Dynamic landscape of the local translation at activated synapses.

The mammalian target of rapamycin (mTOR) signaling pathway is the central regulator of cap-dependent translation at the synapse. Disturbances in mTOR pathway have been associated with several neurological diseases, such as autism and epilepsy. RNA-binding protein FMRP, a negative regulator of translation initiation, is one of the key components of the local translation system. Activation and inactivation of FMRP occurs via phosphorylation by S6 kinase and dephosphorylation by PP2A phosphatase, respectively. S6 kinase and PP2A phosphatase are activated in response to mGluR receptor stimulation through different signaling pathways and at different rates. The dynamic aspects of this system are poorly understood. We developed a mathematical model of FMRP-dependent regulation of postsynaptic density (PSD) protein synthesis in response to mGluR receptor stimulation and conducted in silico experiments to study the regulatory circuit functioning. The modeling results revealed the possibility of generating oscillatory (cyclic and quasi-cyclic), chaotic and even hyperchaotic dynamics of postsynaptic protein synthesis as well as the presence of multiple attractors in a wide range of parameters of the local translation system. The results suggest that autistic disorders associated with mTOR pathway hyperactivation may be due to impaired proteome stability associated with the formation of complex dynamic regimes of PSD protein synthesis in response to stimulation of mGluR receptors on the postsynaptic membrane of excitatory synapses on pyramidal hippocampal cells.

[Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea].

The phenomenon of bacterial persistence, also known as non-inherited antibiotic tolerance in a part of bacterial populations, was described more than 70 years ago. This type of tolerance contributes to the chronization of infectious diseases, including tuberculosis. Currently, the emergence of persistent cells in bacterial populations is associated with the functioning of some stress-induced molecular triggers, including toxin-antitoxin systems. In the presented review, genetic and metabolic peculiarities of persistent cells are considered and the mechanisms of their occurrence are discussed. The hypothesis of the origin of persister cells based on bistability, arising due to the non-linear properties of a coupled transcription-translation system, was proposed. Within this hypothesis, the phenomenon of the bacterial persistence of modern cells is considered as a result of the genetic fixation of the phenotypic multiplicity that emerged in primitive cells in the process of neutrally coupled co-evolution (genetic drift of multiple neutrally coupled mutations). Our hypothesis explains the properties of persister cells, as well as their origin and "ineradicable" nature.

[New evidence of an old problem: the coupling of genome replication to cell growth in bacteria].

The problem of coordinating genome replication with cell growth in bacteria was posed over four decades ago. Unlike for eukaryotes, this problem has not been completely solved even for Escherichia coli, which has been comprehensively studied by molecular biologists, to say nothing of other bacteria. Current models of the bacterial life cycle solve the coupling problem by introducing a phenomenological hypothesis that considers the dynamic coordination of growth and replication but does not unveil the underlying molecular mechanisms. Here we review the mechanisms regulating genome replication initiation with regards to their coupling to growth processes in the three best investigated bacterial species: E. coli, Bacillus subtilis, and Caulobacter crescentus. A putative correlation between the type of cell growth laws and the actual mechanisms regulating the replication of DNA formed during the process of evolution in various classes of bacteria, is discussed, including those intracellular parasites in which degenerative evolution his discarded most of their genomes. We contemplate the concept of a universal growth law for bacterial cells and some features in the formation of a primitive negative replication regulating mechanism in the context of the coupling problem.

[Replication of the subgenomic hepatitis C virus replicon in the presence of the NS3 protease inhibitors: a stochastic model].

The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are relevant to predict the efficacy of potential drugs against virus or host targets. One of the promising targets for development of new drugs is the viral NS3 protease. Here we developed a stochastic model of the subgenomic HCV replicon replication in Huh-7 cells and in the presence of the NS3 protease inhibitors. Along with consideration of the stochastic nature of the subgenomic HCV replicon replication the model takes into account the existence and generation of main NS3 protease drug resistant mutants, namely BILN-2061 (A156T, D168V, R155Q), VX-950 (A156S, A156T, T54A) and SCH-503034 (A156T, A156S, T54A). The model reproduces well the viral RNA kinetics in the cell from the moment of the subgenomic HCV replicon transfection to steady state, as well as the viral RNA suppression kinetics in the presence of NS3 protease inhibitors BILN-2061, VX-950 and SCH-503034. We showed that the resistant mutants should be taken into account for the correct description of biphasic kinetics of the viral RNA suppression. The mutants selected in the presence of different inhibitor concentrations have maximal replication capacity in the given inhibitor concentration range. Our model can be used to interpret the results of the new anti-HCV drug testing in replicon systems, as well as to predict the efficacy of new potential drugs and optimize the regimen of their use.

Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance.

BACKGROUND AND AIMS: The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport. The PIN family of auxin transporters plays a critical role in polar auxin transport, and two mechanisms of auxin maximum formation in the RAM based on PIN-mediated auxin transport have been proposed to date: the reverse fountain and the reflected flow mechanisms. METHODS: The two mechanisms are combined here in in silico studies of auxin distribution in intact roots and roots cut into two pieces in the proximal meristem region. In parallel, corresponding experiments were performed in vivo using DR5::GFP Arabidopsis plants. KEY RESULTS: The reverse fountain and the reflected flow mechanism naturally cooperate for RAM patterning and maintenance in intact root. Regeneration of the RAM in decapitated roots is provided by the reflected flow mechanism. In the excised root tips local auxin biosynthesis either alone or in cooperation with the reverse fountain enables RAM maintenance. CONCLUSIONS: The efficiency of a dual-mechanism model in guiding biological experiments on RAM regeneration and maintenance is demonstrated. The model also allows estimation of the concentrations of auxin and PINs in root cells during development and under various treatments. The dual-mechanism model proposed here can be a powerful tool for the study of several different aspects of auxin function in root.

Causes of global extinctions in the history of life: facts and hypotheses.

Paleontologists define global extinctions on Earth as a loss of about three-quarters of plant and animal species over a relatively short period of time. At least five global extinctions are documented in the Phanerozoic fossil record (~500-million-year period): ~65, 200, 260, 380, and 440 million years ago. In addition, there is evidence of global extinctions in earlier periods of life on Earth - during the Late Cambrian (~500 million years ago) and Ediacaran periods (more than 540 million years ago). There is still no common opinion on the causes of their occurrence. The current study is a systematized review of the data on recorded extinctions of complex life forms on Earth from the moment of their occurrence during the Ediacaran period to the modern period. The review discusses possible causes for mass extinctions in the light of the influence of abiogenic factors, planetary or astronomical, and the consequences of their actions. We evaluate the pros and cons of the hypothesis on the presence of periodicity in the extinction of Phanerozoic marine biota. Strong evidence that allows us to hypothesize that additional mechanisms associated with various internal biotic factors are responsible for the emergence of extinctions in the evolution of complex life forms is discussed. Developing the idea of the internal causes of periodicity and discontinuity in evolution, we propose our own original hypothesis, according to which the bistability phenomenon underlies the complex dynamics of the biota development, which is manifested in the form of global extinctions. The bistability phenomenon arises only in ecosystems with predominant sexual reproduction. Our hypothesis suggests that even in the absence of global abiotic catastrophes, extinctions of biota would occur anyway. However, our hypothesis does not exclude the possibility that in different periods of the Earth's history the biota was subjected to powerful external influences that had a significant impact on its further development, which is reflected in the Earth's fossil record.

[A mathematical model of the intracellular reproduction of the influenza virus].

A mathematical model of the intracellular reproduction of the influenza virus has been constructed, which describes the regulation of transcription, translation, replication, and assembly of the virus in a sensitive noninterferonogenic cell. A structural and parametric verification of the model has been performed, which involves an analysis of alternative mechanisms of regulation of the key events of the reproduction of the influenza virus at the stages of the primary and secondary transcription. It was shown that the dynamics of the concentrations of the system components is in qualitative agreement with the experimental data. An analysis of the model parameters showed a high sensitivity of the model to changes in the parameters that control the efficiency of the binding of the viral polymerase to virus-specific RNAs at the stages of initiation and elongation of transcription and replication of the viral genome. The results obtained suggest that the stages of the virus reproduction sensitive to changes in the parameters are potential targets for drugs. Using the model, a minimal multiplicity of infection at which the formation of viral particles is observed was predicted.

Persister Cells - a Plausible Outcome of Neutral Coevolutionary Drift.

The phenomenon of bacterial persistence - a non-inherited antibiotic tolerance in a minute fraction of the bacterial population, was observed more than 70 years ago. Nowadays, it is suggested that "persister cells" undergo an alternative scenario of the cell cycle; however, pathways involved in its emergence are still not identified. We present a mathematically grounded scenario of such possibility. We have determined that population drift in the space of multiple neutrally coupled mutations, which we called "neutrally coupled co-evolution" (NCCE), leads to increased dynamic complexity of bacterial populations via appearance of cells capable of carrying out a single cell cycle in two or more alternative ways and that universal properties of the coupled transcription-translation system underlie this phenotypic multiplicity. According to our hypothesis, modern persister cells have derived from such cells and regulatory mechanisms that govern the consolidation of this phenomenon represented the trigger. We assume that the described type of neutrally coupled co-evolution could play an important role in the origin of extremophiles, both in bacteria and archaea.

GeneNet in 2005.

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/.

[Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms].

UNLABELLED: Gene expression is known to correlate with degree of codon bias in many unicellular organisms. However, such correlation is absent in some organisms. Recently we demonstrated that inverted complementary repeats within coding DNA sequence must be considered for proper estimation of translation efficiency, since they may form secondary structures that obstruct ribosome movement. We have developed a program for estimation of potential coding DNA sequence expression in defined unicellular organism using its genome sequence. The program computes elongation efficiency index. Computation is based on estimation of coding DNA sequence elongation efficiency, taking into account three key factors: codon bias, average number of inverted complementary repeats, and free energy of potential stem-loop structures formed by the repeats. The influence of these factors on translation is numerically estimated. An optimal proportion of these factors is computed for each organism individually. Quantitative translational characteristics of 384 unicellular organisms (351 bacteria, 28 archaea, 5 eukaryota) have been computed using their annotated genomes from NCBI GenBank. Five potential evolutionary strategies of translational optimization have been determined among studied organisms. A considerable difference of preferred translational strategies between Bacteria and Archaea has been revealed. Significant correlations between elongation efficiency index and gene expression levels have been shown for two organisms (S. cerevisiae and H. pylori) using available microarray data. The proposed method allows to estimate numerically the coding DNA sequence translation efficiency and to optimize nucleotide composition of heterologous genes in unicellular organisms. AVAILABILITY: http://www.mgs.bionet.nsc.ru/mgs/programs/eei-calculator/.

[Mathematical model of auxin distribution in the plant root].

Regulation of plant growth and development by auxin is mediated by the hormone controlled distribution and dose-dependent mechanisms of its action. A mathematical model is proposed, which described the distribution of auxin in the cells extending along the central axis of the Arabidopsis thaliana root. This model reproduces qualitatively both auxin distribution in cells of the root central axis under the normal conditions and under the conditions of decreased active transport and the recovery of auxin distribution and related meristem restoration during root regeneration after ablation of its tip. Different types of distribution of the auxin concentration over the vertical root axis are described, possible variants of root growth and lateral roots formation are proposed, and biological interpretation is given to different regimes of model behavior.

[Molecular weight distribution of polymeric DNA-products, formed upon the action of matrix enzymes]. / Molekuliarno-vesovoe raspredelenie polimernykh DNK-produktov, obrazuiushchikhsia pri deistvii matrichnykh fermentov.

Models of processive and distributive DNA synthesis and degradation catalysed by matrix enzymes were investigated. Distribution of polymer products dependent on the reaction model chosen, on the type of the matrix and on the enzyme-matrix initial concentration ratio were determined by methods of numerical modeling. Conditions were found where the scattering of the reaction polymer products was minimal. The homopolymer matrix choice of experimental condition may generate a distribution of product that obeys the Poisson distribution. Numerical investigations of polymerization (hydrolysis) processes showed that for a number of heteropolymer matrixes a distribution may exist with scattering much less than that for homopolymer matrixes. Conditions are found when processive and distributive models give different distributions of the reaction product.

[On connection of a graph of a gene network with qualitative modes of function]. / O sviazi grafa genno seti s kachestvennymi rezhimami ee funktsionirovaniia.

Theoretical investigation of properties of assumed gene networks constructed from elementary units of two types, genetic elements and control links, was carried out. A test was formulated for a subclass of such networks with cyclic structure called S(n,k)-networks allowing calculation-free prediction of the network limiting properties (the presence/absence and number of stationery and/or cyclic functioning modes) from a graph of the network structure. The obtained data can be useful for constructing gene networks with predefined properties.

[A generalized chemical-kinetic method for modeling gene networks]. / Obobshchennyi khimiko-kineticheskii metod modelirovaniia gennykh setei.

Development of methods for mathematical simulation of biological systems and building specific simulations is an important trend of bioinformatics development. Here we describe the method of generalized chemokinetic simulation generating flexible and adequate simulations of various biological systems. Adequate simulations of complex nonlinear gene networks--control system of cholesterol by synthesis in the cell and erythrocyte differentiation and maturation--are given as the examples. The simulations were expressed in terms of unit processes--biochemical reactions. Optimal sets of parameters were determined and the systems were numerically simulated under various conditions. The simulations allow us to study possible functional conditions of these gene networks, calculate consequences of mutations, and define optimal strategies for their correction including therapeutic ones. Graphical user interface for these simulations is available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneNet/.

[Integrated computer system for regulating eukaryotic gene expression]. / Integrirovannaia komp'iuternaia sistema po reguliatsii ékspressii genov éukariot.

The review describes several modules of the GeneExpress integrated computer system concerning the regulation of gene expression in eukaryotes. Approaches to the presentation of experimental data in databases are considered. The employment of GeneExpress in computer analysis and modeling of the organization and function of genetic systems is illustrated with examples. GeneExpress is available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/.

[Effectiveness of distal gene translation in polycistrons depends upon the arrangement of regulatory signals on a template]. / Effektivnost' transliatsii distal'nogo gena v politsistronakh zavisit ot vzaimnogo raspolozheniia reguliatornykh signalov na matritse.

The role of the translational terminator and initiator signals arrangement for two adjacent genes in polycistronic mRNA has been studied. Semisynthetic beta-galactosidase gene (lacZ) of E. coli and fragment of phage M13 DNA (with promoter PVIII, gene IX, and part of gene VIII) were used for constructing of the IX-VIII-lacZ artificial polycistronic operon. Cloning of the constructs into pBR322 vector resulted in a number of pLZ381N plasmids differing by the mutual arrangement of gene VIII translation terminator codon and SD site and initiator codon (SD-ATG-region) of lacZ gene. The mutual arrangement of gene VIII terminator codon and SDlacZ-ATG region has been altered by means of deletions and insertions that have not affected lacZ translation initiation signals. The beta-galactosidase (beta-Gal) synthesis in E. coli harbouring different types of pLZ381N plasmids has been found to depend on type of cistron coupling (gene VIII and lacZ). The overlapping of terminator and initiator codons (ATGA) for genes VIII and lacZ (type I of polycistrons) provide approximately equal translational level for both cistrons. On the other side, levels of beta-Gal synthesis in case of polycistrons type II (gene VIII stop-codon position at the beginning of SDlacZ or 10 nucleotides upstream) were 20-30 times as high as for type I. Differences in beta-Gal levels have also been found for variants of VIII-lacZ coupling in types IV and III polycistrons (the SDlacZ-ATG region in 27-50 nucleotides downstream from the proximal cistron VIII stop-codon, which, in turn, is 41 nucleotides upstream this terminator). These data cannot be explained on the basis of possible secondary structure including the SDlacZ-ATG region and other parts of polycistronic mRNA. In all these cases similarly stable stem-loop structures have been found. Therefore, the arrangement of the translation termination and initiation signals for two adjacent genes in essential for distal gene translation efficiency. One can imagine that ribosome or its 30S subpartical, stalling on the proximal gene terminator codon, affects the distal gene translation initiation.

[Regulation of translation of the distal lacZ gene in polycistronic mRNA by the ribosome stream from the proximal gene]. / Reguliatsiia transliatsii distal'nogo gena lacZ politsistronnoi mRNK potokom ribosom s proksimal'nogo gena.

Four series of plasmids (pNSI, pNSII, pNLI, and pNLII) with artificial polycistrons containing the lacZ test gene were constructed. These plasmids coded for polycistronic mRNAs with two different types of cistron (orfZ and lacZ) coupling: in pNSI and pNLI, the orfZ termination codon and the lacZ initiation codon overlapped (type I); in pNSII and pNLII, the orfZ termination codon, was located upstream of the lacZ SD sequence. The length of the orfZ cistron was 60 bp in pNSI and pNSII or 300 bp in pNLI and pNLII. Plasmids with the same type of cistron coupling contained the same lacZ translation initiation region, whereas the structure of the orfZ translation initiation region varied, thereby providing varying efficiency of the orfZ gene translation. The effect of these variations on the efficiency of the lacZ gene translation was evaluated by direct measurement of the beta-galactosidase activity in Escherichia coli cells transformed with the corresponding plasmids. We found that the level of translation of the distal lacZ gene depended on the ribosome stream from the proximal gene and was maximal at the optimal ribosome stream level, which, in turn, depended on the type of cistron coupling.

[Model polycistron operon for studying conjugated translation in E. coli cells. The role of a stream of ribosomes]. / Model'nyi politsistronnyi operon dlia izucheniia sopriazhennoi transliatsii v kletkakh E. coli. Rol' potoka ribosom.

The role of "stream" of ribosomes upon translation of polycistronic mRNAs has been studied using an artificial polycistron. It has been found that the levels of activation of cistron Ci + 1 out of two adjacent cistrons (Ci and Ci + 1) depends, in addition to earlier described effects of mutual arrangement of initiation and termination signals, also on efficiency of translation of the foregoing cistron Ci. The results obtained lead to the conclusion that in polycistronic systems the levels of translation of cistron Ci + 1 can be regulated by "stream" of ribosomes resulted from translation of the proximal cistron Ci.

Translation efficiency in yeasts correlates with nucleosome formation in promoters.

Elongation efficiency index (EEI) was suggested earlier to estimate gene expression efficiency by nucleotide context of coding sequence in unicellular organisms. We have analyzed association between EEI and nucleosome formation potential (NFP) in 5' regulatory regions upstream translation initiation site (TIS) from two yeast species. Theoretical estimations of NFP based on DNA sequence were obtained by Recon method. Experimental estimation of nucleosome occupancy was obtained by high-throughput sequencing data of nucleosomal DNA in Saccharomyces cerevisiae . For the sample of all genes correlation coefficient was calculated between two vectors: vector of NFP values for fixed position relative to TIS and vector of EEI values. Profiles of correlation coefficients of NFP and EEI were counted in (-600; +600) regions relative to TIS for gene sequences extracted from GenBank. We found regions of strong negative dependence between NFP and EEI for all genes as well as for 10% highly expressed genes in Schizosaccharomyces pombe (10% of EEI-highest genes). At the same time, we found positive dependence between NFP and EEI for all genes and for low expressed genes in S. cerevisiae (10% of EEI-lowest genes). The association between NFP and EEI could be explained by evolutionary selection of context characteristics of nucleotide sequences for gene expression optimization.

Theoretical analysis of the regulation of interferon expression during priming and blocking.

Interferon superinduction, in the case of cell pretreatment with low doses of interferon (priming), may be explained by activation of 2',5'-oligoadenylate synthetase and endonuclease L, since the latter, as expected, leads to a more rapid amplification of the standard scheme of interferon induction based on the antirepression mechanism. In the given case, endonuclease L will further increase the degradation rates for messages, which encode repressor proteins controlling interferon gene expression. Under ordinary induction, these messages are destroyed only by short-lived nuclease activated by double-stranded RNA. Cell pretreatment with high doses of interferon (blocking) considerably increases the concentrations of protein kinase and 2',5'-oligoadenylate synthetase in the cell. However, it seems that during blocking protein kinase plays the main role in inhibition of interferon synthesis, and this leads to almost complete depression of translation in the cell. When protein kinase is not sufficiently activated, blocking does not occur since treatment of cells with high concentrations of interferon does not hinder priming induced by 2',5'-oligoadenylate synthetase and endonuclease L. The proposed model is consistent with the findings that both interferon-treated primed and blocked cells are able to produce interferon more rapidly than normal cells. The analysis, based on a computer simulation model, suggests that priming and blocking of interferon may be based on processes controlling its induction and antiviral activity.