannealed, the strands having the matching sequences at their 3' ends overlap and act as primers for each other. Extension of this overlap by DNA polymerase produces a molecule in which the original sequences are 'spliced' together. This technique is used to construct a gene encoding a mosaic fusion protein comprised of parts of two different class-I major histocompatibility genes. This simple and widely applicable approach has significant advantages over standard recombinant DNA techniques.

Amino Acid Sequence↗
PubMed2006

The 160-kilobase genome of the bacterial endosymbiont Carsonella.

Previous studies have suggested that the minimal cellular genome could be as small as 400 kilobases. Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. It is by far the smallest and most AT-rich bacterial genome yet characterized. The genome has a high coding density (97%) with many overlapping genes and reduced gene length. Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status.

Amino Acids↗
PubMed1987

Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene.

The 3' boundary of the coat gene of the RNA bacteriophage MS2 lies 46 nucleotides downstream from the beginning of the lysis (L) cistron. The translation of both reading frames is coupled; the synthesis of the lysis protein does not occur unless translation of the overlapping coat gene takes place. In the preceding paper we showed that de novo initiation at the L gene is prevented by a hairpin structure that sequesters the ribosomal binding site. Here we examine how translation of the coat gene activates the L gene start site. The experiments show that the movement of ribosomes through the hairpin is in itself not sufficient to expose the lysis gene. Rather, the endpoint of translation is important. Termination at the natural end of the coat gene triggers the lysis response, but further downstream terminations do not. Activation of the L gene is suppressed when the stability of the lysis initiator hairpin is increased by mutations that create additional base-pairs. We assume that the ribosome, terminating at the coat reading frame, covers part of the lysis hairpin, thereby destabilizing the secondary structure. This may be sufficient to promote the binding of a vacant ribosome to the L gene start. Alternatively, the terminated but not yet released ribosome may reach the L gene start by random lateral movements along the mRNA and reinitiate there. The present findings are also discussed in relation to an earlier proposal for L gene activation.

Bacteriophages↗
PubMed1983

Sequence and linkage of the goat epsilon I and epsilon II beta-globin genes.

Overlapping clones containing beta-globin genes have been isolated from a goat genomic library which establish the linkage arrangement 5'-epsilon I-epsilon II-psi beta X-beta C-3'. The complete nucleotide sequence of the epsilon I and epsilon II genes was determined. The sequences of these two genes, along with those previously reported for psi beta X and beta C, complete the sequence of the genes of this linkage set. The first gene in the quadruplet, epsilon I, shows unexpectedly high homology with the human epsilon globin gene both in coding and non-coding regions, and encodes a globin protein that is 90% homologous to human epsilon. The only major difference between the goat epsilon I gene and the human epsilon gene is the presence of an insertion element in the second intron of epsilon I. This element is repetitive in nature and is similar to those found in the second intron of the gamma, beta C and beta A globin genes of the goat. epsilon II also shows high nucleotide homology to the human epsilon globin gene in coding regions and encodes a protein 79% homologous to human epsilon. Notably, however, epsilon II has equivalent nucleotide homology in coding regions to the gamma and epsilon genes of the human locus. The insertion element present in epsilon I is not present in epsilon II. A comparison of the goat beta globin set described here, based on linkage arrangement, nucleotide homology and divergence analysis indicates that this subset of goat beta globin genes is analogous to the entire beta globin loci of other mammalian species. These analyses further indicate that the embryonic genes in these clusters are evolving more slowly than the adult beta globin genes. Comparison of the 5' flanking sequences of epsilon I and epsilon II with those of the beta-embryonic globin genes of other mammals reveals a conserved sequence, C-A-C-C-C-C-T-G, located 28 to 29 bases upstream from the C-C-A-A-T consensus sequence, which appears at this position in the embryonic genes, but in none of the non-embryonic genes. Significantly, this sequence is selectively conserved in the human alpha embryonic globin gene, zeta, which diverged from the beta embryonic genes 500 million years ago, and it may therefore represent an embryonic recognition or signal sequence.

Amino Acid Sequence↗
PubMed1992

Mapping the putative RNA helicase genes by sequence overlapping.

An 'electronic' gene mapping procedure based on computer-aided search for overlapping gene sequences was used to identify adjacent genes and localize several putative RNA helicase genes to different chromosomes. PRP28 and AMD1 genes map to the right arm of chromosome IV next to sup2, which encodes a tyrosine tRNA. PRP16, previously mapped to chromosome XI, is tightly linked to MRP-L20. PRP22 is adjacent to PRE1, whose chromosomal location is currently unknown. The utility of this approach in yeast gene mapping is evaluated.

Chromosome Mapping↗
PubMed1989

Bacteriophage T4 late gene expression: overlapping promoters direct divergent transcription of the base plate gene cluster.

Eight 5' ends of RNA molecules which encompass the bacteriophage T4 base plate late genes 51 to 26 region have been mapped by S1 nuclease protection and reverse transcription within a 246-bp DNA segment. Two of eight 5' ends are initiated at two absolutely conserved late promoter sites, P51 and P26a, that direct RNA synthesis on opposite strands. These two promoters share four of eight promoter sequence base pairs. A third 5' end arises from another promoter, P26b, which shows one base pair mismatch with respect to the absolutely conserved -10 sequence. All the other 5' ends arise from RNA processing and/or degradation. Since no other late transcription promoter sites were found within the base plate cluster sequence, we propose that the two overlapping late promoters, P51 and P26a, direct the expression of the T4 base plate gene cluster, included between map coordinates 114,000 and 121,038: P51 directs the transcription of genes 51, 27, 28, 29, 48, and 54 on the rDNA strand and P26a the transcription of genes 26 and 25 on the /DNA strand. This peculiar promoter configuration might account for the low level of transcription of these late genes.

Amino Acid Sequence↗
PubMed1990

Cascade of overlapping late genes in bacteriophage T4.

The DNA sequences of genes 9, 10, 11, 12, and wac, which encode the structural proteins in the bacteriophage T4 base plate, were determined. These genes form a single operon which is transcribed in a clockwise direction from a single late promoter in the TATAAATA region located upstream of gene 9 at position -10. A feature of the operon is an overlap between the termination codon of each upstream gene and the initiation codon of its downstream gene. With the exception of gene 10, the open reading frames encode proteins which have a calculated molecular mass close to that obtained experimentally. The reading frame of gene 10 encodes a polypeptide with a calculated molecular mass of 66.2 kDa, which is at least 22 kDa less than that in the phage particle. Thus the mature protein encoded by gene 10 is possibly a product of the fusion of two adjacent phage genes. The hybrid protein may be formed by a frameshift during the translation of messenger RNA at the end of gene 9 or gene 10.

Amino Acid Sequence↗