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Series GSE171411 Query DataSets for GSE171411
Status Public on Apr 02, 2023
Title tRNA-seq of Arabidopsis leaves during pattern-triggered immunity
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary During pattern-triggered immunity (PTI), the first line of active defense against infection in plants, the translatome undergoes rapid reprogamming. To understand how defense proteins are selectively translated, we conducted a genetic screen for regulators of PTI using a translational reporter. We identified a mutant of RNA helicase 12 (RH12) showing compromised reporter translation and pathogen resistance. RH12 is a homolog of yeast DEAD-box Helicase Homolog 1, which targets mRNAs with low codon optimality for decay. Therefore, we sequenced the Arabidopsis tRNAome to determine codon optimality during PTI. We discovered a PTI-associated reduction in overall codon optimality of the transcriptome, and found that the decay of transcripts with reduced optimality is mediated by interaction with RH12. Our results demonstrate the first example of codon optimality-associated decay as part of an adaptive response in which the dynamics of both the tRNAome and the transcriptome facilitate rapid changes in translational output during PTI.
Overall design profiling of tRNA from 3 reps of mock and elf18 treated samples
Contributor(s) Zwack PJ, Dong X
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Submission date Apr 02, 2021
Last update date Apr 02, 2023
Contact name Paul Zwack
Organization name Duke University
Street address Campus Box 90338
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (6)
GSM5225006 Leaf_Mock_1
GSM5225007 Leaf_Mock_2
GSM5225008 Leaf_Mock_3
BioProject PRJNA719400
SRA SRP313272

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Supplementary file Size Download File type/resource
GSE171411_diff_expression.txt.gz 1.1 Kb (ftp)(http) TXT
GSE171411_normalized_counts.txt.gz 2.3 Kb (ftp)(http) TXT
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