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| Status |
Public on Dec 14, 2024 |
| Title |
Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly onto the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Furthermore, pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces.
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| Overall design |
smallRNAseq and RNAseq profiling the RNA content of apoplastic washing fluid and leaf surface wash of Arabidopsis plants.
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| Contributor(s) |
Baldrich P, Borniego L, Singla-Rastogi M, McGregor M, Sampangi-Ramaiah M, Innes R, Meyers B |
| Citation(s) |
39752527 |
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| Submission date |
Dec 10, 2024 |
| Last update date |
Feb 14, 2025 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
pbaldrich@ucdavis.edu
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| Organization name |
University of California - Davis
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| Department |
Genome Center
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| Lab |
Meyers Lab
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| Street address |
451 Health Sciences Dr., Davis, CA 95616
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (1) |
| GPL30821 |
NextSeq 2000 (Arabidopsis thaliana) |
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| Samples (21)
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| GSM8675203 |
small RNA seq, Apoplastic washing fluid, replicate 1 |
| GSM8675204 |
small RNA seq, Apoplastic washing fluid, replicate 2 |
| GSM8675205 |
small RNA seq, Apoplastic washing fluid, replicate 3 |
| GSM8675206 |
small RNA seq, Cell lysate, replicate 1 |
| GSM8675207 |
small RNA seq, Cell lysate, replicate 2 |
| GSM8675208 |
small RNA seq, Cell lysate, replicate 3 |
| GSM8675209 |
small RNA seq, Leaf surface wash, replicate 1 |
| GSM8675210 |
small RNA seq, Leaf surface wash, replicate 2 |
| GSM8675211 |
small RNA seq, Leaf surface wash, replicate 3 |
| GSM8675212 |
RNA seq, Apoplastic washing fluid, replicate 1 |
| GSM8675213 |
RNA seq, Apoplastic washing fluid, replicate 2 |
| GSM8675214 |
RNA seq, Apoplastic washing fluid, replicate 3 |
| GSM8675215 |
RNA seq, Cell lysate, ribodepleted, replicate 1 |
| GSM8675216 |
RNA seq, Cell lysate, ribodepleted, replicate 2 |
| GSM8675217 |
RNA seq, Cell lysate, ribodepleted, replicate 3 |
| GSM8675218 |
RNA seq, Cell lysate, not ribodepleted, replicate 1 |
| GSM8675219 |
RNA seq, Cell lysate, not ribodepleted, replicate 2 |
| GSM8675220 |
RNA seq, Cell lysate, not ribodepleted, replicate 3 |
| GSM8675221 |
RNA seq, Leaf surface wash, replicate 1 |
| GSM8675222 |
RNA seq, Leaf surface wash, replicate 2 |
| GSM8675223 |
RNA seq, Leaf surface wash, replicate 3 |
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| Relations |
| BioProject |
PRJNA1196442 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE283977_RAW.tar |
36.0 Mb |
(http)(custom) |
TAR (of GTF, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
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