The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.

Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation-selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used.

Model of Genetic Code Structure Evolution under Various Types of Codon Reading.

The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the number of encoded labels. This redundancy implies the existence of codons that encode the same genetic information. The size and organization of such synonymous codon blocks are important characteristics of the SGC structure whose evolution is still unclear. Therefore, we studied possible evolutionary mechanisms of the codon block structure. We conducted computer simulations assuming that coding systems at early stages of the SGC evolution were sets of ambiguous codon assignments with high entropy. We included three types of reading systems characterized by different inaccuracy and pattern of codon recognition. In contrast to the previous study, we allowed for evolution of the reading systems and their competition. The simulations performed under minimization of translational errors and reduction of coding ambiguity produced the coding system resistant to these errors. The reading system similar to that present in the SGC dominated the others very quickly. The survived system was also characterized by low entropy and possessed properties similar to that in the SGC. Our simulation show that the unambiguous SGC could emerged from a code with a lower level of ambiguity and the number of tRNAs increased during the evolution.

Models of genetic code structure evolution with variable number of coded labels.

It is assumed that at the early stage of cell evolution its translation machinery was characterized by high noise, i.e. ambiguous assignment of codons to amino acids in the genetic code, which initially encoded only few amino acids. Next, during its evolution new amino acids were added to this code. Taking into account this facts, we investigated theoretical models of genetic code's structure, which evolved from a set of ambiguous codons assignments into a coding system with a low level of uncertainty. We considered three types of translational inaccuracies assuming a different number of fixed codon positions. We applied a modified version of evolutionary algorithm for finding the genetic codes that the most effectively reduced the initial uncertainty in the assignment of codons to encoded labels, i.e. amino acids and a stop translation signal. We examined codes with the number of labels from four to 22. Our results indicated that the quality of genetic code structure is strongly dependent on the number of encoded labels as well as the type of translational mechanism. The more strict assignments of codon to the labels was preferred by the codes encoding more number of labels. The results showed that a smaller degeneracy of codes evolved from a more tolerant coding with the stepwise addition of coded amino acids to the genetic code. The distribution of codon groups in the standard genetic code corresponds well to the translation model assuming two fixed codon positions, whereas the six-codon groups can be relics form previous stages of evolution when the code characterized by a greater uncertainty.

Effect of ampicillin on adhesive properties of bacteria examined by atomic force microscopy.

Discovery of new antibacterial agents requires the development of novel techniques for bacteria surface characterization after treatment with antibiotics. In this study, we investigate the effect of ampicillin at MICs levels on adhesive properties of Gram-positive and Gram-negative bacteria, using atomic force microscopy (AFM). Our results revealed that the treatment leads to changes of bacterial surface properties, especially cell surface roughness. A nanomechanical alteration of the cells led to an increase of adhesive forces and rupture lengths. Changes in adhesive properties are determined not only by the modification of physicochemical cell properties but also by an increase in roughness, leading to an increase of the contact area with a cantilever tip. We discovered that the contribution of non-specific physicochemical interactions in the bacteria attachment to a substrate is not negligible and was significantly influenced by the presence of antibiotic. Ampicillin caused much greater change in the adhesion properties of Bacillus subtilis than Escherichia coli due to the mode of action of ß-lactam antibiotic. Adhesion measurements may by a new way to investigate subtle changes of the bacterial surface properties caused by antibiotic, especially those targeting the bacterial cell wall. In contrast to nanoindentation assays, they provide information on adhesive properties of the bacteria surface.

Nanopuller-open data acquisition platform for AFM force spectroscopy experiments.

Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown.