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SdiA DNA-binding transcriptional dual regulator

Synonyms: SdiA
Summary:
The transcription factor SdiA, for Suppressor of the cell division inhibitor, is possibly positively autoregulated and controls the transcription of the genes involved in cell division [1, 2, 5, 6, 7] SdiA has been shown to increase transcription from the P2 promoter of the ftsQAZ operon [6]by facilitating RNA polymerase binding to the promoter region [2] SdiA activates the expression of ydiV, which is involved in the interaction between two quorum-sensing systems. An sdiA ydiV double mutant reduces cAMP levels, which inhibits quorum-sensing system 2 [4] Expression of sdiAitself is regulated by a mechanism similar to quorum sensing: exposure to conditioned medium results in a 50-80% decrease in sdiA expression [5] The transcriptional activity of SdiA is affected not only by quorum signaling but also by other environmental factors, such as oxidation [8]
Overexpression of SdiA speeds up cell division [1]and causes apparently concomitant morphological changes; in both exponential and stationary phases, cells appear rounder and shorter [9] Overexpression of SdiA also leads to resistance to the DNA-damaging agent mitomycin C as well as to other drugs [7, 9] while an sdiA null mutant strain was not hypersensitive to mitomycin C [9]but was more sensitive to flouroquinolones [10] In addition, SdiA also affects the expression of a number of genes, including a decrease in expression of several motility [3]and chemotaxis [7]genes, a pleiotropic effect over the expression of genes involved in cell division, drug sensitivity, DNA replication and repair, macromolecular metabolism [7] genes involved in the glutamate-dependent acid resistance systems (AR-2) [3] and an increase in the expression of the AcrAB multidrug efflux pump proteins [10]
On the other hand, SdiA is highly homologous to quorum-sensing transcription factors that belong to the LuxR family [11, 12, 13, 14] The molecule inducer is represented by different N-acyl-L-homoserine lactones (AHLs), which are signaling molecules involved in communication between bacteria (quorum-sensing systems) [3, 5, 8, 12, 15, 16, 17, 18, 19] AHLs might control the transcriptional activity of SdiA by enhancing its stability rather than by directly affecting its DNA-binding affinity [8] Lee et al.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
SdiA     nd nd
Evolutionary Family: LuxR/UhpA
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: sdiA
  Genome position: 1996110-1996832
  Length: 723 bp / 240 aa
Operon name: sdiA
TU(s) encoding the TF:
Transcription unit        Promoter
sdiA
sdiAp1
sdiA
sdiAp1b
sdiA
sdiAp2
sdiA
sdiAp2b
sdiA
sdiAp3
sdiA
sdiAp4
sdiA
null


Regulon       
Regulated gene(s) ftsA, ftsQ, ftsZ, gadW, ydiV
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
cell division (3)
membrane (1)
Transcription related (1)
repressor (1)
posttranscriptional (1)
Regulated operon(s) gadAXW, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, ydiV
First gene in the operon(s) ftsQ, ftsQ, gadW, ydiV
Simple and complex regulons GadW,GadX,H-NS,PhoP,SdiA
SdiA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SdiA,-](1)
[SdiA,+](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
  SdiA repressor ftsQp1 Sigma38 -163.5 -451.5 ftsQ, ftsA, ftsZ
tgtgggaatgTCAAAAGTAGTAGCAGAAaatgctctac
102695 102712 [BPP], [GEA] [1], [2]
  SdiA repressor ftsQp1 Sigma38 -161.5 -449.5 ftsQ, ftsA, ftsZ
tgggaatgtcAAAAGTAGTAGCAGAAAAtgctctacaa
102697 102714 [BPP], [GEA] [2]
  SdiA repressor ftsQp1 Sigma38 -15.5 -303.5 ftsQ, ftsA, ftsZ
atacgtattcAACCGTCCGGAACCTTCTatgattatga
102843 102860 [BPP] [2]
  SdiA activator ftsQp2 Sigma38 -36.5 -449.5 ftsQ
tgggaatgtcAAAAGTAGTAGCAGAAAAtgctctacaa
102697 102714 [BPP], [GEA] [2]
  SdiA activator gadWp2 nd nd nd gadW nd nd [GEA] [3]
  SdiA activator ydiVp Sigma24 -53.0 -120.0 ydiV
ataatctaaaAAAAGGACCCCTGAAAAagtggttaac
1792132 1792148 [AIBSCS], [BPP], [GEA] [4]


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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] Wang XD., de Boer PA., Rothfield LI., 1991, A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli., EMBO J. 10(11):3363-72

 [2] Yamamoto K., Yata K., Fujita N., Ishihama A., 2001, Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulator., Mol Microbiol. 41(5):1187-98

 [3] Dyszel JL., Soares JA., Swearingen MC., Lindsay A., Smith JN., Ahmer BM., 2010, E. coli K-12 and EHEC genes regulated by SdiA., PLoS One. 5(1):e8946

 [4] Zhou X., Meng X., Sun B., 2008, An EAL domain protein and cyclic AMP contribute to the interaction between the two quorum sensing systems in Escherichia coli., Cell Res. 18(9):937-48

 [5] Garcia-Lara J., Shang LH., Rothfield LI., 1996, An extracellular factor regulates expression of sdiA, a transcriptional activator of cell division genes in Escherichia coli., J Bacteriol. 178(10):2742-8

 [6] Sitnikov DM., Schineller JB., Baldwin TO., 1996, Control of cell division in Escherichia coli: regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction., Proc Natl Acad Sci U S A. 93(1):336-41

 [7] Wei Y., Lee JM., Smulski DR., LaRossa RA., 2001, Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli., J Bacteriol. 183(7):2265-72

 [8] Kim T., Duong T., Wu CA., Choi J., Lan N., Kang SW., Lokanath NK., Shin D., Hwang HY., Kim KK., 2014, Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor., Acta Crystallogr D Biol Crystallogr. 70(Pt 3):694-707

 [9] Wei Y., Vollmer AC., LaRossa RA., 2001, In vivo titration of mitomycin C action by four Escherichia coli genomic regions on multicopy plasmids., J Bacteriol. 183(7):2259-64

 [10] Rahmati S., Yang S., Davidson AL., Zechiedrich EL., 2002, Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA., Mol Microbiol. 43(3):677-85

 [11] Michael B., Smith JN., Swift S., Heffron F., Ahmer BM., 2001, SdiA of Salmonella enterica is a LuxR homolog that detects mixed microbial communities., J Bacteriol. 183(19):5733-42

 [12] Ahmer BM., 2004, Cell-to-cell signalling in Escherichia coli and Salmonella enterica., Mol Microbiol. 52(4):933-45

 [13] Kanamaru K., Kanamaru K., Tatsuno I., Tobe T., Sasakawa C., 2000, SdiA, an Escherichia coli homologue of quorum-sensing regulators, controls the expression of virulence factors in enterohaemorrhagic Escherichia coli O157:H7., Mol Microbiol. 38(4):805-16

 [14] Yao Y., Martinez-Yamout MA., Dickerson TJ., Brogan AP., Wright PE., Dyson HJ., 2006, Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones., J Mol Biol. 355(2):262-73

 [15] Van Houdt R., Aertsen A., Moons P., Vanoirbeek K., Michiels CW., 2006, N-acyl-L-homoserine lactone signal interception by Escherichia coli., FEMS Microbiol Lett. 256(1):83-9

 [16] Lee J., Maeda T., Hong SH., Wood TK., 2009, Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones., Appl Environ Microbiol. 75(6):1703-16

 [17] DeLisa MP., Valdes JJ., Bentley WE., 2001, Mapping stress-induced changes in autoinducer AI-2 production in chemostat-cultivated Escherichia coli K-12., J Bacteriol. 183(9):2918-28

 [18] Lindsay A., Ahmer BM., 2005, Effect of sdiA on biosensors of N-acylhomoserine lactones., J Bacteriol. 187(14):5054-8

 [19] Walters M., Sperandio V., 2006, Quorum sensing in Escherichia coli and Salmonella., Int J Med Microbiol. 296(2-3):125-31

 [20] Lee J., Jayaraman A., Wood TK., 2007, Indole is an inter-species biofilm signal mediated by SdiA., BMC Microbiol. 7:42

 [21] Lee J., Zhang XS., Hegde M., Bentley WE., Jayaraman A., Wood TK., 2008, Indole cell signaling occurs primarily at low temperatures in Escherichia coli., ISME J. 2(10):1007-23

 [22] Sabag-Daigle A., Soares JA., Smith JN., Elmasry ME., Ahmer BM., 2012, The Acyl Homoserine Lactone Receptor, SdiA, of Escherichia coli and Salmonella enterica Serovar Typhimurium Does Not Respond to Indole., Appl Environ Microbiol. 78(15):5424-31

 [23] Nguyen Y., Nguyen NX., Rogers JL., Liao J., MacMillan JB., Jiang Y., Sperandio V., 2015, Structural and mechanistic roles of novel chemical ligands on the SdiA quorum-sensing transcription regulator., MBio. 6(2)



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