The life and death of RNA across temperatures

Becskei, Attila; Rahaman, Sayanur

doi:10.1016/j.csbj.2022.08.008

Cited by 28 publications

(19 citation statements)

References 149 publications

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“…A signal, which corresponds to a 5-C sugar, was identified by METABOLON as “pentose acid”. The DNA and RNA nucleic acids hydrolysis can yield a pentose, whereby RNA is more susceptible to hydrolysis [ 26 ]. The pentose acid ideally describes the curve of winter rest, of the different dormancy phases, respectively, of the sweet cherry cv.…”

Section: Resultsmentioning

confidence: 99%

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Metabolites That Confirm Induction and Release of Dormancy Phases in Sweet Cherry Buds

Götz

Chmielewski

2023

Metabolites

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Here we report on metabolites found in a targeted profiling of ‘Summit’ flower buds for nine years, which could be indicators for the timing of endodormancy release (t1) and beginning of ontogenetic development (t1*). Investigated metabolites included chrysin, arabonic acid, pentose acid, sucrose, abscisic acid (ABA), and abscisic acid glucose ester (ABA-GE). Chrysin and water content showed an almost parallel course between leaf fall and t1*. After ‘swollen bud’, water content raised from ~60 to ~80% at open cluster, while chrysin content decreased and lost its function as an acetylcholinesterase inhibitor. Both parameters can be suitable indicators for t1*. Arabonic acid showed a clear increase after t1*. Pentose acid would be a suitable metabolite to identify t1 and t1*, but would not allow describing the ecodormancy phase, because of its continuously low value during this time. Sucrose reached a maximum during ecodormancy and showed a significant correlation with air temperature, which confirms its cryoprotective role in this phase. The ABA content showed maximum values during endodormancy and decreased during ecodormancy, reaching 50% of its content t1 at t1*. It appears to be the key metabolite to define the ecodormancy phase. The ABA-GE was present at all stages and phases and was much higher than the ABA content and is a readily available storage pool in cherry buds.

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Section: Resultsmentioning

confidence: 99%

“…The RNA contains mostly hydrogen bonds, which are sensitive to changes in ambient temperature. The RNA is prone to hydrolysis at high temperatures and the appearance of stable RNA structures under cold environmental conditions may reduce reaction rates [ 26 ], shown as minimum pentose acid content during ecodormancy.…”

Section: Resultsmentioning

confidence: 99%

Metabolites That Confirm Induction and Release of Dormancy Phases in Sweet Cherry Buds

Götz

Chmielewski

2023

Metabolites

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“…This difference can be explained by the presence of a highly reactive 2′-hydroxyl group in the RNA ribose unit, which makes RNA more susceptible to hydrolysis than DNA. 8 Studies based on agarose gel electrophoresis demonstrated that RNA is degraded at 95°C for 10 min 13 and DNA at 100–110°C for 5 min. 28 Thus, the nature of RNA and its thermolability are consistent with the low detection rates of viral RNA versus the higher resistance of DNA to heat and the higher detection rates of DNA under identical conditions.…”

Section: Discussionmentioning

confidence: 99%

Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids

et al. 2023

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Based on publications reporting improvements in real-time PCR (rtPCR) performance, we compared protocols based on heat treatment or dilution followed by direct rtPCR to standard extraction and amplification methods for the detection of porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), porcine epidemic diarrhea virus (PEDV), or Mycoplasma hyopneumoniae (MHP) in swine oral fluids (OFs). In part A, we subjected aliquots of positive OF samples to 1 of 4 protocols: protocol 1: heat (95°C × 30 min) followed by direct rtPCR; protocol 2: heat and cool (25°C × 20 min) followed by direct rtPCR; protocol 3: heat, cool, extraction, and rtPCR; protocol 4 (control): extraction and then rtPCR. In part B, positive OF samples were split into 3, diluted (D1 = 1:2 with Tris–borate–EDTA (TBE); D2 = 1:2 with negative OF; D3 = not diluted), and then tested by rtPCR using the best-performing protocol from part A (protocol 4). In part A, with occasional exceptions, heat treatment resulted in marked reduction in the detection of target and internal sample control (ISC) nucleic acids. In part B, sample dilution with TBE or OF produced no improvement in the detection of targets and ISCs. Thus, standard extraction and amplification methods provided superior detection of PRRSV, IAV, PEDV, and MHP nucleic acids in OFs.

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“…Clearly, heat shock induces major effects on information processing, although it can be anticipated that this is not only the result of regulation taking place, but also of RNA and protein denaturation caused by a lack of thermostability and of changes in the synthesis and degradation rates (48), both of which are enzymatically catalyzed and thus inherently dependent on temperature. The use of a pulse-labeling approach enabled us to visualize RNA and protein neosynthesis and to demonstrate that global transcription and translation activity decreases in response to heat shock, albeit with different response dynamics.…”

Section: Discussionmentioning

confidence: 99%

“…In this work, we reveal that a temperature increase above the optimal growth temperature causes large changes in differential abundance in transcripts and proteins in S. acidocaldarius , with a fast and immediate response on the RNA level and a less pronounced and slower response on the protein level. Clearly, heat shock induces major effects on information processing, although it can be anticipated that this is not only the result of regulation taking place, but also of RNA and protein denaturation caused by a lack of thermostability and of changes in the synthesis and degradation rates (48), both of which are enzymatically catalyzed and thus inherently dependent on temperature. The use of a pulse-labeling approach enabled us to visualize RNA and protein neosynthesis and to demonstrate that global transcription and translation activity decreases in response to heat shock, albeit with different response dynamics.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional and translational dynamics underlying heat shock response in the thermophilic CrenarchaeonSulfolobus acidocaldarius

Baes

Grünberger

Ruys

et al. 2022

Preprint

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High-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. In this work, we set out to study heat shock response in the thermoacidophilic model crenarchaeonSulfolobus acidocaldarius, which thrives in volcanic hot springs and has an optimal growth temperature of 75°C. Pulse-labeling experiments demonstrated that a temperature shift to 86°C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and TMT-labeled mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by the more subtle reprogramming of the protein landscape. A limited correlation was observed in differential expression on the RNA and protein level, suggesting that there is a prevalence of post-transcriptional and post-translational regulation upon heat shock. Furthermore, based on the finding that promoter regions of heat shock regulon genes lack a conserved DNA-binding motif, we propose that heat-shock responsive transcription regulation is likely not to be accomplished by a classical transcription factor. Instead, in contrast to histone-harboring Euryarchaeota that have heat-shock transcription factors, it is hypothesized that Sulfolobales and other histone-lacking thermophilic archaea employ an evolutionary ancient mechanism relying on temperature-responsive changes in DNA organization and compaction, induced by the action of nucleoid-associated proteins.

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The life and death of RNA across temperatures

Cited by 28 publications

References 149 publications

Metabolites That Confirm Induction and Release of Dormancy Phases in Sweet Cherry Buds

Metabolites That Confirm Induction and Release of Dormancy Phases in Sweet Cherry Buds

Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids

Transcriptional and translational dynamics underlying heat shock response in the thermophilic CrenarchaeonSulfolobus acidocaldarius

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