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LacI DNA-binding transcriptional repressor

Synonyms: LacI-allolactose, LacI
Summary:
The Lactose inhibitor," LacI, is a DNA-binding transcription factor that represses transcription of the operon involved in transport and catabolism of lactose [5, 7, 8] In the absence of allolactose, LacI represses the lac operon by preventing open promoter complex formation for transcription [7, 9] In this repression system, LacI binds to two operators, and formation of the repressor loop is critical [7, 10, 11, 12] This repressor binds in tandem to inverted repeat sequences that are 21 nucleotides long and possess conserved motifs [7, 10, 11] 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 [13, 14]. Induction occurs when the physiological inducer, allolactose, binds to the lac repressor, preventing it from binding to the operator [5, 7] Nonphysiological analogs, such as β-thiogalactosides, can function as inducers too [15].
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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 nd nd
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
mhpR-lacI
mhpRp2


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,MarA
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 [APIORCISFBSCS], [GS], [SM] [1], [2], [3]
  LacI repressor lacZp1 Sigma70 11.0 -28.0 lacZ, lacY, lacA
tgttgtgtggAATTGTGAGCGGATAACAATTtcacacagga
366323 366343 [GEA], [APIORCISFBSCS], [BPP], [GS], [SM] [3], [4], [5], [6]
  LacI repressor lacZp1 Sigma70 412.0 374.0 lacZ, lacY, lacA
gaatccgacgGGTTGTTACTCGCTCACATTTaatgttgatg
365922 365942 [APIORCISFBSCS], [GS], [SM] [1], [2], [3]


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




Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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

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

 [6] 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

 [7] 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

 [8] Vossen KM, Stickle DF, Fried MG, 1996, The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter., J Mol Biol, 255(1):44 10.1006/jmbi.1996.0005

 [9] 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, 30(19):3940 10.1038/emboj.2011.273

 [10] Fried MG, Hudson JM, 1996, DNA looping and lac repressor-CAP interaction., Science, 274(5294):1930 10.1126/science.274.5294.1930

 [11] Perros M, Steitz TA, 1996, DNA looping and lac repressor-CAP interaction., Science, 274(5294):1929 10.1126/science.274.5294.1929

 [12] Balaeff A, Mahadevan L, Schulten K, 2004, Structural basis for cooperative DNA binding by CAP and lac repressor., Structure, 12(1):123 10.1016/j.str.2003.12.004

 [13] 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, 19(14):3762 10.1093/emboj/19.14.3762

 [14] 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, 41(13):6381 10.1093/nar/gkt351

 [15] 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, 199(9):None 10.1128/JB.00796-16

 [16] Mooney RA, Landick R, 2013, Building a better stop sign: understanding the signals that terminate transcription., Nat Methods, 10(7):618 10.1038/nmeth.2527

 [17] Daber R, Stayrook S, Rosenberg A, Lewis M, 2007, Structural analysis of lac repressor bound to allosteric effectors., J Mol Biol, 370(4):609 10.1016/j.jmb.2007.04.028

 [18] 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, 50(42):9002 10.1021/bi200896t

 [19] 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, 13(6):e0198416 10.1371/journal.pone.0198416

 [20] 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, 101(3):718 10.1016/j.bpj.2011.06.040

 [21] Razo-Mejia M, Barnes SL, Belliveau NM, Chure G, Einav T, Lewis M, Phillips R, 2018, Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction., Cell Syst, 6(4):456 10.1016/j.cels.2018.02.004

 [22] Becker NA, Maher LJ, 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, 112(23):7177 10.1073/pnas.1500412112

 [23] Seckfort D, Montgomery Pettitt B, 2019, Price of disorder in the lac repressor hinge helix., Biopolymers, 110(1):e23239 10.1002/bip.23239

 [24] 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, 11(3):e0152002 10.1371/journal.pone.0152002

 [25] Seckfort D, Lynch GC, Pettitt BM, 2020, The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry., Biochim Biophys Acta Gen Subj, 1864(4):129538 10.1016/j.bbagen.2020.129538

 [26] 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, 271(5253):1247 10.1126/science.271.5253.1247

 [27] Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J, 2012, The lac repressor displays facilitated diffusion in living cells., Science, 336(6088):1595 10.1126/science.1221648

 [28] 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, 590(5):613 10.1002/1873-3468.12094

 [29] Atitey K, Loskot P, Rees P, 2019, Elucidating effects of reaction rates on dynamics of the lac circuit in Escherichia coli., Biosystems, 175(None):1 10.1016/j.biosystems.2018.11.003

 [30] 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, 6(None):19243 10.1038/srep19243

 [31] Yan Y, Leng F, Finzi L, Dunlap D, 2018, Protein-mediated looping of DNA under tension requires supercoiling., Nucleic Acids Res, 46(5):2370 10.1093/nar/gky021

 [32] 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, 112(7):1316 10.1016/j.bpj.2017.02.028

 [33] Stracy M, Schweizer J, Sherratt DJ, Kapanidis AN, Uphoff S, Lesterlin C, 2021, Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins., Mol Cell, 81(7):1499 10.1016/j.molcel.2021.01.039

 [34] Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X, 2020, RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria., mBio, 11(1):None 10.1128/mBio.02926-19

 [35] Tack DS, Tonner PD, Pressman A, Olson ND, Levy SF, Romantseva EF, Alperovich N, Vasilyeva O, Ross D, 2021, The genotype-phenotype landscape of an allosteric protein., Mol Syst Biol, 17(3):e10179 10.15252/msb.202010179



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