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RstA DNA-binding transcriptional dual regulator

Synonyms: RstA-Phosphorylated, RstA
Summary:
RstA appears to control genes involved in different biological processes, such as acid tolerance, curli fimbria formation, and anaerobic respiration, among others |CITS:[ 17468243]|. 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 |CITS:[17293428]|. RstA overproduction causes drug resistance |CITS:[12618449][12951338 ]|.
RstA belongs to the two-component system RstA/RstB |CITS:[15522865]|. 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 |CITS:[ 12813061]|.
rstA expression is reduced in a phoP phoQ double mutant and in phoP phoQ pmrA and phoP phoQ pmrB triple mutants |CITS: [25605366]|. The autophosphorylation of RstB appears to be stimulated by low pH |CITS:[17468243][15522865]|. Subsequently, the phosphate group is transferred from RstB to RstA to activate it |CITS:[15522865]|.
A 14-bp DNA sequence that contains the TACA direct repeat has been identified as the RstA DNA-binding site and is called the RstA box |CITS:[ 17468243]|.


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
rstAB
rstAp


Regulon       
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,RcsAB,RstA
CRP,CpxR,EnvY,Fur,IHF,OmpR,PhoB,RstA
FNR,Fis,IHF,NarL,RstA
FliZ,RstA
H-NS,PhoB,RcdA,RstA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RstA,-](3)
[RstA,+](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
  RstA-Phosphorylated activator asrp Sigma38 -62.0 -111.0 asr
attcagcgttTGTACATATCGTTACACgctgaaacca
1671257 1671273 [BPP], [GEA], [HIBSCS] [2]
  RstA-Phosphorylated repressor csgDp1 Sigma38 -51.0 -199.0 csgD, csgE, csgF, csgG
aatataacgaGTTACATTTAGTTACATgtttaacact
1103387 1103403 [BPP], [GEA], [HIBSCS] [2], [3]
  RstA-Phosphorylated repressor csgDp2 Sigma38 -60.0 -199.0 csgD, csgE, csgF, csgG
aatataacgaGTTACATTTAGTTACATgtttaacact
1103387 1103403 [BPP], [GEA], [HIBSCS] [2], [3]
  RstA-Phosphorylated activator narGp Sigma70 -276.0 -333.0 narG, narH, narJ, narI
ctttttttatGCGTCATTTAGTTACAAcatactaatg
1279523 1279539 [HIBSCS] [2], [4]
  RstA-Phosphorylated repressor ompFp Sigma38 -92.0 -202.0 ompF
ttccttaaatTTTACTTTTGGTTACATattttttctt
987176 987192 [HIBSCS], [NTAS] [2]


Alignment and PSSM for RstA TFBSs    

Aligned TFBS of RstA   
  Sequence
  TACTTTTGGTTACA
  TACATTTAGTTACA
  GTCATTTAGTTACA
  TACATATCGTTACA

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


Evidence    

 [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



Reference(s)    

 [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



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