DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs

Abstract

Gene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs.These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. These RHs function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty. XRN1/4 . These 5' and 3' pathways have substrate specificity, but are not mutually exclusive.When decapping-dependent decay is compromised in Arabidopsis, the 3'-to-5' exoribonuclease SOV can compensate to control mRNA abundance and homeostasis 10,11 . Spatiotemporal regulation of mRNA decay is critical for the cellular transcriptome adjustment in response to both developmental and environmental cues in plants 1 . Dysfunction in decapping due to loss-of-function of non-redundant components results in post-embryonic lethality (DCP1, DCP2, VCS, and DCP5) or severe growth alterations (LSM1 and PAT1) [12][13][14][15][16] .The cause of the developmental defects in some decapping mutants is associated with disruption of mRNA quality control and small interfering (si)RNA production 17 . However, there is limited knowledge of the role of the decay machinery in the spatial and temporal turnover of specific mRNAs and the connections between turnover and mRNA translation and mobilization to PBs and SGs. Mutations in the mRNA decay machinery have been identified in genetic screens for altered sensitivity to biotic and abiotic stresses 16,[18][19][20][21][22][23][24] , yet there is poor understanding of the importance of mRNA decay in restricting accumulation of mRNAs that provide stress resilience but constrain growth.The DHH1/DDX6 family of DEAD-box RNA helicases is conserved across eukaryotes 25 .These proteins function at the nexus between mRNA translation, storage and decay, mediating translational repression and initiating mRNA degradation [26][27][28][29][30][31][32][33] . For example, yeast DHH1 can activate mRNA decapping 34 , promote translational repression 35 , and associate with ribosomes to sense the codon-dependent rate of translational elongation to trigger cotranslational decay 36 . However, the transcript-specific role of these helicases is generally understudied. Here we identify the Arabidopsis DHH1/DDX6-like proteins RNA HELICASE 6 (RH6), RH8, and RH12 as additive and functionally redundant mRNA decay factors required for growth and development.Severe deficiency of RH6, RH8 and RH12 function impairs PB and SG formation, and shifts the transcriptome and translatome homeostasis so that defense-and other stress-responsive mRNAs accumulate despite when grown under standar...

Dynamics and Functions of Stress Granules and Processing Bodies in Plants

“…Under normal conditions, these RHs function to keep the stress- and immunity-related mRNAs at basal levels so that the plant cells can allocate resources to mRNAs for growth and development ( Figure 3 ). Consistent with this notion, the Arabidopsis rh6812 triple mutant exhibited constitutive innate immunity at the expense of growth and development [ 48 ]. Of note, although the assemblies of both p-bodies and SGs were defective in the Arabidopsis rh6812 triple mutant [ 48 ] ( Figure 3 ), the decay of VCS-dependent mRNAs was largely unaffected [ 48 ], so mRNA decay may occur co-translationally or in p-bodies of sizes undetectable by current microscopy technology.…”

“…A recent report integrating sophisticated transcriptome and translatome analyses showed that an Arabidopsis mutant defective in DEAD-box RNA helicase 6 (RH6), RH8, and RH12 showed preferential accumulation and translation of stress- and defense-related mRNAs [ 48 ]. RHs are part of the decapping-dependent 5′ to 3′ mRNA decay machinery and were found to co-localize with both p-body and SG markers [ 48 ]. Under normal conditions, these RHs function to keep the stress- and immunity-related mRNAs at basal levels so that the plant cells can allocate resources to mRNAs for growth and development ( Figure 3 ).…”

“… The dynamics and functions of p-bodies and SGs are regulated by RNA helicases. The numbers of p-bodies (marked by DCP2 or VCS) and SGs (marked by UBP1C) increased in response to coverslip-induced hypoxia in Arabidopsis root epidermal cells, a process requiring specific RNA helicases (RHs) [ 48 ]. Note the reduction of cytoplasmic granules in rh6812 triple mutant under coverslip-induced hypoxia.…”

DEAD-box helicases modulate dicing body formation in Arabidopsis

“…A very recent study showed that RH6, RH8, and RH12 associate with and contribute to the formation of P-bodies and SGs to limit overaccumulation and translation of stress-responsive mRNAs, and malfunction of these helicases leads to a constitutive immune response in plants ( 41 ). It would be interesting to determine the dynamics of P-bodies and SGs upon the infections of TuMV.…”

Cauliflower Mosaic Virus Utilizes Processing Bodies to Escape Translational Repression in Arabidopsis

“…This establishes PBs as pro- viral components in CaMV infection, similarly as observed for other plant viruses (Zhang et al ., 2020; Hafrén et al ., 2015; Ye et al ., 2015). However, as PBs were found to limit viral infections in other contexts (Ng et al ., 2020; Li & Wang, 2018), it appears that viruses have evolved individually to cope with the PB associated functions that also serve in general plant innate immunity (Chantarachot et al ., 2020). An intriguing question is how PB proteins are recruited to VFs, and the exclusion of DCP1 suggests specificity to the process.…”