Degradation of microRNAs by a Family of Exoribonucleases in Arabidopsis

Abstract

microRNAs (miRNAs) play crucial roles in numerous developmental and metabolic processes in plants and animals. The steady-state levels of miRNAs need to be properly controlled to ensure normal development. While the framework of miRNA biogenesis is established, factors involved in miRNA degradation remain unknown. Here, we show that a family of exoribonucleases encoded by the SMALL RNA DEGRADING NUCLEASE (SDN) genes degrades mature miRNAs in Arabidopsis. SDN1 acts specifically on single-stranded miRNAs in vitro, and is sensitive to the 2'-O-methyl modification on the 3' terminal ribose of miRNAs. Simultaneous knockdown of three SDN genes in vivo results in elevated miRNA levels and pleiotropic developmental defects. Therefore, we have uncovered the enzymes that degrade miRNAs and demonstrated that miRNA turnover is crucial for plant development.

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

“…This methylation protects the sRNAs against exonucleolytic shortening and/or nontemplated nucleotide addition [53,54]. For example, Ramachandran and Chen [55] found reduced levels of miRNAs and siRNAs in hen1 Arabidopsis mutants, as well as miRNAs with nontemplated 3 terminal nucleotides and 3 end truncated miRNAs. In our data, we identified two siRNAs mapping the RNAi-5x insert, in very low abundance, but when relaxing the parameters (e.g.…”

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

“…The cross-species conservation of 39 modifications of miRNAs suggests that it is the sequence of the mature miRNA that is the primary determinant of these modifications, both in the wild type and the hen1 mutants. Loss-of-function mutations in the genes that catalyze truncation (possibly via SDN1 and 2) and uridylation (HESO1) have a clear impact on miRNA stability and accumulation (Ramachandran and Chen, 2008;Ren et al, 2012;Zhao et al, 2012b). Therefore, knowing that miRNAs vary substantially in numerous aspects of their biogenesis (e.g., expression, structure, processing, etc.…”

“…This ability to regain the original miRNA size after truncation and tailing implies a memory of the original length. These two examples also suggest that the truncation activity, possibly performed by the SDN family of exonucleases (Ramachandran and Chen, 2008), in cases like miR166 and miR163 could be upstream of the uridylation activity, as tailing may not occur until the miRNA is shortened to a certain length. Other patterns were also apparent, for example, miR156, which targets SPL genes to regulate developmental time (Poethig, 2009), and miR172, which represses the translation of AP2-domain transcription factors (A) To generate the data in (B), the canonical miRNA was removed and all remaining variants were renormalized to add to 100%, enriching the signal for 39 modified variants.…”

“…The U-rich tail of unmethylated miRNAs in Arabidopsis hen1 mutants is added by nucleotidyl transferase HEN1 SUPPRESSOR1 (HESO1), whose mutation can partially rescue the phenotype of hen1 mutants by increasing miRNA accumulation (Ren et al, 2012;Zhao et al, 2012b). A family of SMALL RNA DEGRADING NUCLEASE (SDN) proteins was identified in Arabidopsis that degrades mature miRNAs (Ramachandran and Chen, 2008). Work on plant HEN1 has been primarily performed in Arabidopsis, the characterization of wavy leaf1 (waf1) mutants in rice (Oryza sativa), the ortholog of Arabidopsis HEN1 (Abe et al, 2010), and a newly identified hen1 mutant in maize (Zea mays) represent an opportunity to expand our understanding of HEN1 function into monocots.…”

Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2

“…To explore the mechanisms of this selective miRNA stabilization in detail, further studies will be necessary to identify the poly(U) polymerase for 39 uridylation and the 39-59 exonuclease that destroys miR-122. A recent study identified a family of the small RNA-degrading nuclease (SDN) that degrades mature miRNAs in Arabidopsis (Ramachandran and Chen 2008). A mammalian homolog of SDN might be a candidate gene involved in destabilization of miR-122.…”