title: Specificity of RppH-dependent RNA degradation in Bacillus subtilis.
abstract: Bacterial RNA degradation often begins with conversion of the 5'-terminal triphosphate to a monophosphate, creating a better substrate for subsequent ribonuclease digestion. For example, in Bacillus subtilis and related organisms, removal of the gamma and beta phosphates of primary transcripts by the RNA pyrophosphohydrolase RppH triggers rapid 5'-exonucleolytic degradation by RNase J. However, the basis for the selective targeting of a subset of cellular RNAs by this pathway has remained largely unknown. Here we report that purified B. subtilis RppH requires at least two unpaired nucleotides at the 5' end of its RNA substrates and prefers three or more. The second of these 5'-terminal nucleotides must be G, whereas a less strict preference for a purine is evident at the third position, and A is slightly favored over G at the first position. The same sequence requirements are observed for RppH-dependent mRNA degradation in B. subtilis cells. By contrast, a parallel pathway for 5'-end-dependent RNA degradation in that species appears to involve an alternative phosphate-removing enzyme that is relatively insensitive to sequence variation at the first three positions.
authors.affiliation: Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Ping-kun
authors.initials: PK
authors.lastname: Hsieh
authors.forename: Jamie
authors.initials: J
authors.lastname: Richards
authors.forename: Quansheng
authors.initials: Q
authors.lastname: Liu
authors.forename: Joel G
authors.initials: JG
authors.lastname: Belasco
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000502:physiology*; D015152:Blotting, Northern; D011756:Diphosphates / Q000378:metabolism; D004587:Electrophoresis, Agar Gel; D006151:Guanosine / Q000378:metabolism; D016014:Linear Models; D009838:Oligodeoxyribonucleotides / Q000235:genetics; D016133:Polymerase Chain Reaction; D011755:Pyrophosphatases / Q000235:genetics / Q000378:metabolism*; D012315:RNA Caps / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability / Q000502:physiology*; D012260:Ribonucleases / Q000378:metabolism; D013379:Substrate Specificity; D000096964:Nudix Hydrolases
chemical_list: D011756:Diphosphates; D006151:Guanosine; D009838:Oligodeoxyribonucleotides; D011755:Pyrophosphatases; D012315:RNA Caps; D012260:Ribonucleases; D000096964:Nudix Hydrolases
keywords: BsRppH; YtkD; glpP; yhxA