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PubMed1987

Nucleotide sequence and characterization of the pyrF operon of Escherichia coli K12.

The pyrF gene of Escherichia coli K12, which encodes the pyrimidine biosynthetic enzyme orotidine-5'-monophosphate (OMP) decarboxylase, is part of an operon that includes a downstream gene designated orfF. The orfF gene product is a small polypeptide of unknown function. The nucleotide sequence of a 1549-base pair chromosomal fragment containing this operon was determined. An open reading frame capable of encoding the 27-kDa OMP decarboxylase subunit was identified and shown to be the pyrF structural gene by purifying and characterizing OMP decarboxylase. The subunit molecular weight (Mr = 26,350), amino-terminal amino acid sequence, and amino acid composition of the polypeptide predicted from the nucleotide sequence are in excellent agreement with those properties determined for the purified enzyme. The orfF structural gene was tentatively identified and apparently encodes an 11,396-dalton polypeptide. The orfF translational initiation codon overlaps the pyrF termination codon, which may indicate translational coupling in the expression of these genes. The pyrF promoter was mapped by primer extension of in vivo transcripts. The primary transcriptional initiation site is 51 base pairs upstream of the pyrF structural gene. The level of pyrF transcription and OMP decarboxylase synthesis was found to be coordinately derepressed by pyrimidine limitation, indicating that regulation of pyrF gene expression occurs at the transcriptional level. Inspection of the nucleotide sequence indicates that pyrF gene expression is not regulated by an attenuation control mechanism similar to that described for the pyrBI operon or pyrE gene. Finally, we compared the amino acid sequences of the OMP decarboxylases from E. coli, Saccharomyces cerevisiae, Neurospora crassa, and Ehrlich ascites cells to identify conserved regions.

Amino Acid Sequence↗

PubMed1993

Paralogous origin of the red- and green-sensitive visual pigment genes in vertebrates.

The nucleotide sequence of the red-sensitive visual pigment gene, R007Af, in the fish Astyanax fasciatus, from the initiation codon to the stop codon of this gene, including introns, is 1,592 bp, making it the shortest visual pigment gene known in vertebrates. Analysis of this and other homologous sequence data suggests that vertebrates initially had two duplicate genes and that each ancestor of Astyanax, human, and chicken independently duplicated the gene in the process of developing their red-green color vision. Furthermore, many extant red-green colorblind organisms may be explained simply by the failure of achieving very specific nucleotide substitutions at the three codon positions 180, 277, and 285, rather than by the lack of duplicate loci.

Amino Acid Sequence↗

PubMed1988

Primary sequence domains required for the retention of rotavirus VP7 in the endoplasmic reticulum.

Rotavirus VP7 is a membrane-associated protein of the endoplasmic reticulum (ER). It is the product of rotavirus gene 9 which potentially encodes a protein of 326 amino acids that contains two amino terminal hydrophobic domains, h1 and h2, each preceded by an initiation codon. Comparison of the size of products derived from altered genes containing coding sequences for both h1 and h2 with those lacking the h1 sequence ('dhl' mutants), indicates that initiation takes place at M30 immediately preceding h2 (residues F32 to L48) and that h2 is cleaved, confirming the studies of others (Stirzaker, S.C., P.L. Whitfeld, D.L. Christie, A.R. Bellamy, and G.W. Both. 1987. J. Cell Biol. 105:2897-2903). Our previous work had shown that deletions in the carboxy end of h2, extending to amino acid 61 in the open reading frame, resulted in secretion of VP7. The region from amino acid number 51-61, present in wild-type VP7 but missing in the secreted mutant delta 47-61, was thus implicated to have a role in ER retention. To test this, a series of chimeric genes were constructed by fusing the first 63 codons of wild-type VP7, delta 1-14 or delta 51-61/dhl, to the mouse salivary alpha-amylase gene, a secretory protein, such that the fusion junction was located at the exact mature terminus of amylase. The chimeric proteins VP7(63)/amylase, delta 1-14(63)/amylase and delta 51-61(63)/dhl/amylase were secreted when expressed in cells and the h2 domain was cleaved when mRNA was translated in vitro. These results imply that the sequence 51-61 is necessary but not sufficient for ER retention. When a second series of VP7/amylase chimera were constructed extending the VP7 contribution to amino acid 111, the product expressed by delta 1-14(111)/amylase was not secreted whereas that of delta 47-61(111)/amylase was. Significantly, the intracellular delta 1-14(111)/amylase product exhibited an amylase enzymatic specific activity that was similar to that of the wild-type amylase product. We conclude that two regions of VP7 mediate its retention in the ER, the first lies within the sequence 51-61 and the second within the sequence 62-111, which contains the glycosylation site for VP7. Both regions are necessary for retention, though neither is sufficient alone.

Amino Acid Sequence↗

PubMed1998

Characterization of replication-competent hepatitis A virus constructs containing insertions at the N terminus of the polyprotein.

To determine whether hepatitis A virus (HAV) could tolerate the insertion of exogenous sequences, we constructed full-length HAV cDNAs containing in-frame insertions at the N terminus of the polyprotein and transfected the derived T7 RNA polymerase in vitro transcripts into FRhK-4 cells. Replication of HAVvec1, a construct containing an insertion of 60 nucleotides coding for a polylinker, a 2B/2C cleavage site for HAV protease 3Cpro, and two initiation codons that restored the sequence of the N terminus of the polyprotein, was detected 2 weeks after transfection by indirect immunofluorescence analysis using anti-HAV monoclonal antibodies. Western blot analysis of HAVvec1-infected cells using anti-VP2 and anti-VP4 antibodies failed to detect the expression of the inserted sequences. Insertion of a 24-mer oligonucleotide coding for a FLAG epitope into HAVvec1 resulted in its HAV-mediated expression which was retained upon deletion of a Gln residue from the inserted 2B/2C cleavage site. Western blot analysis using anti-FLAG and anti-VP2 antibodies showed that the FLAG epitope accumulated in infected cells fused to VP0. Replacement of the FLAG epitope with an epitope of the circumsporozoite protein (CSP) of Plasmodium falciparum resulted in its stable HAV-mediated expression for at least six serial passages in FRhK-4 cells. Sedimentation analysis in sucrose density gradients showed that the CSP epitope accumulated in infected cells fused to VP0, forming 80S empty capsids which also contained native VP0. Our data suggest that the HAV internal ribosome entry site can efficiently direct dual initiation of translation of the polyprotein from AUG codons separated by 66 to 78 nucleotides and show that HAV can tolerate insertions at the N terminus of the polyprotein.

3C Viral Proteases↗

PubMed2000

Forced retroevolution of an RNA bacteriophage.

The operator hairpin ahead of the replicase gene in RNA bacteriophage MS2 contains overlapping signals for binding the coat protein and ribosomes. Coat protein binding inhibits further translation of the gene and forms the first step in capsid formation. The hairpin sequence was partially randomized to assess the importance of this structure element for the bacteriophage and to monitor alternative solutions that would evolve on the passaging of mutant phages. The evolutionary reconstruction of the operator failed in the majority of mutants. Instead, a poor imitation developed containing only some of the recognition signals for the coat protein. Three mutants were of particular interest in that they contained double nonsense codons in the lysis reading frame that runs through the operator hairpin. The simultaneous reversion of two stop codons into sense codons has a very low probability of occurring. Therefore the phage solved the problem by deleting the nonsense signals and, in fact, the complete operator, except for the initiation codon of the replicase gene. Several revertants were isolated with activities ranging from 1% to 20% of wild type. The operator, long thought to be a critical regulator, now appears to be a dispensable element. In addition, the results indicate how RNA viruses can be forced to step back to an attenuated form.

Base Sequence↗

PubMed1989

Genomic structure of the human cytosolic aldehyde dehydrogenase gene.

We have isolated and characterized several overlapping clones from two human genomic libraries constructed in cosmid and bacteriophage vectors. They span about 80 kbp and include the entire human cytosolic aldehyde dehydrogenase (ALDH1) gene. Restriction endonuclease mapping, Southern blotting with cDNA and specific oligonucleotide probes, and DNA sequencing were performed to analyze the cloned genomic DNA. The ALDH1 gene is about 53 kbp long and is divided into 13 exons which encode 501 amino acid residues. Primer extension results defined the transcription initiation site to 53 bp upstream from the A of the initiation codon ATG. The promoter region of the gene contains an ATA box and a CCAAT box, which are located 32 and 74 bp upstream, respectively, from the transcription initiation site. The possible functional domains of the protein encoded by exons are discussed. A similar intron-exon organization between the genes of cytosolic ALDH1 and its mitochondrial ALDH2 isozyme in which both enzymes are encoded by 13 exons and 9 of the 12 introns interrupt the coding sequence at homologous positions was observed. This is consistent with the model that the two isozyme genes evolved after the duplication of a common ancestor gene.

Aldehyde Dehydrogenase↗

PubMed2003

The mitochondrial genome of Strongyloides stercoralis (Nematoda) - idiosyncratic gene order and evolutionary implications.

The complete mitochondrial genome sequence of the parasitic nematode Strongyloides stercoralis was determined, and its organisation and structure compared with other nematodes for which complete mitochondrial sequence data were available. The mitochondrial genome of S. stercoralis is 13,758 bp in size and contains 36 genes (all transcribed in the clockwise direction) but lacks the atp8 gene. This genome has a high T content (55.9%) and a low C content (8.3%). Corresponding to this T content, there are 16 (poly-T) tracts of >/=12 Ts distributed across the genome. In protein-coding genes, the T bias is greatest (76.4%) at the third codon position compared with the first and second codon positions. Also, the C content is higher at the first (9.3%) and second (13.4%) codon positions than at the third (2%) position. These nucleotide biases have a significant effect on predicted codon usage patterns and, hence, on amino acid compositions of the mitochondrial proteins. Interestingly, six of the 12 protein-coding genes are predicted to employ a unique initiation codon (TTT), which has not yet been reported for any other animal mitochondrial genome. The secondary structures predicted for the 22 transfer RNA (trn) genes and the two ribosomal RNA (rrn) genes are similar to those of other nematodes. In contrast, the gene arrangement in the mitochondrial genome of S. stercoralis is different from all other nematodes studied to date, revealing only a limited number of shared gene boundaries (atp6-nad2 and cox2-rrnL). Evolutionary analyses of mitochondrial nucleotide and amino acid sequence data sets for S. stercoralis and seven other nematodes demonstrate that the mitochondrial genome provides a rich source of phylogenetically informative characters. In conclusion, the S. stercoralis mitochondrial genome, with its unique gene order and characteristics, should provide a resource for comparative mitochondrial genomics and systematics studies of parasitic nematodes.

Amino Acid Sequence↗

PubMed2003

Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria.

In eubacteria, the dissociation of the 70 S ribosome into the 30 S and 50 S subunits is the essential first step for the translation initiation of canonical mRNAs that possess 5'-leader sequences. However, a number of leaderless mRNAs that start with the initiation codon have been identified in some eubacteria. These have been shown to be translated efficiently in vivo. Here we investigated the process by which leaderless mRNA translation is initiated by using a highly reconstituted cell-free translation system from Escherichia coli. We found that leaderless mRNAs bind preferentially to 70 S ribosomes and that the leaderless mRNA.70 S.fMet-tRNA complex can transit from the initiation to the elongation phase even in the absence of initiation factors (IFs). Moreover, leaderless mRNA translation proceeds more efficiently if the intact 70 S ribosome is involved compared with the 30 S subunit. Furthermore, excess amounts of IF3 inhibit leaderless mRNA translation, probably because it promotes the disassembly of the 70 S ribosome into subunits. Finally, excess amounts of fMet-tRNA facilitate the IF-independent translation of leaderless mRNA. These observations strongly suggest that leaderless mRNA translation is initiated by the assembled 70 S ribosome and thereby bypasses the dissociation process.

Escherichia coli↗

PubMed2004

The SANT domain of human MI-ER1 interacts with Sp1 to interfere with GC box recognition and repress transcription from its own promoter.

To gain insight into the regulation of hmi-er1 expression, we cloned a human genomic DNA fragment containing one of the two hmi-er1 promoters and consisting of 1460 bp upstream of the translation initiation codon of hMI-ER1. Computer-assisted sequence analysis revealed that the hmi-er1 promoter region contains a CpG island but lacks an identifiable TATA element, initiator sequence and downstream promoter element. This genomic DNA was able to direct transcription of a luciferase reporter gene in a variety of human cell lines, and the minimal promoter was shown to be located within-68/+144 bp. Several putative Sp1 binding sites were identified, and we show that Sp1 can bind to the hmi-er1 minimal promoter and increase transcription, suggesting that the level of hmi-er1 expression may depend on the availability of Sp1 protein. Functional analysis revealed that hMI-ER1 represses Sp1-activated transcription from the minimal promoter by a histone deacetylase-independent mechanism. Chromatin immunoprecipitation analysis demonstrated that both Sp1 and hMI-ER1 are associated with the chromatin of the hmi-er1 promoter and that overexpression of hMI-ER1 in cell lines that allow Tet-On-inducible expression resulted in loss of detectable Sp1 from the endogenous hmi-er1 promoter. The mechanism by which this occurs does not involve binding of hMI-ER1 to cis-acting elements. Instead, we show that hMI-ER1 physically associates with Sp1 and that endogenous complexes containing the two proteins could be detected in vivo. Furthermore, hMI-ER1 specifically interferes with binding of Sp1 to the hmi-er1 minimal promoter as well as to an Sp1 consensus oligonucleotide. Deletion analysis revealed that this interaction occurs through a region containing the SANT domain of hMI-ER1. Together, these data reveal a functional role for the SANT domain in the action of co-repressor regulatory factors and suggest that the association of hMI-ER1 with Sp1 represents a novel mechanism for the negative regulation of Sp1 target promoters.

Base Sequence↗

PubMed1983

Yeast ribosomal protein S33 is encoded by an unsplit gene.

The structure of the gene coding for ribosomal protein S33, - a protein which escapes the coordinate control of ribosomal protein synthesis in rna 2 mutant cells -, was determined by sequence analysis. The gene comprises an uninterrupted coding region of 204 nucleotides encoding a protein of 8.9 kD. Like for other yeast ribosomal protein genes that have been sequenced so far, a relatively strong codon bias was observed. By S1 nuclease mapping the 5' end of the S33 mRNA was shown to be located at 11 to 15 nucleotides upstream from the initiation codon.

Amino Acid Sequence↗

PubMed2000

Specific binding of Hoechst 33258 to site 1 thymidylate synthase mRNA.

The translational initiator codon in thymidylate synthetase (TS) mRNA is located in a stem-loop structure with a CC bubble. TS is an important target for anticancer drugs. Aminoglycoside antibiotics have been shown to specifically bind to TS mRNA site 1 constructs and, furthermore, specific binding requires the non-duplex CC bubble region. It is shown here that DNA intercalating agents and DNA minor groove-binding drugs also bind to a TS mRNA site 1 construct. This binding is competitive with aminoglycosides, suggesting that the binding sites overlap. Hoechst 33258 binds with a dissociation constant of 60 nM, a value significantly lower than the approximately 1 microM values found for aminoglycosides. Footprinting and direct binding studies show that the CC bubble is important for binding of the Hoechst compound. However, the exact structure of the bubble is unimportant. Interestingly, mutations in regions adjacent to the bulge also affect binding. These studies point to the important role of non-duplex RNA structures in binding of the DNA minor groove binder Hoechst 33258.

Anti-Bacterial Agents↗

PubMed1993

Gene-specific translational control of the yeast GCN4 gene by phosphorylation of eukaryotic initiation factor 2.

Phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF-2 alpha) is one of the best-characterized mechanisms for down-regulating total protein synthesis in mammalian cells in response to various stress conditions. Recent work indicates that regulation of the GCN4 gene of Saccharomyces cerevisiae by amino acid availability represents a gene-specific case of translational control by phosphorylation of eIF-2 alpha. Four short open reading frames in the leader of GCN4 mRNA (uORFs) restrict the flow of scanning ribosomes from the cap site to the GCN4 initiation codon. When amino acids are abundant, ribosomes translate the first uORF and reinitiate at one of the remaining uORFs in the leader, after which they dissociate from the mRNA. Under conditions of amino acid starvation, many ribosomes which have translated uORF1 fail to reinitiate at uORFs 2-4 and utilize the GCN4 start codon instead. Failure to reinitiate at uORFs 2-4 in starved cells results from a reduction in the GTP-bound form of eIF-2 that delivers charged initiator tRNA(iMet) to the ribosome. When the levels of eIF-2.GTP.Met-tRNA(iMet) ternary complexes are low, many ribosomes will not rebind this critical initiation factor following translation of uORF1 until after scanning past uORF4, but before reaching GCN4. Phosphorylation of eIF-2 by the protein kinase GCN2 decreases the concentration of eIF-2.GTP.Met-tRNA(iMet) complexes by inhibiting the guanine nucleotide exchange factor for eIF-2, which is the same mechanism utilized in mammalian cells to inhibit total protein synthesis by phosphorylation of eIF-2.

Amino Acids↗

PubMed1987

The extracellular portion of HLA-DR alpha chain is composed of two compactly folded domains.

A truncated form of the class II antigen DR alpha chain of the human major histocompatibility complex was produced in bacteria. A cDNA clone encoding the intact chain was modified so that the segment encoding the signal sequence was replaced by an ATG codon and the 3' region downstream to the part corresponding to the third exon was replaced by a stop codon. The new construct was put under the control of the Tac promoter in a bacterial expression vector. The distance between the Shine-Delgarno sequence and the initiation codon was randomized so that clones with optimal expression of the truncated DR alpha chain could be obtained after induced expression and immunoscreening. The truncated DR alpha chain was subjected to limited proteolysis with chymotrypsin, and the resulting cleavage products were analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Two fragments were visualized by western blotting. Electrophoresis in the absence and presence of reducing agents suggested that one of the proteolytic fragments contained a disulphide bridge. It is concluded that the extracellular portion of the DR alpha chain is composed of two compactly folded domains connected by an extended stretch of the polypeptide chain.

Base Sequence↗

PubMed1988

First committed step of lipid A biosynthesis in Escherichia coli: sequence of the lpxA gene.

The min 4 region of the Escherichia coli genome contains genes (lpxA and lpxB) that encode proteins involved in lipid A biosynthesis. We have determined the sequence of 1,350 base pairs of DNA upstream of the lpxB gene. This fragment of DNA contains the complete coding sequence for the 28.0-kilodalton lpxA gene product and an upstream open reading frame capable of encoding a 17-kilodalton protein (ORF17). In addition there appears to be an additional open reading frame (ORF?) immediately upstream of ORF17. The initiation codon for lpxA is a GUG codon, and the start codon for ORF17 is apparently a UUG codon. The start and stop codons overlap between ORF? and ORF17, ORF17 and lpxA, and lpxA and lpxB. This overlap is suggestive of translational coupling and argues that the genes are cotranscribed. Crowell et al. (D.N. Crowell, W.S. Reznikoff, and C.R.H. Raetz, J. Bacteriol. 169:5727-5734, 1987) and Tomasiewicz and McHenry (H.G. Tomasiewicz and C.S. McHenry, J. Bacteriol. 169:5735-5744, 1987) have demonstrated that there are three similarly overlapping coding regions downstream of lpxB including dnaE, suggesting the existence of a complex operon of at least seven genes: 5'-ORF?-ORF17-lpxA-lpxB-ORF23-dnaE-ORF37-3 '.

Acyltransferases↗

PubMed1991

Structure of the human aldose reductase gene.

The structure and sequence of the human gene for aldose reductase (AR) was determined by analysis of cDNA and genomic clones. The AR gene was independently isolated from two different cosmid libraries and the clones were characterized by restriction mapping, Southern blotting, and DNA sequencing. The gene extends over approximately 18 kilobases and consists of 10 exons giving rise to a 1,384 nucleotide mRNA (excluding the poly(A) tail). The human aldose reductase gene codes for a 316-amino acid protein with a molecular mass of 35,858 daltons. The size range for the exons is 82-168 base pairs (bp), whereas that for the introns is 325 to about 7,160 bp. A major site of transcription initiation in liver was mapped to an A residue 31 nucleotides upstream from the A of the ATG initiation codon. The promotor region of the gene contains a TATA (TATTTA) box and a CCAAT box which are located 37 and 104 nucleotides upstream, respectively, from the transcription initiation site. We have found four Alu elements in the AR gene; two are found in intron 1 and one each in intron 4 and intron 9.

Aldehyde Reductase↗

PubMed1993

[Analysis of the secondary structure of the regulatory region of mRNA of the Escherichia coli rpsA gene].

The rpsA gene of E. coli coding for the ribosomal protein S1 was inserted into the plasmid pGEM-3Z under the control of a T7 promoter. The resulted plasmid was used for mRNA preparation in vitro. The toeprint analysis of the rpsA mRNA revealed a strong S1 dependence: 30S ribosomal subunits lacking S1 were inactive in the 30S initiation complex formation; addition of the free S1 restored subunits' ability to bind mRNA; a molar excess of the free S1 over ribosomes was inhibitory. The secondary structure of the rpsA mRNA in the vicinity of the initiation codon was probed with the use of specific ribonucleases. Basing on the experimental data obtained we suggest a model for the structural organisation of the rpsA mRNA translation initiation region.

Base Sequence↗

PubMed1986

Protein synthesis in yeast Saccharomyces cerevisiae. Purification of Co-eIF-2A and 'mRNA-binding factor(s)' and studies of their roles in Met-tRNAf.40S.mRNA complex formation.

Antibodies prepared against a homogeneous preparation of Co-eIF-2A20 [Ahmad et al. (1985) J. Biol. Chem. 260, 6955-6959] reacted with several polypeptides including an 80-kDa polypeptide present in a crude yeast ribosomal salt wash. This 80-kDa polypeptide, containing Co-eIF-2A (Co-eIF-2A80) activity, has been extensively purified using a two-step purification procedure involving an immunoaffinity column chromatograph prepared using antibodies against Co-eIF-2A20 (fraction II) and hydroxyapatite chromatography (fraction III). The factors, eIF-2 + homogeneous Co-eIF-2A80 (fraction III) promoted Met-tRNAf.40S complex formation with an AUG codon but not with a physiological mRNA or a polyribonucleotide messenger poly(U,G) whereas eIF-2 + a partially purified Co-eIF-2A80 preparation (fraction II) promoted Met-tRNAf.40S complex formation with an AUG codon as well as with globin mRNA and poly(U,G) messenger. This factor-promoted Met-tRNAf binding to 40S ribosomes depends absolutely on the presence of a polyribonucleotide messenger containing an initiation codon (such as AUG or GUG). Other polyribonucleotide messengers tested, such as poly(U), poly(A) and poly(A,C) were completely ineffective in this binding reaction. This result indicates that the Met-tRNAf.40S.mRNA complex is formed by a direct interaction between Met-tRNAf, 40S ribosomes and the initiation site in mRNA. A mechanism has been proposed for Met-tRNAf.40S.mRNA complex formation in yeast.

Carrier Proteins↗

PubMed2005

The position of premature termination codons in the hepatocyte nuclear factor -1 beta gene determines susceptibility to nonsense-mediated decay.

The nonsense-mediated decay (NMD) pathway is an mRNA surveillance mechanism that detects and degrades transcripts containing premature termination codons. The position of a truncating mutation can govern the resulting phenotype as mutations in the last exon evade NMD. In this study we investigated the susceptibility to NMD of six truncating HNF-1beta mutations by allele-specific quantitative real-time PCR using transformed lymphoblastoid cell lines. Four of six mutations (R181X, Q243fsdelC, P328L329fsdelCCTCT and A373fsdel29) showed evidence of NMD with levels of mutant transcript at 71% (p=0.009), 24% (p=0.008), 22% (p=0.008) and 3% (p=0.016) of the wild-type allele respectively. Comparable results were derived from lymphoblastoid cells and renal tubule cells isolated from a patient's overnight urine confirming that cell lines provide a good model for mRNA analysis. Two mutations (H69fsdelAC and P159fsdelT) produced transcripts unexpectedly immune to NMD. We conclude that truncating mutant transcripts of the HNF-1beta gene do not conform to the known rules governing NMD susceptibility, but instead demonstrate a previously unreported 5' to 3' polarity. We hypothesise that this may be due to reinitiation of translation downstream of the premature termination codon. Our study suggests that reinitiation of translation may be an important mechanism in the evasion of NMD, but that other factors such as the distance from the native initiation codon may also play a part.

Adolescent↗