Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

Degradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs show that cis and trans factors control mRNA degradation rates. However, transcriptome-wide studies have failed to identify global relationships between transcript properties and mRNA degradation. We investigated the contribution of cis and trans factors to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are associated with mRNA degradation rates and that a model incorporating these factors explains ~50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, abundance, ribosome density, codon adaptation index (CAI) and GC content of the third position in codons. To validate these factors we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the translational start site of the GAP1 transcript increases its degradation rate. Using variants of GFP that differ at synonymous sites, we show that increased GC content of the third position of codons results in decreased mRNA degradation rate. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts related to protein translation rather than specific regulatory mechanisms.

Download Full-text

Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant

Molecular and Cellular Biology ◽

10.1128/mcb.18.9.5062 ◽

1998 ◽

Vol 18 (9) ◽

pp. 5062-5072 ◽

Cited By ~ 82

Author(s):

Ronald Boeck ◽

Bruno Lapeyre ◽

Christine E. Brown ◽

Alan B. Sachs

Keyword(s):

Saccharomyces Cerevisiae ◽

Family Member ◽

Gene Deletion ◽

Binding Protein ◽

Mrna Degradation ◽

Protein Family ◽

Suppressor Mutation ◽

Mrna Decapping ◽

Mrna Species ◽

Degradation Intermediates

ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

Download Full-text

Inhibition of 5' to 3' mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16

RNA ◽

10.1261/rna.5183804 ◽

2004 ◽

Vol 10 (3) ◽

pp. 458-468 ◽

Cited By ~ 13

Author(s):

L. BENARD

Keyword(s):

Saccharomyces Cerevisiae ◽

Mrna Degradation ◽

Stress Conditions

Download Full-text

Global analysis of gene expression dynamics identifies factors required for accelerated mRNA degradation

10.1101/254920 ◽

2018 ◽

Author(s):

Darach Miller ◽

Nathan Brandt ◽

David Gresham

Keyword(s):

Single Molecule ◽

Translational Control ◽

Environmental Changes ◽

Global Analysis ◽

Mrna Degradation ◽

Branched Dna ◽

Degradation Rates ◽

Gene Expression Dynamics ◽

Mrna Destabilization ◽

Barcode Sequencing

AbstractCellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeastSaccharomyces cerevisiaeduring a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen using the pooled deletion collection library fortransfactors that mediate rapidGAP1mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify that the Lsm1-7p/Pat1p complex and general mRNA decay machinery are important forGAP1mRNA clearance. We also find that the decapping modulatorSCD6,translation factor eIF4G2, and the 5’ UTR ofGAP1are important for this repression, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.

Download Full-text

Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin

10.1101/2021.04.24.441238 ◽

2021 ◽

Author(s):

Lina Hamouche ◽

Leonora Poljak ◽

Agamemnon J. Carpousis

Keyword(s):

16S Rrna ◽

Rna Polymerase ◽

Growth Conditions ◽

Rna Degradation ◽

Mrna Degradation ◽

Rnase E ◽

Rifampicin Treatment ◽

Bacterial Rna ◽

Degradation Rates ◽

Rrna Degradation

AbstractRifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment of Escherichia coli results in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete thus permitting the re-initiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.

Download Full-text

Upf1p, Nmd2p, and Upf3p Regulate the Decapping and Exonucleolytic Degradation of both Nonsense-Containing mRNAs and Wild-Type mRNAs

Molecular and Cellular Biology ◽

10.1128/mcb.21.5.1515-1530.2001 ◽

2001 ◽

Vol 21 (5) ◽

pp. 1515-1530 ◽

Cited By ~ 52

Author(s):

Feng He ◽

Allan Jacobson

Keyword(s):

Saccharomyces Cerevisiae ◽

Mrna Decay ◽

Translation Termination ◽

Mrna Degradation ◽

Wild Type ◽

Rapid Degradation ◽

Yeast Strains ◽

Nonsense Mediated Mrna Decay ◽

Exonucleolytic Degradation ◽

Decapping Enzyme

ABSTRACT In Saccharomyces cerevisiae, rapid degradation of nonsense-containing mRNAs requires the decapping enzyme Dcp1p, the 5′-to-3′ exoribonuclease Xrn1p, and the three nonsense-mediated mRNA decay (NMD) factors, Upf1p, Nmd2p, and Upf3p. To identify specific functions for the NMD factors, we analyzed the mRNA decay phenotypes of yeast strains containing deletions of DCP1 orXRN1 and UPF1, NMD2, or UPF3. Our results indicate that Upf1p, Nmd2p, and Upf3p regulate decapping and exonucleolytic degradation of nonsense-containing mRNAs. In addition, we show that these factors also regulate the same processes in the degradation of wild-type mRNAs. The participation of the NMD factors in general mRNA degradation suggests that they may regulate an aspect of translation termination common to all transcripts.

Download Full-text

Degradation of Normal mRNA in the Nucleus of Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.23.16.5502-5515.2003 ◽

2003 ◽

Vol 23 (16) ◽

pp. 5502-5515 ◽

Cited By ~ 86

Author(s):

Biswadip Das ◽

J. Scott Butler ◽

Fred Sherman

Keyword(s):

Saccharomyces Cerevisiae ◽

In Situ Hybridization ◽

Mrna Degradation ◽

Northern Blotting ◽

Mrna Turnover ◽

Restrictive Temperature ◽

Turnover Rates ◽

Rapid Degradation ◽

Cap Binding Complex

ABSTRACT A nuclear mRNA degradation (DRN) system was identified from analysis of mRNA turnover rates in nup116-Δ strains of Saccharomyces cerevisiae lacking the ability to export all RNAs, including poly(A) mRNAs, at the restrictive temperature. Northern blotting, in situ hybridization, and blocking transcription with thiolutin in nup116-Δ strains revealed a rapid degradation of mRNAs in the nucleus that was suppressed by the rrp6-Δ, rai1-Δ, and cbc1-Δ deletions, but not by the upf1-Δ deletion, suggesting that DRN requires Rrp6p, a 3′-to-5′ nuclear exonuclease, the Rat1p, a 5′-to-3′ nuclear exonuclease, and Cbc1p, a component of CBC, the nuclear cap binding complex, which may direct the mRNAs to the site of degradation. We propose that certain normal mRNAs retained in the nucleus are degraded by the DRN system, similar to degradation of transcripts with 3′ end formation defects in certain mutants.

Download Full-text

Analysis of Stored mRNA Degradation in Acceleratedly Aged Seeds of Wheat and Canola in Comparison to Arabidopsis

Plants ◽

10.3390/plants9121707 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1707

Author(s):

Liang Zhao ◽

Hong Wang ◽

Yong-Bi Fu

Keyword(s):

Aging Time ◽

Fragment Size ◽

Mrna Degradation ◽

Recent Analysis ◽

Seed Aging ◽

Degradation Rates ◽

Stable Conditions ◽

Stored Mrna ◽

Aging Conditions ◽

Aged Seeds

Seed aging has become a topic of renewed interest but its mechanism remains poorly understood. Our recent analysis of stored mRNA degradation in aged Arabidopsis seeds found that the stored mRNA degradation rates (estimated as the frequency of breakdown per nucleotide per day or β value) were constant over aging time under stable conditions. However, little is known about the generality of this finding to other plant species. We expanded the analysis to aged seeds of wheat (Triticum aestivum) and canola (Brassica napus). It was found that wheat and canola seeds required much longer periods than Arabidopsis seeds to lose seed germination ability completely under the same aging conditions. As what had been observed for Arabidopsis, stored mRNA degradation (∆Ct value in qPCR) in wheat and canola seeds correlated linearly and tightly with seed aging time or mRNA fragment size, while the quality of total RNA showed little change during seed aging. The generated β values reflecting the rate of stored mRNA degradation in wheat or canola seeds were similar for different stored mRNAs assayed and constant over seed aging time. The overall β values for aged seeds of wheat and canola showed non-significant differences from that of Arabidopsis when aged under the same conditions. These results are significant, allowing for better understanding of controlled seed aging for different species at the molecular level and for exploring the potential of stored mRNAs as seed aging biomarkers.

Download Full-text