SinR

• Description: transcriptional regulator of post-exponential-phase responses genes
  
  

Gene name	sinR
Synonyms	sin, flaD
Essential	no
Product	transcriptional regulator of post-exponential-phase responses genes
Function	control of biofilm formation
Gene expression levels in SubtiExpress: sinR
Interactions involving this protein in SubtInteract: SinR
Metabolic function and regulation of this protein in SubtiPathways: Biofilm, Central C-metabolism, Protein secretion
MW, pI	12 kDa, 7.177
Gene length, protein length	333 bp, 111 aa
Immediate neighbours	sinI, tasA
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

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 gene

Basic information

• Locus tag: BSU24610

Phenotypes of a mutant

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

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: transcription repressor of biofilm genes, acts as co-repressor for SlrR PubMed

• Protein family:

• Paralogous protein(s): SlrR

Extended information on the protein

• Kinetic information:

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

• Modification:

• Cofactor(s):

• Effectors of protein activity:
  • SinI and SlrA are antagonists to SinR PubMed
  • SlrR is also antagonist of SinR PubMed

• Interactions:
  • 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

• Localization:

Database entries

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

• UniProt: P06533

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon:
  • sinI-sinR PubMed
  • sinR PubMed

• Expression browser: 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

• 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

Biological materials

• Mutant: TMB079 sinR::spec, GP736 (tetR), available in Stülke lab
  • 1S97 ( sinR::phleo), PubMed, available at BGSC

• Expression vector:
  • N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380: pGP1083 , available in Stülke lab

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

• FLAG-tag construct: GP960 (spc, based on pGP1331), available in the Stülke lab

• Antibody:

References

Reviews

Hera Vlamakis, Yunrong Chai, Pascale Beauregard, Richard Losick, Roberto Kolter
Sticking together: building a biofilm the Bacillus subtilis way.
Nat Rev Microbiol: 2013, 11(3);157-68
[PubMed:23353768] [WorldCat.org] [DOI] (I p)

Patrick Piggot
Epigenetic switching: bacteria hedge bets about staying or moving.
Curr Biol: 2010, 20(11);R480-2
[PubMed:20541494] [WorldCat.org] [DOI] (I p)

David Dubnau
Swim or chill: lifestyles of a bacillus.
Genes Dev: 2010, 24(8);735-7
[PubMed:20395361] [WorldCat.org] [DOI] (I p)

Modelling of the SinI/SinR switch

Jennifer S Hallinan, Goksel Misirli, Anil Wipat
Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits.
Annu Int Conf IEEE Eng Med Biol Soc: 2010, 2010;768-74
[PubMed:21095906] [WorldCat.org] [DOI] (P p)

Original publications

Sean D Stowe, Andrew L Olson, Richard Losick, John Cavanagh
Chemical shift assignments and secondary structure prediction of the master biofilm regulator, SinR, from Bacillus subtilis.
Biomol NMR Assign: 2014, 8(1);155-8
[PubMed:23475644] [WorldCat.org] [DOI] (I p)

Joseph A Newman, Cecilia Rodrigues, Richard J Lewis
Molecular basis of the activity of SinR protein, the master regulator of biofilm formation in Bacillus subtilis.
J Biol Chem: 2013, 288(15);10766-78
[PubMed:23430750] [WorldCat.org] [DOI] (I p)

Ying Lei, Taku Oshima, Naotake Ogasawara, Shu Ishikawa
Functional analysis of the protein Veg, which stimulates biofilm formation in Bacillus subtilis.
J Bacteriol: 2013, 195(8);1697-705
[PubMed:23378512] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Pascale B Beauregard, Hera Vlamakis, Richard Losick, Roberto Kolter
Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis.
mBio: 2012, 3(4);e00184-12
[PubMed:22893383] [WorldCat.org] [DOI] (I e)

Loralyn M Cozy, Andrew M Phillips, Rebecca A Calvo, Ashley R Bate, Yi-Huang Hsueh, Richard Bonneau, Patrick Eichenberger, Daniel B Kearns
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, 83(6);1210-28
[PubMed:22329926] [WorldCat.org] [DOI] (I p)

Christine Diethmaier, Nico Pietack, Katrin Gunka, Christoph Wrede, Martin Lehnik-Habrink, Christina Herzberg, Sebastian Hübner, Jörg Stülke
A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation.
J Bacteriol: 2011, 193(21);5997-6007
[PubMed:21856853] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol Microbiol: 2011, 81(6);1459-73
[PubMed:21815947] [WorldCat.org] [DOI] (I p)

Vicki L Colledge, Mark J Fogg, Vladimir M Levdikov, Andrew Leech, Eleanor J Dodson, Anthony J Wilkinson
Structure and organisation of SinR, the master regulator of biofilm formation in Bacillus subtilis.
J Mol Biol: 2011, 411(3);597-613
[PubMed:21708175] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Thomas Norman, Roberto Kolter, Richard Losick
Evidence that metabolism and chromosome copy number control mutually exclusive cell fates in Bacillus subtilis.
EMBO J: 2011, 30(7);1402-13
[PubMed:21326214] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Roberto Kolter, Richard Losick
Reversal of an epigenetic switch governing cell chaining in Bacillus subtilis by protein instability.
Mol Microbiol: 2010, 78(1);218-29
[PubMed:20923420] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Thomas Norman, Roberto Kolter, Richard Losick
An epigenetic switch governing daughter cell separation in Bacillus subtilis.
Genes Dev: 2010, 24(8);754-65
[PubMed:20351052] [WorldCat.org] [DOI] (I p)

Prashant Kodgire, K Krishnamurthy Rao
A dual mode of regulation of flgM by ScoC in Bacillus subtilis.
Can J Microbiol: 2009, 55(8);983-9
[PubMed:19898538] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Roberto Kolter, Richard Losick
Paralogous antirepressors acting on the master regulator for biofilm formation in Bacillus subtilis.
Mol Microbiol: 2009, 74(4);876-87
[PubMed:19788541] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Roberto Kolter, Richard Losick
A widely conserved gene cluster required for lactate utilization in Bacillus subtilis and its involvement in biofilm formation.
J Bacteriol: 2009, 191(8);2423-30
[PubMed:19201793] [WorldCat.org] [DOI] (I p)

Frances Chu, Daniel B Kearns, Anna McLoon, Yunrong Chai, Roberto Kolter, Richard Losick
A novel regulatory protein governing biofilm formation in Bacillus subtilis.
Mol Microbiol: 2008, 68(5);1117-27
[PubMed:18430133] [WorldCat.org] [DOI] (I p)

Yunrong Chai, Frances Chu, Roberto Kolter, Richard Losick
Bistability and biofilm formation in Bacillus subtilis.
Mol Microbiol: 2008, 67(2);254-63
[PubMed:18047568] [WorldCat.org] [DOI] (P p)

Prashant Kodgire, Madhulika Dixit, K Krishnamurthy Rao
ScoC and SinR negatively regulate epr by corepression in Bacillus subtilis.
J Bacteriol: 2006, 188(17);6425-8
[PubMed:16923912] [WorldCat.org] [DOI] (P p)

Steven S Branda, Frances Chu, Daniel B Kearns, Richard Losick, Roberto Kolter
A major protein component of the Bacillus subtilis biofilm matrix.
Mol Microbiol: 2006, 59(4);1229-38
[PubMed:16430696] [WorldCat.org] [DOI] (P p)

Frances Chu, Daniel B Kearns, Steven S Branda, Roberto Kolter, Richard Losick
Targets of the master regulator of biofilm formation in Bacillus subtilis.
Mol Microbiol: 2006, 59(4);1216-28
[PubMed:16430695] [WorldCat.org] [DOI] (P p)

Daniel B Kearns, Frances Chu, Steven S Branda, Roberto Kolter, Richard Losick
A master regulator for biofilm formation by Bacillus subtilis.
Mol Microbiol: 2005, 55(3);739-49
[PubMed:15661000] [WorldCat.org] [DOI] (P p)

Alejandro Sánchez, Jorge Olmos
Bacillus subtilis transcriptional regulators interaction.
Biotechnol Lett: 2004, 26(5);403-7
[PubMed:15104138] [WorldCat.org] [DOI] (P p)

Sasha H Shafikhani, Ines Mandic-Mulec, Mark A Strauch, Issar Smith, Terrance Leighton
Postexponential regulation of sin operon expression in Bacillus subtilis.
J Bacteriol: 2002, 184(2);564-71
[PubMed:11751836] [WorldCat.org] [DOI] (P p)

D J Scott, S Leejeerajumnean, J A Brannigan, R J Lewis, A J Wilkinson, J G Hoggett
Quaternary re-arrangement analysed by spectral enhancement: the interaction of a sporulation repressor with its antagonist.
J Mol Biol: 1999, 293(5);997-1004
[PubMed:10547280] [WorldCat.org] [DOI] (P p)

R J Lewis, J A Brannigan, W A Offen, I Smith, A J Wilkinson
An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex.
J Mol Biol: 1998, 283(5);907-12
[PubMed:9799632] [WorldCat.org] [DOI] (P p)

M A Cervin, R J Lewis, J A Brannigan, G B Spiegelman
The Bacillus subtilis regulator SinR inhibits spoIIG promoter transcription in vitro without displacing RNA polymerase.
Nucleic Acids Res: 1998, 26(16);3806-12
[PubMed:9685500] [WorldCat.org] [DOI] (P p)

K Fredrick, J D Helmann
FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant.
J Bacteriol: 1996, 178(23);7010-3
[PubMed:8955328] [WorldCat.org] [DOI] (P p)

M H Rashid, J Sekiguchi
flaD (sinR) mutations affect SigD-dependent functions at multiple points in Bacillus subtilis.
J Bacteriol: 1996, 178(22);6640-3
[PubMed:8932324] [WorldCat.org] [DOI] (P p)

J Hahn, A Luttinger, D Dubnau
Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis.
Mol Microbiol: 1996, 21(4);763-75
[PubMed:8878039] [WorldCat.org] [DOI] (P p)

P Margot, V Lazarevic, D Karamata
Effect of the SinR protein on the expression of the Bacillus subtilis 168 lytABC operon.
Microb Drug Resist: 1996, 2(1);119-21
[PubMed:9158733] [WorldCat.org] [DOI] (P p)

M A Strauch
In vitro binding affinity of the Bacillus subtilis AbrB protein to six different DNA target regions.
J Bacteriol: 1995, 177(15);4532-6
[PubMed:7635837] [WorldCat.org] [DOI] (P p)

U Bai, I Mandic-Mulec, I Smith
SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction.
Genes Dev: 1993, 7(1);139-48
[PubMed:8422983] [WorldCat.org] [DOI] (P p)

P T Kallio, J E Fagelson, J A Hoch, M A Strauch
The transition state regulator Hpr of Bacillus subtilis is a DNA-binding protein.
J Biol Chem: 1991, 266(20);13411-7
[PubMed:1906467] [WorldCat.org] (P p)

N K Gaur, K Cabane, I Smith
Structure and expression of the Bacillus subtilis sin operon.
J Bacteriol: 1988, 170(3);1046-53
[PubMed:3125149] [WorldCat.org] [DOI] (P p)