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PubMed1989

Molecular cloning and the nucleotide sequence of the Clostridium thermocellum trpE gene.

The trpE gene of Clostridium thermocellum, a moderately thermophilic and absolutely anaerobic bacterium, was cloned by its ability to complement growth of an Escherichia coli tryptophan auxotroph (trpE) deficient in anthranilate synthase I. The nucleotide sequence of trpE and its flanking region was determined. The trpE gene overlapped at the termination codon with a putative initiation codon of trpG (trp[G]D), as deduced from the amino acid sequence homology with anthranilate synthase II of Serratia marcescens. S1-nuclease mapping of the trpE transcript produced in E. coli cells suggested that the promoter of C. thermocellum was utilized by E. coli. The amino acid sequence of anthranilate synthase I of C. thermocellum predicted from the nucleotide sequence is more similar to that of an extremely thermophilic bacterium, Thermus thermophilus HB8, than that of mesophilic bacteria.

Amino Acid Sequence↗

PubMed1994

Transgenic plant virus resistance mediated by untranslatable sense RNAs: expression, regulation, and fate of nonessential RNAs.

Haploid leaf tissue of tobacco cultivars K326 and K149 was transformed with several transgenes containing cDNA of the potato virus Y (PVY) coat protein (CP) open reading frame (ORF). The various transgenes containing the PVY CP ORF sequence produced (1) the expected mRNA and CP product, (2) an mRNA rendered untranslatable by introduction of a stop codon immediately after the initiation codon, or (3) an antisense RNA that was untranslatable as a result of the incorrect orientation of the PVY CP ORF behind the transcriptional promoter. Homozygous doubled haploid (DH) (diploid) plants were generated, and selfed progeny from these plants were examined. Resistance was virus specific, functioning only against PVY. An inverse correlation between transgene-derived PVY transcript steady state levels and resistance was generally noted with lines expressing the untranslatable sense version of the PVY CP ORF. A collection of DH lines, derived from a single transformation event of a common haploid plant and isogenic for the PVY transgenes expressing untranslatable sense RNA, displayed different levels of PVY resistance. Lines with actively transcribed, methylated transgene sequences had low steady state levels of transgene transcript and a virus-resistant phenotype. These results are discussed within the context of sense suppression in plants.

Base Sequence↗

PubMed1989

Two genes encode the adenine nucleotide translocator of maize mitochondria. Isolation, characterisation and expression of the structural genes.

Southern blot hybridisation of maize (Zea mays) genomic DNA with a specific cDNA probe and sequence analysis of several cDNAs have revealed that the mitochondrial adenine nucleotide translocator (ADP/ATP carrier) is encoded by two genes, both of which are expressed in dark-grown coleoptile tissue. The structural genes (designated ANT-G1 and ANT-G2), encoding the two translocator polypeptides, have been isolated from a maize genomic library and characterised by DNA sequence analysis, mung bean nuclease mapping and primer extension. The two genes each contain two introns and encode very similar proteins. Transcripts from both genes have long (approximately 200 nucleotides) 5' untranslated leaders which are unusual in that they contain several ATG codons upstream of the initiation codon. Transcript analysis of RNA extracted from serial sections of developing maize leaves reveals that the translocator genes are most actively transcribed in the basal meristem, while transcripts were undetectable in green leaves.

Amino Acid Sequence↗

PubMed1991

Genetic analysis of the attenuator of the Rhizobium meliloti trpE(G) gene.

It was previously reported that transcription of the Rhizobium meliloti trpE(G) gene starts at the adenine residue of the AUG codon of the leader peptide coding sequence (trpL), suggesting that translation of the trpL sequence starts without the Shine-Dalgarno sequence. We constructed mutations replacing the AUG codon of the trpL sequence with AAG or ACG. These mutations reduced the expression of a trpL'-'lacZ fusion gene to 0.1 and 0.2% of the wild-type level, respectively, indicating that the AUG codon is the translation initiation codon for the trpL coding sequence. In addition, these mutations, as well as a mutation converting the eighth codon (UCG) of the trpL sequence to UGA, abolished regulation by attenuation when introduced upstream of the tandem tryptophan codons in a trpE'-'lacZ fusion. Mutations affecting the stability of the probable antiterminator and terminator secondary structures in trpL mRNA were also constructed. Studies using these mutations indicate that the attenuator of R. meliloti functions in a way analogous to that of the Escherichia coli trp attenuator.

Base Sequence↗

PubMed1989

Mating-type control in Saccharomyces cerevisiae: isolation and characterization of mutants defective in repression by a1-alpha 2.

The alpha 2 protein, the product of the MAT alpha 2 cistron, represses various genes specific to the a mating type (alpha 2 repression), and when combined with the MATa1 gene product, it represses MAT alpha 1 and various haploid-specific genes (a1-alpha 2 repression). One target of a1-alpha 2 repression is RME1, which is a negative regulator of a/alpha-specific genes. We have isolated 13 recessive mutants whose a1-alpha 2 repression is defective but which retain alpha 2 repression in a genetic background of ho MATa HML alpha HMRa sir3 or ho MAT alpha HMRa HMRa sir3. These mutations can be divided into three different classes. One class contains a missense mutation, designated hml alpha 2-102, in the alpha 2 cistron of HML, and another class contains two mat alpha 2-202, in the MAT alpha locus. These three mutants each have an amino acid substitution of tyrosine or acid substitution of tyrosine or phenylalanine for cysteine at the 33rd codon from the translation initiation codon in the alpha 2 cistron of HML alpha or MAT alpha. The remaining 10 mutants make up the third class and form a single complementation group, having mutations designated aar1 (a1-alpha 2 repression), at a gene other than MAT, HML, HMR, RME1, or the four SIR genes. Although a diploid cell homozygous for the aarl and sir3 mutations and for the MATa, HML alpha, and HMRa alleles showed alpha mating type, it could sporulate and gave rise to asci containing four alpha mating-type spores. These facts indicate that the domain for alpha2 repression is separable from that for a1-alpha2 protein interaction or complex formation in the alpha2 protein and that an additional regulation gene, AAR1, is associated with the a1-alpha2 repression of the alpha1 cistron and haploid-specific genes.

Amino Acid Sequence↗

PubMed2000

Full or near full length nucleotide sequences of TT virus variants (Types SANBAN and YONBAN) and the TT virus-like mini virus.

TT virus (TTV) is a common virus and consists of many genotypes and variants. In addition, there exists a virus which both differs greatly from and retains a considerable resemblance to TTV, such as the TTV-like mini virus (TLMV) as we reported previously. Here we report the near full length genomic sequences of 4 isolates of a new variant of TTV (designated YONBAN) along with the full length sequences of 2 isolates of the TTV-SANBAN lineage and 7 isolates of the TLMV species derived from human sera. The TTV-YONBAN sequences showed only about 50% identity at the nucleotide level to those of the prototype TTV (TA278) and to SANBAN, and even less to TLMV. Moreover, the ORF1 of YONBAN lacked the ATG initiation codon which is shared by all the TTV and TLMV isolates so far identified in humans; instead, YONBAN had a Kozak's rule-compatible ACG codon as the candidate initiation site for the ORF1 translation. Nevertheless, the overall genetic structure and the conserved amino acid motifs within the ORF1 and the ORF2 were well shared among the prototype TTV strains, the SANBAN and YONBAN variants, and TLMV. The most conserved nucleotide sequence was found in the noncoding region just upstream from the ORF2, allowing construction of a phylogenetic tree which implied that the TTV genotypes and variants, the TLMV, and chicken anemia virus could be coclassified under a superfamily for which we proposed the name of 'Paracircoviridae' in our previous report.

Amino Acid Sequence↗

PubMed1991

Characterization and expression of RAD4 gene involved in nucleotide excision repair of UV-damaged Saccharomyces cerevisiae.

Saccharomyces cerevisiae express RAD4 gene for nucleotide excision repair of UV-induced DNA damages. Upon complementation with rad4-4 mutant, a 7.6 kb clone containing the RAD4 gene designated as pPC1 was isolated from a yeast genomic library. The pPC1 was further narrowed to 2.5 kb flanked with BglII and BamHI sites. The cloned RAD4 gene was found to propagate in E. coli without loss of its complementing activity. Pulse-field gel electrophoresis indicated that the cloned RAD4 gene was localized in the right arm of chromosome V. DNA-tRNA hybridization revealed that the cloned gene did not contain a suppressor tRNA gene. The rad4 mutants with various plasmids containing the cloned RAD4 gene, regardless of their copy number, had enhanced resistance against UV damages equivalent to that found in wild type. As determined by S1 nuclease digestion, the RAD4 transcript was found to be 2.3 kb in size and the S1 nuclease mapping revealed the production of a protected fragment of 760 nucleotides within the transcript. Transcriptional start point was found at 48 base pairs upstream from the first ATG codon of the translation initiation codon. The overexpressed Rad4 protein was estimated to be 89 kD and confirmed the expected size based on the actual length of RAD4 gene. Upon stationary phase culturing, E. coli cells transformed with the cloned RAD4 gene had a delayed entrance into exponential growth phase and produced reduced amount of host proteins. These results have indicated that the pPC1 is a functional RAD4 gene playing a unique role involved in the nucleotide excision repair of yeast without any genetic change during amplication in E. coli.

Cloning, Molecular↗

PubMed1999

Genetic manipulation to identify limiting steps and develop strategies for high-level expression of penicillin acylase in Escherichia coli.

We have identified the bottleneck steps limiting expression of penicillin acylase (PAC) through comparison of the expression performance for various PAC-expression vectors constructed by genetically modulating the efficiencies of transcription and/or translation of the pac gene. To our knowledge, this is the first report demonstrating that expression of PAC could be limited by various steps, such as transcription, translation, and post-translational steps (i.e. translocation and periplasmic processing), depending on the host/vector systems. Results also indicate that the structure of the wild-type pac gene might not be optimal for direct use in production of PAC using recombinant DNA technology. To improve the gene expression, transcription was enhanced by manipulating certain DNA bases in the pac regulatory region, whereas translation was enhanced by enlarging the spacing between the ribosome binding site and the ATG initiation codon to increase the initiation efficiency. The information is useful in terms of developing genetic strategies for overproduction of recombinant PAC in Escherichia coli.

Cloning, Molecular↗

PubMed1987

Translation rate modification by preferential codon usage: intragenic position effects.

We present a model for calculating the protein production rate as a function of the translation rate. The model takes into account that the elongation rate along an mRNA molecule is non-uniform as a result of different tRNA availabilities for different codons. Initiation of ribosomes on an mRNA is normally the rate-limiting step in the translation process, and blocking of the initiation site can be avoided if the codons closest to this site allow fast translation by the ribosome. Hence, different selective forces may act on the choice of synonymous codons in the initiation region than elsewhere on a given mRNA. We show that the elongation rate along the whole mRNA influences the production rate of abundant proteins, whereas only the elongation rate in the initiation region is of importance for the production rate of rare proteins. We also present an analysis of the codon distribution along known mRNAs coding for abundant and rare proteins.

Bacterial Proteins↗

PubMedDate not supplied

Comparative analysis of RNA editing sites in higher plant chloroplasts.

Transcripts of land plant chloroplast genomes undergo C-to-U RNA editing. Systematic search disclosed 31 editing sites in tobacco, 27 in maize, and 21 in rice. Based on these identified sites, potential editing sites have been predicted in the transcripts from four angiosperm chloroplast genomes which have been completely sequenced. Most RNA editing events occur in internal codons, which result in amino-acid substitutions. The initiation codon AUG was found to be created from ACG by RNA editing in the transcripts from rpl2, psbL, and ndhD genes. Comparison of editing patterns raises a possibility that many editing sites were acquired in the evolution of angiosperms.

Binding Sites↗

PubMed2005

Increased expression of the glucocorticoid receptor-A translational isoform as a result of the ER22/23EK polymorphism.

One of the most intriguing polymorphisms in the GR [glucocorticoid (GC) receptor] gene is in codons 22 and 23 [GAGAGG(GluArg) --> GAAAAG (GluLys)]. This polymorphism is associated with a reduced GC sensitivity, a better metabolic and cardiovascular health profile, and an increased survival rate. Recently, Yudt and Cidlowski reported that two different methionine codons in the GR mRNA may be used as initiation codon: AUG-1 and AUG-27, resulting in two isoforms, the GR-A and the GR-B proteins, respectively. They also showed that the GR-B protein had a stronger transactivating effect in transient transfection experiments. In this study, we elucidated the molecular basis for the reduced GC sensitivity by investigating the influence of the ER22/23EK polymorphism on synthesis of GR-A and GR-B by expressing them independently from constructs with and without the polymorphic site. Binding studies with [(3)H]-dexamethasone and transactivation studies showed that, when the ER22/23EK polymorphism is present, approximately 15% more GR-A protein was expressed, whereas total GR levels (GR-A + GR-B) were not affected. These results show that the transcriptional activity in GR(ER22/23EK) carriers is decreased because more of the less transcriptionally active GR-A isoform is formed. This is probably caused by altered secondary mRNA structure.

Alternative Splicing↗

PubMed2001

A somatic mutation in the 5'UTR of BRCA1 gene in sporadic breast cancer causes down-modulation of translation efficiency.

Mutations in the 5' UTR which cause increment/decrement of translation efficiency have been recently described as a novel molecular mechanism of disease. Alterations in the consensus sequence for the translation initiation may promote context-dependent leaky scanning of ribosomes and/or initiation from a downstream AUG codon. Initiation of translation from a downstream in-frame AUG codon in BRCA1 gene was recently identified in normal cells and possibly in breast cancer. Here we present further insight into BRCA1 translational pathophysiology investigating the role of the canonical structure of the initiation consensus sequence of BRCA1. We have analysed the effect of a somatic point mutation (117 G>C) in position -3 with respect to the AUG of the BRCA1 gene, identified in a highly aggressive sporadic breast cancer. We constructed chimeric genes encoding the luciferase reporter sequence downstream of the wild type or the mutated BRCA1 5'UTR. These transcripts were tested for their activity in in vitro and in vivo systems. In in vitro transcription/translation assays the estimated translation efficiency of the construct with the mutated BRCA1 5'UTR was 30-50% lower than that with the wild type BRCA1 5'UTR. The same chimeric genes were analysed for their expression in vivo by transient transfection in human cells. While the two constructs were equally transcribed, the plasmid carrying the mutated sequence produced 70% less luciferase activity compared to the wild type sequence. Finally, to obtain a direct evaluation on translational efficiency in vivo, we analysed mRNA translation on translationally active and non-active ribosomes separated from transfected cells. Mutant mRNA was partially localized in subpolysomal particles analytically confirming a polysome recruitment defect. Thus, characterization of BRCA1 5'UTR and translation efficiency seems to provide new insight into BRCA1 role in breast and ovarian cancer pathogenesis.

5' Untranslated Regions↗

PubMed1998

Involvement of the 5' proximal coding sequences of hepatitis C virus with internal initiation of viral translation.

The 5' nontranslated region (NTR) of hepatitis C virus (HCV) consists of 341 nucleotides (nt). This region comprises the majority of the internal ribosome entry site (IRES) which controls the efficiency of viral translation. Previous studies of the 3' boundary of the HCV IRES yielded conflicting data regarding the involvement of viral coding sequences in IRES activity. We therefore studied the functional significance of the 5' proximal coding sequences of the HCV core gene on IRES activity. We constructed monocistronic and bicistronic DNAs that contained either a chloramphenicol acetyl transferase (CAT) gene or a luciferase (Luc) gene as the reporter. Results from both in vitro and in vivo experiments indicated that the optimal IRES ranged within nt 1-371. Further mutational analyses of sequences surrounding the initiation codon revealed that primary sequences downstream of the AUG initiator rather than the secondary structure are important in regulating optimal IRES function. We are also able to demonstrate that a non-AUG codon could be used to initiate the synthesis of a reporter protein, albeit with lower efficiency. These findings bear important implications for the HCV IRES secondary structures.

5' Untranslated Regions↗

PubMed1998

Molecular cloning and characterization of the human p44 mitogen-activated protein kinase gene.

The complete genomic structure of the human p44(mapk) gene (HMGW-approved symbol PRKM3) has been determined. The gene covers 9 kb and is composed of nine exons and eight introns. This structure is identical to the previously reported mouse p44(mapk) gene, indicating a high degree of evolutionary conservation. A sequence differing by one nucleotide from the consensus TATA box is present 132 positions upstream of the main transcription initiation point. This point has been located 415 nucleotides upstream of the translation initiation codon ATG and perfectly meets the consensus criteria for an initiator element (Inr). Multiple consensus sequences for factors that regulate either basal transcription or gene expression during cell differentiation and proliferation can be found in the putative promoter region. Some of them, such as several G/C boxes located downstream from the transcription initiation point, are also present in the homologous mouse gene, where they were shown to be functional.

5' Untranslated Regions↗

PubMed2004

Translation of a yeast mitochondrial tRNA synthetase initiated at redundant non-AUG codons.

Although initiation of translation at non-AUG codons occurs occasionally in prokaryotes and higher eukaryotes, it has not been reported in yeast until very recently. Evidence presented here shows that redundant ACG codons are recognized as alternative translation start sites for ALA1, the only gene in Saccharomyces cerevisiae coding for alanyl-tRNA synthetase. ALA1 is shown to be a bifunctional gene that provides both cytoplasmic and mitochondrial activities. Unlike most bifunctional genes that contain alternative in-frame AUG initiators, there is only one AUG codon, designated AUG1, close to the 5'-end of the ALA1 open reading frame. Transcriptional mapping identified three overlapping transcripts, with 5'-ends at positions 54, 105, and 117 nucleotides upstream of AUG1, respectively. Site-specific mutagenesis demonstrated that the cytoplasmic and mitochondrial functions of ALA1 are provided by two protein isoforms with distinct amino termini; that is, a short cytoplasmic form initiated at AUG1 and a longer mitochondrial isoform initiated at two upstream in-frame ACG codons, i.e. ACG(-25) and ACG(-24). These two ACG codons function redundantly in initiation of translation. Either codon can function in the absence of the other. The short transcript appears to serve as the template for the cytoplasmic form, whereas the longer transcripts are likely to code for both isoforms via alternative initiation. Because yeast ribosomes in general cannot efficiently recognize a non-AUG initiator, this unique feature of redundancy of non-AUG initiators in a single mRNA may in itself represent a novel paradigm for translation initiation from poor initiators.

Amino Acyl-tRNA Synthetases↗

PubMed2003

The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase.

In an earlier study (S. W. Jordan and J. E. Cronan, Jr., J. Biol. Chem. 272:17903-17906, 1997) we reported a new enzyme, lipoyl-[acyl carrier protein]-protein N-lipoyltransferase, in Escherichia coli and mitochondria that transfers lipoic acid from lipoyl-acyl carrier protein to the lipoyl domains of pyruvate dehydrogenase. It was also shown that E. coli lipB mutants lack this enzyme activity, a finding consistent with lipB being the gene that encoded the lipoyltransferase. However, it remained possible that lipB encoded a positive regulator required for lipoyltransferase expression or action. We now report genetic and biochemical evidence demonstrating that lipB encodes the lipoyltransferase. A lipB temperature-sensitive mutant was shown to produce a thermolabile lipoyltransferase and a tagged version of the lipB-encoded protein was purified to homogeneity and shown to catalyze the transfer of either lipoic acid or octanoic acid from their acyl carrier protein thioesters to the lipoyl domain of pyruvate dehydrogenase. In the course of these experiments the ATG initiation codon commonly assigned to lipB genes in genomic databases was shown to produce a nonfunctional E. coli LipB protein, whereas initiation at an upstream TTG codon gave a stable and enzymatically active protein. Prior genetic results (T. W. Morris, K. E. Reed, and J. E. Cronan, Jr., J. Bacteriol. 177:1-10, 1995) suggested that lipoate protein ligase (LplA) could also utilize (albeit poorly) acyl carrier protein substrates in addition to its normal substrates lipoic acid plus ATP. We have detected a very slow LplA-catalyzed transfer of lipoic acid and octanoic acid from their acyl carrier protein thioesters to the lipoyl domain of pyruvate dehydrogenase. A nonhydrolyzable lipoyl-AMP analogue was found to competitively inhibit both ACP-dependent and ATP-dependent reactions of LplA, suggesting that the same active site catalyzes two chemically diverse reactions.

Acyltransferases↗

PubMed1993

Identification of an alternative 5' untranslated region of the adenomatous polyposis coli gene.

cDNA clones, representing transcripts expressed in human fetal brain, have been isolated that specify the 5' end of the adenomatous polyposis coli (APC) gene. Sequence analyses have revealed an alternative 5' untranslated region (5'UTR) of the APC gene; this region is comprised of at least 103 basepairs. A comparison of this alternative UTR with the published sequence of the APC-gene indicates that these two 5'UTR sequences diverge beyond nucleotide position -20 with respect to the A of the authentic translational initiation codon. These data suggest that two APC-specific promoter elements exist, giving rise to two different untranslated regions. Within the alternative UTR, we have identified 3 additional AUG codons, located 5' to the intrinsic APC initiation site. Two of these AUG codons are located in a nucleotide context that favours initiation of truncated translation products. The relevance of these additional AUG codons to a regulatory mechanism acting at the post-transcriptional level of APC gene expression is discussed.

Adenomatous Polyposis Coli↗

PubMed1992

A putative two-component regulatory system involved in secondary metabolism in Streptomyces spp.

A DNA fragment stimulating actinorhodin, undecylprodigiosin, and A-factor production in Streptomyces lividans 66 was cloned from Streptomyces coelicolor A3(2). Nucleotide sequencing revealed the presence of an open reading frame of 225 codons, named afsQ1, that showed great similarity in amino acid sequence to the response regulators of typical prokaryotic two-component regulatory systems responsible for adaptive responses. The termination codon, TGA, of afsQ1 overlapped the initiation codon, GTG, of a second open reading frame, afsQ2, of 535 codons. The afsQ2 gene product showed homology with the sensory histidine protein kinases of two-component systems. In agreement with the assumption that the AfsQ1 and AfsQ2 proteins comprise an aspartate-histidine phosphotransfer system, an amino acid replacement from Asp to Glu at residue 52 of AfsQ1, generated by site-directed mutagenesis, resulted in loss of the protein's ability to stimulate antibiotic production in S. lividans. Primer extension experiments indicated that transcription of the afsQ1 and afsQ2 genes initiates at the translational start codon (GTG) of the afsQ1 gene. The afsQ1 and afsQ2 genes were physically mapped at a chromosomal position near the actinorhodin biosynthetic gene cluster (act) by hybridization to Southern blots of restriction fragments separated by pulsed-field gel electrophoresis. Disruption of either afsQ1 or afsQ2 on the S. coelicolor chromosome by use of phage phi C31KC515 led to no detectable change in secondary metabolite formation or morphogenesis. The afsQ1 gene on pIJ922 suppressed the S. coelicolor absA mutation and caused actinorhodin production but did not suppress the absB mutation. Southern blot hybridization showed that sequences homologous to afsQ1 and afsQ2 are present in almost all of the actinomycetes examined.

4-Butyrolactone↗