SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

Abstract

<jats:title>Abstract</jats:title> <jats:p>SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.</jats:p>

Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes

“…While Arabidopsis MTR4 is mostly involved in rRNA processing/degradation, its paralog HEN2 targets predominantly non-rRNAs for degradation by nuclear exosome complexes ( Figure 5 ; Lange et al, 2014 ; Kindgren et al, 2018 , 2020 ; Bajczyk et al, 2020 ; Gao et al, 2020 ; Thieffry et al, 2020 ; Thomas et al, 2020 ). HEN2 substrates include long noncoding RNAs (lncRNAs), precursors and processing intermediates of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), and primary microRNAs (miRNAs), as well as by-products produced by miRNA processing.…”

“…HEN2 substrates include long noncoding RNAs (lncRNAs), precursors and processing intermediates of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), and primary microRNAs (miRNAs), as well as by-products produced by miRNA processing. Importantly, loss of HEN2 or the downregulation of Exo9 core subunits does not affect the steady-state levels of mature snoRNAs, snRNAs, or miRNAs and therefore, HEN2 and the exosome are not required for their production ( Chekanova et al, 2007 ; Lange et al, 2014 ; Bajczyk et al, 2020 ; Gao et al, 2020 ).…”

“…Other short-living antisense transcripts degraded by the RNA exosome initiate within 5′-regions of protein-coding genes (convergent antisense [CAS]) or within 3′-untranslated regions (poly(A)-site antisense [PAS]) ( Kindgren et al, 2020 ; Thieffry et al, 2020 ). In addition, hen2 mutants accumulate transcripts with 3′-extensions downstream of the annotated cleavage and polyadenylation sites that correspond to 3′-read-through transcripts ( Lange et al, 2014 ; Bajczyk et al, 2020 ; Parker et al, 2020 ). Finally, HEN2 promotes the degradation of unspliced, mis-spliced, or inefficiently spliced mRNAs ( Lange et al, 2014 ; Hématy et al, 2016 ).…”

“…Arabidopsis NEXT complexes contain HEN2, RBM7, ZCCHC8A, and ZCCHC8B ( Figure 6 ). ZCCHC8A and ZCCHC8B are closely related and can functionally replace each other ( Bajczyk et al, 2020 ). While RBM7 is an RNA-binding protein, ZCCHC8 proteins serve as scaffolds for the assembly of NEXT.…”

“…The sequence conservation between plant and human ZCCHC8 orthologs is not overwhelming. Yet, those domains are also recognizable in plant ZCCHC8A/B proteins, and Arabidopsis ZCCHC8A and B were shown to directly interact with both RBM7 and HEN2 ( Bajczyk et al, 2020 ).…”