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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 [1, 3] 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 [10] It is known that SlyA recognizes a short palindromic DNA sequence of 12 bp [3]


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]
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 (3)
Read more >
Regulated operon(s) casABCDE12, fecIR, gspCDEFGHIJKLMO, hlyE, leuO, paaABCDEFGHIJK, pagP, rmf, rsd
First gene in the operon(s) fecI, hlyE, leuO, paaA, pagP, rmf, rsd, casA, gspC
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
ArcA,McbR,RcdA,SdiA,SlyA
CRP,FNR,Fis,H-NS,SlyA
CRP,H-NS,LeuO,SlyA
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
gtgaatgtgaTTATTGAATTAAttacgccgta
2884233 2884244 [AIBSCS], [BPP], [GEA] [4]
  SlyA repressor fecIp Sigma70 -62.5 -109.5 fecI, fecR
cttataacacTTAGAAAAACAAcatgttaaaa
4518339 4518350 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator gspCp2 Sigma70 -49.5 -100.5 gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO
taaatacataTTACTAATATAAataaattttg
3455472 3455483 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator hlyEp nd -55.5 -127.5 hlyE
tgtttgatatTTATCATATTAAtagaaataaa
1230516 1230527 [BPP], [GEA] [1], [3], [5]
  SlyA activator hlyEp nd -44.5 -116.5 hlyE
tatcatattaATAGAAATAAAGacattgacgc
1230505 1230516 [BPP], [GEA] [1], [3], [5], [6], [7]
  SlyA activator hlyEp nd 52.5 -20.5 hlyE
tcattacaatTTATATATTTAAagaggcgaat
1230409 1230420 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 61.5 -11.5 hlyE
tttatatattTAAAGAGGCGAAtgattatgac
1230400 1230411 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 76.5 4.5 hlyE
aggcgaatgaTTATGACTGAAAtcgttgcaga
1230385 1230396 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 90.5 18.5 hlyE
gactgaaatcGTTGCAGATAAAacggtagaag
1230371 1230382 [BPP], [GEA] [5]
  SlyA activator leuOp Sigma70 -125.5 -305.5 leuO
atgttaagaaTTAATGCATTAAatatataaat
84057 84068 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator leuOp Sigma70 -117.5 -297.5 leuO
aattaatgcaTTAAATATATAAattaattatt
84065 84076 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator paaAp Sigma70 -177.5 -239.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
ttgctaatagTTAAATCGCGAAtcataaaaag
1453682 1453693 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator paaAp Sigma70 -74.5 -136.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
aaataatgatTTATAAAAATAGggtgcgaaat
1453785 1453796 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator paaAp Sigma70 -19.5 -81.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
atttgtgattTTACTTAACTATtgtgtaactt
1453840 1453851 [AIBSCS], [BPP], [GEA] [4]
  SlyA activator pagPp nd -109.5 -140.5 pagP
atctttaatcGATGCGCGGAAAtatttaactt
656411 656422 [GEA], [8]
  SlyA activator pagPp nd -89.0 -120.0 pagP
aatatttaacTTGAACAAGCGGAAataaatagag
656431 656444 [GEA], [8]
  SlyA activator pagPp nd -10.0 -41.0 pagP
taattgtagcTTTGCTATGCTAGTagtagatttt
656510 656523 [GEA], [8]
  SlyA activator rmfp nd nd nd rmf nd nd [BPP], [CV(GEA/GS)], [GEA], [GS] [9]
  SlyA activator rsdp2 Sigma70 nd nd rsd nd nd [BPP], [CV(GEA/GS)], [GEA], [GS] [9]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  SlyA activator slyA nd nd 1720980 1720991 nd [AIBSCS], [BPP], [GEA] [4]
  SlyA activator nd nd nd 997854 997865 nd [AIBSCS], [BPP], [GEA] [4]
  SlyA activator nd nd nd 4568763 4568774 nd [AIBSCS], [BPP], [GEA] [4]
  SlyA activator slyA nd nd 1720841 1720852 nd [AIBSCS], [BPP], [GEA] [4]
  SlyA repressor nd nd nd 4531988 4531999 nd [AIBSCS], [BPP], [GEA] [4]
  SlyA repressor nd nd nd 4531834 4531845 nd [AIBSCS], [BPP], [GEA] [4]


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

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

 [GS] genomic SELEX



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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)

 [10] Wu RY, Zhang RG, Zagnitko O, Dementieva I, Maltzev N, Watson JD, Laskowski R, Gornicki P, Joachimiak A, 2003, Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor., J Biol Chem, 2003 May 30



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