Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters

We present a statistical-mechanical selection theory for the sequence analysis of a set of specific DNA regulatory sites that makes it possible to predict the relationship between individual base-pair choices in the site and specific activity (affinity). The theory is based on the assumption that specific DNA sequences have been selected to conform to some requirement for protein binding (or activity), and that all sequences that can fulfil this requirement are equally likely to occur. In most cases, the number of specific DNA sequences that are known for a certain DNA-binding protein is very small, and we discuss in detail the small-sample uncertainties that this leads to. When applied to the binding sites for cro repressor in phage lambda, the theory can predict, from the sequence statistics alone, their rank order binding affinities in reasonable agreement with measured values. However, the statistical uncertainty generated by such a small sample (only 6 sites known) limits the result to order-of-magnitude comparisons. When applied to the much larger sample of Escherichia coli promoter sequences, the theory predicts the correlation between in vitro activity (k2KB values) and homology score (closeness to the consensus sequence) observed by Mulligan et al. (1984). The analysis of base-pair frequencies in the promoter sample is consistent with the assumption that base-pairs at different positions in the sites contribute independently to the specific activity, except in a few marginal cases that are discussed. When the promoter sites are ordered according to predicted activities, they seem to conform to the Gaussian distribution that results from a requirement for maximal sequence variability within the constraint of providing a certain average activity. The theory allows us to compare the number of specific sites with a certain activity to the number that would be expected from random occurrence in the genome. While strong promoters are "overspecified", in the sense that their probability of random occurrence is very low, random sequences with weak promoter-like properties are expected to occur in very large numbers. This leads to the conclusion that functional specificity is based on other properties in addition to primary sequence recognition; some possibilities are discussed. Finally, we show that the sequence information, as defined by Schneider et al. (1986), can be used directly (at least in the case of equilibrium binding sites) to estimate the number of protein molecules that are specifically bound at random "pseudosites" in the genome.(ABSTRACT TRUNCATED AT 400 WORDS)     

The heat generated by yeast cultures with a mixed metabolism in the transition between respiration and fermentation

The heat generated by both batch and continuous cultures of the yeast K. fragilis was studied using a modified Bench Scale Calorimeter. Batch cultures were used to measure the heat dissipation rates and the heat yields during fully aerobic and completely anaerobic growth, whereas continuous cultures enabled, in addition, a quantitative study of heat dissipation rates during growth on mixed metabolism. In this case, the extent of fermentation versus respiration could be specified and controlled by varying the degree of oxygen limitation. The heat dissipated per unit biomass formed was highest for fully respirative catabolism and fell continuously to a much lower value typical of anaerobic cultures as the catabolism was shifted increasingly to the fermentative mode. The heat generated per mole of oxygen taken up stayed quite close to the fully aerobic value of 506 kJ mol(-1) even when a sizable fraction of the substrate available to catabolism was fermented. If the fraction of respiration in the metabolism is lowered beyond a certain threshold, the ratio of the heat generation to oxygen consumption starts to increase dramatically and finally tends to infinity for fully anaerobic growth. All experimental results were quantitatively analyzed and explained on the basis of a simple model which formally describes the cultures in terms of two parallel "chemical" reactions. In simple cases such as the one presented here, the model enables calculation of the whole stoichiometry of the culture from a single measured heat yield.     

Cleavage-site motifs in mitochondrial targeting peptides

Although mitochondrial targeting peptides lack a common consensus sequence, a certain bias in the positional distribution of amino acids has recently been found. These patterns seem to be associated with cleavage of the precursor proteins by matrix processing proteases. We have extended the previous studies and found new sequence motifs that are conserved within subgroups of mitochondrial targeting peptides. These motifs have certain common themes, indicating that they are associated with cleavage by one single protease. Two of the conserved patterns have a high predictive value, but even for sequences that do not possess these patterns, a fairly accurate prediction of the cleavage site is shown to be possible. We also suggest that a well-conserved RXY decreases (S/A) pattern may be used to engineer efficiently recognized cleavage sites into uncleaved or artificial mitochondrial targeting peptides.     

Hordein variation in the genus Hordeum as recognized by monoclonal antibodies.

The composition of the major storage protein, hordein, in wild barley species has been studied by using gel electrophoresis, Coomassie staining, and immunoblot assays. We have shown earlier that it is possible to obtain cross-reaction outside the cultivated barley, with monoclonal antibodies raised against hordeins from the barley cultivar Bomi. These antibodies have now been used to investigate the hordein composition in all species of the Hordeum genus. The results showed that polypeptides similar to the two major hordein groups of cultivated barley, the B- and C-hordeins, are produced in all wild Hordeum species, and that there are both similarities and differences between the two hordein groups. The similarities indicate a common evolutionary origin, while the distinction between B- and C-hordeins in the entire genus clearly shows that the divergence of their coding genes preceded the divergence of the Hordeum species. The presence of the same antigenic site in two different species indicates that they are evolutionarily related. Among the wild species, two rarely occurring sites were exclusively found in H. vulgare ssp. spontaneum and H. bulbosum, which confirms that they are the cultivated barley's closest relatives. Some of the antibodies also gave an extensive reaction pattern with H. murinum, which suggests a fairly close relationship to H. vulgare, though not as close as between H. vulgare and H. bulbosum.     

Molecular cloning of the mouse 46-kDa mannose 6-phosphate receptor (MPR 46).

A cDNA clone for the mouse 46-kDa mannose 6-phosphate receptor (MPR 46) was isolated from an embryonic mouse cDNA library. Its single open reading frame codes for a protein of 278 residues. It shows an over-all amino-acid identity of 93% with the human receptor. Nine non-conservative amino-acid exchanges are found in the luminal domain, one non-conservative exchange of hydrophobic amino acids is in the transmembrane domain, while the cytoplasmic receptor tails are identical. All five potential N-glycosylation sites are conserved as well as amino acids that are important for ligand binding (Arg 137 and His 131) and disulfide pairing (Cys 32 and 78, Cys 132 and Cys 167, Cys 145 and Cys 179). The absolute identity in the cytoplasmic MPR 46 tail suggests the importance of this amino-acid sequence for the intracellular routing of the MPR 46.     

Primary production data from the south-eastern Weddell Sea

Summary Phytoplankton production for three size classes (<20 m, 20–100 m, >100 m), total primary production and qualitative composition of phytoplankton populations were recorded from 18 stations in the south-eastern Weddell Sea in February/March 1983. Total primary production ranged between 80 and 1670 mg C m^-2 d^-1 with an average of 670 mg C m^-2 d^-1, nearly 70% of which was contributed by the <20 m size fraction (usually pennate and/or centric diatoms). Production of phytoplankton was in the higher range of values reported by other authors for the same region. Variations in primary production could not be attributed to composition of populations, ambient light levels or concentrations of macronutrients (N, P, Si). Phytoplankton populations had a higher diversity in the deeper parts of the Weddell Sea and coincided with different oceanographic situations. Three zones (along the shelf-ice edge from Atka Bay to Halley Bay, west of Halley Bay and off the Filchner/Rønne Ice Shelf) with different communities could be clearly distinguished.     

How signal sequences maintain cleavage specificity

The specificity of the signal sequence cleavage reaction has been postulated to reside in a signal peptidase active site that can bind only to particular (i, i + 2) pairs of amino acids. In this paper, we present further patterns of non-random amino acid utilization in a region around in vivo cleavage sites, and show that they can be interpreted in terms of selection acting to reduce the number of potential competing sites in the vicinity of the correct one.     

A neural cocktail-party processor

Sensory segmentation is an outstanding unsolved problem of theoretical, practical and technical importance. The basic idea of a solution is described in the form of a model. The response of neurons within the sensory field is temporally unstable. Segmentation is expressed by synchronization within segments and desynchronization between segments. Correlations are generated by an autonomous pattern formation process. Neuronal coupling is the result both of peripheral evidence (similarity of local quality) and of central evidence (common membership in a stored pattern). The model is consistent with known anatomy and physiology. However, a new physiological function, synaptic modulation, has to be postulated. The present paper restricts explicit treatment to the peripheral evidence represented by amplitude modulations globally present in all components of a sound spectrum. Generalization to arbitrary sensory qualities will be the subject of a later paper. The model is an application and illustration of the Correlation Theory of brain function.This work has been supported by Grant I/37-821 of the Stiftung Volkswagenwerk.     

Biosynthesis and maturation of arylsulfatase B in normal and mutant cultured human fibroblasts

The biosynthesis of arylsulfatase B in normal and mutant human skin fibroblasts was studied by metabolic labeling with radioactive amino acids, monosaccharides, or 32Pi and by specific immunoprecipitation followed by polyacrylamide gel electrophoresis and fluorography. Three major polypeptides with apparent molecular weights of 47,000, 40,000, and 31,000 were found intracellularly and one of 64,000 in the medium. Pulse-chase labeling and uptake experiments showed that arylsulfatase B synthesized and secreted as a 64,000 precursor was intracellularly processed within less than 24 h via short lived intermediates to two different forms. Form I (chains of 47,000 and 11,500) was labeled earlier and was about twice as stable as form II (chains of 40,000 and 31,000). The secreted 64,000 precursor and the 40,000 chain of form II contained oligosaccharides resistant to endo-beta-N-acetylglucosaminidase H. In the other chains mainly cleavable and phosphorylated oligosaccharides were found. Arylsulfatase B activity was associated with the 64,000 precursor and with form I, but not with form II. Fibroblasts of four patients with the severe form of mucopolysaccharidosis type VI, which were deficient in arylsulfatase B activity, synthesized and secreted the 64,000 precursor at a normal rate. This precursor, however, had little if any catalytic activity and one of its mature forms (I) was rapidly degraded.     

A fluorescence microscope attachment for flow-through cytofluorometry

A flow-through system for rapid automated analysis of intracellular fluorescence parameters is described. In combination with commercially available instrumentation for fluorescence microscopy, fluorometry and pulse height analysis, the hydrodynamic focusing flow-through principle can be successfully applied. The specific advantages and disadvantages of this principle compared with the mechanical focusing system are discussed.