1887

Abstract

The operon encodes three iron–sulfur-containing proteins required for -lactate utilization and involved in biofilm formation. The transcriptional regulator LutR of the GntR family negatively controls expression. The gene, which is situated immediately upstream of , encodes an -lactate permease. Here, we show that expression can be strongly induced by -lactate and is subject to partial catabolite repression by glucose. Disruption of the gene led to a strong derepression of and no further induction by -lactate, suggesting that the LutR repressor can also negatively control expression. Electrophoretic mobility shift assay revealed a LutR-binding site located downstream of the promoter of or and containing a consensus inverted repeat sequence 5′-TCATC-N-GATGA-3′. Reporter gene analysis showed that deletion of each LutR-binding site caused a strong derepression of or . These results indicated that these two LutR-binding sites can function as operators . Moreover, deletion analysis identified a DNA segment upstream of the promoter to be important for expression. In contrast to the truncated LutR of laboratory strains 168 and PY79, the full-length LutR of the undomesticated strain RO-NN-1, and probably many other strains, can directly and negatively regulate transcription. The absence or presence of the N-terminal 21 aa of the full-length LutR, which encompass a small part of the predicted winged helix–turn–helix DNA-binding motif, may probably alter the DNA-binding specificity or affinity of LutR.

Funding
This study was supported by the:
  • National Science Council (Award NSC 102-2311-B-010-003)
  • Ministry of Education of the Republic of China
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.079806-0
2014-10-01
2021-07-26
Loading full text...

Full text loading...

/deliver/fulltext/micro/160/10/2178.html?itemId=/content/journal/micro/10.1099/mic.0.079806-0&mimeType=html&fmt=ahah

References

  1. Aguilera L., Campos E., Giménez R., Badía J., Aguilar J., Baldoma L. ( 2008). Dual role of LldR in regulation of the lldPRD operon, involved in l-lactate metabolism in Escherichia coli. J Bacteriol 190:2997–3005 [View Article][PubMed]
    [Google Scholar]
  2. Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I. & other authors ( 2009). From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758–1775 [View Article][PubMed]
    [Google Scholar]
  3. Blatter E. E., Ross W., Tang H., Gourse R. L., Ebright R. H. ( 1994). Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78:889–896 [View Article][PubMed]
    [Google Scholar]
  4. Chai Y., Kolter R., Losick R. ( 2009). A widely conserved gene cluster required for lactate utilization in Bacillus subtilis and its involvement in biofilm formation. J Bacteriol 191:2423–2430 [View Article][PubMed]
    [Google Scholar]
  5. Contente S., Dubnau D. ( 1979). Characterization of plasmid transformation in Bacillus subtilis: kinetic properties and the effect of DNA conformation. Mol Gen Genet 167:251–258 [View Article][PubMed]
    [Google Scholar]
  6. Deng Y., Zhu Y., Wang P., Zhu L., Zheng J., Li R., Ruan L., Peng D., Sun M. ( 2011). Complete genome sequence of Bacillus subtilis BSn5, an endophytic bacterium of Amorphophallus konjac with antimicrobial activity for the plant pathogen Erwinia carotovora subsp. carotovora. J Bacteriol 193:2070–2071 [View Article][PubMed]
    [Google Scholar]
  7. Dong J. M., Taylor J. S., Latour D. J., Iuchi S., Lin E. C. ( 1993). Three overlapping lct genes involved in l-lactate utilization by Escherichia coli. J Bacteriol 175:6671–6678[PubMed]
    [Google Scholar]
  8. Earl A. M., Eppinger M., Fricke W. F., Rosovitz M. J., Rasko D. A., Daugherty S., Losick R., Kolter R., Ravel J. ( 2012). Whole-genome sequences of Bacillus subtilis and close relatives. J Bacteriol 194:2378–2379 [View Article][PubMed]
    [Google Scholar]
  9. Exley R. M., Goodwin L., Mowe E., Shaw J., Smith H., Read R. C., Tang C. M. ( 2005). Neisseria meningitidis lactate permease is required for nasopharyngeal colonization. Infect Immun 73:5762–5766 [View Article][PubMed]
    [Google Scholar]
  10. Exley R. M., Wu H., Shaw J., Schneider M. C., Smith H., Jerse A. E., Tang C. M. ( 2007). Lactate acquisition promotes successful colonization of the murine genital tract by Neisseria gonorrhoeae. Infect Immun 75:1318–1324 [View Article][PubMed]
    [Google Scholar]
  11. Fedhila S., Msadek T., Nel P., Lereclus D. ( 2002). Distinct clpP genes control specific adaptive responses in Bacillus thuringiensis. J Bacteriol 184:5554–5562 [View Article][PubMed]
    [Google Scholar]
  12. Gajiwala K. S., Burley S. K. ( 2000). Winged helix proteins. Curr Opin Struct Biol 10:110–116 [View Article][PubMed]
    [Google Scholar]
  13. Gajiwala K. S., Chen H., Cornille F., Roques B. P., Reith W., Mach B., Burley S. K. ( 2000). Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature 403:916–921 [View Article][PubMed]
    [Google Scholar]
  14. Gao Y. G., Suzuki H., Itou H., Zhou Y., Tanaka Y., Wachi M., Watanabe N., Tanaka I., Yao M. ( 2008). Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in l-lactate and sugar utilization. Nucleic Acids Res 36:7110–7123 [View Article][PubMed]
    [Google Scholar]
  15. Gao C., Hu C., Zheng Z., Ma C., Jiang T., Dou P., Zhang W., Che B., Wang Y. & other authors ( 2012a). Lactate utilization is regulated by the FadR-type regulator LldR in Pseudomonas aeruginosa. J Bacteriol 194:2687–2692 [View Article][PubMed]
    [Google Scholar]
  16. Gao C., Jiang T., Dou P., Ma C., Li L., Kong J., Xu P. ( 2012b). NAD-independent l-lactate dehydrogenase is required for l-lactate utilization in Pseudomonas stutzeri SDM. PLoS ONE 7:e36519 [View Article][PubMed]
    [Google Scholar]
  17. Georgi T., Engels V., Wendisch V. F. ( 2008). Regulation of l-lactate utilization by the FadR-type regulator LldR of Corynebacterium glutamicum. J Bacteriol 190:963–971 [View Article][PubMed]
    [Google Scholar]
  18. Gibello A., Collins M. D., Domínguez L., Fernández-Garayzábal J. F., Richardson P. T. ( 1999). Cloning and analysis of the l-lactate utilization genes from Streptococcus iniae. Appl Environ Microbiol 65:4346–4350[PubMed]
    [Google Scholar]
  19. Goffin P., Lorquet F., Kleerebezem M., Hols P. ( 2004). Major role of NAD-dependent lactate dehydrogenases in aerobic lactate utilization in Lactobacillus plantarum during early stationary phase. J Bacteriol 186:6661–6666 [View Article][PubMed]
    [Google Scholar]
  20. Gourse R. L., Ross W., Gaal T. ( 2000). UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37:687–695 [View Article][PubMed]
    [Google Scholar]
  21. Guérout-Fleury A. M., Frandsen N., Stragier P. ( 1996). Plasmids for ectopic integration in Bacillus subtilis. Gene 180:57–61 [View Article][PubMed]
    [Google Scholar]
  22. Guo S., Mao Z., Wu Y., Hao K., He P., He Y. ( 2013). Genome sequencing of Bacillus subtilis strain XF-1 with high efficiency in the suppression of Plasmodiophora brassicae. Genome Announc 1:e0006613 [View Article][PubMed]
    [Google Scholar]
  23. Herbert M. A., Hayes S., Deadman M. E., Tang C. M., Hood D. W., Moxon E. R. ( 2002). Signature tagged mutagenesis of Haemophilus influenzae identifies genes required for in vivo survival. Microb Pathog 33:211–223 [View Article][PubMed]
    [Google Scholar]
  24. Higuchi R., Krummel B., Saiki R. K. ( 1988). A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res 16:7351–7367 [View Article][PubMed]
    [Google Scholar]
  25. Hoskisson P. A., Rigali S. ( 2009). Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily. Adv Appl Microbiol 69:1–22 [View Article][PubMed]
    [Google Scholar]
  26. Hueck C. J., Hillen W. ( 1995). Catabolite repression in Bacillus subtilis: a global regulatory mechanism for the Gram-positive bacteria?. Mol Microbiol 15:395–401 [View Article][PubMed]
    [Google Scholar]
  27. Hueck C. J., Hillen W., Saier M. H. Jr ( 1994). Analysis of a cis-active sequence mediating catabolite repression in Gram-positive bacteria. Res Microbiol 145:503–518 [View Article][PubMed]
    [Google Scholar]
  28. Irigül-Sönmez O., Köroğlu T. E., Öztürk B., Kovács A. T., Kuipers O. P., Yazgan-Karataş A. ( 2014). In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase. Microbiology 160:243–260 [View Article][PubMed]
    [Google Scholar]
  29. Kemp M. B. ( 1972). d- and l-lactate dehydrogenases of Pseudomonas aeruginosa. Biochem J 130:307–309[PubMed]
    [Google Scholar]
  30. Lin T. H., Wei G. T., Su C. C., Shaw G. C. ( 2012). AdeR, a PucR-type transcription factor, activates expression of l-alanine dehydrogenase and is required for sporulation of Bacillus subtilis. J Bacteriol 194:4995–5001 [View Article][PubMed]
    [Google Scholar]
  31. Lin T. H., Hu Y. N., Shaw G. C. ( 2014). Two enzymes, TilS and HprT, can form a complex to function as a transcriptional activator for the cell division protease gene ftsH in Bacillus subtilis. J Biochem 155:5–16 [View Article][PubMed]
    [Google Scholar]
  32. Miller J. H. ( 1972). Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  33. Nishito Y., Osana Y., Hachiya T., Popendorf K., Toyoda A., Fujiyama A., Itaya M., Sakakibara Y. ( 2010). Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics 11:243 [View Article][PubMed]
    [Google Scholar]
  34. Pinchuk G. E., Rodionov D. A., Yang C., Li X., Osterman A. L., Dervyn E., Geydebrekht O. V., Reed S. B., Romine M. F. & other authors ( 2009). Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A 106:2874–2879 [View Article][PubMed]
    [Google Scholar]
  35. Rigali S., Derouaux A., Giannotta F., Dusart J. ( 2002). Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277:12507–12515 [View Article][PubMed]
    [Google Scholar]
  36. Ross W., Gosink K. K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R. L. ( 1993). A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407–1413 [View Article][PubMed]
    [Google Scholar]
  37. Schroeder J. W., Simmons L. A. ( 2013). Complete genome sequence of Bacillus subtilis strain PY79. Genome Announc 1:e01085-13 [View Article][PubMed]
    [Google Scholar]
  38. Shine J., Dalgarno L. ( 1974). The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 71:1342–1346 [View Article][PubMed]
    [Google Scholar]
  39. Stansen C., Uy D., Delaunay S., Eggeling L., Goergen J. L., Wendisch V. F. ( 2005). Characterization of a Corynebacterium glutamicum lactate utilization operon induced during temperature-triggered glutamate production. Appl Environ Microbiol 71:5920–5928 [View Article][PubMed]
    [Google Scholar]
  40. Stülke J., Hillen W. ( 2000). Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol 54:849–880 [View Article][PubMed]
    [Google Scholar]
  41. Thomas M. T., Shepherd M., Poole R. K., van Vliet A. H., Kelly D. J., Pearson B. M. ( 2011). Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on l-lactate. Environ Microbiol 13:48–61 [View Article][PubMed]
    [Google Scholar]
  42. Weickert M. J., Chambliss G. H. ( 1990). Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis. Proc Natl Acad Sci U S A 87:6238–6242 [View Article][PubMed]
    [Google Scholar]
  43. Zeigler D. R. ( 2011). The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics. Microbiology 157:2033–2041 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.079806-0
Loading
/content/journal/micro/10.1099/mic.0.079806-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error