Allostery in the LacI/GalR family: variations on a theme.

The lactose repressor protein (LacI) was among the very first genetic regulatory proteins discovered, and more than 1000 members of the bacterial LacI/GalR family are now identified. LacI has been the prototype for understanding how transcription is controlled using small metabolites to modulate protein association with specific DNA sites. This understanding has been greatly expanded by the study of other LacI/GalR homologues. A general picture emerges in which the conserved fold provides a scaffold for multiple types of interactions - including oligomerization, small molecule binding, and protein-protein binding - that in turn influence target DNA binding and thereby regulate mRNA production. Although many different functions have evolved from this basic scaffold, each homologue retains functional flexibility: For the same protein, different small molecules can have disparate impact on DNA binding and hence transcriptional outcome. In turn, binding to alternative DNA sequences may impact the degree of allosteric response. Thus, this family exhibits a symphony of variations by which transcriptional control is achieved.

[1]  M H Saier,et al.  Cyclic AMP-independent catabolite repression in bacteria. , 1996, FEMS microbiology letters.

[2]  Jeffrey Miller,et al.  Genetic Studies of Lac Repressor: 4000 Single Amino Acid Substitutions and Analysis of the Resulting Phenotypes on the Basis of the Protein Structure , 1996, German Conference on Bioinformatics.

[3]  G. Buttin,et al.  [REGULATORY MECHANISMS IN THE BIOSYNTHESIS OF THE ENZYMES OF GALACTOSE METABOLISM IN ESCHERICHIA COLI K 12. I. THE INDUCED BIOSYNTHESIS OF GALACTOKINASE AND THE SIMULTANEOUS INDUCTION OF THE ENZYMATIC SEQUENCE]. , 1963, Journal of Molecular Biology.

[4]  J. Colmer,et al.  Characterization of ptxS, a Pseudomonas aeruginosa gene which interferes with the effect of the exotoxin A positive regulatory gene, ptxR , 1998, Molecular and General Genetics MGG.

[5]  M. Schumacher,et al.  Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate. , 2007, Journal of molecular biology.

[6]  K. Y. Choi,et al.  Structural characterization and corepressor binding of the Escherichia coli purine repressor , 1992, Journal of bacteriology.

[7]  J. Musser,et al.  A direct link between carbohydrate utilization and virulence in the major human pathogen group A Streptococcus , 2008, Proceedings of the National Academy of Sciences.

[8]  C. Wilson,et al.  The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding , 2006, Cellular and Molecular Life Sciences.

[9]  S. Adhya,et al.  A family of bacterial regulators homologous to Gal and Lac repressors. , 1992, The Journal of biological chemistry.

[10]  M. Lewis,et al.  A closer view of the conformation of the Lac repressor bound to operator , 2000, Nature Structural Biology.

[11]  K. McIver,et al.  CcpA-Mediated Repression of Streptolysin S Expression and Virulence in the Group A Streptococcus , 2008, Infection and Immunity.

[12]  K. Matthews,et al.  Operator DNA sequence variation enhances high affinity binding by hinge helix mutants of lactose repressor protein. , 2000, Biochemistry.

[13]  M. Schumacher,et al.  Mechanism of corepressor-mediated specific DNA binding by the purine repressor , 1995, Cell.

[14]  S. Bell,et al.  Charting a course through RNA polymerase , 2000, Nature Structural Biology.

[15]  S. Roy,et al.  The non-inducible nature of super-repressors of the gal operon in Escherichia coli. , 1995, Journal of molecular biology.

[16]  CytR/cAMP-CRP nucleoprotein formation in E. coli: the CytR repressor binds its operator as a stable dimer in a ternary complex with cAMP-CRP. , 1996, Journal of molecular biology.

[17]  Daniel M. Stoebel,et al.  The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products , 2008, Genetics.

[18]  A. Riggs,et al.  Interaction of effecting ligands with lac repressor and repressor-operator complex. , 1975, Biochemistry.

[19]  M. Lewis,et al.  Structural analysis of lac repressor bound to allosteric effectors. , 2007, Journal of molecular biology.

[20]  M. Slijper,et al.  Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. , 1996, Journal of molecular biology.

[21]  V. Tretyachenko-Ladokhina,et al.  Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation. , 2006, Journal of molecular biology.

[22]  S. Adhya,et al.  The galactose regulon of Escherichia coli , 1993, Molecular microbiology.

[23]  A. Sonenshein,et al.  Control of key metabolic intersections in Bacillus subtilis , 2007, Nature Reviews Microbiology.

[24]  K. Matthews,et al.  Functional impact of polar and acidic substitutions in the lactose repressor hydrophobic monomer.monomer interface with a buried lysine. , 2009, Biochemistry.

[25]  D. F. Senear,et al.  Analysis of interactions between CytR and CRP at CytR-regulated promoters. , 1998, Methods in enzymology.

[26]  R. Kaptein,et al.  Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes , 2004, Science.

[27]  J. Trewhella,et al.  Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein. , 2008, Journal of molecular biology.

[28]  T. Steitz,et al.  Crystal structure of lac repressor core tetramer and its implications for DNA looping. , 1995, Science.

[29]  P. Nygaard,et al.  Identification of hypoxanthine and guanine as the co‐repressors for the purine regulon genes of Escherichia coli , 1990, Molecular microbiology.

[30]  R. Rolfes,et al.  Purification of the Escherichia coli purine regulon repressor and identification of corepressors , 1990, Journal of bacteriology.

[31]  Kirsten L. Frieda,et al.  A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell , 2008, Science.

[32]  A. Koehler,et al.  The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. , 1999, Journal of molecular biology.

[33]  J. Chen,et al.  Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation. , 1992, The Journal of biological chemistry.

[34]  H. Nakamura,et al.  Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain. , 1995, Structure.

[35]  C. Jørgensen,et al.  DNA‐binding characteristics of the Escherichia coli CytR regulator: a relaxed spacing requirement between operator half‐sites is provided by a flexible, unstructured interdomain linker , 1998, Molecular microbiology.

[36]  S. Semsey,et al.  Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA. , 2006, Journal of molecular biology.

[37]  K. Matthews,et al.  Lactose repressor protein: functional properties and structure. , 1998, Progress in nucleic acid research and molecular biology.

[38]  Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter. , 1991, The Journal of biological chemistry.

[39]  Benno Müller-Hill,et al.  Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction , 2006, Nucleic acids research.

[40]  K. Y. Choi,et al.  Mutagenesis of amino acid residues required for binding of corepressors to the purine repressor. , 1994, The Journal of biological chemistry.

[41]  W. Hillen,et al.  CcpA Mutants with Differential Activities in Bacillus subtilis , 2006, Journal of Molecular Microbiology and Biotechnology.

[42]  L. Swint-Kruse,et al.  Ligand interactions with lactose repressor protein and the repressor-operator complex: the effects of ionization and oligomerization on binding. , 2007, Biophysical chemistry.

[43]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[44]  Liskin Swint-Kruse,et al.  Integrated insights from simulation, experiment, and mutational analysis yield new details of LacI function. , 2005, Biochemistry.

[45]  N. Fujita,et al.  Repression and activation of transcription by Gal and Lac repressors: involvement of alpha subunit of RNA polymerase. , 1995, The EMBO journal.

[46]  M. Schumacher,et al.  The X-ray Structure of the PurR-Guanine-purF Operator Complex Reveals the Contributions of Complementary Electrostatic Surfaces and a Water-mediated Hydrogen Bond to Corepressor Specificity and Binding Affinity* , 1997, The Journal of Biological Chemistry.

[47]  K. Matthews,et al.  Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity, decreases sequence selectivity, and alters allostery. , 2001, Biochemistry.

[48]  B. Kallipolitis,et al.  Protein–Protein Communication: Structural Model of the Repression Complex Formed by CytR and the Global Regulator CRP , 1997, Cell.

[49]  G. Buttin.  Mécanismes régulateurs dans la biosynthèse des enzymes du métabolisme du galactose chez Escherichia coli K12: I. La biosynthèse induite de la galactokinase et l'induction simultanée de la séquence enzymatique , 1963 .

[50]  E. Koonin,et al.  Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. , 1999, Nucleic acids research.

[51]  G. Chang,et al.  Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer , 1996, Science.

[52]  Y. Fujita,et al.  Specific recognition of the Bacillus subtilis gnt cis‐acting catabolite‐responsive element by a protein complex formed between CcpA and seryl‐phosphorylated HPr , 1995, Molecular microbiology.

[53]  C. Wolz,et al.  Staphylococcus aureus CcpA Affects Virulence Determinant Production and Antibiotic Resistance , 2006, Antimicrobial Agents and Chemotherapy.

[54]  H. Pedersen,et al.  Protein‐induced fit: the CRP activator protein changes sequence‐specific DNA recognition by the CytR repressor, a highly flexible LacI member , 1997, The EMBO journal.

[55]  J. Deutscher,et al.  Phosphorylation of either crh or HPr mediates binding of CcpA to the bacillus subtilis xyn cre and catabolite repression of the xyn operon. , 1999, Journal of molecular biology.

[56]  M. Guthold,et al.  Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments , 2008, PLoS biology.

[57]  Identification of the Subunit of cAMP Receptor Protein (CRP) That Functionally Interacts with CytR in CRP-CytR-mediated Transcriptional Repression* , 2000, The Journal of Biological Chemistry.

[58]  Jianpeng Ma,et al.  Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimer , 2003, Protein science : a publication of the Protein Society.

[59]  J. Trewhella,et al.  Subdividing repressor function: DNA binding affinity, selectivity, and allostery can be altered by amino acid substitution of nonconserved residues in a LacI/GalR homologue. , 2008, Biochemistry.

[60]  Heinrich Sticht,et al.  The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr‐Ser46‐P in Bacillus subtilis , 2006, The FEBS journal.

[61]  T. R. Licht,et al.  A Functional cra Gene Is Required forSalmonella enterica Serovar Typhimurium Virulence in BALB/c Mice , 2000, Infection and Immunity.

[62]  S. Mowbray,et al.  Conformational changes of ribose-binding protein and two related repressors are tailored to fit the functional need. , 1999, Journal of molecular biology.

[63]  Liskin Swint-Kruse,et al.  Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: Bioinformatics‐based predictions generate true positives and false negatives , 2008, Proteins.

[64]  Akira Ishihama,et al.  Systematic search for the Cra‐binding promoters using genomic SELEX system , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[65]  M. Schumacher,et al.  Structural Basis for Allosteric Control of the Transcription Regulator CcpA by the Phosphoprotein HPr-Ser46-P , 2004, Cell.

[66]  R. Brennan,et al.  Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor. , 2002, Biochemistry.

[67]  W. Saenger,et al.  Structure of full-length transcription regulator CcpA in the apo form. , 2007, Biochimica et biophysica acta.

[68]  B. Müller-Hill,et al.  The three operators of the lac operon cooperate in repression. , 1990, The EMBO journal.

[69]  K. Matthews,et al.  Ion concentration and temperature dependence of DNA binding: comparison of PurR and LacI repressor proteins. , 2001, Biochemistry.