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RstA DNA-binding transcriptional dual regulator

Synonyms: RstA-Phosphorylated, RstA
RstA appears to control genes involved in different biological processes, such as acid tolerance, curli fimbria formation, and anaerobic respiration, among others [2] Some phenotypes caused by RstA have been identified by mutational analysis. For example, RstA is a suppressor of a lesion in yjeE, a gene essential for cell growth and whose cellular function is unknown [5] RstA overproduction causes drug resistance [6, 7].
RstA belongs to the two-component system RstA/RstB [1] Both genes, rstA, encoding the response regulator, and rstB, encoding the sensor kinase, are transcribed together in an operon that is induced under low-Mg2+ growth conditions through the PhoP/PhoQ two-component system [8]
rstA expression is reduced in a phoP phoQ double mutant and in phoP phoQ pmrA and phoP phoQ pmrB triple mutants [9].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RstA Non-Functional   Apo [BPP], [IPI] [1]
RstA-Phosphorylated Functional Covalent Holo [BPP], [IPI] [1]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: rstA
  Genome position: 1682159-1682878
  Length: 720 bp / 239 aa
Operon name: rstAB
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) asr, csgD, csgE, csgF, csgG, narG, narH, narI, narJ, ompF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
anaerobic respiration (4)
electron acceptors (3)
membrane (2)
pH (1)
Transcription related (1)
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Regulated operon(s) asr, csgDEFG, narGHJI, ompF
First gene in the operon(s) asr, csgD, csgD, narG, ompF
Simple and complex regulons BasR,CRP,CpxR,Cra,CsgD,FliZ,IHF,MlrA,MqsA,OmpR,RcdA,RcsB,RstA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  RstA-Phosphorylated activator asrp Sigma38 -62.0 -111.0 asr
1671257 1671273 [BPP], [GEA], [HIBSCS] [2]
  RstA-Phosphorylated repressor csgDp1 Sigma38 -51.0 -199.0 csgD, csgE, csgF, csgG
1103387 1103403 [BPP], [GEA], [HIBSCS] [2], [3]
  RstA-Phosphorylated repressor csgDp2 Sigma38 -60.0 -199.0 csgD, csgE, csgF, csgG
1103387 1103403 [BPP], [GEA], [HIBSCS] [2], [3]
  RstA-Phosphorylated activator narGp Sigma70 -276.0 -333.0 narG, narH, narJ, narI
1279523 1279539 [HIBSCS] [2], [4]
  RstA-Phosphorylated repressor ompFp Sigma38 -92.0 -202.0 ompF
987176 987192 [HIBSCS], [NTAS] [2]

Alignment and PSSM for RstA TFBSs    

Aligned TFBS of RstA   

Position weight matrix (PWM).   
A	0	3	0	3	0	1	0	2	0	0	0	4	0	4
C	0	0	4	0	0	0	0	1	0	0	0	0	4	0
G	1	0	0	0	0	0	0	1	4	0	0	0	0	0
T	3	1	0	1	4	3	4	0	0	4	4	0	0	0

PWM logo   


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


 [BPP] Binding of purified proteins

 [IPI] Inferred from physical interaction

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [NTAS] Non-traceable author statement


 [1] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem. 280(2):1448-56

 [2] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol. 189(13):4791-9

 [3] Ogasawara H., Yamada K., Kori A., Yamamoto K., Ishihama A., 2010, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors., Microbiology. 156(Pt 8):2470-83

 [4] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol. 46(1):281-91

 [5] Campbell TL., Ederer C., Allali-Hassani A., Brown ED., 2007, Isolation of the rstA gene as a multicopy suppressor of YjeE, an essential ATPase of unknown function in Escherichia coli., J Bacteriol. 189(8):3318-21

 [6] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Bacteriol. 185(6):1851-6

 [7] Hirakawa H., Nishino K., Yamada J., Hirata T., Yamaguchi A., 2003, Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Antimicrob Chemother. 52(4):576-82

 [8] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol. 185(13):3696-702

 [9] Rubin EJ., Herrera CM., Crofts AA., Trent MS., 2015, PmrD is required for modifications to escherichia coli endotoxin that promote antimicrobial resistance., Antimicrob Agents Chemother. 59(4):2051-61