A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis.
The enzyme Dicer is central to the production of small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs). Like other insects, Drosophila melanogaster uses different Dicers to make siRNAs and miRNAs: Dicer-1 produces miRNAs from pre-miRNAs, whereas Dicer-2 generates siRNAs from long double-stranded RNA (dsRNA). How do the 2 Dicers achieve their substrate specificity? Here, we review recent findings that inorganic phosphate restricts the substrate specificity of Dicer-2 to long dsRNA. Inorganic phosphate inhibits Dicer-2 from binding and cleaving pre-miRNAs, without affecting the processing of long dsRNA. Crystal structures of a fragment of human Dicer in complex with an RNA duplex identify a phosphate-binding pocket that recognizes both the 5'-monophosphate of a substrate RNA and inorganic phosphate. We propose that inorganic phosphate occupies the phosphate-binding pocket in the fly Dicer-2, blocking binding of pre-miRNA and restricting pre-miRNA processing to Dicer-1. Thus, a small molecule can alter the substrate specificity of a nucleic acid-processing enzyme.
Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA.
Ryuya
R
Fukunaga
Howard Hughes Medical Institute; RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology; University of Massachusetts Medical School; Worcester, MA USA.
Phillip D
PD
Zamore
D000595:Amino Acid Sequence; D000818:Animals; D020029:Base Pairing; D053487:DEAD-box RNA Helicases / Q000737:chemistry; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics*; D040461:Gene Components / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010755:Organophosphates / Q000494:pharmacology*; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000096:biosynthesis* / Q000737:chemistry / Q000378:metabolism; D043244:Ribonuclease III / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity / Q000187:drug effects / Q000235:genetics
D029721:Drosophila Proteins; D010755:Organophosphates; D058727:RNA, Small Untranslated; C478069:DCR-2 protein, Drosophila; C515033:Dcr-1 protein, Drosophila; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases
dicer; dsRNA; miRNA; phosphate; siRNA