Archives of Microbiology

, Volume 192, Issue 7, pp 569–580 | Cite as

Identification of the sequences recognized by the Bacillus subtilis response regulator YclJ

Original Paper


The Bacillus subtilis yclJ gene encodes an OmpR-type response regulator of a two-component regulatory system with unknown function. A previous DNA microarray experiment suggested that multicopy yclJ greatly enhances the expression of several operons in a cognate kinase (YclK)-deficient strain. To confirm this, lacZ fusion analysis was performed in the yclK background with overexpressed yclJ. As a result, yclHI, ykcBC, and yngABC were indeed positively regulated by YclJ. Gel retardation and DNase I footprint analyses revealed that YclJ binds to the promoter regions of yclHI, ykcBC, and yngABC. Nucleotide sequence analysis of the binding regions suggested that YclJ recognizes a direct repeat of the consensus sequence TTCATANTTT, the upstream half of which has close similarity to the consensus binding sequence of the other OmpR family response regulator PhoP. LacZ fusion analysis of the control region of yngA with deletion or point mutation confirmed that the YclJ-binding sequence is required for the YclJ-mediated activation of yngA. Furthermore, we identified two more YclJ-regulated genes, yycA and yfjR, using bioinformatic analysis of the B. subtilis genome, and it was shown that YclJ binds to those promoters and controls the expression of those genes.


YclJ DNA-binding Response regulator 



This work was supported by a Grant-in-aid for Scientific Research on Priority Areas (C) “Genome Biology” to T. T., and a Grant-in-aid for Scientific Research (C) to M. O., and (B) to T. T., from the Ministry of Education, Culture, Sports, Science and Technology of Japan. We thank K. Kobayashi for a bacterial strain. We also thank N. Takahashi, T. Furukawa, K. Yamashita, T. Fujio, H. Nishida, Y. Hanawa, and M. Tanaka for technical assistance.

Supplementary material

203_2010_586_MOESM1_ESM.pdf (344 kb)
Supplementary material 1 (PDF 344 kb)


  1. Fabret C, Feher VA, Hoch JA (1999) Two-component signal transduction in Bacillus subtilis: how one organism sees its world. J Bacteriol 181:1975–1983PubMedGoogle Scholar
  2. Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP (1999) Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nat Struct Biol 6:775–784CrossRefPubMedGoogle Scholar
  3. Geng H, Zhu Y, Mullen K, Zuber CS, Nakano MM (2007) Characterization of ResDE-dependent fnr transcription in Bacillus subtilis. J Bacteriol 189:1745–1755CrossRefPubMedGoogle Scholar
  4. Guan S, Bastin DA, Verma NK (1999) Functional analysis of the O antigen glucosylation gene cluster of Shigella flexneri bacteriophage SfX. Microbiology 145:1263–1273CrossRefPubMedGoogle Scholar
  5. Hartig E, Geng H, Hartmann A, Hubacek A, Munch R, Ye RW, Jahn D, Nakano MM (2004) Bacillus subtilis ResD induces expression of the potential regulatory genes yclJK upon oxygen limitation. J Bacteriol 186:6477–6784CrossRefPubMedGoogle Scholar
  6. Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M (2005) The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis. J Bacteriol 187:6659–6666CrossRefPubMedGoogle Scholar
  7. Hayashi K, Kensuke T, Kobayashi K, Ogasawara N, Ogura M (2006) Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon. Mol Microbiol 59:1714–1729CrossRefPubMedGoogle Scholar
  8. Hulett FM (2002) The PhoP regulon. In: Sonenshine AL, Hoch JA, Losick R (eds) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press, Washington, DC, pp 193–202Google Scholar
  9. Huyen NTT, Eiamphungporn W, Mader U, Liebeke M, Lalk M, Hecker M, Helmann JD, Antelmann H (2009) Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase Adha and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR). Mol Microbiol 71:876–894CrossRefGoogle Scholar
  10. Joseph P, Fichant G, Quentin Y, Denizot F (2002) Regulatory relationship of two-component and ABC transport systems and clustering of their genes in the Bacillus/Clostridium group, suggest a functional link between them. J Mol Microbiol Biotechnol 4:503–513PubMedGoogle Scholar
  11. Jürgen B, Hanschke R, Sarvas M, Hecker M, Schweder T (2001) Proteome and transcriptome based analysis of Bacillus subtilis cells overproducing an insoluble heterologous protein. Appl Microbiol Biotechnol 55:326–332CrossRefPubMedGoogle Scholar
  12. Kobayashi K, Ogura M, Yamaguchi H, Yoshida K, Ogasawara N, Tanaka T, Fujita Y (2001) Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. J Bacteriol 183:7365–7370CrossRefPubMedGoogle Scholar
  13. Kobayashi K, Ehrlich D, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S et al (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100:4678–4683CrossRefPubMedGoogle Scholar
  14. Langdon RH, Cuccui J, Wren BW (2009) N-linked glycosylation in bacteria: an unexpected application. Future Microbiol 4:401–412CrossRefPubMedGoogle Scholar
  15. Lommel M, Strahl S (2009) Protein O-mannosylation: conserved from bacteria to humans. Glycobiology 19:816–828CrossRefPubMedGoogle Scholar
  16. Mukai K, Kawata M, Tanaka T (1990) Isolation and phosphorylation of the Bacillus subtilis degS and degU gene products. J Biol Chem 265:20000–20006PubMedGoogle Scholar
  17. Ogura M, Tanaka T (1996) Transcription of Bacillus subtilis degR is σD-dependent and suppressed by multicopy proB through σD. J Bacteriol 178:216–222PubMedGoogle Scholar
  18. Ogura M, Tanaka T (2002) Recent progress in Bacillus subtilis two-component regulation. Front Biosci 7:1815–1824CrossRefGoogle Scholar
  19. Ogura M, Tanaka T (2009) Bacillus subtilis late competence operon comE is transcriptionally regulated by yutB and under post-transcription initiation control of comN (yrzD). J Bacteriol 191:949–958CrossRefPubMedGoogle Scholar
  20. Ogura M, Ohshiro Y, Hirao S, Tanaka T (1997) A new Bacillus subtilis gene, med, encodes a positive regulator of comK. J Bacteriol 179:6244–6253PubMedGoogle Scholar
  21. Ogura M, Yamaguchi H, Yoshida K, Fujita Y, Tanaka T (2001) DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of Bacillus subtilis two-component regulatory systems. Nucleic Acids Res 29:3804–3813CrossRefPubMedGoogle Scholar
  22. Ogura M, Shimane K, Asai K, Ogasawara N, Tanaka T (2003) Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis. Mol Microbiol 49:1685–1697CrossRefPubMedGoogle Scholar
  23. Ogura M, Tsukahara K, Hayashi K, Tanaka T (2007) The Bacillus subtilis NatK-NatR two-component system regulates expression of the natAB operon encoding an ABC transporter for sodium ion extrusion. Microbiology 153:667–675CrossRefPubMedGoogle Scholar
  24. Ogura M, Ohsawa T, Tanaka T (2008) Identification of the sequences recognized by the Bacillus subtilis response regulator YrkP. Biosci Biotech Biochem 72:186–196CrossRefGoogle Scholar
  25. Pirrung MC (1999) Histidine kinases and two-component signal transduction systems. Chem Biol 6:167–175CrossRefGoogle Scholar
  26. Quentin Y, Fichant G, Denizot F (1999) Inventory, assembly and analysis of Bacillus subtilis ABC transport systems. J Mol Biol 287:467–484CrossRefPubMedGoogle Scholar
  27. Schilling CH, Held L, Torre M, Saier MH (2000) GRASP DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs. J Mol Microbiol Biotechnol 2:495–500PubMedGoogle Scholar
  28. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18:6097–6100CrossRefPubMedGoogle Scholar
  29. Serizawa M, Sekiguchi J (2005) The Bacillus subtilis YdfHI two-component system regulates the transcription of ydfJ, a member of the RND superfamily. Microbiology 151:1769–1778CrossRefPubMedGoogle Scholar
  30. Shimane K, Ogura M (2004) Mutational analysis of the helix–turn–helix region of Bacillus subtilis response regulator DegU, and identification of cis-acting sequences for DegU in the aprE and comK promoters. J Biochem 136:387–397CrossRefPubMedGoogle Scholar
  31. Stock JB, Ninfa AJ, Stock AM (1989) Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev 53:450–490PubMedGoogle Scholar
  32. Stragier P, Bonamy C, Karmazyn-Campelli C (1988) Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression. Cell 527:697–704CrossRefGoogle Scholar
  33. Tsukahara K, Ogura M (2008) Promoter selectivity of the Bacillus subtilis response regulator DegU, a positive regulator of the fla/che operon and sacB. BMC Microbiol 8:8CrossRefPubMedGoogle Scholar
  34. Vagner V, Dervyn E, Ehrlich SD (1998) A vector for systematic gene inactivation in Bacillus subtilis. Microbiology 144:3097–3104CrossRefPubMedGoogle Scholar
  35. Varon D, Boylan SA, Okamoto K, Price CW (1993) Bacillus subtilis gtaB encodes UDP-glucose pyrophosphorylase and is controlled by stationary-phase transcription factor sigma B. J Bacteriol 175:3964–3971PubMedGoogle Scholar
  36. Wach A (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259–265CrossRefPubMedGoogle Scholar
  37. Ye RW, Tao W, Bedzyk L, Young T, Chen M, Liao LI (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182:4458–4465CrossRefPubMedGoogle Scholar
  38. Yoshida K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res 29:683–692CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Institute of Oceanic Research and DevelopmentTokai UniversityShizuokaJapan

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