The primary structure of the<i>Saccharomyces cerevisiae</i>gene for 3-phosphogrycerate kinase

Hitzeman, Ronald A.; Hagie, Frank E.; Hayflick, Joei S.; Chen, Christina Y.; Seeburg, Peter H.; Derynck, Rik

doi:10.1093/nar/10.23.7791

Cited by 183 publications

(85 citation statements)

References 63 publications

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“…cer.) (32), and humans (36). The percentages at the end of the sequences indicate degrees of identity to the C. glutamicum PGK.…”

Section: Resultsmentioning

confidence: 99%

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Eikmanns

1992

J Bacteriol

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To investigate a possible chromosomal clustering of glycolytic enzyme genes in Corynebacterium glutamicum, a 6.4-kb DNA 27,198). The amino acid sequences of the three enzymes show up to 62% (GAPDH), 48% (PGK), and 44% (TPI) identity in comparison with respective enzymes from other organisms. The gap, pgk, tpi, and ppc genes were cloned into the C. glutamicum-Escherichia coli shuttle vector pEKO and introduced into C. glutamicum. Relative to the wild type, the recombinant strains showed up to 20-fold-higher specific activities of the respective enzymes. On the basis of codon usage analysis of gap, pgk, tpi, and previously sequenced genes from C. glutamicum, a codon preference profile for this organism which differs significantly from those of E. coli and Bacillus subtilis is presented.

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“…cer.) (32), and humans (36). The percentages at the end of the sequences indicate degrees of identity to the C. glutamicum PGK.…”

Section: Resultsmentioning

confidence: 99%

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Eikmanns

1992

J Bacteriol

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“…The DNA fragment containing PGK1-1L (PGK1-1, the full-length downstream element [ Fig. 2]), was generated by PCR with the plasmid pUC9PGK1(-AU), harboring the PGK1 gene (32), as the template and with oligonucleotides 4 and 6 as the primers (Table 1). Similarly, oligonucleotides 5 and 4 were used as primers in the PCR described above to prepare a DNA fragment containing the downstream element PGK1-1S (lacking two copies of the sequence motif [ Fig.…”

Section: Methodsmentioning

confidence: 99%

Identification and Characterization of a Sequence Motif Involved in Nonsense-Mediated mRNA Decay

Zhang

Ruiz-Echevarría²,

Quan

et al. 1995

Molecular and Cellular Biology

123

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In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3 of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3 of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5 of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3 of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3 of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed.The rates at which mRNAs decay play an important role in regulating gene expression. mRNA half-lives can vary from each other by as much as 100-fold (28,55,59,62,64), and this variation determines, in part, the cytoplasmic abundance of these RNAs. In addition, the decay rate of an mRNA can be modulated, and its half-life can vary depending on the cell type or the environmental situation of the cell (e.g., hormones, stress, cell cycle, etc. [3,55,62]). The goal of our work is to understand the cellular mechanisms that determine the stability of mRNAs.We are studying mRNA decay in the yeast Saccharomyces cerevisiae. Our results, as well as work from other laboratories, strongly indicate that the processes of mRNA turnover and translation are intimately linked and that understanding of this relationship is critical in elucidating the mechanism of mRNA decay (2, 5, 9, 11, 15, 21, 23, 29-31, 41, 53, 55-59, 76). The role of translation in determination of mRNA decay rates is direct, and, for certain instability elements identified in protein coding regions and 3Ј untranslated regions (3Ј-UTRs), translation of the protein coding region must occur in order for them to function (2,11,15,21,23,29,41,53,60,66,76).One clear example of the relationship between translation and mRNA decay is the observation that nonsense mutati...

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“…Transformation of a ura3 strain by this fragment allowed its integration into the chromosome. Subsequent mating of a Ura+ transformant with an rnal4 ura3 strain, meiosis, and genetic analysis of the spores showed that the integration had occurred at the RNA14 locus, proving that the cloned gene was the RNA14 wild-type gene (16 [43]) was cloned in the M13 bacteriophage to obtain singlestranded DNA carrying either the sense strand (unable to hybridize with the PGK mRNA) or the antisense strand (able to hybridize with the PGK mRNA). These probes were loaded on three independent nitrocellulose filters and incubated with the radioactive RNAs for 2 days at 37°C, washed, RNase A treated, and assayed for radioactivity by scintillation counting for at least 10 min.…”

Section: Methodsmentioning

confidence: 99%

Mutations in the yeast RNA14 and RNA15 genes result in an abnormal mRNA decay rate; sequence analysis reveals an RNA-binding domain in the RNA15 protein.

Minvielle‐Sebastia¹,

Winsor²,

Bonneaud³

et al. 1991

Mol. Cell. Biol.

126

110

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In Saccharomyces cerevisiae, temperature-sensitive mutations in the genes RNA14 and RNA15 correlate with a reduction of mRNA stability and poly(A) tail length. Although mRNA transcription is not abolished in these mutants, the transcripts are rapidly deadenylated as in a strain carrying an RNA polymerase B(II) temperature-sensitive mutation. This suggests that the primary defect could be in the control of the poly(A) status of the mRNAs and that the fast decay rate may be due to the loss of this control. By complementation of their temperature-sensitive phenotype, we have cloned the wild-type genes. They are essential for cell viability and are unique in the haploid genome. The RNA14 gene, located on chromosome II, is transcribed as three mRNAs, one major and two minor, which are 2.2, 1.5, and 1.1 kb in length. The RNA15 gene gives rise to a single 1.2-kb transcript and maps to chromosome XVI. Sequence analysis indicates that RNA14 encodes a 636-amino-acid protein with a calculated molecular weight of 75,295. No homology was found between RNA14 and RNA15 or between RNA14 and other proteins contained in data banks. The RNA15 DNA sequence predicts a protein of 296 amino acids with a molecular weight of 32,770. Sequence comparison reveals an N-terminal putative RNA-binding domain in the RNA15-encoded protein, followed by a glutamine and asparagine stretch similar to the opa sequences. Both RNA14 and RNA15 wild-type genes, when cloned on a multicopy plasmid, are able to suppress the temperature-sensitive phenotype of strains bearing either the rnal4 or the rnal5 mutation, suggesting that the encoded proteins could interact with each other.In yeast cells, all known mRNAs terminate in a poly(A) tail that is probably added to the 3' end of the pre-mature RNA in the nucleus in a posttranscriptional manner (18), as was previously shown to be the case in higher eucaryotes (57). One of the major roles for the poly(A) tail was suggested by its involvement in protein biosynthesis (47,63), and in yeast cells the poly(A)-binding protein (PABP [1,68]) was shown to be required for translation initiation (69). More recently, in vitro data have supported the idea that the poly(A) tail enhances translation through the interaction of an initiation factor or the ribosomal subunit with the PABP (59).Besides the implication of the poly(A) tail in translation (reviewed in reference 46), its role in mRNA half-life has been evoked as many times (30,44,82,83,86), sometimes in association with the PABP (11, 12, 17), as refuted (41,49,69,72). Nevertheless, it appears that the poly(A) tail is not solely responsible for determination of the stability of mRNA in vivo, but that it acts in association with other factors.To obtain mutants of Saccharomyces cerevisiae impaired in poly(A) mRNA metabolism, two mutants simultaneously cordycepin (3'-deoxyadenosine) sensitive and temperature sensitive were isolated by using a selective approach (13). The mutations, located at two independent loci, were renamed rnal4 and rnal5 for reasons of homonymy (see...

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The primary structure of theSaccharomyces cerevisiaegene for 3-phosphogrycerate kinase

Cited by 183 publications

References 63 publications

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Identification and Characterization of a Sequence Motif Involved in Nonsense-Mediated mRNA Decay

Mutations in the yeast RNA14 and RNA15 genes result in an abnormal mRNA decay rate; sequence analysis reveals an RNA-binding domain in the RNA15 protein.

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