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FhlA DNA-binding transcriptional activator

Synonyms: FhlA, FhlA-formate
Summary:
The transcription factor FhlA, for "Formate hydrogen lyase Activator," is positively autoregulated and controls the transcription of the operons involved in formate metabolism to produce dihydrogen and carbon dioxide [2, 6, 7, 12, 13, 14, 15, 16, 17, 18]nd genes involved in the proton motive force generation during fermentation [18]. Transcription of the FhlA regulon is induced when E. coli is grown under anaerobic growth conditions and when the physiological inducer, formate, binds to the FhlA protein [2, 12, 14, 15] When formate binds to FhlA, the protein becomes active as the binding affinity of FhlA increases, and it activates the transcription of σ54-dependent promoters. HycA may inactivate the function of the FhlA protein and prevent the binding of FhlA to target sequences, but the mechanism of the negative regulation by HycA is unknown [16, 19] FhlA is subject to posttranscriptional regulation by the sRNA OxyS [20, 21, 22] This sRNA binds to FhlA mRNA and inhibits translation by interfering with the binding of the mRNA and the ribosome [21, 22, 23] As a member of the group of σ54-dependent transcriptional regulators, FhlA contains three domains: a possible sensory domain located in the N terminus that probably modulates the activity of the C-terminal domain [24, 25] the central domain, which is probably involved in open complex formation, ATP hydrolysis, and interaction with σ54 and formate [25, 26, 27] and the C-terminal domain, which contains a helix-turn-helix motif for DNA binding [1] FhlA shows 46% identity to the HyfR protein, a member of the same group.
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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
FhlA Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
FhlA-formate Functional Allosteric Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS] S [1]
Evolutionary Family: EBP
TFBs length: 14
TFBs symmetry: inverted-repeat
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: fhlA
  Genome position: 2854338-2856416
  Length: 2079 bp / 692 aa
Operon name: hypABCDE-fhlA
TU(s) encoding the TF:
Transcription unit        Promoter
hypABCDE-fhlA
hypAp
hypBCDE-fhlA
hypBp


Regulon       
Regulated gene(s) fdhF, fhlA, focB, hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI, hydN, hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, hypA, hypB, hypC, hypD, hypE, hypF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
anaerobic respiration (16)
fermentation (11)
membrane (9)
posttranslational modification (4)
operon (3)
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Regulated operon(s) fdhF, hycABCDEFGHI, hydN-hypF, hyfABCDEFGHIJR-focB, hypABCDE-fhlA
First gene in the operon(s) fdhF, hycA, hydN, hyfA, hypA
Simple and complex regulons CRP,FNR,FhlA,HyfR
FNR,FhlA,NarL,NarP
FhlA,FlhDC
FhlA,IHF,ModE,NsrR
FhlA,IHF,NsrR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[FhlA,+](5)


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
  FhlA-formate activator fdhFp Sigma54 -129.5 -170.5 fdhF
gcgtgatggcTGTCACGCGGTATTtcgtttcgtc
 4299530 4299543 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [2], [3], [4], [5], [6]
  FhlA-formate activator fdhFp Sigma54 -104.5 -145.5 fdhF
cgtttcgtcaCGTCAAAACTGACGacagcctgtt
 4299505 4299518 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [2], [3]
  FhlA-formate activator hycAp Sigma54 -98.0 -124.0 hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI
aatgtcgatgATGTCGAAATGACAcgtcgacacg
 2850553 2850566 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3], [7], [7], [8]
  FhlA-formate activator hycAp Sigma54 -84.5 -110.5 hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI
cgaaatgacaCGTCGACACGGCGAcgaaattcat
 2850539 2850552 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3], [7], [7]
  FhlA-formate activator hydNp Sigma54 nd nd hydN, hypF
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [9], [9]
  FhlA-formate activator hyfAp Sigma54 -130.0 -160.0 hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB
gctttcccctGCGACACGGGTGTCgaatccattt
 2601034 2601047 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10], [11]
  FhlA-formate activator hypAp Sigma54 -751.5 -771.5 hypA, hypB, hypC, hypD, hypE, fhlA
ctcaggtgatTGTCATTTTTGACGaaaacatgcc
 2849869 2849882 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3], [7], [7]
  FhlA-formate activator hypAp Sigma54 -720.5 -740.5 hypA, hypB, hypC, hypD, hypE, fhlA
gccgatgaaaTGTCATTTTCGACActcatcgaca
 2849900 2849913 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3], [7], [7]


Alignment and PSSM for FhlA TFBSs    

Aligned TFBS of FhlA   
  Sequence
  GTCGCCGTGTCGACGTG
  TCGTCAGTTTTGACGTG
  ATGTCATTTTCGACACT
  TTGTCATTTTTGACGAA
  ACACCCGTGTCGCAGGG
  ATGGCTGTCACGCGGTA
  CGTGTCATTTCGACATC

Position weight matrix (PWM). FhlA matrix-quality result    
A	3	0	1	0	0	3	1	0	0	1	0	0	5	1	2	1	2
C	1	2	1	1	6	3	0	0	1	0	5	0	2	5	0	1	1
G	1	1	4	3	0	0	4	0	2	0	0	7	0	1	5	1	3
T	2	4	1	3	1	1	2	7	4	6	2	0	0	0	0	4	1

Consensus    
;	consensus.strict             	atggCcgTttCGaCGtg
;	consensus.strict.rc          	CACGTCGAAACGGCCAT
;	consensus.IUPAC              	aygkCmgTktCGmCGtg
;	consensus.IUPAC.rc           	CACGKCGAMACKGMCRT
;	consensus.regexp             	a[ct]g[gt]C[ac]gT[gt]tCG[ac]CGtg
;	consensus.regexp.rc          	CACG[GT]CGA[AC]AC[GT]G[AC]C[AG]T

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

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

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [1] Leonhartsberger S., Ehrenreich A., Bock A., 2000, Analysis of the domain structure and the DNA binding site of the transcriptional activator FhlA., Eur J Biochem 267(12):3672-84

 [2] Schlensog V., Lutz S., Bock A., 1994, Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli., J Biol Chem 269(30):19590-6

 [3] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [4] Birkmann A., Bock A., 1989, Characterization of a cis regulatory DNA element necessary for formate induction of the formate dehydrogenase gene (fdhF) of Escherichia coli., Mol Microbiol 3(2):187-95

 [5] Birkmann A., Zinoni F., Sawers G., Bock A., 1987, Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli., Arch Microbiol 148(1):44-51

 [6] Schlensog V., Bock A., 1990, Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli., Mol Microbiol 4(8):1319-27

 [7] Hopper S., Babst M., Schlensog V., Fischer HM., Hennecke H., Bock A., 1994, Regulated expression in vitro of genes coding for formate hydrogenlyase components of Escherichia coli., J Biol Chem 269(30):19597-604

 [8] Self WT., Shanmugam KT., 2000, Isolation and characterization of mutated Fh1A proteins which activate transcription of the hyc operon (formate hydrogenlyase) of Escherichia coli in the absence of molybdate(1)., FEMS Microbiol Lett 184(1):47-52

 [9] Maier T., Binder U., Bock A., 1996, Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism., Arch Microbiol 165(5):333-41

 [10] Self WT., Hasona A., Shanmugam KT., 2004, Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli., J Bacteriol 186(2):580-7

 [11] Skibinski DA., Golby P., Chang YS., Sargent F., Hoffman R., Harper R., Guest JR., Attwood MM., Berks BC., Andrews SC., 2002, Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR., J Bacteriol 184(23):6642-53

 [12] Maupin JA., Shanmugam KT., 1990, Genetic regulation of formate hydrogenlyase of Escherichia coli: role of the fhlA gene product as a transcriptional activator for a new regulatory gene, fhlB., J Bacteriol 172(9):4798-806

 [13] Sankar P, Lee JH, Shanmugam KT, 1988, Gene-product relationships of fhlA and fdv genes of Escherichia coli., J Bacteriol, 170(12):5440 10.1128/jb.170.12.5440-5445.1988

 [14] Rossmann R, Sawers G, Böck A, 1991, Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon., Mol Microbiol, 5(11):2807 10.1111/j.1365-2958.1991.tb01989.x

 [15] Iuchi S., Lin EC., 1993, Adaptation of Escherichia coli to redox environments by gene expression., Mol Microbiol 9(1):9-15

 [16] Maeda T, Sanchez-Torres V, Wood TK, 2007, Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli., Appl Microbiol Biotechnol, 77(4):879 10.1007/s00253-007-1217-0

 [17] Maeda T, Sanchez-Torres V, Wood TK, 2007, Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities., Appl Microbiol Biotechnol, 76(5):1035 10.1007/s00253-007-1086-6

 [18] Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K, 2021, The role of Escherichia coli FhlA transcriptional activator in generation of proton motive force and FO F1 -ATPase activity at pH 7.5., IUBMB Life, 73(6):883 10.1002/iub.2470

 [19] Sauter M., Bohm R., Bock A., 1992, Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli., Mol Microbiol 6(11):1523-32

 [20] Repoila F, Majdalani N, Gottesman S, 2003, Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm., Mol Microbiol, 48(4):855 10.1046/j.1365-2958.2003.03454.x

 [21] Argaman L., Altuvia S., 2000, fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex., J Mol Biol 300(5):1101-12

 [22] Altuvia S., Zhang A., Argaman L., Tiwari A., Storz G., 1998, The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding., EMBO J 17(20):6069-75

 [23] Altuvia S., Weinstein-Fischer D., Zhang A., Postow L., Storz G., 1997, A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator., Cell 90(1):43-53

 [24] Self WT, Hasona A, Shanmugam KT, 2001, N-terminal truncations in the FhlA protein result in formate- and MoeA-independent expression of the hyc (formate hydrogenlyase) operon of Escherichia coli., Microbiology (Reading), 147(Pt 11):3093 10.1099/00221287-147-11-3093

 [25] Hopper S, Böck A, 1995, Effector-mediated stimulation of ATPase activity by the sigma 54-dependent transcriptional activator FHLA from Escherichia coli., J Bacteriol, 177(10):2798 10.1128/jb.177.10.2798-2803.1995

 [26] Weiss DS, Batut J, Klose KE, Keener J, Kustu S, 1991, The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription., Cell, 67(1):155 10.1016/0092-8674(91)90579-n

 [27] Korsa I, Böck A, 1997, Characterization of fhlA mutations resulting in ligand-independent transcriptional activation and ATP hydrolysis., J Bacteriol, 179(1):41 10.1128/jb.179.1.41-45.1997

 [28] Andrews SC., Berks BC., McClay J., Ambler A., Quail MA., Golby P., Guest JR., 1997, A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system., Microbiology 143 ( Pt 11):3633-47


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