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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 [4, 5]. 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 [5]. SlyA activity and expression are not regulated by ppGpp [2].


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
SlyA Functional   nd nd nd
Evolutionary Family: MarR
TFBs length: 12
TFBs symmetry: inverted-repeat
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  SlyA activator casAp Sigma70 81.5 -100.5 casA, casB, casC, casD, casE, cas1, cas2
gtgaatgtgaTTATTGAATTAAttacgccgta
 2884233 2884244 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SlyA repressor fecIp Sigma70 -62.5 -109.5 fecI, fecR
cttataacacTTAGAAAAACAAcatgttaaaa
 4518339 4518350 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SlyA activator gspCp2 Sigma70 -49.5 -100.5 gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO
taaatacataTTACTAATATAAataaattttg
 3455472 3455483 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SlyA activator hlyEp nd -55.5 -127.5 hlyE
tgtttgatatTTATCATATTAAtagaaataaa
 1230516 1230527 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3], [4], [5], [5]
  SlyA activator hlyEp nd -44.5 -116.5 hlyE
tatcatattaATAGAAATAAAGacattgacgc
 1230505 1230516 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3], [4], [5], [5], [6], [7]
  SlyA activator hlyEp nd 52.5 -20.5 hlyE
tcattacaatTTATATATTTAAagaggcgaat
 1230409 1230420 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3]
  SlyA activator hlyEp nd 61.5 -11.5 hlyE
tttatatattTAAAGAGGCGAAtgattatgac
 1230400 1230411 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3]
  SlyA activator hlyEp nd 76.5 4.5 hlyE
aggcgaatgaTTATGACTGAAAtcgttgcaga
 1230385 1230396 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3]
  SlyA activator hlyEp nd 90.5 18.5 hlyE
gactgaaatcGTTGCAGATAAAacggtagaag
 1230371 1230382 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [3], [3]
  SlyA activator leuOp Sigma70 -125.5 -305.5 leuO
atgttaagaaTTAATGCATTAAatatataaat
 84057 84068 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SlyA activator leuOp Sigma70 -117.5 -297.5 leuO
aattaatgcaTTAAATATATAAattaattatt
 84065 84076 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  SlyA activator paaAp Sigma70 -177.5 -239.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
ttgctaatagTTAAATCGCGAAtcataaaaag
 1453682 1453693 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  SlyA activator paaAp Sigma70 -74.5 -136.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
aaataatgatTTATAAAAATAGggtgcgaaat
 1453785 1453796 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  SlyA activator paaAp Sigma70 -19.5 -81.5 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
atttgtgattTTACTTAACTATtgtgtaactt
 1453840 1453851 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2]
  SlyA activator pagPp nd -109.5 -140.5 pagP
atctttaatcGATGCGCGGAAAtatttaactt
 656411 656422 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-PATTERN-DISCOVERY] W [8], [8]
  SlyA activator pagPp nd -89.0 -120.0 pagP
aatatttaacTTGAACAAGCGGAAataaatagag
 656431 656444 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-PATTERN-DISCOVERY] W [8], [8]
  SlyA activator pagPp nd -10.0 -41.0 pagP
taattgtagcTTTGCTATGCTAGTagtagatttt
 656510 656523 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-PATTERN-DISCOVERY] W [8], [8]
  SlyA activator rmfp nd nd nd rmf
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [9], [9]
  SlyA activator rsdp2 Sigma70 nd nd rsd
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [9], [9]



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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  SlyA activator slyA Transcription-Unit nd
taaagaatatTTATTAATCTAAcgcaatatat
1720980 1720991 1720985.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2]
  SlyA activator slyA Transcription-Unit nd
ctccttataaTTAGCTTGCTAAgatattatgc
1720841 1720852 1720846.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2]
  SlyA activator elfA Transcription-Unit nd
tacgaagagaTCAGGATGATAAcgatgaaaaa
997854 997865 997859.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  SlyA activator mdtM-yjiN Transcription-Unit nd
gcatagaaaaTATACACCTTAAgtgtaattaa
4568763 4568774 4568768.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  SlyA repressor sgcXBCQAER Transcription-Unit nd
agaccagtgaTTATGGTTGAAAtaatgaggat
4531834 4531845 4531839.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  SlyA repressor sgcXBCQAER Transcription-Unit nd
aggtcgttggTTCCCAGCATAAtgtaagaaaa
4531988 4531999 4531993.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


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    

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [COMP-HINF-PATTERN-DISCOVERY] Manually curated inference based on sequence pattern discovery

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] 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

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

 [3] 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

 [4] 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

 [5] 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

 [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., 2018, 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, 278(22):20240 10.1074/jbc.M300292200


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