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LsrR DNA-binding transcriptional repressor

Synonyms: LsrR-4,5-dihydroxy-2,3-pentanedione-P, LsrR, LsrR-4,5-dihydroxy-2,3-pentanedione
Summary:
Using particular analysis and high-throughput analysis (microarrays), it was established that LsrR regulates expression of many genes involved in several processes, such as autoinducer 2 uptake and processing [1, 3], biofilm architecture [1, 7], host invasion, stress responses, and foreign DNA, among others [1]. It also regulates the expression of small riboregulators [1].
LrsR pertains to the quorum-sensing system, which involves autoinducer-based bacterial cell-to-cell communication [8]. It was demonstrated in Salmonella enterica serovar Typhimurium that LsrR directly senses and binds the molecule 4,5-dihydroxy-2,3-pentanedione (DPD), phosphorylated [2] and dephosphorylated [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
LsrR Functional Allosteric Holo [IEP], [IMP], [IPI] [1], [2]
LsrR-4,5-dihydroxy-2,3-pentanedione Non-Functional Allosteric Holo [IEP], [IMP] [1]
LsrR-4,5-dihydroxy-2,3-pentanedione-P Non-Functional Allosteric Holo [IPI] [2]
Evolutionary Family: Sugar_binding domain
Connectivity class: Local Regulator
Gene name: lsrR
  Genome position: 1600288-1601241
  Length: 954 bp / 317 aa
Operon name: lsrRK
TU(s) encoding the TF:
Transcription unit        Promoter
lsrRK
lsrRp


Regulon       
Regulated gene(s) lsrA, lsrB, lsrC, lsrD, lsrF, lsrG, lsrK, lsrR, tam
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
ABC superfamily, membrane component (2)
membrane (2)
ABC superfamily ATP binding cytoplasmic component (1)
ABC superfamily, periplasmic binding component (1)
regulation (1)
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Regulated operon(s) lsrACDBFG-tam, lsrRK
First gene in the operon(s) lsrA, lsrR
Simple and complex regulons CRP,LsrR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[LsrR,-](2)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  LsrR repressor lsrAp Sigma38 nd nd lsrA, lsrC, lsrD, lsrB, lsrF, lsrG, tam nd nd [BPP], [GEA], [SM] [3], [4]
  LsrR repressor lsrRp Sigma70 nd nd lsrR, lsrK nd nd [BPP], [GEA], [SM] [4], [5], [6]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [IEP] Inferred from expression pattern

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation



Reference(s)    

 [1] Li J., Attila C., Wang L., Wood TK., Valdes JJ., Bentley WE., 2007, Quorum sensing in Escherichia coli is signaled by AI-2/LsrR: effects on small RNA and biofilm architecture., J Bacteriol. 189(16):6011-20

 [2] Xavier KB., Miller ST., Lu W., Kim JH., Rabinowitz J., Pelczer I., Semmelhack MF., Bassler BL., 2007, Phosphorylation and processing of the quorum-sensing molecule autoinducer-2 in enteric bacteria., ACS Chem Biol. 2(2):128-36

 [3] Wang L., Hashimoto Y., Tsao CY., Valdes JJ., Bentley WE., 2005, Cyclic AMP (cAMP) and cAMP receptor protein influence both synthesis and uptake of extracellular autoinducer 2 in Escherichia coli., J Bacteriol. 187(6):2066-76

 [4] Xue T., Zhao L., Sun H., Zhou X., Sun B., 2009, LsrR-binding site recognition and regulatory characteristics in Escherichia coli AI-2 quorum sensing., Cell Res. 19(11):1258-68

 [5] Wang L., Li J., March JC., Valdes JJ., Bentley WE., 2005, luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling., J Bacteriol. 187(24):8350-60

 [6] Wu M., Tao Y., Liu X., Zang J., 2013, Structural basis for phosphorylated autoinducer-2 modulation of the oligomerization state of the global transcription regulator LsrR from Escherichia coli., J Biol Chem. 288(22):15878-87

 [7] Zhang XS., Garcia-Contreras R., Wood TK., 2008, Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)., ISME J. 2(6):615-31

 [8] Fuqua WC., Winans SC., Greenberg EP., 1994, Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators., J Bacteriol. 176(2):269-75

 [9] Xavier KB., Bassler BL., 2005, Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli., J Bacteriol. 187(1):238-48

 [10] Ha JH., Eo Y., Grishaev A., Guo M., Smith JA., Sintim HO., Kim EH., Cheong HK., Bentley WE., Ryu KS., 2013, Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition., J Am Chem Soc. 135(41):15526-35

 [11] Taga ME., Miller ST., Bassler BL., 2003, Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium., Mol Microbiol. 50(4):1411-27

 [12] Mitra A., Herren CD., Patel IR., Coleman A., Mukhopadhyay S., 2016, Integration of AI-2 Based Cell-Cell Signaling with Metabolic Cues in Escherichia coli., PLoS One. 11(6):e0157532

 [13] Krisko A., Copi T., Gabaldon T., Lehner B., Supek F., 2014, Inferring gene function from evolutionary change in signatures of translation efficiency., Genome Biol. 15(3):R44



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