Difference between revisions of "PMID:11844765"

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'''Pease, AJ, Roa, BR, Luo, W and Winkler, ME'''  (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12.''J. Bacteriol.'' '''184''':1359-69
 
'''Pease, AJ, Roa, BR, Luo, W and Winkler, ME'''  (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12.''J. Bacteriol.'' '''184''':1359-69
 
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We found that transcription of the pdxA and pdxB genes, which mediate steps in the biosynthesis of the essential coenzyme pyridoxal 5"-phosphate, and the ksgA gene, which encodes an rRNA modification enzyme and is partly cotranscribed with pdxA, is subject to positive growth rate regulation in Escherichia coli K-12. The amounts of the pdxA-ksgA cotranscript and pdxB- and ksgA-specific transcripts and expression from pdxA- and pdxB-lacZ fusions increased as the growth rate increased. The half-lives of ksgA- and pdxB-specific transcripts were not affected by the growth rate, whereas the half-life of the pdxA-ksgA cotranscript was too short to be measured accurately. A method of normalization was applied to determine the amount of mRNA synthesized per gene and the rate of protein accumulation per gene. Normalization removed an apparent anomaly at fast growth rates and demonstrated that positive regulation of pdxB occurs at the level of transcription initiation over the whole range of growth rates tested. RNA polymerase limitation and autoregulation could not account for the positive growth rate regulation of pdxA, pdxB, and ksgA transcription. On the other hand, growth rate regulation of the amount of the pdxA-ksgA cotranscript was abolished by a fis mutation, suggesting a role for the Fis protein. In contrast, the fis mutation had no effect on pdxB- or ksgA-specific transcript amounts. The amounts of the pdxA-ksgA cotranscript and ksgA-specific transcript were repressed in the presence of high intracellular concentrations of guanosine tetraphosphate; however, this effect was independent of relA function for the pdxA-ksgA cotranscript. Amounts of the pdxB-specific transcript remained unchanged during amino acid starvation in wild-type and relA mutant strains.
 
We found that transcription of the pdxA and pdxB genes, which mediate steps in the biosynthesis of the essential coenzyme pyridoxal 5"-phosphate, and the ksgA gene, which encodes an rRNA modification enzyme and is partly cotranscribed with pdxA, is subject to positive growth rate regulation in Escherichia coli K-12. The amounts of the pdxA-ksgA cotranscript and pdxB- and ksgA-specific transcripts and expression from pdxA- and pdxB-lacZ fusions increased as the growth rate increased. The half-lives of ksgA- and pdxB-specific transcripts were not affected by the growth rate, whereas the half-life of the pdxA-ksgA cotranscript was too short to be measured accurately. A method of normalization was applied to determine the amount of mRNA synthesized per gene and the rate of protein accumulation per gene. Normalization removed an apparent anomaly at fast growth rates and demonstrated that positive regulation of pdxB occurs at the level of transcription initiation over the whole range of growth rates tested. RNA polymerase limitation and autoregulation could not account for the positive growth rate regulation of pdxA, pdxB, and ksgA transcription. On the other hand, growth rate regulation of the amount of the pdxA-ksgA cotranscript was abolished by a fis mutation, suggesting a role for the Fis protein. In contrast, the fis mutation had no effect on pdxB- or ksgA-specific transcript amounts. The amounts of the pdxA-ksgA cotranscript and ksgA-specific transcript were repressed in the presence of high intracellular concentrations of guanosine tetraphosphate; however, this effect was independent of relA function for the pdxA-ksgA cotranscript. Amounts of the pdxB-specific transcript remained unchanged during amino acid starvation in wild-type and relA mutant strains.
 
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11844765 PubMed]
 
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11844765 PubMed]
  
 
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Bacterial Proteins; Carbohydrate Dehydrogenases; Carrier Proteins; Culture Media; Escherichia coli; Escherichia coli Proteins; Factor For Inversion Stimulation Protein; Gene Expression Regulation, Bacterial; Guanosine Tetraphosphate; Integration Host Factors; Methyltransferases; Mutation; Oxidoreductases; Pyridoxal Phosphate; Recombinant Fusion Proteins; Transcription, Genetic
 
Bacterial Proteins; Carbohydrate Dehydrogenases; Carrier Proteins; Culture Media; Escherichia coli; Escherichia coli Proteins; Factor For Inversion Stimulation Protein; Gene Expression Regulation, Bacterial; Guanosine Tetraphosphate; Integration Host Factors; Methyltransferases; Mutation; Oxidoreductases; Pyridoxal Phosphate; Recombinant Fusion Proteins; Transcription, Genetic
  
 
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==Phenotype Annotations==
 
==Phenotype Annotations==
 
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!|Annotation ID!!Qualifier!!OMP ID!!OMP term name!!Relative phenotype information!!Experimental condition!!ECO ID!!ECO term name!!Reference!!Annotation Extension!!Notes
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!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
 
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a mutation or genetic difference within a strain
 
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*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
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Mutants with ''lacZ'' translation fusion showed expression of ''pdxB'' incease in proportion to the growth rate, Fig 2. expression leads to PLP biosynthesis.
 
Mutants with ''lacZ'' translation fusion showed expression of ''pdxB'' incease in proportion to the growth rate, Fig 2. expression leads to PLP biosynthesis.
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*Taxon: Escherichia coli
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*NCBI Taxon ID: [http://www.ncbi.nlm.nih.gov/taxonomy?term=83333 83333]
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Growth rate regulation of the amount of the ''pdxA-ksgA'' contranscript was abolished by mutation, figure 7.
 
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Latest revision as of 13:24, 6 June 2017

Citation

Pease, AJ, Roa, BR, Luo, W and Winkler, ME (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12.J. Bacteriol. 184:1359-69

Abstract

We found that transcription of the pdxA and pdxB genes, which mediate steps in the biosynthesis of the essential coenzyme pyridoxal 5"-phosphate, and the ksgA gene, which encodes an rRNA modification enzyme and is partly cotranscribed with pdxA, is subject to positive growth rate regulation in Escherichia coli K-12. The amounts of the pdxA-ksgA cotranscript and pdxB- and ksgA-specific transcripts and expression from pdxA- and pdxB-lacZ fusions increased as the growth rate increased. The half-lives of ksgA- and pdxB-specific transcripts were not affected by the growth rate, whereas the half-life of the pdxA-ksgA cotranscript was too short to be measured accurately. A method of normalization was applied to determine the amount of mRNA synthesized per gene and the rate of protein accumulation per gene. Normalization removed an apparent anomaly at fast growth rates and demonstrated that positive regulation of pdxB occurs at the level of transcription initiation over the whole range of growth rates tested. RNA polymerase limitation and autoregulation could not account for the positive growth rate regulation of pdxA, pdxB, and ksgA transcription. On the other hand, growth rate regulation of the amount of the pdxA-ksgA cotranscript was abolished by a fis mutation, suggesting a role for the Fis protein. In contrast, the fis mutation had no effect on pdxB- or ksgA-specific transcript amounts. The amounts of the pdxA-ksgA cotranscript and ksgA-specific transcript were repressed in the presence of high intracellular concentrations of guanosine tetraphosphate; however, this effect was independent of relA function for the pdxA-ksgA cotranscript. Amounts of the pdxB-specific transcript remained unchanged during amino acid starvation in wild-type and relA mutant strains.

Links

PubMed

Keywords

Bacterial Proteins; Carbohydrate Dehydrogenases; Carrier Proteins; Culture Media; Escherichia coli; Escherichia coli Proteins; Factor For Inversion Stimulation Protein; Gene Expression Regulation, Bacterial; Guanosine Tetraphosphate; Integration Host Factors; Methyltransferases; Mutation; Oxidoreductases; Pyridoxal Phosphate; Recombinant Fusion Proteins; Transcription, Genetic

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Main Points of the Paper

Please summarize the main points of the paper.

Materials and Methods Used

Please list the materials and methods used in this paper (strains, plasmids, antibodies, etc).

Phenotype Annotations

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Annotation ID Qualifier OMP ID OMP term name Relative phenotype information Experimental condition ECO ID ECO term name Reference Annotation Extension Notes
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Phenotype of Taxon Information Genotype Information (if known) Condition Information OMP ID OMP Term Name ECO ID ECO Term Name Notes Status

a mutation or genetic difference within a strain

  • Taxon: Escherichia coli
  • Strain: K-12
  • Substrain: NU1187
  • NCBI Taxon ID: 83333
  • Genotype of Reference Strain: pdxA
  • Genotype of Experimental Strain : pdxA:minimudI lacZ
  • Reference Condition:

Proximal surface mutation exhibit a 2.3 to 3.2-fold decrease in affinity to DsrA, a small regulatory RNA, compared to wildtype Hfq. Thus translation cannot continue because DsrA is required in order to enhance translation of rpoS mRNA which encodes a transcription factor, table 1.

  • Taxon: Escherichia coli
  • Strain: K-12
  • Substrain: NU1702
  • NCBI Taxon ID: 83333
  • Genotype of Reference Strain: pdxB
  • Genotype of Experimental Strain : pdxB:minimudIacZ
  • Reference Condition:

Mutants with lacZ translation fusion showed expression of pdxB incease in proportion to the growth rate, Fig 2. expression leads to PLP biosynthesis.

  • Taxon: Escherichia coli
  • Strain: K-12
  • Substrain: TX3333
  • NCBI Taxon ID: 83333
  • Genotype of Reference Strain:
  • Reference Condition:

Growth rate regulation of the amount of the pdxA-ksgA contranscript was abolished by mutation, figure 7.


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Notes

References

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