Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Jun;177(12):3427–3437. doi: 10.1128/jb.177.12.3427-3437.1995

Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis.

D Garmyn 1, T Ferain 1, N Bernard 1, P Hols 1, B Delplace 1, J Delcour 1
PMCID: PMC177045  PMID: 7539419

Abstract

The gene encoding D-lactate dehydrogenase was isolated on a 2.9-kb insert from a library of Pediococcus acidilactici DNA by complementation for growth under anaerobiosis of an Escherichia coli lactate dehydrogenase and pyruvate-formate lyase double mutant. The nucleotide sequence of ldhD encodes a protein of 331 amino acids (predicted molecular mass of 37,210 Da) which shows similarity to the family of D-2-hydroxyacid dehydrogenases. The enzyme encoded by the cloned fragment is equally active on pyruvate and hydroxypyruvate, indicating that the enzyme has both D-lactate and D-glycerate dehydrogenase activities. Three other open reading frames were found in the 2.9-kb insert, one of which (rpsB) is highly similar to bacterial genes coding for ribosomal protein S2. Northern (RNA) blotting analyses indicated the presence of a 2-kb dicistronic transcript of ldhD (a metabolic gene) and rpsB (a putative ribosomal protein gene) together with a 1-kb monocistronic rpsB mRNA. These transcripts are abundant in the early phase of exponential growth but steadily fade away to disappear in the stationary phase. Primer extension analysis identified two distinct promoters driving either cotranscription of ldhD and rpsB or transcription of rpsB alone.

Full Text

The Full Text of this article is available as a PDF (1,015.7 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. An G., Bendiak D. S., Mamelak L. A., Friesen J. D. Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts. Nucleic Acids Res. 1981 Aug 25;9(16):4163–4172. doi: 10.1093/nar/9.16.4163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arndt E., Scholzen T., Krömer W., Hatakeyama T., Kimura M. Primary structures of ribosomal proteins from the archaebacterium Halobacterium marismortui and the eubacterium Bacillus stearothermophilus. Biochimie. 1991 Jun;73(6):657–668. doi: 10.1016/0300-9084(91)90045-3. [DOI] [PubMed] [Google Scholar]
  3. Arthur M., Molinas C., Dutka-Malen S., Courvalin P. Structural relationship between the vancomycin resistance protein VanH and 2-hydroxycarboxylic acid dehydrogenases. Gene. 1991 Jul 15;103(1):133–134. doi: 10.1016/0378-1119(91)90405-z. [DOI] [PubMed] [Google Scholar]
  4. Azevedo V., Sorokin A., Ehrlich S. D., Serror P. The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci. Mol Microbiol. 1993 Oct;10(2):397–405. doi: 10.1111/j.1365-2958.1993.tb02671.x. [DOI] [PubMed] [Google Scholar]
  5. Bernard N., Ferain T., Garmyn D., Hols P., Delcour J. Cloning of the D-lactate dehydrogenase gene from Lactobacillus delbrueckii subsp. bulgaricus by complementation in Escherichia coli. FEBS Lett. 1991 Sep 23;290(1-2):61–64. doi: 10.1016/0014-5793(91)81226-x. [DOI] [PubMed] [Google Scholar]
  6. Bernard N., Johnsen K., Ferain T., Garmyn D., Hols P., Holbrook J. J., Delcour J. NAD(+)-dependent D-2-hydroxyisocaproate dehydrogenase of Lactobacillus delbrueckii subsp. bulgaricus. Gene cloning and enzyme characterization. Eur J Biochem. 1994 Sep 1;224(2):439–446. doi: 10.1111/j.1432-1033.1994.00439.x. [DOI] [PubMed] [Google Scholar]
  7. Bernard N., Johnsen K., Holbrook J. J., Delcour J. D175 discriminates between NADH and NADPH in the coenzyme binding site of Lactobacillus delbrueckii subsp. bulgaricus D-lactate dehydrogenase. Biochem Biophys Res Commun. 1995 Mar 28;208(3):895–900. doi: 10.1006/bbrc.1995.1419. [DOI] [PubMed] [Google Scholar]
  8. Chen J. D., Morrison D. A. Construction and properties of a new insertion vector, pJDC9, that is protected by transcriptional terminators and useful for cloning of DNA from Streptococcus pneumoniae. Gene. 1988 Apr 15;64(1):155–164. doi: 10.1016/0378-1119(88)90489-1. [DOI] [PubMed] [Google Scholar]
  9. Chen L. H., Emory S. A., Bricker A. L., Bouvet P., Belasco J. G. Structure and function of a bacterial mRNA stabilizer: analysis of the 5' untranslated region of ompA mRNA. J Bacteriol. 1991 Aug;173(15):4578–4586. doi: 10.1128/jb.173.15.4578-4586.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chistoserdova L. V., Lidstrom M. E. Genetics of the serine cycle in Methylobacterium extorquens AM1: identification of sgaA and mtdA and sequences of sgaA, hprA, and mtdA. J Bacteriol. 1994 Apr;176(7):1957–1968. doi: 10.1128/jb.176.7.1957-1968.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Contag P. R., Williams M. G., Rogers P. Cloning of a lactate dehydrogenase gene from Clostridium acetobutylicum B643 and expression in Escherichia coli. Appl Environ Microbiol. 1990 Dec;56(12):3760–3765. doi: 10.1128/aem.56.12.3760-3765.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Crow V. L., Pritchard G. G. Fructose 1,6-diphosphate-activated L-lactate dehydrogenase from Streptococcus lactis: kinetic properties and factors affecting activation. J Bacteriol. 1977 Jul;131(1):82–91. doi: 10.1128/jb.131.1.82-91.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dunn C. R., Wilks H. M., Halsall D. J., Atkinson T., Clarke A. R., Muirhead H., Holbrook J. J. Design and synthesis of new enzymes based on the lactate dehydrogenase framework. Philos Trans R Soc Lond B Biol Sci. 1991 May 29;332(1263):177–184. doi: 10.1098/rstb.1991.0047. [DOI] [PubMed] [Google Scholar]
  14. Ferain T., Garmyn D., Bernard N., Hols P., Delcour J. Lactobacillus plantarum ldhL gene: overexpression and deletion. J Bacteriol. 1994 Feb;176(3):596–601. doi: 10.1128/jb.176.3.596-601.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fitzsimons A., Duffner F., Curtin D., Brophy G., O'kiely P., O'connell M. Assessment of Pediococcus acidilactici as a Potential Silage Inoculant. Appl Environ Microbiol. 1992 Sep;58(9):3047–3052. doi: 10.1128/aem.58.9.3047-3052.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Garmyn D., Ferain T., Bernard N., Hols P., Delcour J. Cloning, nucleotide sequence, and transcriptional analysis of the Pediococcus acidilactici L-(+)-lactate dehydrogenase gene. Appl Environ Microbiol. 1995 Jan;61(1):266–272. doi: 10.1128/aem.61.1.266-272.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Garvie E. I. Bacterial lactate dehydrogenases. Microbiol Rev. 1980 Mar;44(1):106–139. doi: 10.1128/mr.44.1.106-139.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Georgellis D., Barlow T., Arvidson S., von Gabain A. Retarded RNA turnover in Escherichia coli: a means of maintaining gene expression during anaerobiosis. Mol Microbiol. 1993 Jul;9(2):375–381. doi: 10.1111/j.1365-2958.1993.tb01698.x. [DOI] [PubMed] [Google Scholar]
  19. Goldberg J. D., Yoshida T., Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J Mol Biol. 1994 Mar 4;236(4):1123–1140. doi: 10.1016/0022-2836(94)90016-7. [DOI] [PubMed] [Google Scholar]
  20. Grant G. A. A new family of 2-hydroxyacid dehydrogenases. Biochem Biophys Res Commun. 1989 Dec 29;165(3):1371–1374. doi: 10.1016/0006-291x(89)92755-1. [DOI] [PubMed] [Google Scholar]
  21. Graves M. C., Rabinowitz J. C. In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for "extended" promoter elements in gram-positive organisms. J Biol Chem. 1986 Aug 25;261(24):11409–11415. [PubMed] [Google Scholar]
  22. Jensen K. F., Pedersen S. Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol Rev. 1990 Jun;54(2):89–100. doi: 10.1128/mr.54.2.89-100.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kochhar S., Chuard N., Hottinger H. Glutamate 264 modulates the pH dependence of the NAD(+)-dependent D-lactate dehydrogenase. J Biol Chem. 1992 Oct 5;267(28):20298–20301. [PubMed] [Google Scholar]
  24. Kochhar S., Hottinger H., Chuard N., Taylor P. G., Atkinson T., Scawen M. D., Nicholls D. J. Cloning and overexpression of Lactobacillus helveticus D-lactate dehydrogenase gene in Escherichia coli. Eur J Biochem. 1992 Sep 15;208(3):799–805. doi: 10.1111/j.1432-1033.1992.tb17250.x. [DOI] [PubMed] [Google Scholar]
  25. Kochhar S., Hunziker P. E., Leong-Morgenthaler P., Hottinger H. Primary structure, physicochemical properties, and chemical modification of NAD(+)-dependent D-lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site. J Biol Chem. 1992 Apr 25;267(12):8499–8513. [PubMed] [Google Scholar]
  26. Lamzin V. S., Aleshin A. E., Strokopytov B. V., Yukhnevich M. G., Popov V. O., Harutyunyan E. H., Wilson K. S. Crystal structure of NAD-dependent formate dehydrogenase. Eur J Biochem. 1992 Jun 1;206(2):441–452. doi: 10.1111/j.1432-1033.1992.tb16945.x. [DOI] [PubMed] [Google Scholar]
  27. Lamzin V. S., Dauter Z., Popov V. O., Harutyunyan E. H., Wilson K. S. High resolution structures of holo and apo formate dehydrogenase. J Mol Biol. 1994 Feb 25;236(3):759–785. doi: 10.1006/jmbi.1994.1188. [DOI] [PubMed] [Google Scholar]
  28. Lerch H. P., Blöcker H., Kallwass H., Hoppe J., Tsai H., Collins J. Cloning, sequencing and expression in Escherichia coli of the D-2-hydroxyisocaproate dehydrogenase gene of Lactobacillus casei. Gene. 1989 May 15;78(1):47–57. doi: 10.1016/0378-1119(89)90313-2. [DOI] [PubMed] [Google Scholar]
  29. Llanos R. M., Harris C. J., Hillier A. J., Davidson B. E. Identification of a novel operon in Lactococcus lactis encoding three enzymes for lactic acid synthesis: phosphofructokinase, pyruvate kinase, and lactate dehydrogenase. J Bacteriol. 1993 May;175(9):2541–2551. doi: 10.1128/jb.175.9.2541-2551.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Llanos R. M., Hillier A. J., Davidson B. E. Cloning, nucleotide sequence, expression, and chromosomal location of ldh, the gene encoding L-(+)-lactate dehydrogenase, from Lactococcus lactis. J Bacteriol. 1992 Nov;174(21):6956–6964. doi: 10.1128/jb.174.21.6956-6964.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mat-Jan F., Alam K. Y., Clark D. P. Mutants of Escherichia coli deficient in the fermentative lactate dehydrogenase. J Bacteriol. 1989 Jan;171(1):342–348. doi: 10.1128/jb.171.1.342-348.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Minowa T., Iwata S., Sakai H., Masaki H., Ohta T. Sequence and characteristics of the Bifidobacterium longum gene encoding L-lactate dehydrogenase and the primary structure of the enzyme: a new feature of the allosteric site. Gene. 1989 Dec 21;85(1):161–168. doi: 10.1016/0378-1119(89)90476-9. [DOI] [PubMed] [Google Scholar]
  33. Nilsson G., Belasco J. G., Cohen S. N., von Gabain A. Growth-rate dependent regulation of mRNA stability in Escherichia coli. Nature. 1984 Nov 1;312(5989):75–77. doi: 10.1038/312075a0. [DOI] [PubMed] [Google Scholar]
  34. Ogasawara N., Nakai S., Yoshikawa H. Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res. 1994;1(1):1–14. doi: 10.1093/dnares/1.1.1. [DOI] [PubMed] [Google Scholar]
  35. Ostendorp R., Liebl W., Schurig H., Jaenicke R. The L-lactate dehydrogenase gene of the hyperthermophilic bacterium Thermotoga maritima cloned by complementation in Escherichia coli. Eur J Biochem. 1993 Sep 15;216(3):709–715. doi: 10.1111/j.1432-1033.1993.tb18190.x. [DOI] [PubMed] [Google Scholar]
  36. Pease A. J., Wolf R. E., Jr Determination of the growth rate-regulated steps in expression of the Escherichia coli K-12 gnd gene. J Bacteriol. 1994 Jan;176(1):115–122. doi: 10.1128/jb.176.1.115-122.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rasmussen L. J., Marinus M. G., Løbner-Olesen A. Novel growth rate control of dam gene expression in Escherichia coli. Mol Microbiol. 1994 May;12(4):631–638. doi: 10.1111/j.1365-2958.1994.tb01050.x. [DOI] [PubMed] [Google Scholar]
  38. Resnekov O., Rutberg L., von Gabain A. Changes in the stability of specific mRNA species in response to growth stage in Bacillus subtilis. Proc Natl Acad Sci U S A. 1990 Nov;87(21):8355–8359. doi: 10.1073/pnas.87.21.8355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rossmann M. G., Moras D., Olsen K. W. Chemical and biological evolution of nucleotide-binding protein. Nature. 1974 Jul 19;250(463):194–199. doi: 10.1038/250194a0. [DOI] [PubMed] [Google Scholar]
  40. Rowley D. L., Pease A. J., Wolf R. E., Jr Genetic and physical analyses of the growth rate-dependent regulation of Escherichia coli zwf expression. J Bacteriol. 1991 Aug;173(15):4660–4667. doi: 10.1128/jb.173.15.4660-4667.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sanangelantoni A. M., Calogero R. C., Buttarelli F. R., Gualerzi C. O., Tiboni O. Organization and nucleotide sequence of the genes for ribosomal protein S2 and elongation factor Ts in Spirulina platensis. FEMS Microbiol Lett. 1990 Jan 1;54(1-3):141–145. doi: 10.1016/0378-1097(90)90272-r. [DOI] [PubMed] [Google Scholar]
  42. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Schuster W. Ribosomal protein gene rpl5 is cotranscribed with the nad3 gene in Oenothera mitochondria. Mol Gen Genet. 1993 Sep;240(3):445–449. doi: 10.1007/BF00280399. [DOI] [PubMed] [Google Scholar]
  44. Taguchi H., Ohta T. D-lactate dehydrogenase is a member of the D-isomer-specific 2-hydroxyacid dehydrogenase family. Cloning, sequencing, and expression in Escherichia coli of the D-lactate dehydrogenase gene of Lactobacillus plantarum. J Biol Chem. 1991 Jul 5;266(19):12588–12594. [PubMed] [Google Scholar]
  45. Taguchi H., Ohta T. Histidine 296 is essential for the catalysis in Lactobacillus plantarum D-lactate dehydrogenase. J Biol Chem. 1993 Aug 25;268(24):18030–18034. [PubMed] [Google Scholar]
  46. Thomas T. D., Ellwood D. C., Longyear V. M. Change from homo- to heterolactic fermentation by Streptococcus lactis resulting from glucose limitation in anaerobic chemostat cultures. J Bacteriol. 1979 Apr;138(1):109–117. doi: 10.1128/jb.138.1.109-117.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Thomas T. D., Turner K. W., Crow V. L. Galactose fermentation by Streptococcus lactis and Streptococcus cremoris: pathways, products, and regulation. J Bacteriol. 1980 Nov;144(2):672–682. doi: 10.1128/jb.144.2.672-682.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Vanet A., Plumbridge J. A., Alix J. H. Cotranscription of two genes necessary for ribosomal protein L11 methylation (prmA) and pantothenate transport (panF) in Escherichia coli K-12. J Bacteriol. 1993 Nov;175(22):7178–7188. doi: 10.1128/jb.175.22.7178-7188.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Vinals C., Depiereux E., Feytmans E. Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase. Biochem Biophys Res Commun. 1993 Apr 15;192(1):182–188. doi: 10.1006/bbrc.1993.1398. [DOI] [PubMed] [Google Scholar]
  50. Wierenga R. K., Terpstra P., Hol W. G. Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J Mol Biol. 1986 Jan 5;187(1):101–107. doi: 10.1016/0022-2836(86)90409-2. [DOI] [PubMed] [Google Scholar]
  51. Wigley D. B., Gamblin S. J., Turkenburg J. P., Dodson E. J., Piontek K., Muirhead H., Holbrook J. J. Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution. J Mol Biol. 1992 Jan 5;223(1):317–335. doi: 10.1016/0022-2836(92)90733-z. [DOI] [PubMed] [Google Scholar]
  52. Yamada T., Carlsson J. Regulation of lactate dehydrogenase and change of fermentation products in streptococci. J Bacteriol. 1975 Oct;124(1):55–61. doi: 10.1128/jb.124.1.55-61.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Yomano L. P., Scopes R. K., Ingram L. O. Cloning, sequencing, and expression of the Zymomonas mobilis phosphoglycerate mutase gene (pgm) in Escherichia coli. J Bacteriol. 1993 Jul;175(13):3926–3933. doi: 10.1128/jb.175.13.3926-3933.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES