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Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.

Adamo A, Pinney JW, Kunova A, Westhead DR, Meyer P - PLoS ONE (2008)

Bottom Line: We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A)-specific RNA probes, and that these transcript levels are significantly enhanced after heat treatment.We found that the affected transcripts were uncapped transcripts of mitochondrial origin, which were polyadenylated at multiple sites within their 3'region.As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.

View Article: PubMed Central - PubMed

Affiliation: Center for Plant Sciences, University of Leeds, Leeds, United Kingdom.

ABSTRACT

Background: Polyadenylation of RNA has a decisive influence on RNA stability. Depending on the organisms or subcellular compartment, it either enhances transcript stability or targets RNAs for degradation. In plant mitochondria, polyadenylation promotes RNA degradation, and polyadenylated mitochondrial transcripts are therefore widely considered to be rare and unstable. We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A)-specific RNA probes, and that these transcript levels are significantly enhanced after heat treatment.

Methodology/principal findings: As the Columbia genome contains a complete set of mitochondrial genes, we had to identify polymorphisms to differentiate between nuclear and mitochondrial copies of a mitochondrial transcript. We found that the affected transcripts were uncapped transcripts of mitochondrial origin, which were polyadenylated at multiple sites within their 3'region. Heat-induced enhancement of these transcripts was quickly restored during a short recovery period.

Conclusions/significance: Our results show that polyadenylated transcripts of mitochondrial origin are more stable than previously suggested, and that their steady-state levels can even be significantly enhanced under certain conditions. As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.

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Related in: MedlinePlus

Turnover rates of polyadenylated rpl2 transcripts are not significantly affected by heat treatment.When standardized to EF1α, rpl2 transcript levels remain stable 1, 2 and 4 hours after Cordycepin treatment of 10-day-old seedlings both at 24°C and 40°C. Transcript levels of the nuclear SMG gene were used as a positive control for the efficiency of Cordycepin treatment.
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pone-0002889-g005: Turnover rates of polyadenylated rpl2 transcripts are not significantly affected by heat treatment.When standardized to EF1α, rpl2 transcript levels remain stable 1, 2 and 4 hours after Cordycepin treatment of 10-day-old seedlings both at 24°C and 40°C. Transcript levels of the nuclear SMG gene were used as a positive control for the efficiency of Cordycepin treatment.

Mentions: To assess if the increased temperature affects the stability of polyadenylated rpl2 transcripts, their level was measured at 24°C and 40°C in the presence of 0.6mM cordycepin [12], which inhibits transcript synthesis. Transcript levels were normalised to EF1α. Since EF1α is also affected by the treatment, the calculations performed in this way actually show whether the turnover of the tested gene is faster or slower than the turnover of EF1α. Over a period of four hours, rpl2 transcript turnover rates were comparable to EF1α and no changes were detectable for the two temperature treatments with respect to rpl2 transcript turnover (Fig. 5), which suggests that heat treatment does not significantly alter the turnover rate of polyadenylated rpl2 transcripts.


Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.

Adamo A, Pinney JW, Kunova A, Westhead DR, Meyer P - PLoS ONE (2008)

Turnover rates of polyadenylated rpl2 transcripts are not significantly affected by heat treatment.When standardized to EF1α, rpl2 transcript levels remain stable 1, 2 and 4 hours after Cordycepin treatment of 10-day-old seedlings both at 24°C and 40°C. Transcript levels of the nuclear SMG gene were used as a positive control for the efficiency of Cordycepin treatment.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2483354&req=5

pone-0002889-g005: Turnover rates of polyadenylated rpl2 transcripts are not significantly affected by heat treatment.When standardized to EF1α, rpl2 transcript levels remain stable 1, 2 and 4 hours after Cordycepin treatment of 10-day-old seedlings both at 24°C and 40°C. Transcript levels of the nuclear SMG gene were used as a positive control for the efficiency of Cordycepin treatment.
Mentions: To assess if the increased temperature affects the stability of polyadenylated rpl2 transcripts, their level was measured at 24°C and 40°C in the presence of 0.6mM cordycepin [12], which inhibits transcript synthesis. Transcript levels were normalised to EF1α. Since EF1α is also affected by the treatment, the calculations performed in this way actually show whether the turnover of the tested gene is faster or slower than the turnover of EF1α. Over a period of four hours, rpl2 transcript turnover rates were comparable to EF1α and no changes were detectable for the two temperature treatments with respect to rpl2 transcript turnover (Fig. 5), which suggests that heat treatment does not significantly alter the turnover rate of polyadenylated rpl2 transcripts.

Bottom Line: We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A)-specific RNA probes, and that these transcript levels are significantly enhanced after heat treatment.We found that the affected transcripts were uncapped transcripts of mitochondrial origin, which were polyadenylated at multiple sites within their 3'region.As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.

View Article: PubMed Central - PubMed

Affiliation: Center for Plant Sciences, University of Leeds, Leeds, United Kingdom.

ABSTRACT

Background: Polyadenylation of RNA has a decisive influence on RNA stability. Depending on the organisms or subcellular compartment, it either enhances transcript stability or targets RNAs for degradation. In plant mitochondria, polyadenylation promotes RNA degradation, and polyadenylated mitochondrial transcripts are therefore widely considered to be rare and unstable. We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A)-specific RNA probes, and that these transcript levels are significantly enhanced after heat treatment.

Methodology/principal findings: As the Columbia genome contains a complete set of mitochondrial genes, we had to identify polymorphisms to differentiate between nuclear and mitochondrial copies of a mitochondrial transcript. We found that the affected transcripts were uncapped transcripts of mitochondrial origin, which were polyadenylated at multiple sites within their 3'region. Heat-induced enhancement of these transcripts was quickly restored during a short recovery period.

Conclusions/significance: Our results show that polyadenylated transcripts of mitochondrial origin are more stable than previously suggested, and that their steady-state levels can even be significantly enhanced under certain conditions. As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.

Show MeSH
Related in: MedlinePlus