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At least 145 records · Page 8Linked to original sources
PubMed2000

Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences.

MOTIVATION: In the previous works, we developed ATGpr, a computer program for predicting the fullness of a cDNA, i.e. whether it contains an initiation codon or not. Statistical information of short nucleotide fragments was fully exploited in the prediction algorithm. However, sequence similarities to known proteins, which are becoming increasingly available due to recent rapid growth of protein database, were not used in the prediction. In this work, we present a new prediction algorithm based on both statistical and similarity information, which provides better performance in sensitivity and specificity. RESULTS: We evaluated the accuracy of ATGpr for predicting fullness of cDNA sequences from human clustered ESTs of UniGene, and we obtained specificity, sensitivity, and correlation coefficient of this prediction. Specificity and sensitivity crossed at 46% over the ATGpr score threshold of 0.33 and the maximum correlation coefficient of 0.34 was obtained at this threshold. Without ATGpr we found it effective to use alignments with known proteins for predicting the fullness of cDNA sequences. That is, specificity increased monotonously as similarity (identity of the alignments) increased. Specificity was achieved greater than 80% if identity was greater than 40%. For more effective prediction of fullness of cDNA sequences we combined the similarity (identity of query sequence) with known proteins and ATGpr score. As a result, specificity became greater than 80% if identity was greater than 20%. AVAILABILITY: The prediction program, called ATGpr_ sim, is available at http://www.hri.co.jp/atgpr/ATGpr_sim.html CONTACT: nisikawa@crl.hitachi.co.jp

Amino Acid Sequence↗
PubMed1998

Compilation of mRNA sequences surrounding the AUG translation initiation codon in the green alga Chlamydomonas reinhardtii.

Sequences of 118 mRNAs of the green alga Chlamydomonas reinhardtii in the GenBank data base were compiled to examine the consensus sequence surrounding the AUG translation initiation codon. The consensus sequence for C. reinhardtii was found to be gc(A/C)A(A/C)(A/C) AUGGC. The AUG context of chloroplast proteins (nuclear coded) and non-chloroplast proteins were compared by a separate compilation, and some distinctive features in AUG context of chloroplast proteins were found.

Algal Proteins↗
PubMed1985

Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression.

Roy et al. [Roy, A., Haziza, C. & Danchin, A. (1983) EMBO J. 2, 791-797] established that translation of Escherichia coli adenylate cyclase initiates at a UUG codon, and they suggested this might decrease the efficiency of translation. We investigated the effect of varying the initiation codon on the expression of the adenylate cyclase (cya) gene. Using oligonucleotide-directed mutagenesis, we changed the UUG initiation codon to GUG and the more common initiator AUG and assayed for cya gene expression in a number of ways. First, the GUG initiation codon, in place of UUG, doubled cya expression when cya was expressed from the dual cya P1/P2 promoters. The corresponding AUG codon construct was nonviable. Second, when the cya gene was placed under the transcriptional control of the thermoinducible phage lambda PL promoter, the relative amounts of cya gene product were 1:2:6 for the UUG, GUG, and AUG initiation codons, respectively. Finally, the cya P2 promoter, Shine-Dalgarno sequence, and the DNA corresponding to the first 86 codons of cya were fused to DNA encoding the E. coli galactokinase gene beginning at the second codon. The relative amounts of the fusion polypeptides, which had galactokinase activity, were 1:2:3 for the UUG, GUG, and AUG initiation codons, respectively. These results demonstrate that the cya UUG initiation codon limits cya expression at the level of translation.

Adenylyl Cyclases↗
PubMed1986

Alpha-thalassemia due to the deletion of nucleotides -2 and -3 preceding the AUG initiation codon affects translation efficiency both in vitro and in vivo.

We previously hypothesized that a 2 nucleotide deletion, causing a A-greater than C change at position -3 preceding the ATG initiation codon of alpha globin gene, reduced translation efficiency of alpha globin mRNA and was responsible for a form of alpha + thalassemia displayed by an Algerian patient. We presently show that this deletion leads to a 30-45% reduction in translation efficiency of synthetic alpha globin mRNA in rabbit reticulocyte lysate. In other experiments, we constructed alpha/G gamma hybrid globin genes in which the 3' end of normal or mutated alpha globin genes downstream to the ATG initiation codon was substituted by the 3' part of a G gamma globin gene. COS cells transfected with either of these 2 hybrid genes were shown to synthesize a similar amount of alpha/G gamma hybrid mRNAs but 50% less G gamma globin when transfected with the alpha/G gamma hybrid gene carrying the deletion. These results definitively establish that the 2 nucleotide deletion reduces translation efficiency by 30-50%. This contrasts with the 93% reduction induced by a similar A-greater than C change at position -3 in the different nucleotide context preceding the ATG codon of the rat preproinsulin gene.

Base Sequence↗
PubMed1987

At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells.

Sequences flanking the AUG initiator codon influence its recognition by eukaryotic ribosomes. From a comparison of several hundred mRNA sequences, CCA/GCCAUGG emerged as the consensus sequence for initiation in higher eukaryotes. Systematic mutagenesis of a cloned preproinsulin gene confirmed the facilitating effect of A or G in position -3 (i.e. 3 nucleotides upstream from the AUG codon), C in positions -1 and -2, and G immediately following the AUG codon. The analysis of a new set of mutants now reveals that sequences slightly farther upstream are also influential, the optimal context for initiation being (GCC)GCCA/GCCAUGG. Possible mechanistic implications of the repeating GCC motif are discussed.

Base Sequence↗
PubMed2002

Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3' side.

The downstream region (DR) located immediately after the initiation codon acts as a translational enhancer and depending on its sequence gene expression can vary considerably. In order to determine the influence of the DR on the apparent translation initiation, we have analyzed several naturally occurring DRs (a stretch of five codons) in a lacZ reporter gene. The efficiency of expression, associated with these DRs did not show any correlation to the expression levels connected with the natural genes. Changes of the iso-codon composition in the DR, thus maintaining the amino acid sequence in the gene product, gave significant variations in gene expression. Thus, the messenger RNA base sequence, and not the encoded amino acid sequence, in the early coding region is the determinant for the apparent efficiency of translation initiation and/or early elongation.

Base Sequence↗
PubMed2006

A mutation in the translation initiation codon of Gata-1 disrupts megakaryocyte maturation and causes thrombocytopenia.

We have generated mice from a N-ethyl-N-nitrosourea mutagenesis screen that carry a mutation in the translation initiation codon of Gata-1, termed Plt13, which is equivalent to mutations found in patients with acute megakaryoblastic leukemia and Down syndrome. The Gata-1 locus is present on the X chromosome in humans and in mice. Male mice hemizygous for the mutation (Gata-1Plt13/Y) failed to produce red blood cells and died during embryogenesis at a similar stage to Gata-1-null animals. Female mice that carry the Plt13 mutation are mosaic because of random inactivation of the X chromosome. Adult Gata-1Plt13/+ females were not anemic, but they were thrombocytopenic and accumulated abnormal megakaryocytes without a concomitant increase in megakaryocyte progenitor cells. Gata-1Plt13/+ mice contained large numbers of blast-like colony-forming cells, particularly in the fetal liver, but also in adult spleen and bone marrow, from which continuous mast cells lines were readily derived. Although the equivalent mutation to Gata-1Plt13 in humans results in production of GATA-1s, a short protein isoform initiated from a start codon downstream of the mutated initiation codon, Gata-1s was not detected in Gata-1Plt13/+ mice.

Alkylating Agents↗
PubMed1987

Expression of the Rous sarcoma virus env gene from a simian virus 40 late-region replacement vector: effects of upstream initiation codons.

Expression of the Rous sarcoma virus envelope gene (env) from a simian virus 40 (SV40) late-region replacement vector is dependent on the position of env within the SV40 late-region sequences. The difference in expression levels appeared to be due to differences in the efficiency with which the env-specific transcripts were translated, because transcription levels from different constructions were similar. Deletion of the nucleotides encoding the agnoprotein initiator codon, located upstream of the env sequences in the poorly expressed construct, resulted in high levels of env expression. The agnoprotein initiator codon and overlapping open reading frame thus act as strong barriers to further ribosome scanning and prevent initiation at the env AUG codon. We conclude that AUG codons present in the late region of SV40 can reduce expression of inserted genes positioned downstream. Nevertheless, intrinsic properties of the gene may determine its ultimate level of expression.

Animals↗
PubMed1983

Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5' of an ATG initiation codon.

The nine base pairs immediately 5' of the initiation codon for the bovine growth hormone (BGH) structural gene have been mutagenized. The mutagenesis method employs the ligation of an ambiguously synthesized oligonucleotide duplex into a previously engineered gap in an expression plasmid for BGH. The mutation method, coupled with hybridization screening, is efficient at isolating 1 and 2 base pair changes within the targeted region. The E. coli cultures harboring the mutant plasmids were assayed for relative levels of BGH expression. The most notable result is the varied effect of substitution of G into the mRNA at various positions in this region.

Animals↗
PubMed1996

Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo.

In a genetic selection designed to isolate Escherichia coli mutations that increase expression of the IS 10 transposase gene (tnp), we unexpectedly obtained viable mutants defective in translation initiation factor 3 (IF3). Several lines of evidence led us to conclude that transposase expression, per se, was not increased. Rather, these mutations appear to increase expression of the tnp'-'lacZ gene fusions used in this screen, by increasing translation initiation at downstream, atypical initiation codons. To test this hypothesis we undertook a systematic analysis of start codon requirements and measured the effects of IF3 mutations on initiation from various start codons. Beginning with an efficient translation initiation site, we varied the AUG start codon to all possible codons that differed from AUG by one nucleotide. These potential start codons fall into distinct classes with regard to translation efficiency in vivo: Class I codons (AUG, GUG, and UUG) support efficient translation; Class IIA codons (CUG, AUU, AUC, AUA, and ACG) support translation at levels only 1-3% that of AUG; and Class IIB codons (AGG and AAG) permit levels of translation too low for reliable quantification, importantly, the IF3 mutations had no effect on translation from Class I codons, but they increased translation from Class II codons 3-5-fold, and this same effect was seen in other gene contexts. Therefore, IF3 is generally able to discriminate between efficient and inefficient codons in vivo, consistent with earlier in vitro observations. We discuss these observations as they relate to IF3 autoregulation and the mechanism of IF3 function.

Bacterial Proteins↗
PubMed2003

Vitamin D receptor initiation codon polymorphism, bone density and inflammatory activity of patients with ankylosing spondylitis.

OBJECTIVES: Osteoporosis is a common finding in ankylosing spondylitis (AS) and may contribute to spinal deformity and bone pain. Bone metabolism as well as inflammatory processes are influenced by the vitamin D receptor gene (VDR). We investigated initiation codon ( FokI) and 3'UTR ( BsmI) polymorphisms of the VDR for whether there could be an association with bone mineral density (BMD) in relation to bone metabolism or inflammatory activity in patients with AS. METHODS: In this study, 104 patients with AS (m/w 71/33, mean age 41+/-12 years) were investigated for their lumbar and femoral BMD by DEXA and in part by QCT measurements and compared to 54 healthy controls. Disease activity indices, serum markers of bone metabolism and inflammation were recorded. FokI and BsmI polymorphisms of the VDR were genotyped using genomic DNA from peripheral leukocytes with present or absent restriction sites defined as alleles " f" and " b" or " F" and " B," respectively. RESULTS: In male AS patients, FokI genotypes were significantly associated with spinal but not with femoral BMD values ( P=0.01) as independent predictors of low BMD, which was also influenced by BMI, and inflammatory and pain indices. CRP and ESR values were also significantly associated with FokI genotypes. BMD in female patients showed no significant association with either FokI or BsmI genotypes of the VDR. CONCLUSION: This is the first evidence that the VDR gene may be involved in BMD differences, bone metabolism and inflammatory processes in ankylosing spondylitis. A possible interaction of the vitamin D system, cytokines and bone could define new diagnostic and therapeutic implications in ankylosing spondylitis.

Absorptiometry, Photon↗
PubMed1997

Improved translational efficiency of subtilisin YaB gene with different initiation codons in Bacillus subtilis and alkalophilic Bacillus YaB.

The ale gene specifying the subtilisin YaB produced by alkalophilic Bacillus YaB, has an unusual start codon UUG. Changing this codon to AUG and GUG increased expression of the ale gene in B. subtilis DB104 and in an ale deficient mutant strain YaB-DEC4. The relative translational efficiency order of the three initiation codons is AUG > GUG > UUG in B. subtilis DB104 and in YaB-DEC4. These data suggest that the preferred initiation codon is AUG for ale gene expression in Bacillus.

Bacillus subtilis↗
PubMed1995

The sequence surrounding the translation initiation codon of the pea plastocyanin gene increases translational efficiency of a reporter gene.

The 5'-upstream region of the pea plastocyanin gene (petE) directed 5-10-fold higher levels of beta-glucuronidase (GUS) activity than the cauliflower mosaic virus 35S promoter in transgenic tobacco plants, although the levels of GUS mRNA were similar. The sequence (AAAAAUGG) around the translation initiation codon of petE enhanced translation of the GUS mRNA 10-fold compared to translation from the GUS translation initiation codon in transgenic tobacco plants and transfected protoplasts.

Base Sequence↗
PubMed2000

Identification of the initiation codon for the atpB gene in Chlamydomonas chloroplasts excludes translation of a precursor form of the beta subunit of the ATP synthase.

The chloroplast atpB gene of Chlamydomonas reinhardtii, which encodes the beta subunit of the ATP synthase, contains three in-frame ATGs that are candidate translation initiation codons. An earlier study revealed that the N terminus of the assembled beta subunit maps at the +2 position with respect to the second in-frame methionine codon (Fiedler et al. 1995). Using chloroplast transformation, we have examined the possibility that either of the two additional in-frame ATG codons is competent for translation initiation. We provide evidence that translation of atpB is initiated exclusively at the second ATG codon. We conclude that the beta subunit is not synthesized with an N-terminal leader before its assembly into a functional ATP synthase complex.

5' Untranslated Regions↗
PubMed1990

[Rare initiation codons are regulators of expression of the rpoC gene].

Translation of the rpoC genes in Escherichia coli and Salmonella typhimurium is known to start from the GUG codon. Now, using toeprint analysis we have shown UUG to be the initiation codon of the Pseudomonas putida rpoC gene. IF3 does not seem to proofread initiation at the UUG codon. The rpoC genes of P. putida, E. coli, and S. typhimurium, which use rare start codons, have strong SD-domains AGGAGG (P. p.) and GGGAG (E. c., S. t.), optimal seven-nucleotide spacing between SD and start codons, and good second codon AAA. We suggest that rpoC presents an infrequent case of the regulation of translation initiation by selecting the start codon.

Base Sequence↗
PubMed1992

An initiation codon mutation in CD18 in association with the moderate phenotype of leukocyte adhesion deficiency.

Leukocyte adhesion deficiency (LAD) is an autosomal recessive disease caused by mutations in the CD18 gene which codes for the beta 2 integrin subunit. We studied two patients, the first of which had a moderate LAD phenotype and expressed only 9% of CD11/CD18 on blood leukocytes. RNA from lymphoblasts was reverse-transcribed, and the cDNA was amplified, cloned, and sequenced. An ATG to AAG alteration in the initiation codon was detected in 39 of 45 (87%) cDNA clones. This mutation was detected in the father, but not in the mother. The maternal defect was shown to be a frameshift mutation with the deletion of a single T in the aspartic acid codon at position 690 (GAT), 11 amino acids N-terminal to the beginning of the transmembrane domain. This mutation predicts a polypeptide which would terminate without transmembrane or cytoplasmic domains. The frameshift mutation was also found in the second patient who had the severe phenotype of LAD (less than 1% of CD11/CD18), indicating that this allele does not encode a functional protein. The partial expression in the patient with a moderate phenotype must be derived from the initiation codon mutation and may be due to a low level of initiation of translation of the CD18 mRNA at the second codon (CUG).

Antigens, CD↗
PubMed1993

Influence of the three nucleotides upstream of the initiation codon on expression of the Escherichia coli lacZ gene in Saccharomyces cerevisiae.

By introducing synthetic oligonucleotides into a lacZ-yeast expression vector a set of 47 plasmids (out of 64 possible) was generated, differing only in the three bases immediately upstream of the AUG initiation codon of the Escherichia coli lacZ gene. Expression of the beta-galactosidase fusion protein encoded by the different plasmids was determined in Saccharomyces cerevisiae by immunogel electrophoresis. Among the clones tested we found a factor 3 difference in expression. A slight nucleotide preference was found in positions -3(A > G > C = U) and -2 (G > C = U > A). The choice of the nucleotide at position -1 immediately 5' of the AUG did not effect translation efficiency. Increasing homology to the yeast consensus sequence (AAAAAAAUGUCU) was not concomitant with an increased translation efficiency. Our results indicate that the choice of nucleotides immediately preceding the initiation codon in yeast does not dramatically influence translation efficiency, as in prokaryotes or higher eukaryotes.

Base Sequence↗