High local concentration: a fundamental strategy of life

Local increase in concentration is a basic principle of transcriptional control. Closer inspection reveals that it is a major force governing all interactions within and between proteins and DNA. Local increase in concentration acts on all levels of organization of living matter. The structures and functions of two central molecules of life-the linear polymers DNA and protein-are particularly illuminating examples. Local increase in concentration leads to cooperative or competitive interactions between molecules. It is an important principle of life.

“Cold-Sensitive” Mutants of the Lac Repressor

Thirteen of more than 4,000 single-amino-acid-replacement mutants of the Lac repressor, generated by suppression of amber nonsense mutants, were characterized as having a cold-sensitive phenotype. However, when expressed as missense mutations, none of the replacements cause cold sensitivity, implicating the suppression mechanism as being responsible for this phenotype.

What is life? The paradigm of DNA and protein cooperation at high local concentrations

Many chemical reactions need high concentrations of the molecules involved in order to work efficiently. It is usually impossible for the cell to achieve the necessary high concentrations of all relevant molecules in unconfined solutions but this becomes possible if the high concentration is restricted around a relevant molecule. High local concentrations of interacting molecules have been observed many times in many different biological systems. The examples of Lac and Lambda repressors of Escherichia coli are presented and discussed here as useful paradigms of mechanisms for achieving high local concentrations of interacting protein protomers.

Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction

In vivo induction of the Escherichia coli lactose operon as a function of inducer concentration generates a sigmoidal curve, indicating a non-linear response. Suggested explanations for this dependence include a 2:1 inducer–repressor stoichiometry of induction, which is the currently accepted view. It is, however, known for decades that, in vitro, operator binding as a function of inducer concentration is not sigmoidal. This discrepancy between in vivo and in vitro data has so far not been resolved. We demonstrate that the in vivo non-linearity of induction is due to cooperative repression of the wild-type lac operon through DNA loop formation. In the absence of DNA loops, in vivo induction curves are hyperbolic. In the light of this result, we re-address the question of functional molecular inducer–repressor stoichiometry in induction of the lac operon.

[Remembrance and denial. A critical look into correspondence of Adolf Butenandt, MPG president 1960-1972]

Adolf Butenandt was one of the great biochemists of the last century. He was also a most successful organiser of science. Which price did he have to pay to be a success in the Third Reich? He persistently avoided seeing or hearing the blatant injustice around him. Injustice he knew nothing about did not exist. So he became the perfect model for the postwar generation of German scientists. Is he still a model today?

Genetics of susceptibility to tuberculosis: Mengele's experiments in Auschwitz

Great experiments will always be remembered. I highlight an experiment that was conducted during the Nazi regime in Germany. Not only did the experiment fail, it was also linked to fraud and crimes against humanity. This failed experiment will never be forgotten.

High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells

The speed of chemical reactions is proportional to the concentration of molecules involved. Since proteins catalyze most of the essential reactions inside a living cell, their concentration should be as high as possible. An economical way to achieve this is through the establishment of small cell compartments. We propose that within these compartments, two types of local concentration effects are at work. (1) With local concentration type I reactions, multimeric proteins bound to a specific DNA sequence have an increased local concentration for a second DNA site sufficiently close-by, or for proteins bound to such a site. (2) For type II effects, DNA can be used as a scaffold to build unique nucleoprotein complexes that would otherwise not exist free in solution. These complexes are proficient in establishing longer-range interactions with similarly unique complexes located far away on the genome. We discuss the consequences of these local concentration effects in the light of the markedly different sizes of prokaryotic and eukaryotic cells and of their genomes.

Reflections on the use of interviews in the history of science: who will write the history of science?

Interviews are an excellent source of information for historians of science. They should be done by historians who understand science in detail and, if possible, better than the scientists they interview. In the case of applied industrial or governmental sciences, historians must have detailed knowledge of economic or historic sources. Again they should know more in these areas than those they interview. If, on the contrary, the interviewers are not scientists at heart who know science, the history they write will become at best literature but at worst pseudoscientific abracadabra.

On the conservation of protein sequences in evolution

The amino acid sequences of enzymes like alcohol dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase are strongly conserved across all phyla. We suggest that the amino acid conservation of such enzymes might be a result of the fact that they function as part of a multi-enzyme complex. The specific interactions between the proteins involved would hinder evolutionary change of their surfaces.

Strengthening the dimerisation interface of Lac repressor increases its thermostability by 40 deg. C

We increased drastically the heat stability of Lac repressor (LacR) of Escherichia coli. Wild-type tetrameric LacR denatures irreversibly at 53 degrees C. Improving hydrophobic packing at the dimerisation interface by a single substitution increases LacR heat-resistance by 40 deg. C without abolishing inducer binding at high and low temperatures. Tetrameric LacR mutants carrying substitutions of the positively charged amino acid Lys84 by each of the hydrophobic amino acids Leu, Ile and Met resist heating to temperatures up to 93 degrees C. We performed IPTG binding assays at 80 degrees C and found the mutant Lac repressors active and, thus, the core intact. Furthermore, the activity of LacR following heating is shown at room temperature by a gel retardation assay, which demonstrates normal oligomerisation state and function of the headpiece. The same mutations (K84L/I/M) in the dimer LacR331stop, carrying a stop codon in amino acid 331, increase thermostability of the dimer from 47 degrees C to 87 degrees C. LacRK84M represses beta-galactosidase activity in vivo as well as the wild-type and is sufficiently induced to allow growth on lactose. The results with both tetramer and dimer variants of LacR indicate mutual stabilisation of the tetramerisation region and the stable core.

Dimerisation mutants of Lac repressor. II. A single amino acid substitution, D278L, changes the specificity of dimerisation

Assembly of the lactose repressor tetramer involves two subunit interfaces, the C-terminal heptad repeats, and the monomer-monomer interface. Dimerisation between two monomers of Lac repressor of Escherichia coli lacking the two C-terminal heptad repeats occurs through the interactions between three alpha-helices of each monomer, which form a highly hydrophobic interface. Residues possibly involved in specific dimer formation are known from X-ray studies and from the phenotypes of more than 4000 single amino acid substitutions. During the examination of numerous mutants within the dimerisation interface of Lac repressor, we found that substitution of one amino acid, D278 to leucine, is sufficient to change the specificity of dimerisation. Analysis of this single substitution indicates that D278L mutant Lac repressor represses like wild-type. However, it no longer forms heterodimers with wild-type Lac repressor.

Dimerisation mutants of Lac repressor. I. A monomeric mutant, L251A, that binds Lac operator DNA as a dimer

Dimer formation between monomers of the Escherichia coli Lac repressor is substantially specificed by the interactions between three alpha-helices in each monomer which form a hydrophobic interface. As a first step in analysing the specificity of this interaction, we examined the mutant L251A. LacR bearing this mutation in a background lacking the C-terminal heptad repeats is completely incapable of forming dimers in solution, with a dimer-monomer equilibrium dissociation constant, or Kd, higher than 10(-5)M. This correlates with a 200-fold decrease in its ability to repress the lac operon in vivo compared to dimeric LacR. Surprisingly, the mutant is still capable of forming dimers upon binding to short operator DNA in vitro. Analysis of the kinetic parameters of binding of the mutant to operator DNA reveals a 2000 to 3000-fold increase in the equilibrium dissociation constant (Kd) of the mutant-DNA complex in comparison to dimeric LacR-operator complexes, with the change almost entirely due to a greater than 1000-fold decrease in association rate. The dissociation rate varies only by a factor of about two, in comparison to dimeric LacR. This change reflects a kinetic pathway in which dimer formation, in solution or on DNA, is the rate-limiting step. These findings have implications for the specificity and stability of the protein-protein interface in question.

Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances

Transcription factors that are bound specifically to DNA often interact with each other over thousands of base pairs [1] [2]. Large DNA loops resulting from such interactions have been observed in Escherichia coli with the transcription factors deoR [3] and NtrC [4], but such interactions are not, as yet, well understood. We propose that unique protein complexes, that are not present in solution, may form specifically on DNA. Their uniqueness would make it possible for them to interact tightly and specifically with each other. We used the repressor and operators of coliphage lambda to construct a model system in which to test our proposition. lambda repressor is a dimer at physiological concentrations, but forms tetramers and octamers at a hundredfold higher concentration. We predict that two lambda repressor dimers form a tetramer in vitro when bound to two lambda operators spaced 24 bp apart and that two such tetramers interact to form an octamer. We examined, in vitro, relaxed circular plasmid DNA in which such operator pairs were separated by 2,850 bp and 2,470 bp. Of these molecules, 29% formed loops as seen by electron microscopy (EM). The loop increased the tightness of binding of lambda repressor to lambda operator. Consequently, repression of the lambda PR promoter in vivo was increased fourfold by the presence of a second pair of lambda operators, separated by a distance of 3,600 bp.

The blood from Auschwitz and the silence of the scholars

The Kaiser Wilhelm Institute for Anthropology, Human Genetics and Eugenics in Berlin-Dahlem was the centre of scientific racism in Nazi Germany. Its bad history culminated in a research project to analyse the molecular basis of racial differences in the susceptibility to various infectious diseases such as tuberculosis. Josef Mengele, a former postdoc of the director of the institute, Otmar von Verschuer, collected blood samples and other material in Auschwitz from families and twins of Jews and Gypsies. The blood samples were analysed by Günther Hillmann in the Berlin laboratory of Nobel Prize winner Adolf Butenandt. Butenandt had just moved to Tübingen. The project was paid for by the Deutsche Forschungsgemeinschaft. Butenandt, Hillmann and von Verschuer made scientific careers in the Federal Republic. To the present day this past has not been acknowledged by the Max-Planck-Gesellschaft as part of its history.

Dimeric lac repressors exhibit phase-dependent co-operativity

Transcription of the lac operon in Escherichia coli is repressed by the binding of Lac repressor (LacR) to lac operator O1, a pseudo-palindromic sequence centred 11 bp downstream of the transcription start. Full repression of the wild-type promoter by wild-type, tetrameric LacR requires the presence of at least two operator sequences that must not only be in close proximity to O1, 401 bp and 92 bp for the auxiliary operators O2 and O3, respectively, but must also be present on the same side of the DNA helix. LacR mutants lacking the C-terminal heptad repeat and thus only capable of dimer formation still repress, but at a much reduced level. Their repression of the lac promoter is comparable to repression by tetrameric LacR when both auxiliary operators are destroyed. We have examined the residual repression, by dimeric LacR, of a series of constructs containing a CAP-independent promoter and two lac operators, O1 and Oid, separated by a series of spacers increasing in size by single base-pair increments. Surprisingly, repression of these constructs still exhibits phase dependence. The periodicity of maxima is similar to the helical repeat of DNA in vivo, as measured by phase-dependent repression with tetrameric LacR, although the magnitude of repression is much smaller than that obtained in previous experiments with tetrameric LacR. Two additional variants of dimeric LacR with altered C termini that were tested also show phase dependence. Control experiments show that the presence of O1 is required for repression in this system. In the absence of O1, occupancy of the auxiliary operator does not lead to repression. The magnitudes of repression maxima correlate best with the overall basic nature of the C terminus. Weak, unspecific contacts by this region with DNA seem sufficient to explain the observed periodicity. It remains to be seen whether additional factors are also involved in this residual repression.

Towards a mutant analysis of the tertiary structures of functional DNA-binding motifs

Transcription factors have specific regions, often alpha helices, with which they recognise DNA. These regions are more or less disordered off DNA. Some examples are listed here. However, a detailed mutant analysis of this phenomenon is missing. It could show to what extent DNA binding in vitro and in vivo is harmed when such a region is artificially made rigid by suitable substitutions and could reveal how much transcription factors have improved by having been selected to carry unstable recognition domains.

The function of auxiliary operators

Gene regulation by control of transcription has been analysed in great detail both in prokaryotes and in eukaryotes. The frequency of transcription may be decreased by repressors or increased by activators. A repressor may work by decreasing the concentration of RNA polymerase at a promoter capable of forming an open complex. An activator may work by increasing the concentration of RNA polymerase at a promoter capable of forming an open complex. For this purpose, a strategy is used over and over again. It is called increase in local concentration. How Escherichia coli uses this strategy efficiently is discussed.

Some repressors of bacterial transcription

For a long time, repression of transcription in Escherichia coli was thought to be generally caused by one repressor binding to one operator. Recent work has indicated the frequent presence of auxiliary operators and helper proteins. The recent solution of the X-ray structures of Lac and Pur repressors were breakthroughs; yet, it has become painfully clear that important aspects of repression are still not understood.

Enhanced GFAP expression in astrocytes of transgenic mice expressing the human brain-specific trypsinogen IV

We recently identified a cDNA encoding a human brain specific trypsinogen (trypsinogen IV). In order to test whether trypsinogen IV is involved in CNS diseases of, or injury response in, mammalian brain, a mouse model was developed in which the human trypsinogen IV was expressed specifically in neurons. Immunocytochemical analysis of the brains of transgenic mice revealed a striking enhancement of glial fibrillar acidic protein (GFAP) expression in astrocytes. This remarkable astrocytic reaction was detected in the brains of mice as young as 2 months and did not diminish in the older animals we tested. However, we did not find gross evidence for neurodegeneration, nor for reactive microglial cells. The long-term survival of these animals should provide a model with which to study the mechanism of nerve-astroglia interactions. In addition, the possible participation of trypsin IV in the metabolism of the Alzheimer precursor protein (APP) was investigated by immunostaining brains from transgenic mice with beta-amyloid (betaA4) antibodies. Immunocytochemical staining of brains from one year old transgenic mice revealed an intense intracellular betaA4-like signal in neurons.

A positive selection vector for cloning of long polymerase chain reaction fragments based on a lethal mutant of the crp gene of Escherichia coli

We have constructed a cloning vector with a tight positive selection for recombinant clones in Escherichia coli. The positive selection pressure results from a lethal mutation within the E. coli gene coding for the catabolite gene activator protein CAP, which is disrupted whenever a fragment is successfully inserted. Here, we show that this "suicide" vector, pCAPs, is suitable for cloning of PCR products as long as 9.3 kb into several unique restriction sites which are scattered throughout the lethal gene.

A lethal mutant of the catabolite gene activator protein CAP of Escherichia coli

The dimeric catabolite gene activator protein (CAP) of Escherichia coli uses its recognition helix to bind with each subunit the DNA sequence motif 5' G-7T-6G-5A-4 3'. It makes a direct amino acid-base contact with E181 and cytosine in position-5' on the reverse strand. While testing mutants of CAP in position 181 for specificity changes, we found that CAP E181Q is lethal in high amounts for the E. coli strains we used for cloning. We cloned this CAP mutant successfully in cya- strains, where CAP is inactive. Examination of the in vitro binding activities of CAP E181Q, and of in vivo activity when present in low, non-lethal amounts, revealed loss of specificity but not of binding capacity for its DNA targets. It binds well to CAP consensus with G or T in position-5, better to CAP consensus with A, C in position-5, quite well to lambda consensus operator with G in position-7 and rather weakly to lambda consensus.

How AraC interacts specifically with its target DNAs

Previous work indicates that one subunit of the AraC protein dimer binds to a DNA target araI1, of 17 base-pairs. We systematically substituted every base-pair in a synthetic araI1 target with the three possible alternatives and then tested binding of araI1 and of these 51 DNA targets to AraC by quantitative gel shift analysis in the presence of L-arabinose. We found that every substitution of the underlined bases reduces AraC binding tenfold or more: 5' TAGCATTTTTATCCATA 3'. Substitutions at other bases have little or no effect. In the absence of L-arabinose we observed a sixfold reduction of binding of AraC to araI1. We have designated the 5' AGC sequence the A-box and the 5'TCCATA sequence the B-box. We synthesised DNA targets containing either two A or two B-boxes with the natural araI1-I2 spacing. Wild-type AraC binds both targets in the presence of L-arabinose in a gel shift-experiment. In the absence of L-arabinose, AraC binds only to the double B-box. We then tested various AraC mutant proteins in the same way. S208A and H212A bind to the double B-box but not to the double A-box in the presence or absence of L-arabinose. D256A binds to the double A-box, but not to the double B-box, in the presence of L-arabinose but not in its absence. The implications of these results for the mechanism of AraC induction by L-arabinose are discussed.

Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure

Each amino acid from position 2 to 329 of Lac repressor was replaced by 12 or 13 of the 20 natural occurring amino acids. The resulting phenotypes are discussed on the basis of (1) the recently published structure of the Lac repressor core complexed with the inducer IPTG and (2) a model of the dimeric Lac repressor built by homology modelling from the X-ray structure of the purine repressor-corepressor-operator complex. This phenotype analysis, based on 4000 well-defined mutants, yields a functional description of each amino acid position of Lac repressor. In most cases, mutant effects can be directly correlated with the structure and function of the protein. This connection between the amino acid position and the structure and function of the protein is in most cases direct and not complicated: amino acids which are directly involved in sugar binding are affected in Lac repressor mutants of the Is type; small amino acids which can only be replaced by other small acids are located in the core of the protein; positions at which nearly all amino acids are tolerated are in most cases located on the surface of the protein. Amino acids which are highly conserved throughout the LacI family of repressors, and not directly involved in specific functions of the protein like DNA recognition or sugar binding, form a network of contacts with other amino acids. Such amino acids are either located inside one subunit, mostly at the interface between secondary structure elements, or are involved in the dimerisation interface.

Mutants in position 69 of the Trp repressor of Escherichia coli K12 with altered DNA-binding specificity

Structural analysis by X-ray crystallography has indicated that direct contact occurs between Arg69, the second residue of the first helix of the helix-turnhelix (HTH) motif of the Trp repressor, and guanine in position 9 of the alpha-centred consensus trp operator. We therefore replaced residue 69 of the Trp repressor with Gly, Ile, Leu or Gln and tested the resultant repressor mutants for their binding to synthetic symmetrical alpha- or beta-centred trp operator variants, in vivo and in vitro. We present genetic and biochemical evidence that Ile in position 69 of the Trp repressor interacts specifically with thymine in position 9 of the alpha-centred trp operator. There are also interactions with other bases in positions 8 and 9 of the alpha-centred trp operator. In vitro, the Trp repressor of mutant RI69 binds to the consensus alpha-centred trp operator and a similar trp operator variant that carries a T in position 9. In vivo analysis of the interactions of Trp repressor mutant RI69 with symmetrical variants of the beta-centred trp operator shows a change in the specificity of binding to a beta-centred symmetrical trp operator variant with a gua-nine to thymine substitution in position 5, which corresponds to position 9 of the alpha-centred trp operator.

The side-chain of the amino acid residue in position 110 of the Lac repressor influences its allosteric equilibrium

Binding of the Lac repressor to its operator DNA controls the expression of the genes of the lac operon of Escherichia coli. Lac repressor's affinity for the lac operator is diminished by an inducer that affects the structure of the repressor tetramer. Here we report the cloning and sequencing of the mutant Lac repressor i-t gene, whose product, the LacR-t repressor, shows a higher affinity for the inducer isopropyl-beta-D-thiogalactopyranoside (IPTG) and a lower affinity for the lac operator than the wild-type repressor. We show that the altered phenotype is due to a single amino acid residue replacement; the alanine residue at position 110 in the wild-type is replaced by threonine in i-t. Other amino acid residues in position 110 have been shown to result in an i-s phenotype. For the i-s-substitution of alanine 110 with lysine we demonstrate an increase in the affinity for operator DNA and a decrease in the affinity for IPTG. Thus, A110--> K shows the opposite effect to A110-->T on the repressor protein. We explain the phenotype of the LacR mutants by displacements of the conformational equilibrium for the dimeric repressor unit between RR (high operator affinity, low inducer affinity) and R*R* (low operator affinity, high inducer affinity) towards R*R* in the i-t and towards RR in the i-s mutant in position 110 with respect to the wild-type. The putative structures of the wild-type and mutant Lac repressors confirm this conclusion.

Co-operative binding of two Trp repressor dimers to alpha- or beta-centred trp operators

The alpha-centred trp operator binds one dimer of the Trp repressor, whereas the beta-centred trp operator binds two dimers of the Trp repressor (Carey et al., 1991; Haran et al., 1992). The Trp repressor with a Tyr-Gly-7 substitution binds almost as well as the wild-type Trp repressor to the alpha-centred trp operator, but it does not bind to the beta-centred trp operator. This confirms that Tyr-7 is involved in the interaction between Trp repressor dimers, as seen in the crystal structure (Lawson and Carey, 1993). Further experiments with alpha-centred trp operator variants showed that positions +/-1 of the alpha-centred trp operators play a crucial role in tetramerisation. The two innermost base pairs of the alpha-centred trp operator are not involved in contacts with the dimer of the Trp repressor binding to it. However, substitutions in these positions (T-A to G-T) effectively transform the alpha-centred trp operator into a beta-centred trp operator, and thus encourage the binding of two Trp repressor dimers to this operator. Finally, we demonstrate, with suitable heterodimers, that one subunit of each dimer suffices to bind to a beta-centred trp operator.

Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator

The tetrameric Lac repressor can bind simultaneously to two lac operators on the same DNA molecule, thereby including the formation of a DNA loop. We investigated the phasing dependence of DNA loop formation between lac operator O1 and an auxiliary ideal lac operator (O(id)) on the bacterial chromosome, with inter-operator distances varying from 57.5 to 1493.5 bp. Repression of a CAP-independent lac UV5 promoter by O1 at its natural position increased up to 50-fold in the presence of an optimally positioned auxiliary O(id)). Repression values alternated between local maxima and minima with a periodicity of 11.0 to 11.3 bp, suggesting that the chromosomal helical repeat is in this range in vivo. Repression increased significantly with decreasing inter-operator DNA length, indicating that the local Lac repressor concentration at O1 is crucial for tight repression. Maximal repression, attributed to stable DNA loop formation, was obtained at an operator spacing of 70.5 bp. Other repression maxima occurred at operator distances of 92.5 and 115.5 bp, corresponding to natural operator spacings in the lac and in the gal operon, respectively. Substitution of the auxiliary O(id) with the weaker binding lac operator O3 lowered repression efficiency, presumably due to the reduced local concentration of Lac repressor.

Mutant bZip-DNA complexes with four quasi-identical protein-DNA interfaces

The complex between the yeast transcriptional activator GCN4 and the palindromic ATF/CREB site 5'- A4T3G2A1C0*G0'T1'C2'A3'T4'-3' shows dyad symmetry. The basic region of GCN4 contains a segment of 18 amino acids with a partially palindromic sequence: N-LKRARNTEA*ARRSRARKL-C. Symmetric residues are underlined. Apart from the ATF/CREB site, GCN4 also binds well to the symmetric variants with guanine in position 4 (5'-G4T3G2A1C0*G0'T1'C2'A3'C4'-3') or thymine in position 0 (5'-A4T3G2A1T0*A0'T1'C2'A3'T4'-3'). The half-sites of these sequences can be regarded as short pseudo-palindromes with central guanine 2/cytosine 2' base pairs. We investigated whether the geometry of the peptide of the basic region of GCN4 could be functionally related to the pseudo-palindromic character of some target half-sites. Since inspection of the X-ray structures of GCN4-DNA complexes reveals that several amino acid-DNA interactions are symmetric within the wild-type half-complexes, we introduced mutations into a GCN4 bZip peptide that improve the symmetry of the peptide. We found that most of the constructs retain specific DNA recognition. For one mutant, we conclude that it is not only capable of forming DNA complexes showing the well-known overall dyad symmetry, but that the protein-DNA interface of each half-complex can be divided further into two quasi-identical, quasi-symmetric substructures.

A comparison of the different DNA binding specificities of the bZip proteins C/EBP and GCN4

The bZip proteins GCN4 and C/EBP differ in their DNA binding specificities: GCN4 binds well to the pseudopalindromic AP1 site 5'-A4T3G2A1C0T1C2'A3'T4'-3' and to the palindromic ATF/CREB sequence 5'-A4T3G2A1-C0*G0'T1'C2'A3'T4'-3'; C/EBP preferentially recognizes the palindromic sequence 5'-A4T3T2G1C0*G0'C1'A2'-A3'T4'-3'. According to the X-ray structures of GCN4-DNA complexes, five residues of the basic region of GCN4 are involved in specific base contacts: asparagine -18, alanine -15, alanine -14, serine -11 and arginine -10 (numbered relative to the start point of the leucine zipper, which we define as +1). In the basic region of C/EBP position -14 is occupied by valine instead of alanine, the other four residues being identical. Here we analyse the role of valine -14 in C/EBP-DNA complex formation. Starting from a C/EBP-GCN4 chimeric bZip peptide which displays C/EBP specificity, we systematically mutated position -14 of its basic region and characterized the DNA binding specificities of the 20 possible different peptides by gel mobility shift assays with various target sites. We present evidence that valine -14 of C/EBP interacts more strongly with thymine 2 than with cytosine 1' of the C/EBP binding site, unlike the corresponding alanine -14 of GCN4, which exclusively contacts thymine 1' of the GCN4 binding sites.

A basic tail increases repression by dimeric lac repressor

Tetrameric Lac repressor achieves cooperative repression by binding simultaneously to O1 and to one of the auxiliary operators O2 or O3, thereby forcing the intervening DNA into a loop. Dimeric Lac repressor is not able to form DNA loops and consequently shows no cooperative repression. We constructed a dimeric Lac repressor mutant which exhibits increased repression to the lac operon that does not depend on specific operator-repressor-operator loops. This Lac repressor carries a synthetic tail of basic residues attached to its C terminus. With this construct, we observe an increase of the in vivo repression upon addition of auxiliary lac operators to a chromosomal lac operon controlled by O1. This suggests that the basic tail enables dimeric Lac repressor to enhance its repression by additional non-specific DNA contacts.

The possible roles of residues 79 and 80 of the Trp repressor from Escherichia coli K-12 in trp operator recognition

We constructed mutants of the Trp repressor from Escherichia coli K-12 with all possible single amino acid exchanges at positions 79 and 80 (residues 1 and 2 of the recognition helix). We tested these mutants in vivo by measuring the repression of synthesis of beta-galactosidase with symmetric variants of alpha- and beta-centered trp operators, which replace the lac operator in a synthetic lac system. The Trp repressor carrying a substitution of isoleucine 79 by lysine, showed a marked specificity change with respect to base pair 7 of the alpha-centered trp operator. Gel retardation experiments confirmed this result. Trp repressor mutant IR79 specifically recognizes a trp operator variant with substitutions in positions 7 and 8. Another mutant, with glycine in position 79, exhibited loss of contact at base pair 7. We speculate that the side chain of Ile79 interacts with the AT base pairs 7 and 8 of the alpha-centered trp operator, possibly with the methyl groups of thymines. Replacement of thymine in position 7 or 8 by uracil confirms the involvement of the methyl group of thymine 8 in repressor binding. Several Trp repressor mutants in position 80 (i.e. A180, AL80, AM80 and AP80) broaden the specificity of the Trp repressor for alpha-centered trp operator variants with exchanges in positions 3, 4 and 5.

Replacement of invariant bZip residues within the basic region of the yeast transcriptional activator GCN4 can change its DNA binding specificity

Two residues are invariant in all bZip basic regions: asparagine -18 and arginine -10 (we define the first leucine of the leucine zipper of GCN4 as +1). X-ray structures of two specific GCN4-DNA complexes (Ellenberger et al., Cell, 71, 1223-1237, 1992; König & Richmond, J. Mol. Biol., 233, 139-154, 1993) demonstrate the involvement of both residues in specific base pair recognition. We replaced either asparagine -18 or arginine -10 with all other amino acids and tested the DNA binding properties of the resulting mutant peptides by gel mobility shift assays. Peptides with histidine -18 or tyrosine -10 bind with changed specificities to variants of the ATF/CREB site 5'A4T3G2A1C0*G0'T1'C2'A3'T4'3' with symmetric exchanges in positions 2/2' or 0/0', respectively. The double mutant with histidine -18 and tyrosine -10 combines the features of the parental single mutants and binds specifically to the respective double exchange target. Furthermore, the tyrosine -10 mutant clearly prefers the palindrome 5'ATGATATCAT3' over the corresponding pseudo-palindrome 5'ATGATTCA-T3', whereas the lysine -10 mutant binds better to the pseudo-palindromic AP1 site 5'ATGACTCAT3' than to the palindromic ATF/CREB site. Thus, although invariant within natural bZip proteins, asparagine -18 or arginine -10 can be functionally replaced by other amino acids, and their replacement can lead to new DNA binding specificities.

Lambda cI repressor mutants altered in transcriptional activation

We analysed the in vivo functions of three lambda cI repressor mutants which are phenotypically defective in positive control (pc). For this purpose, we constructed a lambda cI repressor expression system which allows controlled expression of various amounts of lambda cI repressor or its mutants. A five-fold activation of the PRM promoter by wild-type lambda cI repressor is measured in this in vivo system. Two of the pc mutants (pc 1: G43-R and pc 3: E34-K) repress the PRM promoter over a wide range of intracellular concentrations, the lowest being almost identical to the concentration of wild-type lambda cI repressor at which it activates the transcription of its own gene. Only the third pc mutant (pc 2: D38-N) behaves in a manner that would be expected of a true pc mutant, which is unaffected in its DNA binding activity but has lost its activation function. We studied the DNA binding properties of cI repressor and its three pc mutants with a variety of operator constructs in vivo and found that the four repressor proteins differed significantly with respect to their affinities for all operators tested. We also probed the necessity of an acidic residue at position 38 of cI repressor for activation and found that the substitution of aspartic acid 38 by tyrosine does not reduce activation of PRM. Furthermore a substitution with phenylalanine improves the activator function of cI repressor. Our results suggest that amino acid replacements at position 34 or 43 of lambda cI repressor predominantly affect the binding properties of the repressor while some hydrophobic amino acid residues at position 38 are at least as functional in activation as the acidic wild-type amino acid residue.

Quality and position of the three lac operators of E. coli define efficiency of repression

Repression of the lac promoter may be achieved in two different ways: either by interference with the action of RNA polymerase or by interference with CAP activation. We investigated cooperative repression of the Escherichia coli lac operon by systematic conversion of its three natural operators (O1, O2 and O3) on the chromosome. We find that cooperative repression by tetrameric Lac repressor increases with both quality and proximity of the interacting operators. A short distance of 92 bp allows effective repression by two very weak operators (O3, O3). The cooperativity of lac operators is discussed in terms of a local increase of repressor concentration. This increase in concentration depends on flexible DNA which allows loop formation.

Creating new DNA binding specificities in the yeast transcriptional activator GCN4 by combining selected amino acid substitutions

The specificity of the GCN4/DNA complex is mediated by a complicated network of interactions between the basic regions of both GCN4 monomers and their target halfsites. According to X-ray analyses (1, 2) one particular thymine of the target sequence is recognized by serine -11 and alanine -15 (we define the leucine in the first d-position of the heptad repeats as +1). We replaced serine -11 or alanine -15 with all other amino acids and analysed the DNA binding properties of the resulting stable GCN4 derivatives by electrophoretic mobility shift assays. Among these, mutants with tryptophan in position -11, or glutamic acid and glutamine in position -15, differ significantly from GCN4 in their DNA binding specificities. We then constructed selected double mutants, which differ from GCN4 in positions -11, -15 or -14 (3) of the basic region. The double mutants with tryptophan in position -11 and asparagine or serine in position -14 show drastically altered DNA binding specificities, presumably due to additive effects.