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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 [] 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
null


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
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 (3)
sigma factors, anti-sigmafactors (2)
Read more >
Regulated operon(s) casABCDE12, fecIR, gspCDEFGHIJKLMO, hlyE, leuO, paaABCDEFGHIJK
First gene in the operon(s) casA, fecI, gspC, hlyE, leuO, paaA
Simple and complex regulons CRP,FNR,Fis,H-NS,SlyA
CRP,H-NS,LeuO,SlyA
CRP,IHF,PaaX,SlyA
Fur,SlyA
H-NS,LeuO,LrhA,SlyA
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SlyA,+](5)
[SlyA,-](1)


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
tacggcgtaaTTAATTCAATAAtcacattcac
2884233 2884244 [AIBSCS], [BPP], [GEA] [4]
  SlyA repressor fecIp Sigma70 -62.5 -109.5 fecI, fecR
ttttaacatgTTGTTTTTCTAAgtgttataag
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
tttatttctaTTAATATGATAAatatcaaaca
1230516 1230527 [BPP], [GEA] [1], [3], [5]
  SlyA activator hlyEp nd -44.5 -116.5 hlyE
gcgtcaatgtCTTTATTTCTATtaatatgata
1230505 1230516 [BPP], [GEA] [1], [3], [5], [6], [7]
  SlyA activator hlyEp nd 52.5 -20.5 hlyE
attcgcctctTTAAATATATAAattgtaatga
1230409 1230420 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 61.5 -11.5 hlyE
gtcataatcaTTCGCCTCTTTAaatatataaa
1230400 1230411 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 76.5 3.5 hlyE
tctgcaacgaTTTCAGTCATAAtcattcgcct
1230385 1230396 [BPP], [GEA] [5]
  SlyA activator hlyEp nd 90.5 17.5 hlyE
cttctaccgtTTTATCTGCAACgatttcagtc
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]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  SlyA activator slyA nd nd 1720980 1720991 [AISGDTU] nd
  SlyA activator elfA nd nd 997854 997865 [ICWHO] nd
  SlyA activator mdtM-yjiN nd nd 4568763 4568774 [ICWHO] nd
  SlyA activator slyA nd nd 1720841 1720852 [AISGDTU] nd
  SlyA repressor sgcXBCQAER nd nd 4531988 4531999 [ICWHO] nd
  SlyA repressor sgcXBCQAER nd nd 4531834 4531845 [ICWHO] nd


Alignment and PSSM for SlyA TFBSs    

Position weight matrix (PWM).   
A	6	0	4	2	1	1	5	3	5	0	6
C	0	0	1	0	0	0	0	2	0	0	0
G	0	1	0	1	0	1	1	0	0	6	0
T	0	5	1	3	5	4	0	1	1	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    

 [IE] Inferred from experiment

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AISGDTU] Automated inference that a single-gene directon is a transcription unit

 [ICWHO] Inferred computationally without human oversight



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 T., Abacha F., Hibberd S., Rolfe M., Lacey M., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology

 [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



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