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RstA DNA-binding transcriptional dual regulator

Synonyms: RstA, RstA-phosphorylated
Summary:
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
RstA Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
RstA-phosphorylated Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: OmpR
TFBs length: 17
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, narG, ompF
Simple and complex regulons BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
CRP,CpxR,EnvY,Fur,IHF,OmpR,PhoB,RstA
FNR,Fis,IHF,NarL,RstA
FliZ,RstA
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RstA,+](3)
[RstA,-](6)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  RstA-phosphorylated activator asrp Sigma70 -62.0 -111.0 asr
attcagcgttTGTACATATCGTTACACgctgaaacca
 1671257 1671273 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  RstA-phosphorylated activator asrp2 Sigma38 -62.0 -111.0 asr
attcagcgttTGTACATATCGTTACACgctgaaacca
 1671257 1671273 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  RstA-phosphorylated repressor csgDp Sigma38 -59.5 -198.5 csgD, csgE, csgF, csgG
atataacgagTTACATTTAGTTACAtgtttaacac
 1103388 1103402 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  RstA-phosphorylated repressor csgDp1 Sigma70 -50.5 -198.5 csgD, csgE, csgF, csgG
atataacgagTTACATTTAGTTACAtgtttaacac
 1103388 1103402 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  RstA-phosphorylated repressor csgDp2 Sigma70 -59.5 -198.5 csgD, csgE, csgF, csgG
atataacgagTTACATTTAGTTACAtgtttaacac
 1103388 1103402 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  RstA-phosphorylated repressor csgDp3 Sigma38 -50.5 -198.5 csgD, csgE, csgF, csgG
atataacgagTTACATTTAGTTACAtgtttaacac
 1103388 1103402 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  RstA-phosphorylated activator narGp Sigma70 -276.0 -333.0 narG, narH, narJ, narI
ctttttttatGCGTCATTTAGTTACAAcatactaatg
 1279523 1279539 [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2], [4], [4]
  RstA-phosphorylated repressor ompFp Sigma70 -92.0 -202.0 ompF
ttccttaaatTTTACTTTTGGTTACATattttttctt
 987176 987192 [AS-NAS], [AS-NAS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  RstA-phosphorylated repressor ompFp2 Sigma38 -92.0 -202.0 ompF
ttccttaaatTTTACTTTTGGTTACATattttttctt
 987176 987192 [AS-NAS], [AS-NAS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2], [2]


Alignment and PSSM for RstA TFBSs    

Aligned TFBS of RstA   
  Sequence
  AACATGTAACTAAATGTAAC
  AGCGTGTAACGATATGTACA
  AATATGTAACCAAAAGTAAA
  ATGTTGTAACTAAATGACGC

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

Consensus    
;	consensus.strict             	AacaTGTAACtAaAtGtaac
;	consensus.strict.rc          	GTTACATTTAGTTACATGTT
;	consensus.IUPAC              	ArsrTGTAACbAaAtGtmvm
;	consensus.IUPAC.rc           	KBKACATTTVGTTACAYSYT
;	consensus.regexp             	A[ag][cg][ag]TGTAAC[cgt]AaAtGt[ac][acg][ac]
;	consensus.regexp.rc          	[GT][CGT][GT]ACATTT[ACG]GTTACA[CT][CG][CT]T

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    

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [AS-NAS] 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

 [5] Campbell TL, Ederer CS, 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 10.1128/JB.00131-06

 [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 10.1128/AAC.05052-14

 [10] Yao Y, Ma Y, Chen X, Bade R, Lv C, Zhu R, 2018, Absence of RstA results in delayed initiation of DNA replication in Escherichia coli., PLoS One, 13(7):e0200688 10.1371/journal.pone.0200688

 [11] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661


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