Optimization of error-correction processes with respect to time. Comparison to free energy aspects

Rates of nucleotide substitution in sexual and anciently asexual rotifers

The class Bdelloidea of the phylum Rotifera is the largest well studied eukaryotic taxon in which males and meiosis are unknown, and the only one for which these indications of ancient asexuality are supported by cytological and molecular genetic evidence. We estimated the rates of synonymous and nonsynonymous substitutions in the hsp82 heat shock gene in bdelloids and in facultatively sexual rotifers of the class Monogononta, employing distance based and maximum likelihood methods. Relative-rate tests, using acanthocephalan rotifers as an outgroup, showed slightly higher rates of nonsynonymous substitution and slightly lower rates of synonymous substitution in bdelloids as compared with monogononts. The opposite trend, however, was seen in intraclass pairwise comparisons. If, as it seems, bdelloids have evolved asexually, an equality of bdelloid and monogonont substitution rates would suggest that the maintenance of sexual reproduction in monogononts is not attributable to an effect of sexual reproduction in limiting the load of deleterious nucleotide substitutions.

Deleterious mutations and the evolution of sexual reproduction

The origin and maintenance of sexual reproduction continues to be an important problem in evolutionary biology. If the deleterious mutation rate per genome per generation is greater than 1, then the greater efficiency of selection against these mutations in sexual populations may be responsible for the evolution of sex and related phenomena. In modern human populations detrimental mutations with small individual effects are probably accumulating faster than they are being eliminated by selection.

Site dependent time optimization of protein synthesis with special regard to accuracy

The efficiency of protein synthesis is determined by its rate, accuracy, and energy consumption. With the energy consumption fixed, we optimize the system with respect to time and accuracy. Using an analytic model for a simple system and computer simulations for more complex systems, where also the possibility of errors is included, we demonstrate how different parts of the messenger RNA influence the protein production rate differently. The first part of the coding sequence is of major importance, since the availability of empty initiation sites is crucial, and queuing back to that region may interfere with initiation. The elongation rate at different positions depends on codon usage, on the concentrations of substrate and co-factors, and on the kinetic rate constants, including those of the proofreading branch(es). Ribosomal proofreading is a time consuming process and by allowing for more errors in the beginning of a protein, it is possible to increase the production rate of that protein. We calculate the mean translation time per functioning protein for various translation accuracies, and discuss the different strategies open to living cells.

Free energy and time economy for the mutual selection of monomers in biosynthesis, primarily protein synthesis

The starting point of this work is the fact that the correction of errors in biosynthesis must be paid for by an increased dissipation (free energy loss) or a time delay. Further, a low accuracy is wasteful in this respect as the cell then produces a number of non-functioning products with a significant "production cost". One can then look for the situations of best "economy" for the selection processes. This is particularly obvious in reciprocal selections, where in some cases a substrate A shall be selected but discriminated against a competitor B, and in other cases, the opposite is true, B shall be selected with A as a competitor. It can be expected only in certain symmetric situations that these reciprocal selections are made in an equal way. Because one substrate shall be selected more often or it may be more relevant for the product, it may occur in higher concentrations and/or be selected more accurately (at a higher cost). The opposite selection may then be less accurate. The work studies various aspects of this.

Theoretical modelling of protein synthesis

This article provides an overview of the use of mathematical and computer modelling in furthering the understanding of protein synthesis. In particular, we discuss issues such as the nature of the rate limiting step(s), error rates, tRNA-codon adaptation, codon bias, attenuation control, and problems of selection and error corrections, focussing on their theoretical treatment.