Lev I. Rubanov

Lack of conservation of bacterial type promoters in plastids of Streptophyta.

We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes psaA, psbA, psbB, psbE, rbcL. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, de novo emergence of the promoters, their loss together with plastome genes; functional substitution of the promoter boxes by transcription activation factor binding sites.ReviewersThis article was reviewed by Dr. Arcady Mushegian, and by Dr. Alexander Bolshoy and Dr. Yuri Wolf (both nominated by Dr. Purificación López-García).

Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level

BackgroundModeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases. This process involves RNA polymerases collision followed by transcription termination.ResultsA mathematical and computer simulation model is developed to describe the competition of RNA polymerases during genes transcription on complementary DNA strands. E.g., in the barley Hordeum vulgare the polymerase competition occurs in the locus containing plastome genes psbA, rpl23, rpl2 and four bacterial type promoters. In heat shock experiments on isolated chloroplasts, a twofold decrease of psbA transcripts and even larger increase of rpl23-rpl2 transcripts were observed, which is well reproduced in the model. The model predictions are in good agreement with virtually all relevant experimental data (knockout, heat shock, chromatogram data, etc.). The model allows to hypothesize a mechanism of cell response to knockout and heat shock, as well as a mechanism of gene expression regulation in presence of RNA polymerase competition. The model is implemented for multiprocessor platforms with MPI and supported on Linux and MS Windows. The source code written in C++ is available under the GNU General Public License from the laboratory website. A user-friendly GUI version is also provided at http://lab6.iitp.ru/en/rivals.ConclusionsThe developed model is in good agreement with virtually all relevant experimental data. The model can be applied to estimate intensities of binding of the holoenzyme and phage type RNA polymerase to their promoters using data on gene transcription levels, as well as to predict characteristics of RNA polymerases and the transcription process that are difficult to measure directly, e.g., the intensity (frequency) of holoenzyme binding to the promoter in correlation to its nucleotide composition and the type of σ-subunit, the amount of transcription initiation aborts, etc. The model can be used to make functional predictions, e.g., heat shock response in isolated chloroplasts and changes of gene transcription levels under knockout of different σ-subunits or RNA polymerases or due to gene expression regulation.ReviewersThis article was reviewed by Dr. Anthony Almudevar, Dr. Aniko Szabo, Dr. Yuri Wolf (nominated by Dr. Peter Olofsson) and Prof. Marek Kimmel.

Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios

BackgroundA long recognized problem is the inference of the supertree S that amalgamates a given set {Gj} of trees Gj, with leaves in each Gj being assigned homologous elements.We ground on an approach to find the tree S by minimizing the total cost of mappings αj of individual gene trees Gj into S. Traditionally, this cost is defined basically as a sum of duplications and gaps in each αj. The classical problem is to minimize the total cost, where S runs over the set of all trees that contain an exhaustive non-redundant set of species from all input Gj.ResultsWe suggest a reformulation of the classical NP-hard problem of building a supertree in terms of the global minimization of the same cost functional but only over species trees S that consist of clades belonging to a fixed set P (e.g., an exhaustive set of clades in all Gj). We developed a deterministic solving algorithm with a low degree polynomial (typically cubic) time complexity with respect to the size of input data.We define an extensive set of elementary evolutionary events and suggest an original definition of mapping β of tree G into tree S. We introduce the cost functional c(G, S, f ) and define the mapping β as the global minimum of this functional with respect to the variable f, in which sense it is a generalization of classical mapping α.We suggest a reformulation of the classical NP-hard mapping (reconciliation) problem by introducing time slices into the species tree S and present a cubic time solving algorithm to compute the mapping β. We introduce two novel definitions of the evolutionary scenario based on mapping β or a random process of gene evolution along a species tree.ConclusionsDeveloped algorithms are mathematically proved, which justifies the following statements. The supertree building algorithm finds exactly the global minimum of the total cost if only gene duplications and losses are allowed and the given sets of gene trees satisfies a certain condition. The mapping algorithm finds exactly the minimal mapping β, the minimal total cost and the evolutionary scenario as a minimum over all possible distributions of elementary evolutionary events along the edges of tree S.The algorithms and their effective software implementations provide useful tools in many biological studies. They facilitate processing of voluminous tree data in acceptable time still largely avoiding heuristics. Performance of the tools is tested with artificial and prokaryotic tree data.ReviewersThis article was reviewed by Prof. Anthony Almudevar, Prof. Alexander Bolshoy (nominated by Prof. Peter Olofsson), and Prof. Marek Kimmel.

Model of gene expression regulation in bacteria via formation of RNA secondary structures

A model was proposed for the classical attenuating mRNA regulation of gene expression via transcription termination. The model is based on the concept of secondary structure macrostates in the RNA regulatory region between the ribosome and RNA polymerase, utilizes resonant equations for estimating the deceleration of RNA polymerase by a set of hairpins located in this RNA region, and takes into account views on the initiation and elongation of transcription and translation. Special attention was paid to selecting the model parameters. To test the model, computations were performed to estimate, in particular, the probability of translation termination as dependent on the charged tRNA concentration and the amino acid concentration for several regulatory regions of the bacterial genome (as exemplified by trpE of Streptomyces spp., Bradyrhizobium japonicum, and Escherichia coli). Analysis was performed with different values of three parameters isolated as major ones. The resulting dependences agreed with the available experimental data, including those characterizing an enzymatic activity as dependent on the amino acid concentration in a culture (e.g., the anthranylate synthase activity as dependent on the tryptophan concentration in S. venezuelae). The following possible application was proposed for the model. Attenuating regulation is usually predicted on the basis of multiple sequence alignment, which requires several sequences. With the model, an individual sequence can be analyzed with proper parameters to generate a concentration-enzymatic activity curve. The curve characteristic of attenuation or its absence provides an additional argument for the presence or absence of attenuation.

A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata

BackgroundPerfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between apicomplexans can be very high, in particular, due to the positive selection pressure on them. This complicates the identification of highly conserved elements in alveolates, which is overcome by the proposed algorithm.ResultsA novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed.ConclusionWe proposed an algorithm for the identification of highly conserved elements. The multitude of identified elements was used to infer the phylogeny of Alveolata.

Modeling RNA polymerase interaction in mitochondria of chordates.

BackgroundIn previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA secondary structures during transcription, including transcription initiation and termination. The model accurately reproduces changes of gene transcription level observed in polymerase sigma-subunit knockout and heat shock experiments in plant plastids. The corresponding computer program and a user guide are available at http://lab6.iitp.ru/en/rivals. Here we apply the model to the analysis of transcription and (partially) translation processes in the mitochondria of frog, rat and human. Notably, mitochondria possess only phage-type polymerases. We consider the entire mitochondrial genome so that our model allows RNA polymerases to complete more than one circle on the DNA strand.ResultsOur model of RNA polymerase interaction during transcription initiation and elongation accurately reproduces experimental data obtained for plastids. Moreover, it also reproduces evidence on bulk RNA concentrations and RNA half-lives in the mitochondria of frog, human with or without the MELAS mutation, and rat with normal (euthyroid) or hyposecretion of thyroid hormone (hypothyroid). The transcription characteristics predicted by the model include: (i) the fraction of polymerases terminating at a protein-dependent terminator in both directions (the terminator polarization), (ii) the binding intensities of the regulatory protein factor (mTERF) with the termination site and, (iii) the transcription initiation intensities (initiation frequencies) of all promoters in all five conditions (frog, healthy human, human with MELAS syndrome, healthy rat, and hypothyroid rat with aberrant mtDNA methylation). Using the model, absolute levels of all gene transcription can be inferred from an arbitrary array of the three transcription characteristics, whereas, for selected genes only relative RNA concentrations have been experimentally determined. Conversely, these characteristics and absolute transcription levels can be obtained using relative RNA concentrations and RNA half-lives known from various experimental studies. In this case, the “inverse problem” is solved with multi-objective optimization.ConclusionsIn this study, we demonstrate that our model accurately reproduces all relevant experimental data available for plant plastids, as well as the mitochondria of chordates. Using experimental data, the model is applied to estimate binding intensities of phage-type RNA polymerases to their promoters as well as predicting terminator characteristics, including polarization. In addition, one can predict characteristics of phage-type RNA polymerases and the transcription process that are difficult to measure directly, e.g., the association between the promoter’s nucleotide composition and the intensity of polymerase binding. To illustrate the application of our model in functional predictions, we propose a possible mechanism for MELAS syndrome development in human involving a decrease of Phe-tRNA, Val-tRNA and rRNA concentrations in the cell. In addition, we describe how changes in methylation patterns of the mTERF binding site and three promoters in hypothyroid rat correlate with changes in intensities of the mTERF binding and transcription initiations. Finally, we introduce an auxiliary model to describe the interaction between polysomal mRNA and ribonucleases.

Easily computable invariants for hypersurface recognition

A method is proposed for the short description of an algebraic hypersurface with the help of descriptors that depend on a small number of coefficients of the corresponding polynomial form and are invariant with respect to the orthogonal transformations of the enveloping space. These invariants, which can easily be computed even for high dimensionalities, allow to compare quickly the shapes of hypersurfaces in the general position and can be used as features in applied problems of object description and recognition as well as for the solution of combinatorial problems. The transformation of real multilinear cubic forms is specially considered.

Gene expression regulation of the PF00480 or PF14340 domain proteins suggests their involvement in sulfur metabolism

The paper studies proteins with domains PF00480 or PF14340, as well as some other poorly characterized proteins, encoded by genes associated with leader peptide genes containing a tract of cysteine codons. Such proteins are hypothetically regulated with cysteine-dependent transcription attenuation, namely the Rho-dependent or classic transcription attenuation. Cysteine is an important structural amino acid in various proteins and is required for synthesis of many sulfur-containing compounds, such as methionine, thiamine, glutathione, taurine and the lipoic acid. Earlier a few species of mycobacteria were predicted by the authors to have cysteine-dependent regulation of operons containing the cysK gene. In Escherichia coli this regulation is absent, and the same operon is regulated by the CysB transcription activator. The paper also studies Rho-dependent and classic transcription regulations in all annotated genes of mycobacteria available in GenBank and their orthologs in Actinomycetales. We predict regulations for many genes involved in sulfur metabolism and transport of sulfur-containing compounds; these regulations differ considerably among species. On the basis of predictions, we assign a putative role to proteins encoded by the regulated genes with unknown function, and also describe the structure of corresponding regulons, predict the lack of such regulations for many genes. Thus, all proteins with the uncharacterized Pfam domains PF14340 and PF00480, as well as some others, are predicted to be involved in sulfur metabolism. We also surmise the affinity of some transporters to sulfur-containing compounds. The obtained results considerably extend earlier large-scale studies of Rho-dependent and classic transcription attenuations.

Gibbs field approach for evolutionary analysis of regulatory signal of gene expression

We propose a new approach to modeling a nucleotide sequence evolution subject to constraints on the secondary structure. The approach is based on the problem of optimizing a functional that involves both standard evolution of the primary structure and a condition of secondary structure conservation. We discuss simulation results in the example of evolution in the case of classical attenuation regulation.

Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates

Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome.