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LacI DNA-binding transcriptional repressor

Synonyms: LacI, LacI-allolactose
Summary:
The Lactose inhibitor," LacI, is a DNA-binding transcription factor that represses transcription of the operon involved in transport and catabolism of lactose [19, 21, 22] In the absence of allolactose, LacI represses the lac operon by preventing open promoter complex formation for transcription [21, 23] In this repression system, LacI binds to two operators, and formation of the repressor loop is critical [21, 24, 25, 26] This repressor binds in tandem to inverted repeat sequences that are 21 nucleotides long and possess conserved motifs [21, 24, 25] LacI is negatively autoregulated when it binds to two DNA-binding sites, one located downstream of the lacI gene and the other one located in the coding sequence for the C terminus of LacI. The protein when bound to these sites forms a loop that inhibits the transcription elongation, thus producing truncated proteins that are tagged for degradation by the small peptide SsrA [27, 28]. Induction occurs when the physiological inducer, allolactose, binds to the lac repressor, preventing it from binding to the operator [19, 21] Nonphysiological analogs, such as β-thiogalactosides, can function as inducers too [29].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
LacI Functional   Apo [IE] [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]
LacI-allolactose Non-Functional Allosteric Holo nd nd
Evolutionary Family: GalR/LacI
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: lacI
  Genome position: 366428-367510
  Length: 1083 bp / 360 aa
Operon name: mhpR-lacI
TU(s) encoding the TF:
Transcription unit        Promoter
lacI
lacIp
mhpR-lacI
mhpRp1
null
mhpRp


Regulon       
Regulated gene(s) lacA, lacY, lacZ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (3)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) lacZYA
First gene in the operon(s) lacZ
Simple and complex regulons CRP,H-NS,LacI
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[LacI,-](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
  LacI repressor lacZp1 Sigma70 -82.0 -120.0 lacZ, lacY, lacA
ctggaaagcgGGCAGTGAGCGCAACGCAATTaatgtgagtt
366415 366435 , [HIBSCS], [SM] [13], [14], [15], [16]
  LacI repressor lacZp1 Sigma70 11.0 -28.0 lacZ, lacY, lacA
tgttgtgtggAATTGTGAGCGGATAACAATTtcacacagga
366323 366343 [BPP], [GEA], , [HIBSCS], [SM] [13], [15], [16], [17], [18], [19], [20]
  LacI repressor lacZp1 Sigma70 412.0 373.0 lacZ, lacY, lacA
gaatccgacgGGTTGTTACTCGCTCACATTTaatgttgatg
365922 365942 , [HIBSCS], [SM] [13], [15], [16], [19]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [IE] Inferred from experiment

 [GS] genomic SELEX

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] Beyreuther K., Adler K., Fanning E., Murray C., Klemm A., Geisler N., 1975, Amino-acid sequence of lac repressor from Escherichia coli. Isolation, sequence analysis and sequence assembly of tryptic peptides and cyanogen-bromide fragments., Eur J Biochem 59(2):491-509

 [2] Boelens R., Lamerichs RM., Rullmann JA., van Boom JH., Kaptein R., 1988, The interaction of lac repressor headpiece with its operator: an NMR view., Protein Seq Data Anal 1(6):487-98

 [3] Farabaugh PJ., 1978, Sequence of the lacI gene., Nature 274(5673):765-9

 [4] Ganem D., Miller JH., Files JG., Platt T., Weber K., 1973, Reinitiation of a lac repressor fragment at a codon other than AUG., Proc Natl Acad Sci U S A 70(11):3165-9

 [5] Gordon AJ., Burns PA., Fix DF., Yatagai F., Allen FL., Horsfall MJ., Halliday JA., Gray J., Bernelot-Moens C., Glickman BW., 1988, Missense mutation in the lacI gene of Escherichia coli. Inferences on the structure of the repressor protein., J Mol Biol 200(2):239-51

 [6] Jacob F., Monod J., 1961, Genetic regulatory mechanisms in the synthesis of proteins., J Mol Biol 3:318-56

 [7] Kisters-Woike B., Lehming N., Sartorius J., von Wilcken-Bergmann B., Muller-Hill B., 1991, A model of the lac repressor-operator complex based on physical and genetic data., Eur J Biochem 198(2):411-9

 [8] Lamerichs RM., Boelens R., van der Marel GA., van Boom JH., Kaptein R., Buck F., Fera B., Ruterjans H., 1989, H NMR study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator., Biochemistry 28(7):2985-91

 [9] Lehming N., Sartorius J., Kisters-Woike B., von Wilcken-Bergmann B., Muller-Hill B., 1990, Mutant lac repressors with new specificities hint at rules for protein--DNA recognition., EMBO J 9(3):615-21

 [10] Markiewicz P., Kleina LG., Cruz C., Ehret S., Miller JH., 1994, Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence., J Mol Biol 240(5):421-33

 [11] Pardee AB., Prestidge LS., 1959, On the nature of the repressor of beta-galactosidase synthesis in Escherichia coli., Biochim Biophys Acta 36:545-7

 [12] Platt T., Files JG., Weber K., 1973, Lac repressor. Specific proteolytic destruction of the NH 2 -terminal region and loss of the deoxyribonucleic acid-binding activity., J Biol Chem 248(1):110-21

 [13] Flashner Y., Gralla JD., 1988, Dual mechanism of repression at a distance in the lac operon., Proc Natl Acad Sci U S A 85(23):8968-72

 [14] Jimenez CR., Li KW., Smit AB., Janse C., 2005, Auto-inhibitory control of peptidergic molluscan neurons and reproductive senescence., Neurobiol Aging NIL

 [15] Oehler S., Eismann ER., Kramer H., Muller-Hill B., 1990, The three operators of the lac operon cooperate in repression., EMBO J 9(4):973-9

 [16] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [17] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [18] Hoare AM., McLeish A., Thompson H., Alexander-Williams J., 1978, Selection of patients for bile diversion surgery: use of bile acid measurement in fasting gastric aspirates., Gut 19(3):163-5

 [19] Lewis M., 2005, The lac repressor., C R Biol 328(6):521-48

 [20] Rastinejad F., Artz P., Lu P., 1993, Origin of the asymmetrical contact between lac repressor and lac operator DNA., J Mol Biol 233(3):389-99

 [21] Hudson JM., Fried MG., 1990, Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter., J Mol Biol 214(2):381-96

 [22] Vossen KM, Stickle DF, Fried MG, 1996, The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter., J Mol Biol, 1996 Jan 12

 [23] Sanchez A, Osborne ML, Friedman LJ, Kondev J, Gelles J, 2011, Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules., EMBO J, 2011 Aug 9

 [24] Fried MG, Hudson JM, 1996, DNA looping and lac repressor-CAP interaction., Science, 1996 Dec 13

 [25] Perros M, Steitz TA, 1996, DNA looping and lac repressor-CAP interaction., Science, 1996 Dec 13

 [26] Balaeff A, Mahadevan L, Schulten K, 2004, Structural basis for cooperative DNA binding by CAP and lac repressor., Structure, 2004 Jan

 [27] Abo T, Inada T, Ogawa K, Aiba H, 2000, SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon., EMBO J, 2000 Jul 17

 [28] Semsey S, Jauffred L, Csiszovszki Z, Erdossy J, Stéger V, Hansen S, Krishna S, 2013, The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli., Nucleic Acids Res, 2013 Jul

 [29] Narang A, Oehler S, 2017, Effector Overlap between the lac and mel Operons of Escherichia coli: Induction of the mel Operon with ?-Galactosides., J Bacteriol, 2017 May 1

 [30] Mooney RA, Landick R, 2013, Building a better stop sign: understanding the signals that terminate transcription., Nat Methods, 2013 Jul

 [31] Daber R, Stayrook S, Rosenberg A, Lewis M, 2007, Structural analysis of lac repressor bound to allosteric effectors., J Mol Biol, 2007 Jul 20

 [32] Xu J, Liu S, Chen M, Ma J, Matthews KS, 2011, Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor., Biochemistry, 2011 Oct 25

 [33] Kipper K, Eremina N, Marklund E, Tubasum S, Mao G, Lehmann LC, Elf J, Deindl S, 2018, Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI., PLoS One, 2018

 [34] Hirsh AD, Lillian TD, Lionberger TA, Perkins NC, 2011, DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays., Biophys J, 2011 Aug 3

 [35] Becker NA, Maher LJ 3rd, 2015, High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli., Proc Natl Acad Sci U S A, 2015 Jun 9

 [36] Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R, 2016, The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study., PLoS One, 2016

 [37] Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P, 1996, Crystal structure of the lactose operon repressor and its complexes with DNA and inducer., Science, 1996 Mar 1

 [38] Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J, 2012, The lac repressor displays facilitated diffusion in living cells., Science, 2012 Jun 22

 [39] Fulcrand G, Chapagain P, Dunlap D, Leng F, 2016, Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope., FEBS Lett, 2016 Mar

 [40] Atitey K, Loskot P, Rees P, 2019, Elucidating effects of reaction rates on dynamics of the lac circuit in Escherichia coli., Biosystems, 2019 Jan

 [41] Fulcrand G, Dages S, Zhi X, Chapagain P, Gerstman BS, Dunlap D, Leng F, 2016, DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli., Sci Rep, 2016 Jan 14

 [42] Yan Y, Leng F, Finzi L, Dunlap D, 2018, Protein-mediated looping of DNA under tension requires supercoiling., Nucleic Acids Res, 2018 Mar 16

 [43] Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN, 2017, Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor., Biophys J, 2017 Apr 11



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