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SlyA DNA-binding transcriptional dual regulator

Synonyms: SlyA
Summary:
SlyA (for "hemolytic protein in Salmonella") was initially identified in Salmonella, although little is known about the regulator role of SlyA. It has been demonstrated that SlyA increases expression of hemolysin E by antagonizing the negative effects of H-NS [2, 4] SlyA belongs to the MarR family of transcriptional regulators. This protein consist of two domains, an amino-terminal domain involved in dimerization and a carboxy-terminal domain indispensable for DNA recognition [] It is known that SlyA recognizes a short palindromic DNA sequence of 12 bp [4] SlyA activity and expression are not regulated by ppGpp [1]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
SlyA Functional   [IE] [1], [2], [3], [4]
Evolutionary Family: MarR
Connectivity class: Local Regulator
Gene name: slyA
  Genome position: 1720390-1720824
  Length: 435 bp / 144 aa
Operon name: slyA
TU(s) encoding the TF:
Transcription unit        Promoter
slyA
 


Regulon       
Regulated gene(s) cas1, cas2, casA, casB, casC, casD, casE, fecI, fecR, gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO, hlyE, leuO, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, pagP, rmf, rsd
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Putative uncharacterized transport protein (11)
carbon compounds (10)
defense/survival (7)
Transcription related (4)
sigma factors, anti-sigmafactors (2)
Read more >
Regulated operon(s) casABCDE12, fecIR, gspCDEFGHIJKLMO, hlyE, leuO, paaABCDEFGHIJK, pagP, rmf, rsd
First gene in the operon(s) casA, fecI, gspC, hlyE, leuO, paaA, pagP, rmf, rsd
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
ArcA,McbR,RcdA,SdiA,SlyA
CRP,DksA-ppGpp,FNR,Fis,H-NS,SlyA
CRP,H-NS,LeuO,SlyA,StpA
CRP,IHF,PaaX,SlyA
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SlyA,-](1)
[SlyA,+](8)


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
  SlyA activator casAp Sigma70 81.5 -100.5 casA, casB, casC, casD, casE, cas1, cas2
tgtgattattGaattaattac
 2884239 2884238 [AIBSCS], [BPP], [GEA] [5]
  SlyA repressor fecIp Sigma70 -62.5 -109.5 fecI, fecR
aacacttagaAaaacaacatg
 4518345 4518344 [AIBSCS], [BPP], [GEA] [5]
  SlyA activator gspCp2 Sigma70 -49.5 -100.5 gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO
catattactaAtataaataaa
 3455478 3455477 [AIBSCS], [BPP], [GEA] [5]
  SlyA activator hlyEp nd -55.5 -127.5 hlyE
gatatttatcAtattaataga
 1230522 1230521 [BPP], [GEA] [1], [2], [4], [6]
  SlyA activator hlyEp nd -44.5 -116.5 hlyE
tattaatagaAataaagacat
 1230511 1230510 [BPP], [GEA] [1], [2], [4], [6], [7], [8]
  SlyA activator hlyEp nd 52.5 -20.5 hlyE
acaatttataTatttaaagag
 1230415 1230414 [BPP], [GEA] [1], [6]
  SlyA activator hlyEp nd 61.5 -11.5 hlyE
atatttaaagAggcgaatgat
 1230406 1230405 [BPP], [GEA] [1], [6]
  SlyA activator hlyEp nd 76.5 4.5 hlyE
aatgattatgActgaaatcgt
 1230391 1230390 [BPP], [GEA] [1], [6]
  SlyA activator hlyEp nd 90.5 18.5 hlyE
aaatcgttgcAgataaaacgg
 1230377 1230376 [BPP], [GEA] [1], [6]
  SlyA activator leuOp Sigma70 -125.5 -305.5 leuO
agaattaatgCattaaatata
 84063 84062 [AIBSCS], [BPP], [GEA] [5]
  SlyA activator leuOp Sigma70 -117.5 -297.5 leuO
tgcattaaatAtataaattaa
 84071 84070 [AIBSCS], [BPP], [GEA] [5]
  SlyA activator paaAp Sigma70 -177.5 -239.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
atagttaaatCgcgaatcata
 1453688 1453687 [AIBSCS], [BPP], [GEA] [1], [5]
  SlyA activator paaAp Sigma70 -74.5 -136.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
tgatttataaAaatagggtgc
 1453791 1453790 [AIBSCS], [BPP], [GEA] [1], [5]
  SlyA activator paaAp Sigma70 -19.5 -81.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
gattttacttAactattgtgt
 1453846 1453845 [AIBSCS], [BPP], [GEA] [1], [5]
  SlyA activator pagPp nd -109.5 -140.5 pagP
aatcgatgcgCggaaatattt
 656417 656416 [GEA], [MCIBSPD] [9]
  SlyA activator pagPp nd -89.0 -120.0 pagP
aatatttaacTTGAACAAGCGGAAataaatagag
 656431 656444 [GEA], [MCIBSPD] [9]
  SlyA activator pagPp nd -10.0 -41.0 pagP
taattgtagcTTTGCTATGCTAGTagtagatttt
 656510 656523 [GEA], [MCIBSPD] [9]
  SlyA activator rmfp nd nd nd rmf
nd
 nd nd [BPP], [GEA], [IGI] [10]
  SlyA activator rsdp2 Sigma70 nd nd rsd
nd
 nd nd [BPP], [GEA], [IGI] [10]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  SlyA activator slyA Transcription-Unit nd
nd
1720847 1720846 1720846.5 nd [AIBSCS], [BPP], [GEA] [1], [5]
  SlyA activator elfA Transcription-Unit nd
nd
997860 997859 997859.5 nd [AIBSCS], [BPP], [GEA] [5]
  SlyA activator mdtM-yjiN Transcription-Unit nd
nd
4568769 4568768 4568768.5 nd [AIBSCS], [BPP], [GEA] [5]
  SlyA activator slyA Transcription-Unit nd
nd
1720986 1720985 1720985.5 nd [AIBSCS], [BPP], [GEA] [1], [5]
  SlyA repressor sgcXBCQAER Transcription-Unit nd
nd
4531840 4531839 4531839.5 nd [AIBSCS], [BPP], [GEA] [5]
  SlyA repressor sgcXBCQAER Transcription-Unit nd
nd
4531994 4531993 4531993.5 nd [AIBSCS], [BPP], [GEA] [5]


Alignment and PSSM for SlyA TFBSs    

Aligned TFBS of SlyA   
  Sequence
  ATTACTAATATAAAT
  ATTAAATATATAAAT
  ATGATTTATAAAAAT
  ATTAATGCATTAAAT
  TTTAAATATATAAAT
  ATTATTGAATTAATT
  ATTAATATGATAAAT
  TTTATTTCTATTAAT
  TTCGCCTCTTTAAAT
  ATTCGCGATTTAACT
  ATAGTTAAGTAAAAT
  AACACTTAGAAAAAC
  ATGACTGAAATCGTT
  GTTGCAGATAAAACG

Position weight matrix (PWM). SlyA matrix-quality result    
A	10	1	1	10	4	3	3	10	3	9	4	12	13	10	0
C	0	0	2	1	5	2	0	3	0	0	0	1	0	2	1
G	1	0	2	3	1	0	5	0	3	0	0	0	1	0	1
T	3	13	9	0	4	9	6	1	8	5	10	1	0	2	12

Consensus    
;	consensus.strict             	aTtactgatatAAaT
;	consensus.strict.rc          	ATTTATATCAGTAAT
;	consensus.IUPAC              	aTtrctkmkwtAAaT
;	consensus.IUPAC.rc           	ATTTAWMKMAGYAAT
;	consensus.regexp             	aTt[ag]ct[gt][ac][gt][at]tAAaT
;	consensus.regexp.rc          	ATTTA[AT][AC][GT][AC]AG[CT]AAT

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    

 [IE] Inferred from experiment

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [MCIBSPD] Manually curated inference based on sequence pattern discovery

 [IGI] Inferred from genetic interaction


Reference(s)    

 [1] Bartoli J., Viala JP., Bouveret E., 2020, SlyA Transcriptional Regulator Is Not Directly Affected by ppGpp Levels., Front Microbiol 11:1856

 [2] Ludwig A., Bauer S., Benz R., Bergmann B., Goebel W., 1999, Analysis of the SlyA-controlled expression, subcellular localization and pore-forming activity of a 34 kDa haemolysin (ClyA) from Escherichia coli K-12., Mol Microbiol 31(2):557-67

 [3] Spory A., Bosserhoff A., von Rhein C., Goebel W., Ludwig A., 2002, Differential regulation of multiple proteins of Escherichia coli and Salmonella enterica serovar Typhimurium by the transcriptional regulator SlyA., J Bacteriol 184(13):3549-59

 [4] Wyborn NR., Stapleton MR., Norte VA., Roberts RE., Grafton J., Green J., 2004, Regulation of Escherichia coli hemolysin E expression by H-NS and Salmonella SlyA., J Bacteriol 186(6):1620-8

 [5] Curran TD., Abacha F., Hibberd SP., Rolfe MD., Lacey MM., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology 163(3):400-409

 [6] Lithgow JK., Haider F., Roberts IS., Green J., 2007, Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12., Mol Microbiol 66(3):685-98

 [7] Oscarsson J., Mizunoe Y., Uhlin BE., Haydon DJ., 1996, Induction of haemolytic activity in Escherichia coli by the slyA gene product., Mol Microbiol 20(1):191-9

 [8] Westermark M., Oscarsson J., Mizunoe Y., Urbonaviciene J., Uhlin BE., 2000, Silencing and activation of ClyA cytotoxin expression in Escherichia coli., J Bacteriol 182(22):6347-57

 [9] Klitgaard RN., Jana B., Guardabassi L., Nielsen KL., Lobner-Olesen A., 2018, DNA Damage Repair and Drug Efflux as Potential Targets for Reversing Low or Intermediate Ciprofloxacin Resistance in E. coli K-12., Front Microbiol 9:1438

 [10] 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)


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