SubtiBank SubtiBank

It will happen very soon:

International Conference on Bacilli and Gram-positive bacteria

June 11 - 15, 2017, Berlin, Germany

Check out the program here

Categories containing this gene/protein

transcription factors and their control, transition state regulators, biofilm formation

This gene is a member of the following regulons

AbrB regulon, ScoC regulon, Spo0A regulon

The SinR regulon


  • Coordinates on the chromosome (coding sequence): 2,552,653 -> 2,552,988
  • Phenotypes of a mutant

  • the mutation suppresses the galactose toxicity to a galE mutant PubMed
  • The protein

    Catalyzed reaction/ biological activity

  • transcription regulator of biofilm genes, acts as a true repressor of the tapA-sipW-tasA operon and as an anti-activator (prevents binding of the activator protein RemA) of the epsA-epsB-epsC-epsD-epsE-epsF-epsG-epsH-epsI-epsJ-epsK-epsL-epsM-epsN-epsO operon PubMed
  • acts as co-repressor for SlrR PubMed
  • Protein family

  • Xre family
  • Paralogous protein(s)

  • SlrR
  • Kinetic information


  • DNA-binding N-terminal domain (aa 1-69) PubMed
  • SinI-binding C-terminal domain (aa 74-111) PubMed
  • Modification


    Effectors of protein activity

  • SinI and SlrA are antagonists to SinR PubMed
  • SlrR is also antagonist of SinR PubMed
  • Structure

  • 2YAL (C-terminal domain, aa 74-111) PubMed
  • 3QQ6 (N-terminal domain, aa 1-69) PubMed
  • 1B0N (complex SinR-SinI) PubMed
  • Localization


  • SlrA-SinR PubMed, K(D) 10.6 nM PubMed
  • SlrR-SinR PubMed, K(D) 47.5 nM PubMed, Veg may inhibit this interaction PubMed
  • SinR-SinI PubMed, K(D) 1.8 nM PubMed
  • SinR-ScoC
  • Additional information

    Expression and Regulation


  • sinI-sinR PubMed
  • sinR PubMed
  • Sigma factor

  • sinI: SigA PubMed
  • sinR: SigA PubMed
  • Regulation

  • sinI: repressed under conditions that trigger sporulation (Spo0A) PubMed
  • sinI: repressed during exponential growth (ScoC) PubMed
  • sinI: repressed during logrithmic growth (AbrB) PubMed
  • sinI: repressed during vegetative growth (SinR) PubMed
  • sinR is bimodally expressed and this depends on RNase Y PubMed
  • Regulatory mechanism

  • Spo0A: transcription repression PubMed
  • ScoC: transcription repression PubMed
  • AbrB: transcription repression PubMed
  • SinR: transcription repression PubMed
  • Additional information

  • the mRNA is substantially stabilized upon depletion of RNase Y (the half-life of the mRNA increases from 3.5 to 13 min) PubMed
  • RNA degradation by RNase Y was reported to depend on the interaction of RNase Y with the complex of YmcA-YlbF-YaaT PubMed
  • Biological materials


  • GP923 (sinR::spec) PubMed, available in Jörg Stülke's lab
  • GP736 (sinR::tetR) PubMed, available in Jörg Stülke's lab
  • 1S97 (sinR::phleo), PubMed, available at BGSC
  • GP1672 (sinR-tasA::cat) PubMed, available in Jörg Stülke's lab
  • GP1663 (yqhG-sinI-sinR-tasA), available in Jörg Stülke's lab
  • Expression vector

  • N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380: pGP1083 , available in Jörg Stülke's lab
  • lacZ fusion

  • pGP1930 (aphA3) based on pAC7, available in Jörg Stülke's lab
  • GFP fusion

    two-hybrid system

  • B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • FLAG-tag construct

  • GP960 (spc, based on pGP1331), available in Jörg Stülke's lab
  • Antibody

    Labs working on this gene/protein



    Cairns LS, Hobley L, Stanley-Wall NR

    Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms

    Mol Microbiol. 2014 Aug;93(4):587-98. doi: 10.1111/mmi.12697. Epub 2014 Jul 18. Review. PubMed PMID: 24988880; PubMed Central PMCID: PMC4238804.
    Vlamakis H, Chai Y, Beauregard P, Losick R, Kolter R

    Sticking together: building a biofilm the Bacillus subtilis way

    Nat Rev Microbiol. 2013 Mar;11(3):157-68. doi: 10.1038/nrmicro2960. Epub 2013 Jan 28. Review. PubMed PMID: 23353768; PubMed Central PMCID: PMC3936787.
    Piggot P

    Epigenetic switching: bacteria hedge bets about staying or moving

    Curr Biol. 2010 Jun 8;20(11):R480-2. doi: 10.1016/j.cub.2010.04.020. PubMed PMID: 20541494.
    Dubnau D

    Swim or chill: lifestyles of a bacillus

    Genes Dev. 2010 Apr 15;24(8):735-7. doi: 10.1101/gad.1923110. PubMed PMID: 20395361; PubMed Central PMCID: PMC2854387.

    Modelling of the SinI/SinR switch

    Hallinan JS(1), Misirli G, Wipat A.

    Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits.

    Conf Proc IEEE Eng Med Biol Soc. 2010;2010:768-74. doi: 10.1109/IEMBS.2010.5626353.

    Original publications

    Ogura M

    Post-transcriptionally generated cell heterogeneity regulates biofilm formation in Bacillus subtilis

    Genes Cells. 2016 Apr;21(4):335-49. doi: 10.1111/gtc.12343. Epub 2016 Jan 28. PubMed PMID: 26819068.
    DeLoughery A, Dengler V, Chai Y, Losick R

    Biofilm formation by Bacillus subtilis requires an endoribonuclease-containing multisubunit complex that controls mRNA levels for the matrix gene repressor SinR

    Mol Microbiol. 2016 Jan;99(2):425-37. doi: 10.1111/mmi.13240. Epub 2015 Oct 26. PubMed PMID: 26434553; PubMed Central PMCID: PMC4989519.
    Gao T, Greenwich J, Li Y, Wang Q, Chai Y

    The Bacterial Tyrosine Kinase Activator TkmA Contributes to Biofilm Formation Largely Independently of the Cognate Kinase PtkA in Bacillus subtilis

    J Bacteriol. 2015 Nov;197(21):3421-32. doi: 10.1128/JB.00438-15. Epub 2015 Aug 17. PubMed PMID: 26283769; PubMed Central PMCID: PMC4621062.
    Leiman SA, Arboleda LC, Spina JS, McLoon AL

    SinR is a mutational target for fine-tuning biofilm formation in laboratory-evolved strains of Bacillus subtilis

    BMC Microbiol. 2014 Nov 30;14:301. doi: 10.1186/s12866-014-0301-8. PubMed PMID: 25433524; PubMed Central PMCID: PMC4258274.
    Subramaniam AR, Deloughery A, Bradshaw N, Chen Y, O'Shea E, Losick R, Chai Y

    A serine sensor for multicellularity in a bacterium

    Elife. 2013 Dec 17;2:e01501. doi: 10.7554/eLife.01501. PubMed PMID: 24347549; PubMed Central PMCID: PMC3862929.
    Ogura M, Yoshikawa H, Chibazakura T

    Regulation of the response regulator gene degU through the binding of SinR/SlrR and exclusion of SinR/SlrR by DegU in Bacillus subtilis

    J Bacteriol. 2014 Feb;196(4):873-81. doi: 10.1128/JB.01321-13. Epub 2013 Dec 6. PubMed PMID: 24317403; PubMed Central PMCID: PMC3911177.
    Norman TM, Lord ND, Paulsson J, Losick R

    Memory and modularity in cell-fate decision making

    Nature. 2013 Nov 28;503(7477):481-6. doi: 10.1038/nature12804. Epub 2013 Nov 20. PubMed PMID: 24256735; PubMed Central PMCID: PMC4019345.
    Gupta M, Dixit M, Rao KK

    Spo0A positively regulates epr expression by negating the repressive effect of co-repressors, SinR and ScoC, in Bacillus subtilis

    J Biosci. 2013 Jun;38(2):291-9. PubMed PMID: 23660663.
    Winkelman JT, Bree AC, Bate AR, Eichenberger P, Gourse RL, Kearns DB

    RemA is a DNA-binding protein that activates biofilm matrix gene expression in Bacillus subtilis

    Mol Microbiol. 2013 Jun;88(5):984-97. doi: 10.1111/mmi.12235. Epub 2013 May 7. PubMed PMID: 23646920; PubMed Central PMCID: PMC3732408.
    Stowe SD, Olson AL, Losick R, Cavanagh J

    Chemical shift assignments and secondary structure prediction of the master biofilm regulator, SinR, from Bacillus subtilis

    Biomol NMR Assign. 2014 Apr;8(1):155-8. doi: 10.1007/s12104-013-9473-7. Epub 2013 Mar 10. PubMed PMID: 23475644; PubMed Central PMCID: PMC3739994.
    Newman JA, Rodrigues C, Lewis RJ

    Molecular basis of the activity of SinR protein, the master regulator of biofilm formation in Bacillus subtilis

    J Biol Chem. 2013 Apr 12;288(15):10766-78. doi: 10.1074/jbc.M113.455592. Epub 2013 Feb 21. PubMed PMID: 23430750; PubMed Central PMCID: PMC3624457.
    Lei Y, Oshima T, Ogasawara N, Ishikawa S

    Functional analysis of the protein Veg, which stimulates biofilm formation in Bacillus subtilis

    J Bacteriol. 2013 Apr;195(8):1697-705. doi: 10.1128/JB.02201-12. Epub 2013 Feb 1. PubMed PMID: 23378512; PubMed Central PMCID: PMC3624561.
    Chai Y, Beauregard PB, Vlamakis H, Losick R, Kolter R

    Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis

    MBio. 2012 Aug 14;3(4):e00184-12. doi: 10.1128/mBio.00184-12. Print 2012. Erratum in: MBio. 2013;4(1). doi:10.1128/mBio.00555-12. PubMed PMID: 22893383; PubMed Central PMCID: PMC3419520.
    Cozy LM, Phillips AM, Calvo RA, Bate AR, Hsueh YH, Bonneau R, Eichenberger P, Kearns DB

    SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σ(D) in Bacillus subtilis

    Mol Microbiol. 2012 Mar;83(6):1210-28. doi: 10.1111/j.1365-2958.2012.08003.x. Epub 2012 Feb 22. PubMed PMID: 22329926; PubMed Central PMCID: PMC3303961.
    Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J

    A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation

    J Bacteriol. 2011 Nov;193(21):5997-6007. doi: 10.1128/JB.05360-11. Epub 2011 Aug 19. PubMed PMID: 21856853; PubMed Central PMCID: PMC3194898.
    Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J

    RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y

    Mol Microbiol. 2011 Sep;81(6):1459-73. doi: 10.1111/j.1365-2958.2011.07777.x. Epub 2011 Aug 4. PubMed PMID: 21815947.
    Colledge VL, Fogg MJ, Levdikov VM, Leech A, Dodson EJ, Wilkinson AJ

    Structure and organisation of SinR, the master regulator of biofilm formation in Bacillus subtilis

    J Mol Biol. 2011 Aug 19;411(3):597-613. doi: 10.1016/j.jmb.2011.06.004. Epub 2011 Jun 25. PubMed PMID: 21708175; PubMed Central PMCID: PMC3163267.
    Chai Y, Norman T, Kolter R, Losick R

    Evidence that metabolism and chromosome copy number control mutually exclusive cell fates in Bacillus subtilis

    EMBO J. 2011 Apr 6;30(7):1402-13. doi: 10.1038/emboj.2011.36. Epub 2011 Feb 15. PubMed PMID: 21326214; PubMed Central PMCID: PMC3094124.
    Chai Y, Kolter R, Losick R

    Reversal of an epigenetic switch governing cell chaining in Bacillus subtilis by protein instability

    Mol Microbiol. 2010 Oct;78(1):218-29. doi: 10.1111/j.1365-2958.2010.07335.x. PubMed PMID: 20923420; PubMed Central PMCID: PMC2998389.
    Kodgire P, Rao KK

    A dual mode of regulation of flgM by ScoC in Bacillus subtilis

    Can J Microbiol. 2009 Aug;55(8):983-9. doi: 10.1139/w09-049. PubMed PMID: 19898538.
    Chai Y, Kolter R, Losick R

    Paralogous antirepressors acting on the master regulator for biofilm formation in Bacillus subtilis

    Mol Microbiol. 2009 Nov;74(4):876-87. doi: 10.1111/j.1365-2958.2009.06900.x. Epub 2009 Sep 28. PubMed PMID: 19788541; PubMed Central PMCID: PMC2805041.
    Chai Y, Kolter R, Losick R

    A widely conserved gene cluster required for lactate utilization in Bacillus subtilis and its involvement in biofilm formation

    J Bacteriol. 2009 Apr;191(8):2423-30. doi: 10.1128/JB.01464-08. Epub 2009 Feb 6. PubMed PMID: 19201793; PubMed Central PMCID: PMC2668416.
    Chu F, Kearns DB, McLoon A, Chai Y, Kolter R, Losick R

    A novel regulatory protein governing biofilm formation in Bacillus subtilis

    Mol Microbiol. 2008 Jun;68(5):1117-27. doi: 10.1111/j.1365-2958.2008.06201.x. Epub 2008 Apr 21. PubMed PMID: 18430133; PubMed Central PMCID: PMC2430766.
    Chai Y, Chu F, Kolter R, Losick R

    Bistability and biofilm formation in Bacillus subtilis

    Mol Microbiol. 2008 Jan;67(2):254-63. Epub 2007 Nov 28. PubMed PMID: 18047568; PubMed Central PMCID: PMC2430929.
    Kodgire P, Dixit M, Rao KK

    ScoC and SinR negatively regulate epr by corepression in Bacillus subtilis

    J Bacteriol. 2006 Sep;188(17):6425-8. PubMed PMID: 16923912; PubMed Central PMCID: PMC1595376.
    Branda SS, Chu F, Kearns DB, Losick R, Kolter R

    A major protein component of the Bacillus subtilis biofilm matrix

    Mol Microbiol. 2006 Feb;59(4):1229-38. PubMed PMID: 16430696.
    Chu F, Kearns DB, Branda SS, Kolter R, Losick R

    Targets of the master regulator of biofilm formation in Bacillus subtilis

    Mol Microbiol. 2006 Feb;59(4):1216-28. PubMed PMID: 16430695.
    Kearns DB, Chu F, Branda SS, Kolter R, Losick R

    A master regulator for biofilm formation by Bacillus subtilis

    Mol Microbiol. 2005 Feb;55(3):739-49. PubMed PMID: 15661000.
    Sánchez A, Olmos J

    Bacillus subtilis transcriptional regulators interaction

    Biotechnol Lett. 2004 Mar;26(5):403-7. PubMed PMID: 15104138.
    Shafikhani SH, Mandic-Mulec I, Strauch MA, Smith I, Leighton T

    Postexponential regulation of sin operon expression in Bacillus subtilis

    J Bacteriol. 2002 Jan;184(2):564-71. PubMed PMID: 11751836; PubMed Central PMCID: PMC139554.
    Scott DJ, Leejeerajumnean S, Brannigan JA, Lewis RJ, Wilkinson AJ, Hoggett JG

    Quaternary re-arrangement analysed by spectral enhancement: the interaction of a sporulation repressor with its antagonist

    J Mol Biol. 1999 Nov 12;293(5):997-1004. PubMed PMID: 10547280.
    Lewis RJ, Brannigan JA, Offen WA, Smith I, Wilkinson AJ

    An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex

    J Mol Biol. 1998 Nov 13;283(5):907-12. Review. PubMed PMID: 9799632.
    Cervin MA, Lewis RJ, Brannigan JA, Spiegelman GB

    The Bacillus subtilis regulator SinR inhibits spoIIG promoter transcription in vitro without displacing RNA polymerase

    Nucleic Acids Res. 1998 Aug 15;26(16):3806-12. PubMed PMID: 9685500; PubMed Central PMCID: PMC147748.
    Margot P, Lazarevic V, Karamata D

    Effect of the SinR protein on the expression of the Bacillus subtilis 168 lytABC operon

    Microb Drug Resist. 1996 Spring;2(1):119-21. PubMed PMID: 9158733.
    Fredrick K, Helmann JD

    FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant

    J Bacteriol. 1996 Dec;178(23):7010-3. PubMed PMID: 8955328; PubMed Central PMCID: PMC178607.
    Rashid MH, Sekiguchi J

    flaD (sinR) mutations affect SigD-dependent functions at multiple points in Bacillus subtilis

    J Bacteriol. 1996 Nov;178(22):6640-3. PubMed PMID: 8932324; PubMed Central PMCID: PMC178554.
    Hahn J, Luttinger A, Dubnau D

    Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis

    Mol Microbiol. 1996 Aug;21(4):763-75. PubMed PMID: 8878039.
    Bai U, Mandic-Mulec I, Smith I

    SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction

    Genes Dev. 1993 Jan;7(1):139-48. PubMed PMID: 8422983.
    Strauch MA

    In vitro binding affinity of the Bacillus subtilis AbrB protein to six different DNA target regions

    J Bacteriol. 1995 Aug;177(15):4532-6. PubMed PMID: 7635837; PubMed Central PMCID: PMC177209.
    Gaur NK, Cabane K, Smith I

    Structure and expression of the Bacillus subtilis sin operon

    J Bacteriol. 1988 Mar;170(3):1046-53. PubMed PMID: 3125149; PubMed Central PMCID: PMC210872.
    Kallio PT, Fagelson JE, Hoch JA, Strauch MA

    The transition state regulator Hpr of Bacillus subtilis is a DNA-binding protein

    J Biol Chem. 1991 Jul 15;266(20):13411-7. PubMed PMID: 1906467.
    No login