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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, 6, 7, 8] 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 [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 [5] 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 [6] The transcriptional activity of SdiA is affected not only by quorum signaling but also by other environmental factors, such as oxidation [9] 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 [] Overexpression of SdiA also leads to resistance to the DNA-damaging agent mitomycin C as well as to other drugs [8] while an sdiA null mutant strain was not hypersensitive to mitomycin C []but was more sensitive to flouroquinolones [] In addition, SdiA also affects the expression of a number of genes, including a decrease in expression of several motility [3]and chemotaxis [8]genes, a pleiotropic effect over the expression of genes involved in cell division, drug sensitivity, DNA replication and repair, macromolecular metabolism [8] 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 [] Strains overexpressing SdiA had a chain-type cell morphology [] On the other hand, SdiA is highly homologous to quorum-sensing transcription factors that belong to the LuxR family [10] 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, 6, 9] AHLs might control the transcriptional activity of SdiA by enhancing its stability rather than by directly affecting its DNA-binding affinity [9] 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 Functional   [IE] 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
 
 


Regulon       
Regulated gene(s) ftsA, ftsQ, ftsZ, gadW, rmf, rsd, ydiV
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)
translation (1)
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Regulated operon(s) gadAXW, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, rmf, rsd, ydiV
First gene in the operon(s) ftsQ, gadW, rmf, rsd, ydiV
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
ArcA,McbR,RcdA,SdiA,SlyA
GadW,GadX,H-NS,PhoP,SdiA
SdiA
SdiA,ppGpp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SdiA,-](1)
[SdiA,+](5)


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 ftsQp1 Sigma38, Sigma70 -163.5 -451.5 ftsQ, ftsA, ftsZ
tgtgggaatgTCAAAAGTAGTAGCAGAAaatgctctac
 102695 102712 [BPP], [GEA] [1], [2]
  SdiA repressor ftsQp1 Sigma38, Sigma70 -161.5 -449.5 ftsQ, ftsA, ftsZ
tgggaatgtcAAAAGTAGTAGCAGAAAAtgctctacaa
 102697 102714 [BPP], [GEA] [2]
  SdiA repressor ftsQp1 Sigma38, Sigma70 -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 nd [GEA] [3]
  SdiA activator rmfp nd nd nd rmf
nd
 nd nd [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/GS)], [CV(GEA/ROMA)], [GEA], [GS] [4]
  SdiA activator rsdp2 Sigma70 nd nd rsd
nd
 nd nd [BPP], [CV(CHIP-SV/GEA/GS)], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/GS)], [CV(GEA/ROMA)], [GEA], [GS] [4]
  SdiA activator ydiVp Sigma24 -53.0 -120.0 ydiV
gataatctaaAAAAAGGACCCCTGAAAAagtggttaac
 1792132 1792149 [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [5]


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


Evidence    

 [IE] Inferred from experiment

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [CV(CHIP-SV/GEA/GS)] cross validation(CHIP-SV/GEA/GS)

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(GEA/GS)] cross validation(GEA/GS)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GS] genomic SELEX

 [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] Yoshida H., Shimada T., Ishihama A., null, 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] 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

 [9] 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, 2014 Mar

 [10] 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


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