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. 1989 Nov;171(11):6084–6092. doi: 10.1128/jb.171.11.6084-6092.1989

Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12.

P V Schoenlein 1, B B Roa 1, M E Winkler 1
PMCID: PMC210475  PMID: 2681152

Abstract

We report the DNA sequence and in vivo transcription start of pdxB, which encodes a protein required for de novo biosynthesis of pyridoxine (vitamin B6). The DNA sequence confirms results from previous minicell experiments showing that pdxB encodes a 41-kilodalton polypeptide. RNase T2 mapping of in vivo transcripts and corroborating experiments with promoter expression vector pKK232-8 demonstrated that the pdxB promoter shares its -10 region with an overlapping, divergent promoter. Thus, pdxB must be the first gene in the complex pdxB-hisT operon. The steady-state transcription level from these divergent promoters, which probably occlude each other, is approximately equal in bacteria growing in rich medium at 37 degrees C. The divergent transcript could encode a polypeptide whose amino-terminal domain is rich in proline and glutamine residues. Similarity searches of protein data bases revealed a significant number of amino acid matches between the pdxB gene product and D-3-phosphoglycerate dehydrogenase, which is encoded by serA and catalyzes the first step in the phosphorylated pathway of serine biosynthesis. FASTA and alignment score analyses indicated that PdxB and SerA are indeed homologs and share a common ancestor. The amino acid alignment between PdxB and SerA implies that PdxB is a 2-hydroxyacid dehydrogenase and suggests possible NAD+, substrate binding, and active sites of both enzymes. Furthermore, the fact that 4-hydroxythreonine, a probable intermediate in pyridoxine biosynthesis, is structurally related to serine strongly suggests that the pdxB gene product is erythronate-4-phosphate dehydrogenase. The homology between PdxB and SerA provides considerable support for Jensen's model of enzyme recruitment as the basis for the evolution of different biosynthetic pathways.

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Selected References

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  1. Arps P. J., Marvel C. C., Rubin B. C., Tolan D. A., Penhoet E. E., Winkler M. E. Structural features of the hisT operon of Escherichia coli K-12. Nucleic Acids Res. 1985 Jul 25;13(14):5297–5315. doi: 10.1093/nar/13.14.5297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arps P. J., Winkler M. E. An unusual genetic link between vitamin B6 biosynthesis and tRNA pseudouridine modification in Escherichia coli K-12. J Bacteriol. 1987 Mar;169(3):1071–1079. doi: 10.1128/jb.169.3.1071-1079.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arps P. J., Winkler M. E. Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette. J Bacteriol. 1987 Mar;169(3):1061–1070. doi: 10.1128/jb.169.3.1061-1070.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beck C. F., Warren R. A. Divergent promoters, a common form of gene organization. Microbiol Rev. 1988 Sep;52(3):318–326. doi: 10.1128/mr.52.3.318-326.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Birktoft J. J., Banaszak L. J. The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase. J Biol Chem. 1983 Jan 10;258(1):472–482. doi: 10.2210/pdb2mdh/pdb. [DOI] [PubMed] [Google Scholar]
  6. Bognar A. L., Osborne C., Shane B. Primary structure of the Escherichia coli folC gene and its folylpolyglutamate synthetase-dihydrofolate synthetase product and regulation of expression by an upstream gene. J Biol Chem. 1987 Sep 5;262(25):12337–12343. [PubMed] [Google Scholar]
  7. Bognar A., Pyne C., Yu M., Basi G. Transcription of the folC gene encoding folylpolyglutamate synthetase-dihydrofolate synthetase in Escherichia coli. J Bacteriol. 1989 Apr;171(4):1854–1861. doi: 10.1128/jb.171.4.1854-1861.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brosius J. Plasmid vectors for the selection of promoters. Gene. 1984 Feb;27(2):151–160. doi: 10.1016/0378-1119(84)90136-7. [DOI] [PubMed] [Google Scholar]
  9. Cho K. O., Yanofsky C. Sequence changes preceding a Shine-Dalgarno region influence trpE mRNA translation and decay. J Mol Biol. 1988 Nov 5;204(1):51–60. doi: 10.1016/0022-2836(88)90598-0. [DOI] [PubMed] [Google Scholar]
  10. Connolly D. M., Winkler M. E. Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12. J Bacteriol. 1989 Jun;171(6):3233–3246. doi: 10.1128/jb.171.6.3233-3246.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Costa R. H., Lai E., Darnell J. E., Jr Transcriptional control of the mouse prealbumin (transthyretin) gene: both promoter sequences and a distinct enhancer are cell specific. Mol Cell Biol. 1986 Dec;6(12):4697–4708. doi: 10.1128/mcb.6.12.4697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
  13. Dayhoff M. O., Barker W. C., Hunt L. T. Establishing homologies in protein sequences. Methods Enzymol. 1983;91:524–545. doi: 10.1016/s0076-6879(83)91049-2. [DOI] [PubMed] [Google Scholar]
  14. Feng D. F., Johnson M. S., Doolittle R. F. Aligning amino acid sequences: comparison of commonly used methods. J Mol Evol. 1984;21(2):112–125. doi: 10.1007/BF02100085. [DOI] [PubMed] [Google Scholar]
  15. Goncharoff P., Nichols B. P. Evolution of aminobenzoate synthases: nucleotide sequences of Salmonella typhimurium and Klebsiella aerogenes pabB. Mol Biol Evol. 1988 Sep;5(5):531–548. doi: 10.1093/oxfordjournals.molbev.a040512. [DOI] [PubMed] [Google Scholar]
  16. Goncharoff P., Nichols B. P. Nucleotide sequence of Escherichia coli pabB indicates a common evolutionary origin of p-aminobenzoate synthetase and anthranilate synthetase. J Bacteriol. 1984 Jul;159(1):57–62. doi: 10.1128/jb.159.1.57-62.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Henikoff S., Haughn G. W., Calvo J. M., Wallace J. C. A large family of bacterial activator proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Henikoff S., Wallace J. C. Detection of protein similarities using nucleotide sequence databases. Nucleic Acids Res. 1988 Jul 11;16(13):6191–6204. doi: 10.1093/nar/16.13.6191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jensen R. A. Enzyme recruitment in evolution of new function. Annu Rev Microbiol. 1976;30:409–425. doi: 10.1146/annurev.mi.30.100176.002205. [DOI] [PubMed] [Google Scholar]
  20. Kaplan J. B., Merkel W. K., Nichols B. P. Evolution of glutamine amidotransferase genes. Nucleotide sequences of the pabA genes from Salmonella typhimurium, Klebsiella aerogenes and Serratia marcescens. J Mol Biol. 1985 Jun 5;183(3):327–340. doi: 10.1016/0022-2836(85)90004-x. [DOI] [PubMed] [Google Scholar]
  21. Kaplan J. B., Nichols B. P. Nucleotide sequence of Escherichia coli pabA and its evolutionary relationship to trp(G)D. J Mol Biol. 1983 Aug 15;168(3):451–468. doi: 10.1016/s0022-2836(83)80295-2. [DOI] [PubMed] [Google Scholar]
  22. Marvel C. C., Arps P. J., Rubin B. C., Kammen H. O., Penhoet E. E., Winkler M. E. hisT is part of a multigene operon in Escherichia coli K-12. J Bacteriol. 1985 Jan;161(1):60–71. doi: 10.1128/jb.161.1.60-71.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Nixon B. T., Ronson C. W., Ausubel F. M. Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7850–7854. doi: 10.1073/pnas.83.20.7850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nonet M. L., Marvel C. C., Tolan D. R. The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons. J Biol Chem. 1987 Sep 5;262(25):12209–12217. [PubMed] [Google Scholar]
  25. Parsot C. Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase. EMBO J. 1986 Nov;5(11):3013–3019. doi: 10.1002/j.1460-2075.1986.tb04600.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Roa B. B., Connolly D. M., Winkler M. E. Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12. J Bacteriol. 1989 Sep;171(9):4767–4777. doi: 10.1128/jb.171.9.4767-4777.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schuller D. J., Fetter C. H., Banaszak L. J., Grant G. A. Enhanced expression of the Escherichia coli serA gene in a plasmid vector. Purification, crystallization, and preliminary X-ray data of D-3 phosphoglycerate dehydrogenase. J Biol Chem. 1989 Feb 15;264(5):2645–2648. [PubMed] [Google Scholar]
  29. Squires C. H., De Felice M., Devereux J., Calvo J. M. Molecular structure of ilvIH and its evolutionary relationship to ilvG in Escherichia coli K12. Nucleic Acids Res. 1983 Aug 11;11(15):5299–5313. doi: 10.1093/nar/11.15.5299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Stokes H. W., Hall B. G. Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor. Mol Biol Evol. 1985 Nov;2(6):478–483. doi: 10.1093/oxfordjournals.molbev.a040373. [DOI] [PubMed] [Google Scholar]
  31. Stokes H. W., Hall B. G. Topological repression of gene activity by a transposable element. Proc Natl Acad Sci U S A. 1984 Oct;81(19):6115–6119. doi: 10.1073/pnas.81.19.6115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Tobey K. L., Grant G. A. The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase. J Biol Chem. 1986 Sep 15;261(26):12179–12183. [PubMed] [Google Scholar]
  33. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  34. Zalkin H., Argos P., Narayana S. V., Tiedeman A. A., Smith J. M. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. J Biol Chem. 1985 Mar 25;260(6):3350–3354. [PubMed] [Google Scholar]

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