Changes in the transcriptional activity of barley plastome genes under heat shock

Zubo, Ya. O.; Lysenko, E. A.; Aleinikova, A. Yu.; Kusnetsov, V. V.; Pshibytko, N. L.

doi:10.1134/s1021443708030011

Cited by 12 publications

(8 citation statements)

References 24 publications

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“…4). Zubo et al (2008a) found a significantly reduced expression of several genes in barley chloroplasts in response to heat stress. Moreover, when applied to detached leaves, ABA (Yamburenko et al, unpublished data) and methyl jasmonate (Zubo et al, 2011), hormones known to be involved in the response of plants to abiotic and biotic stresses, drastically inhibited the transcription of plastid genes (Fig.…”

Section: Exogenous and Endogenous Factors Affecting Plastid Transcripmentioning

confidence: 97%

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Liere

Weihe

Börner

2011

Journal of Plant Physiology

202

174

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Section: Exogenous and Endogenous Factors Affecting Plastid Transcripmentioning

confidence: 97%

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Liere

Weihe

Börner

2011

Journal of Plant Physiology

202

174

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“…In heat shock experiments the estimates of the averaged HT/WT ratio and its dispersion (HT is the transcription level after heat shock, WT is that in the wild type) are formally similar with σ-subunit knockout studies. Response to heat shock is essentially different in native and isolated chloroplasts, as experimentally shown in [6]. The ratio of transcription level in shocked vs. intact isolated chloroplasts was assessed in [6] for several genes.…”

Section: Introductionmentioning

confidence: 99%

“…Response to heat shock is essentially different in native and isolated chloroplasts, as experimentally shown in [6]. The ratio of transcription level in shocked vs. intact isolated chloroplasts was assessed in [6] for several genes. In isolated chloroplasts gene transcription levels depend mainly on the polymerase elongation rate and the promoters' binding intensities, which reduces the effect of the nucleus to changes in σ-subunit concentrations.…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, averaged ratios MT/WT of transcription level in mutant (MT) to that in the wild type (WT) and their dispersions in experimental assays were estimated for the cases of sig4- knockout [ 4 ] and sig3- knockout [ 5 ]. Analogous are heat shock and phytohormons level variation studies [ 6 , 7 ]. In heat shock experiments the estimates of the averaged HT/WT ratio and its dispersion (HT is the transcription level after heat shock, WT is that in the wild type) are formally similar with σ-subunit knockout studies.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2011

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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.

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“…halving) and +100% (i.e. doubling) are considered “insignificant” [33]. By this measure, almost all model predictions differ insignificantly from experimental data (Table 4, Table 5, Table 7).…”

Section: Methodsmentioning

confidence: 99%

Modeling RNA polymerase interaction in mitochondria of chordates

et al. 2012

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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 sy...

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Changes in the transcriptional activity of barley plastome genes under heat shock

Cited by 12 publications

References 24 publications

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

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

Modeling RNA polymerase interaction in mitochondria of chordates

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