A. V. Seliverstov

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).

Plastid-encoded protein families specific for narrow taxonomic groups of algae and protozoa

Protein clustering is useful for refining protein annotations and searching for proteins by their phylogenetic profile. We have performed the clustering of proteins encoded in the plastoms of Rhodophyta, as well as other plastid-containing species related to the Rhodophyta branch. The corresponding database and cluster search according to protein phylogenetic profile are available at http://lab6.iitp.ru/ppc/redline. Plastome-encoded proteins specific for small taxonomic groups of algae and protozoa have been found based on this database, and the search for and analysis of RNA polymerase in the nuclear genomes of Apicomplexa has been performed.

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.

Analysis of the 5′-leader regions of several plastid genes in protozoa of the phylum apicomplexa and red algae

Apicomplexan parasites contain so-called apicoplasts, which are similar to chloroplasts of red algae. Multiple alignments of the 5′-leader regions of plastid-encoded genes revealed several conserved noncoding regions in parasites as well as in red algae. The regions were assumed to be sites for RNA interactions with regulatory proteins. Conserved sites were found upstream of ycf24, which is required for [Fe-S] cluster development, and several other genes. In particular, a simultaneous regulation was predicted for ycf24, rps4, and rpo B in Toxoplasma gondii. The prediction agreed with the known data that apicoplasts are only required for a short time, but confer pathogenicity on T. gondii. Another site was predicted upstream of rpo B, which encodes the β subunit of RNA polymerase, in red algae Porphyra spp. and parasites Eimeria tenella and Theileria parva.

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.

Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch

A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed.

Geometric relationship between parallel hyperplanes, quadrics, and vertices of a hypercube

In a space of dimension 30 we find a pair of parallel hyperplanes, uniquely determined by vertices of a unit cube lying on them, such that strictly between the hyperplanes there are no vertices of the cube, though there are integer points. A similar two-sided example is constructed in dimension 37. We consider possible locations of empty quadrics with respect to vertices of the cube, which is a particular case of a discrete optimization problem for a quadratic polynomial on the set of vertices of the cube. We demonstrate existence of a large number of pairs of parallel hyperplanes such that each pair contains a large number of points of a prescribed set.

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.

Attenuation regulation of the amino acid and aminoacyl-tRNA biosynthesis operons in bacteria: A comparative genomic analysis

A large-scale search for attenuation regulation in bacteria was performed using two original computer programs, which modeled the attenuation regulation and multiple alignment along a phylogenetic tree. The programs are available at http://lab6.iitp.ru. Candidate attenuations were predicted for many organisms belonging to α-, ß-, γ-, and δ-proteobacteria, Actinobacteria, Bact eroidetes/Chlorobi, Firmicutes, and Thermotoga; in Cloroflexi, the corresponding sites were found upstream of hisG, hisZ, hisS, pheA, pheST, trpEG, trpA, trpB, trpE, trpS, thrA, thrS, leuA, leuS, ilvB, ilvI, ilvA, ilvC, ilvD, and ilvG. Searches were conducted across all bacterial genomes contained in GenBank, NCBI. Other bacterial taxa were not predicted to have attenuation. It was possible to assume, in some cases, that RNA triplexes play a substantial role in the formation of an active antiterminator and terminator or pseudoknots during termination. The attenuation regulation of Lactobacillus lactis lysQ was assumed to depend on the histidyl-tRNA concentration. Several types of attenuation regulation and the evolution of attenuation are discussed.

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.