RegulonDB RegulonDB 11.1: Operon Form
   

dusB-fis operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: dusB-fis
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: dusB-fis
Synonym(s): OP00028, fis, yhdG-fis
Gene(s): dusB, fis   Genome Browser M3D Gene expression COLOMBOS
Note(s): Nasser et al. Nasser W,2002reported multiple promoters preceding the dusB-fis operon; however, Mallik et al. Mallik P,2004demonstrated that just one promoter transcribes the operon.
Fis is autoregulated negatively and forms multiple complexes at the region upstream of operon dusB-fis. Pratt et al. (1997) found that FIS binds cooperatively to six sites in the region upstream of the promoter dusBp and showed that the binding site that overlaps the -35 box plays a predominant role in autoregulation Pratt TS,1997.
Based on the bacteriostatic antibiotic-induced persister model, 37 and 9 genes were found to produce defects in rifampin- and tetracycline-induced persister formation, respectively. Only six mutants were found to overlap in both treatment-induced persister screens: recA, recC, ruvA, uvrD, fis, and acrB. Four of these mutants (recA, recC, ruvA, and uvrD) mapped to the DNA repair pathway, one mutant mapped to a global transcriptional regulator (fis), and one to a gene for an efflux protein (acrB) Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y,2018 Other genes that mapped to transporters, membrane biogenesis, LPS biosynthesis, flagellum biosynthesis, metabolism (folate and energy), and translation were more specific to rifampin-induced persisters Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y,2018
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Ball CA., et al., 1992
[2] Ninnemann O., et al., 1992
Promoter
Name: dusBp
+1: 3410246
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 34
Sequence: ctcagaggattggtcaaagtttggcctttcatctcgtgcaaaaaatgcgtaatatacgccGccttgcagtcacagtatggt
                           -35                    -10       +1                   
Note(s): The DksA protein binds directly to RNA polymerase, destabilizing transcription complexes and increasing the effect of the alarmone ppGpp on transcription initiation Mallik P,2006 DksA together with ppGpp is required for transcription inhibition of the dusBp (Pfis) promoter in mid-log and late-log growth phases and in stationary phase Mallik P,2006
dusBp, also known as fisp, is one of the few known promoters that initiates transcription predominantly with CTP Walker KA, Osuna R,2002 which is a feature strongly conserved in dusBp (fisp) in other bacteria Mallik P,2004
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Mallik P., et al., 2004
[5] Nasser W., et al., 2002
[6] Nasser W., et al., 2001
[7] Walker KA., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: tgcttgattaAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTttataggtgt
Reference(s): [1] Ball CA., et al., 1992
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator dusBp 3409983 3410004 -252.5 acgcggggcgAAGTGCGAGCAAGCTCACAAAAggcacgtaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
remote CRP-cyclic-AMP activator dusBp 3410068 3410089 -167.5 cataaagaaaAATTGAGAACTTACTCAAATTTctttgagtgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]
proximal CRP-cyclic-AMP activator dusBp 3410172 3410193 -63.0 tttaaatgcaATTCTTTGATCCATCTCAGAGGattggtcaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP repressor dusBp 3410172 3410193 -63.0 tttaaatgcaATTCTTTGATCCATCTCAGAGGattggtcaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor dusBp 3410018 3410032 -221.0 acgtaaatttGCCGATTATTTACGCaaatttgcgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [9]
remote Fis repressor dusBp 3410096 3410110 -143.0 atttctttgaGTGTAAATTTTAGTCactattttct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [9]
remote Fis repressor dusBp 3410138 3410152 -101.0 tgatttttatGAGTAATTATCGCACcacgctcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [9]
proximal Fis repressor dusBp 3410156 3410170 -83.0 atcgcaccacGCTCATTTTAAATGCaattctttga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [9]
proximal Fis repressor dusBp 3410197 3410211 -42.0 tcagaggattGGTCAAAGTTTGGCCtttcatctcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [9]
proximal Fis repressor dusBp 3410264 3410278 26.0 gtcacagtatGGTCATTTCTTAACTcatgcgcatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [9]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator dusBp 3410126 3410138 -114.0 tttctaatatGATGATTTTTATGagtaattatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [9]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition dusBp nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[10]
  ppGpp inhibition dusBp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[10]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [10] Mallik P., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [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-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Ball CA., Osuna R., Ferguson KC., Johnson RC., 1992, Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli., J Bacteriol 174(24):8043-56

 [2] Ninnemann O., Koch C., Kahmann R., 1992, The E.coli fis promoter is subject to stringent control and autoregulation., EMBO J 11(3):1075-83

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Mallik P., Pratt TS., Beach MB., Bradley MD., Undamatla J., Osuna R., 2004, Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli., J Bacteriol 186(1):122-35

 [5] Nasser W., Rochman M., Muskhelishvili G., 2002, Transcriptional regulation of fis operon involves a module of multiple coupled promoters., EMBO J 21(4):715-24

 [6] Nasser W., Schneider R., Travers A., Muskhelishvili G., 2001, CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes., J Biol Chem 276(21):17878-86

 [7] Walker KA., Atkins CL., Osuna R., 1999, Functional determinants of the Escherichia coli fis promoter: roles of -35, -10, and transcription initiation regions in the response to stringent control and growth phase-dependent regulation., J Bacteriol 181(4):1269-80

 [8] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [9] Pratt TS., Steiner T., Feldman LS., Walker KA., Osuna R., 1997, Deletion analysis of the fis promoter region in Escherichia coli: antagonistic effects of integration host factor and Fis., J Bacteriol 179(20):6367-77

 [10] Mallik P., Paul BJ., Rutherford ST., Gourse RL., Osuna R., 2006, DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli., J Bacteriol 188(16):5775-82

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