Benno Müller-Hill

Easy identification of cDNA clones.

A set of six cloning vectors, pUR 278, 288, 289, 290, 291, 292 is presented. These vectors have the cloning sites, BamHI, SalI, PstI, XbaI and HindIII, in all frames at the 3′ end of the lacZ gene. Insertion of cDNA in the proper cloning sites leads to a fusion protein of active beta‐galactosidase and the peptide encoded by the cDNA. A simple immunoenzymatic assay can be used to identify clones in such a cDNA library.

The three operators of the lac operon cooperate in repression

We tested the effect of systematic destruction of all three lac operators of the chromosomal lac operon of Escherichia coli on repression by Lac repressor. Absence of just one ‘pseudo‐operator’ O2 or O3 decreases repression by wild‐type tetrameric Lac repressor approximately 2‐ to 3‐fold; absence of both ‘pseudo‐operators’ decreases repression greater than 50‐fold. O1 alone represses under these conditions only approximately 20‐fold. Dimeric active Lac repressor (iadi) represses the wild‐type lac operon to about the same low extent. This indicates that cooperative interaction between lac operators is due to DNA loop formation mediated by tetrameric Lac repressor. Under conditions where loop formation is impossible, occupation of O3 but not of O2 may lead to weak repression. This suggests that under these conditions CAP activation may be inhibited and that stopping transcription at O2 does not significantly contribute to repression.

Sequence of the lacZ gene of Escherichia coli.

The nucleotide sequence of the lacZ gene coding for beta‐galactosidase (EC 3.2.1.23) in Escherichia coli has been determined. Beta‐Galactosidase is predicted to consist of 1023 residues, resulting in a protein with a mol. wt. of 116 353 per subunit. The protein sequence originally determined by Fowler and Zabin was shown to be essentially correct and in an Appendix these authors comment on the discrepancies.

Differential splicing of Alzheimer's disease amyloid A4 precursor RNA in rat tissues: PreA4695 mRNA is predominantly produced in rat and human brain

Alzheimers disease is characterized by filamentous depositions of amyloid A4 protein in the brain. The first precursor of A4 protein that has been described consists of 695 amino acids (PreA4(695)). Until now, three types of amyloid precursor mRNAs (PreA4(770), PreA4(751) and PreA4(695)), produced by alternative splicing, have been detected. We analysed the differential expression of these mRNAs in various rat tissues by PCR and show that (1) there exists a fourth type of mRNA, PreA4(714); (2) in all tissues except the brain the PreA4(695) mRNA is less abundant than the other types of mRNAs; in the brain, however, the PreA4(695) mRNA predominates by far. The same observations hold true for human tissues. The possible function of this differential splicing is discussed.

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

Abstract 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 λ to construct a model system in which to test our proposition. λ repressor is a dimer at physiological concentrations, but forms tetramers and octamers at a hundredfold higher concentration. We predict that two λ repressor dimers form a tetramer in vitro when bound to two λ 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 λ repressor to λ operator. Consequently, repression of the λ PR promoter in vivo was increased fourfold by the presence of a second pair of λ operators, separated by a distance of 3,600 bp.

Amplification of the lactose carrier protein in Escherichia coli using a plasmid vector.

SummaryThe isolation and properties of a hybrid plasmid carrying the Y gene of the lac operon of Escherichia coli are described. The lactose carrier protein, coded for by the Y gene, is readily identified upon lac operon induction in strains carrying the plasmid. The protein comprises about 15% of the cytoplasmic membrane protein synthesized in the first generation after induction, compared with a wild type strain induced under the same conditions where lactose carrier protein comprises 1.4% of the cytoplasmic membrane protein.

The interaction of the recognition helix of lac repressor with lac operator.

We have constructed a system which allows systematic testing of repressor–operator interactions. The system consists of two plasmids. One of them carries a lac operon in which lac operator has been replaced by a unique restriction site into which synthetic operators can be cloned. The other plasmid carries the gene coding for the repressor, in our case a semisynthetic lacI gene of which parts can be exchanged in a cassette‐like manner. A galE host allows us to select for mutants which express repressors with altered specificities. Here we report the change of specificity in the lac system by changing residues 1 and 2 of the recognition helix of lac repressor. The specificity changes are brought about cooperatively by the change of both residues. Exchanges of just one residue broaden the specificity. Our results hint that the recognition helix of lac repressor may possibly have the opposite orientation to those in Lambda cro protein or 434 CI repressor.

DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor.

We have used a gel retardation assay to investigate the influence of DNA supercoiling on loop formation between lac repressor and two lac operators. A series of 15 DNA minicircles of identical size (452 bp) was constructed carrying two lac operators at distances ranging from 153 to 168 bp. Low positive or negative supercoiling (sigma = +/‐ 0.023) changed the spacing between the two lac operators required for the formation of the most stable loops. This reveals the presence of altered double helical repeats (ranging from 10.3 to 10.7 bp) in supercoiled DNA minicircles. At elevated negative supercoiling (sigma = −0.046) extremely stable loops were formed at all operator distances tested, with a slight spacing periodicity remaining. After relaxation of minicircle‐repressor complexes with topoisomerase I one superhelical turn was found to be constrained in those minicircles which carry operators at distances corresponding to a non‐integral number of helical turns. This indicates that DNA loop formation can define local DNA domains with altered topological properties of the DNA helix.

How Lac repressor finds lac operator in vitro

Filter-binding and gel mobility shift assays were used to analyse the kinetics of the interaction of Lac repressor with lac operator. A comparison of the two techniques reveals that filter-binding assays with tetrameric Lac repressor have often been misinterpreted. It has been assumed that all complexes of Lac repressor and lac operator DNA bind with equal affinity to nitrocellulose filters. This assumption is wrong. Sandwich or loop complexes where two lac operators bind to one tetrameric Lac repressor are not or are only badly retained on nitrocellulose filters under normal conditions. Taking this into account, dimeric and tetrameric Lac repressor do not show any DNA-length dependence of their association and dissociation rate constants when they bind to DNA fragments smaller than 2455 base-pairs carrying a single symmetric ideal lac operator. A ninefold increased association rate to ideal lac operator on lambda DNA is observed for tetrameric but not dimeric Lac repressor. It is presumably due to intersegment transfer involving lac operator-like sequences.

How Trp repressor binds to its operator.

We propose that the generally accepted model of a single Trp repressor dimer binding to a center of symmetry in the natural trp operator (Otwinowski et al., 1988) is wrong. We show here that the Trp repressor binds to a sequence whose center is located four base pairs either to the right or to the left of the central axis of symmetry that was previously identified. We show that: (i) the oligonucleotide used by Otwinowski et al. is not retarded by the Trp repressor in a mobility shift assay under conditions wherein a shorter oligonucleotide carrying our consensus sequence is retarded, (ii) that methylation protection experiments on the full natural operator sequence and the short oligonucleotide protect similar patterns and (iii) that by varying every base in the shorter oligonucleotide, we can demonstrate an optimal sequence for Trp repressor binding.