Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast

Abstract

Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed to directly influence protein abundances. However, the correlation between RNA-Seq and proteomics data is in general quite limited owing to differences in protein stability and translational regulation. Here we perform RNA-Seq, ribosome profiling and proteomics analyses in baker’s yeast cells grown in rich media and oxidative stress conditions to examine gene expression regulation at various levels. With the exception of a small set of genes involved in the maintenance of the redox state, which are regulated at the transcriptional level, modulation of protein expression is largely driven by changes in the relative ribosome density across conditions. The majority of shifts in mRNA abundance are compensated by changes in the opposite direction in the number of translating ribosomes and are predicted to result in no net change at the protein level. We also identify a subset of mRNAs which is likely to undergo specific translational repression during stress and which includes cell cycle control genes. The study suggests that post-transcriptional buffering of gene expression may be more common than previously anticipated.

Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response inArabidopsis

“…This indicates that posttranscriptional regulation of RNA might be an important part of the stress response to aphid feeding. Indeed, posttranscriptional regulation of RNA metabolism is a known regulator of the stress response in eukaryotes (Blevins, Tavella et al, 2019, Harvey, Dezi et al, 2017, Jung, Park et al, 2013, Marondedze, Thomas et al, 2019. These mechanisms could buffer excessive TE transcription to avoid their activity and maintain genome stability during stressinduced transcriptional reprogramming (in our case, loss of 24 nt sRNAs).…”

Protein Biogenesis Demands of the Early Secretory Pathway in Komagataella Phaffii

“…Thus, by comparing the distribution of reads, we can answer our first question and identify which transcripts sequester ribosomes and ribosome-associated factors, like the sec translocon. As a method to predict the abundance of polypeptide chains, Ribo-seq has greater sensitivity than mass spectrometry, and more closely matches measurements of protein abundance than RNA-seq [60]. To answer our second question, the number of nascent polypeptide chains produced per unit time can be approximated using a modified form of the transcripts per million (TPM) metric used in RNA-seq.…”

Expanding Role of Ubiquitin in Translational Control

“…This range suggests that significant regulation occurs post-transcriptionally, including at the level of translation [12][13][14][15][16]. This is supported by the increased accuracy of newly developed ribosome profiling techniques such as Ribo-seq, which show that ribosome occupancy has a higher correlation range with protein abundance than mRNA levels [11,17,18]. As protein production is an energetically costly process [19] and is responsible for shaping proteome dynamics, regulation at the translational level is essential to ensure proper cellular function and health.…”

“…Due to advances in next generation sequencing, RNA-seq has become an efficient way to measure the transcriptome and is commonly used as an estimation for protein levels [7]. Despite its widespread implementation, recent studies suggest that only partial correlation exists between the transcriptome and proteome, ranging from a 0.4-0.7 correlation coefficient in yeast [8][9][10][11]. This range suggests that significant regulation occurs post-transcriptionally, including at the level of translation [12][13][14][15][16].…”