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CysB DNA-binding transcriptional dual regulator

Synonyms: CysB-N-acetyl-L-serine, CysB-Sulphide, CysB-Thiosulfate, CysB-O-acetyl-L-serine, CysB


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CysB     nd nd
CysB-N-acetyl-L-serine Functional Allosteric Holo [BPP], [GEA], [IDA], [SM] [1], [2], [3]
CysB-O-acetyl-L-serine Functional Allosteric Holo [GEA], [IDA] [3]
CysB-Sulphide Non-Functional Allosteric Holo [GEA], [IDA] [3]
CysB-Thiosulfate Non-Functional Allosteric Holo [BPP], [IDA] [2]
Evolutionary Family: LysR
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: cysB
  Genome position: 1333855-1334829
  Length: 975 bp / 324 aa
Operon name: cysB
TU(s) encoding the TF:
Transcription unit        Promoter
cysB
cysBp


Regulon       
Regulated gene(s) cbl, cysA, cysB, cysC, cysD, cysH, cysI, cysJ, cysK, cysM, cysN, cysP, cysU, cysW, dgcZ, hslJ, ssuA, ssuB, ssuC, ssuD, ssuE, tauA, tauB, tauC, tauD, tcyJ, tcyP, ybdN, yciW, yfbR, ygeH, yoaC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
sulfur metabolism (18)
cysteine (4)
ABC superfamily, periplasmic binding component (4)
ABC superfamily, membrane component (4)
membrane (4)
Read more >
Regulated operon(s) alaA-yfbR, cbl, cysB, cysDNC, cysJIH, cysK, cysPUWAM, dgcZ, fliAZ-tcyJ, hslJ, ssuEADCB, tauABCD, tcyP, ybdN, yciW, ygeH, yoaC
First gene in the operon(s) cbl, cysB, cysD, cysJ, cysK, cysP, dgcZ, hslJ, ssuE, tauA, tcyJ, tcyP, ybdN, yciW, yfbR, ygeH, yoaC
Simple and complex regulons ArcA,CysB,FNR
Cbl,CysB
Cbl,CysB,FNR,IHF
CpxR,CysB
CysB
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CysB,+](10)
[CysB,-](3)


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
  CysB-O-acetyl-L-serine activator cblp Sigma70 nd nd cbl nd nd [BPP], [GEA] [4]
  CysB repressor cysBp Sigma70 nd nd cysB nd nd [HIBSCS] [5]
  CysB-O-acetyl-L-serine activator cysDp Sigma70 -85.0 -123.5 cysD, cysN, cysC
cggtgccttaAGCACTTTTTGATATTAGCTTTGCCAAATCGTTATTCCGTTAaggaactact
2876432 2876473 [BCE] [6], [7]
  CysB-O-acetyl-L-serine activator cysJp Sigma70 -55.0 -120.5 cysJ, cysI, cysH
attgctaaaaCAGGTTAGTCGATTTGGTTATTAGTTATCGCTATCCCGTCTTtaatccacac
2891998 2892039 [HIBSCS] [8]
  CysB-O-acetyl-L-serine activator cysKp1 Sigma70 -79.0 -111.5 cysK
gtggcttatgCCGCCCCTTATTCCATCTTGCATGTCATTATTTCCCTTCTGTatatagatat
2532277 2532318 [HIBSCS], [SM] [8]
  CysB-O-acetyl-L-serine activator cysPp Sigma70 -65.0 -93.5 cysP, cysU, cysW, cysA, cysM
aaccaagttcTTATTCCCTTTTCAACTTCCAAATCACCAAACGGTATATAAAaccgttactc
2543601 2543642 [BPP], [GEA] [9], [10], [11]
  CysB-O-acetyl-L-serine activator dgcZp Sigma70 -164.5 -193.5 dgcZ
gggccattagGGTATTGGGTTATGCTATTTGTCATCCTTTTATTTACGATAAtgcagaggta
1624023 1624064 [AIBSCS] [12]
  CysB-O-acetyl-L-serine repressor hslJp Sigma70 -16.0 -52.5 hslJ
agctgattcaGATAATCCCCAATGACCTTTCATCCTCTATTCTTAAAATAGTcctgagtcag
1441775 1441816 [AIBSCS], [BPP], [GEA] [13], [14]
  CysB-O-acetyl-L-serine repressor ssuEp Sigma70 -18.0 -68.5 ssuE, ssuA, ssuD, ssuC, ssuB
cacaaaatttATATTTGGAATTTTCTTGTCTCTCCGACAGACTGACCGAATTgttatcaatg
997560 997601 [BPP], [GEA] [15], [16]
  CysB-O-acetyl-L-serine activator tauAp nd -202.0 -229.5 tauA, tauB, tauC, tauD
aatataatagTTTTATTATATGTATTGATATTGATAGAAATAATGAAGTAATaaatctcgta
384982 385023 [BPP], [GEA] [17]
  CysB-O-acetyl-L-serine activator tauAp nd -93.0 -120.5 tauA, tauB, tauC, tauD
attgttagaaCGGAGTAATTGCATATTTAATCTTTCCTTAGCCGTTTTTTTGctaagaataa
385091 385132 [BPP], [GEA] [17]
  CysB-O-acetyl-L-serine activator tauAp nd -38.0 -65.5 tauA, tauB, tauC, tauD
agaataaaatCATCTGTGCGATAACGACTAATTCTTTTAATGAATGTTTTTAttcctgaata
385146 385187 [BPP], [GEA] [17]
  CysB activator tcyJp nd nd nd tcyJ nd nd [GEA] [18]
  CysB activator tcyPp nd nd nd tcyP nd nd [GEA] [18]
  CysB-O-acetyl-L-serine activator ybdNp Sigma70 -177.5 -294.5 ybdN
atttactgggAATAGTCCCCTATGAACTTTATAATTCCTACCGTGACTTTCTtaacttaaaa
636843 636884 [AIBSCS] [12]
  CysB-O-acetyl-L-serine activator yciWp Sigma70 -50.5 -75.5 yciW
cgttatctctGTTATACCTTTCTGATATTTGTTATCGCCGATCCGTCTTTCTccccttcccg
1350162 1350203 [AIBSCS], [GEA] [12]
  CysB-O-acetyl-L-serine activator yfbRp3 Sigma32 -977.5 -1008.5 yfbR
gtggcatgcgTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCggagcttatc
2407833 2407874 [AIBSCS] [12]
  CysB-O-acetyl-L-serine activator ygeHp10 Sigma70 -573.5 -788.5 ygeH
cagaaacaatTGAAATATTCAATAATAGTGATGAATGGGCAAATCAACTAAAacacgcatta
2991285 2991326 [AIBSCS] [12]
  CysB-O-acetyl-L-serine activator yoaCp1 Sigma24 -145.5 -312.5 yoaC
agatattactGTTGATGCTTCTGCTAATTCATTATTTATATTTATAATTTCAattttatcta
1893800 1893841 [AIBSCS] [12]


Alignment and PSSM for CysB TFBSs    

Aligned TFBS of CysB   
  Sequence
 

Position weight matrix (PWM).   
A	2	2	9	4	1	3	2	9	2	1	2	1	2	5	7	8	1	0	4	6	3	2	9	0	0	4	2	3	7	5	2	2	4	2	4	8	0	3
C	1	0	2	1	1	5	7	2	1	2	2	2	4	3	2	2	0	0	7	3	2	2	0	1	7	3	10	4	4	4	4	6	4	0	0	4	1	0
G	0	1	2	5	3	2	2	0	0	0	3	5	7	0	0	0	2	2	0	4	0	0	1	0	2	3	0	0	1	0	3	2	2	7	1	0	0	0
T	11	11	1	4	9	4	3	3	11	11	7	6	1	6	5	4	11	12	3	1	9	10	4	13	5	4	2	7	2	5	5	4	4	5	9	2	13	11

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    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IDA] Inferred from direct assay

 [SM] Site mutation

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] 11038360., null, null, null

 [2] Hryniewicz MM, Kredich NM., 1991, The cysP promoter of Salmonella typhimurium: characterization of two binding sites for CysB protein, studies of in vivo transcription initiation, and demonstration of the anti-inducer effects of thiosulfate., J. Bacteriol.

 [3] Ostrowski J, Kredich NM., 1990, In vitro interactions of CysB protein with the cysJIH promoter of Salmonella typhimurium: inhibitory effects of sulfide., J Bacteriol.

 [4] Iwanicka-Nowicka R., Hryniewicz MM., 1995, A new gene, cbl, encoding a member of the LysR family of transcriptional regulators belongs to Escherichia coli cys regulon., Gene. 166(1):11-7

 [5] Ostrowski J., Kredich NM., 1991, Negative autoregulation of cysB in Salmonella typhimurium: in vitro interactions of CysB protein with the cysB promoter., J Bacteriol. 173(7):2212-8

 [6] Kredich NM., 1992, The molecular basis for positive regulation of cys promoters in Salmonella typhimurium and Escherichia coli., Mol Microbiol. 6(19):2747-53

 [7] Leyh TS., Vogt TF., Suo Y., 1992, The DNA sequence of the sulfate activation locus from Escherichia coli K-12., J Biol Chem. 267(15):10405-10

 [8] Monroe RS., Ostrowski J., Hryniewicz MM., Kredich NM., 1990, In vitro interactions of CysB protein with the cysK and cysJIH promoter regions of Salmonella typhimurium., J Bacteriol. 172(12):6919-29

 [9] Lochowska A., Iwanicka-Nowicka R., Plochocka D., Hryniewicz MM., 2001, Functional dissection of the LysR-type CysB transcriptional regulator. Regions important for DNA binding, inducer response, oligomerization, and positive control., J Biol Chem. 276(3):2098-107

 [10] Lochowska A., Iwanicka-Nowicka R., Zaim J., Witkowska-Zimny M., Bolewska K., Hryniewicz MM., 2004, Identification of activating region (AR) of Escherichia coli LysR-type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter., Mol Microbiol. 53(3):791-806

 [11] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol. 178(2):183-204

 [12] Kawano Y., Ohtsu I., Takumi K., Tamakoshi A., Nonaka G., Funahashi E., Ihara M., Takagi H., 2015, Enhancement of L-cysteine production by disruption of yciW in Escherichia coli., J Biosci Bioeng. 119(2):176-9

 [13] Jovanovic M., Lilic M., Savic DJ., Jovanovic G., 2003, The LysR-type transcriptional regulator CysB controls the repression of hslJ transcription in Escherichia coli., Microbiology. 149(Pt 12):3449-59

 [14] Lilic M., Jovanovic M., Jovanovic G., Savic DJ., 2003, Identification of the CysB-regulated gene, hslJ, related to the Escherichia coli novobiocin resistance phenotype., FEMS Microbiol Lett. 224(2):239-46

 [15] Bykowski T., van der Ploeg JR., Iwanicka-Nowicka R., Hryniewicz MM., 2002, The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess., Mol Microbiol. 43(5):1347-58

 [16] van Der Ploeg JR., Iwanicka-Nowicka R., Bykowski T., Hryniewicz MM., Leisinger T., 1999, The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl., J Biol Chem. 274(41):29358-65

 [17] van der Ploeg JR., Iwanicka-Nowicka R., Kertesz MA., Leisinger T., Hryniewicz MM., 1997, Involvement of CysB and Cbl regulatory proteins in expression of the tauABCD operon and other sulfate starvation-inducible genes in Escherichia coli., J Bacteriol. 179(24):7671-8

 [18] Chonoles Imlay KR., Korshunov S., Imlay JA., 2015, Physiological Roles and Adverse Effects of the Two Cystine Importers of Escherichia coli., J Bacteriol. 197(23):3629-44



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