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

Lyubetsky VA, Zverkov OA, Rubanov LI, Seliverstov AV - Biol. Direct (2011)

Bottom Line: Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics.The source code written in C++ is available under the GNU General Public License from the laboratory website.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Bolshoy Karetny per,, Moscow, Russia. lyubetsk@iitp.ru

ABSTRACT

Background: Modeling 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.

Results: A 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.

Conclusions: The 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.

Show MeSH

Related in: MedlinePlus

Examples of loci. (a) Locus 1 from Arabidopsis, (b) Locus 2 from Hordeum, (c) Locus 3 from Arabidopsis. PEP-promoters are designated with P, NEP-promoters - with N; T1 and T2 are predicted terminators. Positions of transcription initiation sites are given relative to start codons of the corresponding genes. DNA strand containing the promoter and the gene is marked with arrow and color, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3038987&req=5

Figure 1: Examples of loci. (a) Locus 1 from Arabidopsis, (b) Locus 2 from Hordeum, (c) Locus 3 from Arabidopsis. PEP-promoters are designated with P, NEP-promoters - with N; T1 and T2 are predicted terminators. Positions of transcription initiation sites are given relative to start codons of the corresponding genes. DNA strand containing the promoter and the gene is marked with arrow and color, respectively.

Mentions: Besides σ-subunit knockout and heat shock studies, modeling explains chromatogram data [8], however, with less accuracy. Chromatograms can be used to compare levels of the gene transcription from different promoters or before and after the knockout of phage type RNA polymerase. A lower accuracy is related to a poorer resolution of blotting methods, limited (a max. of two in [8]) assay replicates and ambiguous quantitative interpretation of chromatograms. For example, our analyses of chromatogram data in Figure 5c (see [8]) show that different promoters produce different transcription levels of gene ycf1 (ref. Figure 1c): RpoTp-dependent ycf1-39 is more effective compared to RpoTmp-dependent promoter ycf1-104, and is twice as effective as PEP-dependent ycf1-34/33. This data is in good agreement with the model prediction. Under RpoTp knockout (when promoter ycf1-39 is not functioning) the transcription level from ycf1-104 adheres to the same level, and from ycf1-34/33 it rather increases. We do not discuss the RpoTp knockout in this publication.


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

Lyubetsky VA, Zverkov OA, Rubanov LI, Seliverstov AV - Biol. Direct (2011)

Examples of loci. (a) Locus 1 from Arabidopsis, (b) Locus 2 from Hordeum, (c) Locus 3 from Arabidopsis. PEP-promoters are designated with P, NEP-promoters - with N; T1 and T2 are predicted terminators. Positions of transcription initiation sites are given relative to start codons of the corresponding genes. DNA strand containing the promoter and the gene is marked with arrow and color, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3038987&req=5

Figure 1: Examples of loci. (a) Locus 1 from Arabidopsis, (b) Locus 2 from Hordeum, (c) Locus 3 from Arabidopsis. PEP-promoters are designated with P, NEP-promoters - with N; T1 and T2 are predicted terminators. Positions of transcription initiation sites are given relative to start codons of the corresponding genes. DNA strand containing the promoter and the gene is marked with arrow and color, respectively.
Mentions: Besides σ-subunit knockout and heat shock studies, modeling explains chromatogram data [8], however, with less accuracy. Chromatograms can be used to compare levels of the gene transcription from different promoters or before and after the knockout of phage type RNA polymerase. A lower accuracy is related to a poorer resolution of blotting methods, limited (a max. of two in [8]) assay replicates and ambiguous quantitative interpretation of chromatograms. For example, our analyses of chromatogram data in Figure 5c (see [8]) show that different promoters produce different transcription levels of gene ycf1 (ref. Figure 1c): RpoTp-dependent ycf1-39 is more effective compared to RpoTmp-dependent promoter ycf1-104, and is twice as effective as PEP-dependent ycf1-34/33. This data is in good agreement with the model prediction. Under RpoTp knockout (when promoter ycf1-39 is not functioning) the transcription level from ycf1-104 adheres to the same level, and from ycf1-34/33 it rather increases. We do not discuss the RpoTp knockout in this publication.

Bottom Line: Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics.The source code written in C++ is available under the GNU General Public License from the laboratory website.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Bolshoy Karetny per,, Moscow, Russia. lyubetsk@iitp.ru

ABSTRACT

Background: Modeling 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.

Results: A 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus