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SdiA DNA-binding transcriptional dual regulator

Synonyms: SdiA
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, 6, 7, 8, 9] and acid tolerance [3]. SdiA has been shown to increase transcription from the P2 promoter of the ftsQAZ operon [7] by facilitating RNA polymerase binding to the promoter region [1]. 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 [5]. Expression of sdiA itself is regulated by a mechanism similar to quorum sensing: exposure to conditioned medium results in a 50-80% decrease in sdiA expression [6].
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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 Functional   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

Regulated gene(s) ftsA, ftsQ, ftsZ, gadW, gadY, rflP, rmf, rsd
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
cell division (3)
Transcription related (2)
membrane (1)
repressor (1)
antisense RNA (1)
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Regulated operon(s) gadAXW, gadY, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, rflP, rmf, rsd
First gene in the operon(s) ftsQ, gadW, gadY, rmf, rsd, rflP
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

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 ftsQp Sigma38 -163.5 -451.5 ftsQ, ftsA, ftsZ
102695 102712 [GEA], [BPP] [1]
  SdiA repressor ftsQp Sigma38 -161.5 -449.5 ftsQ, ftsA, ftsZ
102697 102714 [GEA], [BPP] [1]
  SdiA repressor ftsQp Sigma38 -15.5 -303.5 ftsQ, ftsA, ftsZ
102843 102860 [BPP] [1]
  SdiA repressor ftsQp1 Sigma70 -163.5 -451.5 ftsQ, ftsA, ftsZ
102695 102712 [GEA], [BPP] [1]
  SdiA repressor ftsQp1 Sigma70 -161.5 -449.5 ftsQ, ftsA, ftsZ
102697 102714 [GEA], [BPP] [1]
  SdiA repressor ftsQp1 Sigma70 -15.5 -303.5 ftsQ, ftsA, ftsZ
102843 102860 [BPP] [1]
  SdiA activator ftsQp2 Sigma38 -36.5 -449.5 ftsQ
102697 102714 [GEA], [BPP] [1]
  SdiA activator gadWp2 nd nd nd gadW nd nd [GEA], [BPP] [2], [3]
  SdiA activator gadYp Sigma38 nd nd gadY nd nd [GEA], [BPP] [3]
  SdiA activator rmfp nd nd nd rmf nd nd [GEA], [BPP] [4]
  SdiA activator rsdp2 Sigma70 nd nd rsd nd nd [GEA], [BPP] [4]
  SdiA activator ydiVp Sigma24 -53.0 -120.0 rflP
1792132 1792149 [GEA], [AIBSCS], [BPP] [5]

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


 [1] 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

 [2] 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

 [3] Ma X., Zhang S., Xu Z., Li H., Xiao Q., Qiu F., Zhang W., Long Y., Zheng D., Huang B., Chen C., Lu Y., 2020, SdiA Improves the Acid Tolerance of E. coli by Regulating GadW and GadY Expression., Front Microbiol 11:1078

 [4] Yoshida H., Shimada T., Ishihama A., 2018, Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase., mSystems 3(5)

 [5] 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

 [6] García-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, 1996 May

 [7] 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

 [8] 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

 [9] 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

 [10] 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 10.1107/S1399004713032355

 [11] 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 10.1128/JB.183.7.2259-2264.2001

 [12] 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 10.1046/j.1365-2958.2002.02773.x

 [13] Cho S, Choe D, Lee E, Kim SC, Palsson B, Cho BK, 2018, High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli., ACS Synth Biol, 7(4):1085 10.1021/acssynbio.7b00462

 [14] 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

 [15] Ahmer BM, 2004, Cell-to-cell signalling in Escherichia coli and Salmonella enterica., Mol Microbiol, 52(4):933 10.1111/j.1365-2958.2004.04054.x

 [16] 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 10.1046/j.1365-2958.2000.02171.x

 [17] 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 10.1016/j.jmb.2005.10.041

 [18] 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 10.1111/j.1574-6968.2006.00103.x

 [19] 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 10.1128/AEM.02081-08

 [20] 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 10.1128/JB.183.9.2918-2928.2001

 [21] Lindsay A, Ahmer BM, 2005, Effect of sdiA on biosensors of N-acylhomoserine lactones., J Bacteriol, 187(14):5054 10.1128/JB.187.14.5054-5058.2005

 [22] Walters M, Sperandio V, 2006, Quorum sensing in Escherichia coli and Salmonella., Int J Med Microbiol, 296(2-3):125 10.1016/j.ijmm.2006.01.041

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

 [24] 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 10.1038/ismej.2008.54

 [25] 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 10.1128/AEM.00046-12

 [26] 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):None 10.1128/mBio.02429-14

 [27] Grabski H, Ginosyan S, Tiratsuyan S, 2021, Molecular Simulations and Markov State Modeling Reveal Inactive Form of Quorum Sensing Regulator SdiA of Escherichia Coli., IEEE/ACM Trans Comput Biol Bioinform, 18(6):2835 10.1109/TCBB.2021.3074567