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

Abstract

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.

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

“…The observed stimulation of NEP-dependent transcription might be connected to the higher accumulation of RPOTp transcripts in white albostrians leaves (Emanuel et al, 2004). Additionally or alternatively, PEP, being the more abundant and active RNA polymerase in mature chloroplasts, might hinder the access of NEP to its promoters if they are located in close proximity to PEP promoters (Lyubetsky et al, 2011). We indeed observed many examples of NEP promoters in the neighborhood of PEP promoters.…”

Transcription Regulation of Plastid Genes Involved in Sulfate Transport in Viridiplantae

“…Relevant promoter sequences and the evolutionary impact of DNA point mutations on polymerase binding affinity are described in [15, 16]; experimental evidence was obtained using the psbA promoter of Sinapis alba [17]. …”

Modeling RNA polymerase interaction in mitochondria of chordates

“…G-quadruplex implicates DNA regions, but cross-hairpins typical for plastid [1] and bacterial genome DNA [28] are likely absent from the mitochondrial genomes of the animals under study.…”

“…Let us recall our model of interaction between RNA polymerases themselves, factors, and structures in DNA or RNA [1]. RNA polymerases can potentially attempt to bind with all promoters at a given locus.…”

“…In this work, we use the model developed and applied to study plant plastids [1] in the analysis of transcription in the mitochondria of chordates. The model is generally applicable to plastids and mitochondria, prokaryotes, and nuclear DNA.…”