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PubMed1994

Interdependence of gene expression for early steps of cephalosporin synthesis in Streptomyces clavuligerus.

The early steps of cephamycin synthesis by S. clavuligerus are catalyzed sequentially by lysine epsilon-aminotransferase (LAT), delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) and isopenicillin N synthase (cyclase, IPNS). The genes (lat, pcbAB, and pcbC, respectively) are closely linked in the same order as the enzymes act in the biosynthetic pathway and are transcribed in the same direction. Four cephamycin non- (or low-) producing mutants are pleiotropic in that they have undetectable or markedly diminished levels of ACVS and cyclase; two mutants almost completely lack LAT activity. All four mutants are complemented in cephamycin formation by transformation with pNBR1, a plasmid containing a 7.2-kb genomic region of S. clavuligerus in vector pIJ702. The cloned DNA was found to possess no part of the cyclase gene, but instead it contained lat and the 5' upstream part of pcbAB. Doran et al. reported that the 31-bp region between pcbAB and pcbC contains no recognizable promoter or transcription termination sequences. We found that there are 153 bp between the lat ORF and the pcbAB start codon. A potential transcriptional terminator begins 4 to 6 bp downstream of the lat ORF. In the 111-bp segment between the end of the "terminator" and the pcbAB start codon, there are no Streptomyces-like or Escherichia coli-like promoter consensus sequences. However, upstream of the "terminator," that is, in the downstream portion of the lat ORF, are two regions resembling a Streptomyces consensus promoter. Promoter activity in gene fusion constructions was demonstrated in this region. A third potential promoter is upstream of the lat ORF, but only the--10 part is on the cloned DNA. The mechanism by which the cloned DNA (containing lat, the 5' part of pcbAB, and the intervening sequence) influences the expression of the downstream genes encoding ACVS and IPNS, even in strains that possess LAT activity, is an intriguing target of future investigation.

Cephalosporins↗

PubMed1997

Roles of the tnaC-tnaA spacer region and Rho factor in regulating expression of the tryptophanase operon of Proteus vulgaris.

To localize the DNA regions responsible for basal-level and induced expression of the tryptophanase (tna) operon of Proteus vulgaris, short deletions were introduced in the 115-bp spacer region separating tnaC, the leader peptide coding region, from tnaA. Deletions were incorporated into a tnaA'-'lacZ reporter construct containing the intact tna promoter-leader region. Expression was examined in Escherichia coli. Deletions that removed 28 to 30 bp from the region immediately following tnaC increased basal-level expression about threefold and allowed threefold induction by 1-methyltryptophan. A deletion removing 34 bp from the distal segment of the leader permitted basal and induced expression comparable to that of the parental construct. The mutant with the largest spacer deletion, 89 bp, exhibited a 30-fold increase in basal-level expression, and most importantly, inducer presence reduced operon expression by ca. 60%. Replacing the tnaC start codon or replacing or removing Trp codon 20 of tnaC of this deletion derivative eliminated inducer inhibition of expression. These findings suggest that the spacer region separating tnaC and tnaA is essential for Rho action. They also suggest that juxtaposition of the tnaC stop codon and the tnaA ribosome binding site in the 89-bp deletion derivative allows the ribosome that has completed translation of tnaC to inhibit translation initiation at the tnaA start codon when cells are exposed to inducer. These findings are consistent with results in the companion article that suggest that inducer allows the TnaC peptide to inhibit ribosome release at the tnaC stop codon.

Bacterial Proteins↗

PubMed1989

Dual translational initiation sites control function of the lambda S gene.

Lysis gene S of phage lambda has a 107 codon reading frame beginning with the codons Met1-Lys2-Met3. Genetic data have suggested that translational initiation occurs at both Met1 and Met3, generating two polypeptides, S107 and S105 respectively. We have proposed a model in which the proper scheduling of lysis depends on the partition of translational initiations between the two start codons. Here, using in vitro methods, we show that two stem-loop structures, one immediately upstream of the reading frame and a second approximately 10 codons within the gene, control the partitioning event. Utilizing primer-extension inhibition or 'toeprinting', we show that the two S start codons are served by two adjacent Shine-Dalgarno sequences. Moreover, the timing of lysis supported by the wild-type and a number of mutant alleles in vivo can be correlated with the ratio of ternary complex formation over Met1 and Met3 in vitro. Thus the regulation of the S gene is unique in that the products of two adjacent in-frame initiation events have opposing function.

Bacteriolysis↗

PubMed1989

High molecular mass forms of basic fibroblast growth factor are initiated by alternative CUG codons.

A 6.75-kilobase human hepatoma-derived basic fibroblast growth factor (bFGF) cDNA was cloned and sequenced. An amino-terminal sequence generated from a purified hepatoma bFGF was found to correspond to the nucleotide sequence and to begin 8 amino acids upstream from the putative methionine start codon thought to initiate a 154-amino acid bFGF translation product. This sequence suggests that a form of bFGF of at least 163 amino acids exists. The hepatoma cDNA was transcribed in vitro into RNA; in vitro translation of this RNA generated three forms of bFGF with molecular masses of 18, 21, and 22.5 kDa. By use of in vitro mutagenesis, it was found that the 22.5-kDa bFGF and possibly the 21-kDa form were initiated with CUG start codons. The 18-kDa bFGF was initiated with an AUG codon. By transfecting into COS cells human hepatoma bFGF cDNA and a construct from which the AUG initiator was eliminated, it was found that the higher molecular mass forms of bFGF were as biologically active as the 18-kDa form.

Amino Acid Sequence↗

PubMed2003

Non-AUG translation initiation of mRNA encoding acidic ribosomal P2A protein in Candida albicans.

The eukaryotic 60S ribosomal subunit has a set of very acidic proteins (P-proteins), which form a distinct lateral protuberance called the stalk structure. This protein complex is directly involved in the elongation step of polypeptide synthesis. In our study on acidic ribosomal P-proteins from the human opportunistic pathogen Candida albicans, we isolated and characterized one of the genes, called CARP2A, and its product, the P2A protein. The CARP2A gene is intron-less, present in a single copy per haploid genome, and transcriptionally active. The open reading frame of the studied gene contains information for a sequence of 108 amino acids. Based on this, the molecular mass and isoelectric point of the P2A protein were theoretically calculated to be 10.85 kDa and 3.7, respectively. The characteristic feature of the CARP2A gene transcript is the presence of a GUG start codon, which is rare in eukaryotic organisms and not previously reported in yeast. To our knowledge this is the first report showing the presence of a naturally occurring non-AUG start codon on mRNA in yeast species.

Amino Acid Sequence↗

PubMed1994

TSH and TSH receptor antibody-binding sites in fibroblasts of pretibial myxedema are related to the extracellular domain of entire TSH receptor.

The role of TSH receptor antibodies in the pathogenesis of pretibial myxedema is still unclear. This study was designed to determine whether patients with pretibial myxedema had higher serum titers of TSH receptor antibodies, and whether there were TSH and TSH receptor antibody-binding sites on plasma membranes of fibroblasts derived from the skin of pretibial myxedema. If there were, were the binding sites similar to the TSH receptor? The TSH receptor antibodies were determined with radioreceptor assay in 20 normal subjects, 18 hyperthyroid Graves' disease patients without ophthalmopathy, 26 hyperthyroid Graves' disease patients with ophthalmopathy, and 11 patients with pretibial myxedema associated with Graves' ophthalmopathy. TSH and TSH receptor antibody-binding sites were studied on plasma membranes of fibroblasts cultured from the skin of pretibial myxedema with radioreceptor assay. RNA was also extracted from the fibroblasts of pretibial myxedema and reverse transcribed using random primers as the primers for cDNA synthesis. The resulting cDNAs were subjected to amplification by polymerase chain reaction with the use of a set of primers spanning the 5' region (+256/+275 and +616/+635) and the 3' region (+1819/+1838 and +2405/+2424) of the TSH receptor cDNA (+1 transcription start codon). They were further identified by Southern blot hybridization, with the probe spanning the 5' region (+272/+612) and the 3' region (+1908/+2268) of the TSH receptor cDNA (+ 1 transcription start codon), and sequencing. The results showed that patients with pretibial myxedema had higher titers of TSH receptor antibodies in the serum. TSH and TSH receptor antibody-binding sites were present on plasma membranes of fibroblasts derived from the skin of pretibial myxedema patients and related to the extracellular domain of the TSH receptor. These data suggest a common antigenic site in the skin and in the thyroid as a putative target for TSH receptor antibodies or lymphocytes of Graves' disease.

Adult↗

PubMed1996

The human connexin32 gene is transcribed from two tissue-specific promoters.

The connexin32 (cx32) gene codes for the gap junction protein found in liver, pancreas and nervous tissue. Recently mutations in the coding region of this gene have been associated with the dominant X-linked form of Charcot-Marie-Tooth (CMTX1) neuropathy. Since some CMTX1 patients show no mutations in their cx32 gene coding region, it was speculated that these patients carry mutations in the promoter region of the gene. This paper describes the organization of the human cx32 gene and its tissue-specific transcription. The gene consists of three exons that are alternatively spliced to produce mRNAs with different 5'-untranslated regions (UTRs). Transcription is initiated from two tissue-specific promoters. In liver and pancreas, promoter P1, located more than 8 kb upstream of the translation start codon, is used, and the transcript is processed to remove a large intron. In contrast, in nerve cells, transcription is initiated from promoter P2, located 497 bp upstream from the translation start codon, and the transcript is processed to remove a small 355-pb intron. The downstream exon, which includes the entire coding sequence, is shared by both mRNAs. CMTX1 patients with a normal cx32 coding region are expected to have mutations in this newly described promoter P2 rather than the known promoter P1.

Alternative Splicing↗

PubMed1998

The stability of mRNA from the gsiB gene of Bacillus subtilis is dependent on the presence of a strong ribosome binding site.

In Bacillus subtilis IS58 starved of glucose or exposed to heat shock, ethanol or salt stress, the sigmaB-dependent general stress protein GsiB is accumulated to a higher level than other general stress proteins. This high-level accumulation of GsiB can at least partially be attributed to the remarkably long half-life (approximately 20 min) of the gsiB mRNA. Analysis of different gsiB-lacZ fusions revealed that this stability is not determined by sequences at the 3' end of the transcript but rather by sequences upstream of the translational start codon. Site-directed mutagenesis established that a strong ribosome binding site was crucial for the increased stability of the gsiB mRNA. A comparison of the sequences upstream of the translational start codons of three general stress genes, gsiB, gspA and ctc, revealed a direct correlation between mRNA stability and the strength of their translational signals.

Bacillus subtilis↗

PubMed2003

Two novel spliced presenilin 2 transcripts in human lymphocyte with oxidant stress and brain.

We identified two novel spliced human presenilin 2 (PS2) transcripts. The first, PS2deltaEx3-7, lacked part ofexon 3, all of exons 4, 5, and 6, and part of exon 7, resulting in an in-frame shift and inclusion of the natural start codon and proteolytic region. This transcript was detected in cerebral cortex and peripheral lymphocytes. The second transcript, PS2deltaEx4, lacked exon 4, resulting in a frame shift and inclusion of the natural start codon, and was transcribed in peripheral lymphocytes and heart but not in brain. Quantitative RT-PCR analysis revealed that the PS2deltaEx3-7 significantly increased in lymphocytes treated with H2O2, suggesting that this transcript is a novel genetic marker that can be used to study the pathogenesis of Alzheimer's disease.

Amino Acid Sequence↗

PubMed1996

Position-dependent ATT initiation during plant pararetrovirus rice tungro bacilliform virus translation.

The expression of the rice tungro bacilliform virus open reading frame I was studied in transiently transfected protoplasts. Expression occurs despite the presence of a long leader sequence and the absence of a proper ATG initiation codon. Translation is initiated at an ATT codon. The efficiency of initiation in rice protoplasts depends strongly on the mechanism by which ribosomes reach this codon. From the effects of scanning-inhibiting structures inserted into different leader regions, it can be deduced that this mechanism is related to the ribosome shunt described for cauliflower mosaic virus 35S RNA. The process delivers initiation-competent ribosomes to the region downstream of the leader and is so precise that only the second of two potential start codons only 12 nucleotides apart is recognized. The ATT codon that is used when it is present downstream of the leader is hardly recognized as a start codon by ribosomes that reach it by scanning.

Base Sequence↗

PubMed2002

Analysis of Mesorhizobium loti glycogen operon: effect of phosphoglucomutase (pgm) and glycogen synthase (g/gA) null mutants on nodulation of Lotus tenuis.

The phosphoglucomutase (pgm) gene codes for a key enzyme required for the formation of UDP-glucose and ADP-glucose, the sugar donors for the biosynthesis of glucose containing polysaccharides. A Mesorhizobium loti pgm null mutant obtained in this study contains an altered form of lipopolysaccharide (LPS), lacks exopolysaccharide (EPS), beta cyclic glucan, and glycogen and is unable to nodulate Lotus tenuis. The nonnodulating phenotype of the pgm mutant was not due to the absence of glycogen, since a glycogen synthase (glgA) null mutant effectively nodulates this legume. In M. loti, pgm is part of the glycogen metabolism gene cluster formed by GlgP (glycogen phosphorylase), glgB (glycogen branching), glgC (ADP-glucose pyrophosphorylase), glgA, pgm, and glgX (glycogen debranching). The genes are transcribed as a single transcript from glgP to at least pgm under the control of a strong promoter (promoter I) upstream of glgP. An alternative promoter (promoter II), mapping in a 154-bp DNA fragment spanning 85 bp upstream of the glgA start codon and the first 69 bp of the glgA coding region, controls the expression of glgA and pgm, independently of the rest of the upstream genes. Primer extension experiments showed that transcription starts 19 bp upstream of the glgA start codon.

1,4-alpha-Glucan Branching Enzyme↗

PubMed1995

Isolation and characterization of the promoter of the human 5'-nucleotidase (CD73)-encoding gene.

Ecto-5'-nucleotidase (NT, CD73) is a purine salvage-pathway enzyme located on the surface of various cell types, including subsets of human lymphocytes and certain leukemias and lymphomas. In addition to purine salvage, NT has proposed roles in lymphocyte maturation and activation, and its expression has been associated with the resistance of some tumor cell lines to chemotherapeutic agents. To better understand the regulation of NT gene expression in normal lymphocyte development and the elevated expression seen in some drug-resistant tumor cell lines, we isolated NT genomic clones containing the promoter region. The genomic DNA upstream from the NT start codon is high in G+C content, with one cAMP-responsive element and five consensus Sp-1 binding sites, but no TATAA box. RNase protection assays identified a cluster of potential transcription start points (tsp). One tsp, at -63 bp relative to the start codon, was confirmed as authentic by 5'-RACE (rapid amplification of cDNA ends) cloning. Transient transfection experiments utilizing luc as a reporter gene have demonstrated that a 155-bp NT genomic DNA segment inclusive of the tsp functions as a promoter in both NT+ (WI-L2 and MG) and NT- (Jurkat, Hela and Raji) cell lines. The addition of 5'-flanking sequences extending as far as -1.9 kb did not confer cell-type-specific expression to the core promoter. However, nuclear run-on analysis of nascent NT transcripts suggested that differential transcription initiation is at least partially responsible for the regulation of NT expression. Thus, additional information is necessary, either at the chromatin level, or within elements outside of the promoter region, to direct tissue-specific expression of NT.

5'-Nucleotidase↗

PubMed1984

Coordinate increase in major transcripts from the high pI alpha-amylase multigene family in barley aleurone cells stimulated with gibberellic acid.

The purpose of this study was to identify specifically genes and transcripts for the high pI isozyme of barley alpha-amylase. From hybridization of coding sequence probes to blots of genomic DNA digested with restriction enzymes that do not cut within our cloned high pI alpha-amylase cDNA, it is estimated that about 7 alpha-amylase genes or pseudogenes exist. No difference could be detected between barley aleurone cell and sprout DNAs. Experiments using probes from the 5' and 3' untranslated sequences of the high pI alpha-amylase cDNA clone identified three HindIII fragments that probably carry high pI sequences. Primer extension experiments used as a primer the terminal 5' coding sequence from our cDNA clone; this primer would not cross-hybridize to low pI alpha-amylase transcripts. Two major transcripts were identified. These shared a conserved 23-base sequence immediately 5' to the ATG start codon, although a C----G transversion and a 3-base deletion were present within this sequence. An unusual 8-base pair GC palindrome was present in the conserved region immediately preceding the ATG start codon. Distal to the conserved sequence there was no apparent homology. One transcript carrying a 97-base untranslated region was identical to our high pI cDNA clone E. The gene for the other was recovered from a lambda phage genomic library. The 5' coding sequence was very similar, but not identical to clone E, demonstrating that these transcripts arise from separate genes. The two transcripts increased coordinately in aleurone cells stimulated with gibberellic acid. These data indicate that there is a high pI alpha-amylase multigene family with at least two active members, both of which are regulated in some manner by the plant hormone gibberellic acid.

Base Sequence↗

PubMed2005

Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation.

Genetic studies in yeast have shown that the translation initiation factor eIF5 plays an important role in the selection of the AUG start codon. In order to ensure translation fidelity, the hydrolysis of GTP bound to the 40S preinitiation complex (40S.Met-tRNA(i).eIF2.GTP), promoted by eIF5, must occur only when the complex has selected the AUG start codon. However, the mechanism that prevents the eIF5-promoted GTP hydrolysis, prior to AUG selection by the ribosomal machinery, is not known. In this work, we show that the presence of initiation factors eIF1, eIF1A and eIF3 in the 40S preinitiation complex (40S.eIF1.eIF1A.eIF3.Met-tRNA(i).eIF2.GTP) and the subsequent binding of the preinitiation complex to eIF4F bound at the 5'-cap structure of mRNA are necessary for preventing eIF5-promoted hydrolysis of GTP in the 40S preinitiation complex. This block in GTP hydrolysis is released upon AUG selection by the 40S preinitiation complex. These results, taken together, demonstrate the biochemical requirements for regulation of GTP hydrolysis and its coupling to the AUG selection process during translation initiation.

Animals↗

PubMed1995

Structural organization and chromosomal assignment of the human obese gene.

The obese (ob) gene has been identified through a positional cloning approach; the mutation of this gene causes marked hereditary obesity and diabetes mellitus in mice. We report here the isolation and characterization of the human ob gene. Southern blot analysis demonstrated a single copy of the ob gene in the human genome. The human ob gene spanned approximately 20 kilobases (kb) and contained three exons separated by two introns. The first intron, approximately 10.6 kb in size, occurred in the 5'-untranslated region, 29 base pair (bp) upstream of the ATG start codon. The second intron of 2.3 kb in size was located at glutamine +49. By rapid amplification of 5'-cDNA ends, the transcription initiation sites were mapped 54-57 bp upstream of the ATG start codon. The 172-bp 5'-flanking region of the human ob gene contained a TATA box-like sequence and several cis-acting regulatory elements (three copies of GC boxes, an AP-2-binding site, and a CCAAT/enhancer-binding protein-binding site). By the fluorescence in situ hybridization technique, the ob gene was assigned to human chromosome 7q31.3. This study should establish the genetic basis for ob gene research in humans, thereby leading to the better understanding of the molecular mechanisms underlying the ob gene.

Amino Acid Sequence↗

PubMed2002

[Generation of a series of recombinant herpes simplex viruses which can provide replicating and packaging functions for recombinant adeno-associated virus].

BACKGROUND: To construct a series of recombinant herpes simplex viruses that can provide replicating and packaging functions for recombinant adeno-associated virus (rAAV), and to select the strains possessing stronger functions for large-scale production of rAAV. METHODS: A set of cosmids that represents the whole genome of HSV-1 was used to generate recombinant HSV-1 expressing rep and cap proteins of AAV-2. An ATG-to-ACG mutation in the start codon of AAV-2 rep protein was generated by site-directed mutagenesis. rep and cap genes, under control of their native promoters, with or without the ATG-to-ACG mutation in the start codon of rep, were inserted into the Xba site of UL2 or UL44 genes, respectively, resulting in the recombinant cosmids cos6-rmc/ UL2, cos56-rc/ UL44 and cos56-rmc/ UL44. Homologous recombination among the HSV-1 fragment on the recombinant cosmids and the rest fragments of HSV-1 genome resulted in three strains of recombinant HSV-1. Together with the one was constructed previously, there were four strains of recombinant HSV-1named HSV1-rc/ UL2, HSV1-rmc/ UL2, HSV1-rc/ UL44 and HSV1-rmc/ UL44 respectively. RESULTS: PCR detection confirmed the existence of rep- gene in the genomes of all four strains of the recombinant HSV-1. Recombinant AAV was produced after infecting the AAV vector cell line that carrying the GFP expression cassette with the four strains of recombinant HSV-1 respectively. However, HSV1-rc/ UL2 and HSV1-rmc/ UL2 produced much more rAAV than HSV1-rc/ UL44 and HSV1c/ UL44 did. CONCLUSIONS: All the four strains of recombinant HSV-1 support rAAV replication and packaging. HSV1 UL2 and HSV1-rmc/ UL2 that provide much stronger functions may be useful for large-scale production of rAAV.

Animals↗

PubMed2000

A portion of the nucleotide sequence corresponding to the N-terminal coding region of livJ is essential for its transcriptional regulation.

We investigated the regulation of the livJ and livKHMGF operons, which are involved in branched-chain amino acid high-affinity transport in Salmonella typhimurium. When livJ was fused to lacZ at the second codon of livJ to make a livJ-lacZ protein fusion, expression from the livJ promoter was not repressed even under repressing growth conditions; however, expression of an analogous construct of livK-lacZ was repressed. When livJ was fused to lacZ at the twelfth codon of livJ, the expression level under unrepressing growth conditions was elevated, resulting in apparent repressibility of the livJ-lacZ protein fusion. Expression from the livJ-lacZ operon fusion, in which livJ was fused to lacZ 159 bp downstream from the A of the start codon of livJ, was relatively normal under unrepressing growth conditions. Deletion analysis and site-directed base-substitution analysis strongly suggested that cis-acting element for regulation of livJ transcription, 5'-GGCAGGATGTATCG-3', starting at +21 and ending at +34 downstream from the A of the start codon of livJ, was present in the N-terminal coding region of livJ.

Bacterial Proteins↗

PubMed1984

The complete nucleotide sequence of the TL-DNA of the Agrobacterium tumefaciens plasmid pTiAch5.

We have determined the complete primary structure (13 637 bp) of the TL-region of Agrobacterium tumefaciens octopine plasmid pTiAch5 . This sequence comprises two small direct repeats which flank the TL-region at each extremity and are involved in the transfer and/or integration of this DNA segment in plants. TL-DNA specifies eight open-reading frames corresponding to experimentally identified transcripts in crown gall tumor tissue. The eight coding regions are not interrupted by intervening sequences and are separated from each other by AT-rich regions. Potential transcriptional control signals upstream of the 5' and 3' ends of all the transcribed regions resemble typical eukaryotic signals: (i) transcriptional initiation signals ('TATA' or Goldberg- Hogness box) are present upstream to the presumed translational start codons; (ii) ' CCAAT ' sequences are present upstream of the proposed 'TATA' box; (iii) polyadenylation signals are present in the 3'-untranslated regions. Furthermore, no Shine-Dalgarno sequences are present upstream of the presumed translational start codons.

Amino Acid Oxidoreductases↗