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    Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III

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    Characterization of RNA sequence ...
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    Genre
    Journal Article
    Date
    2006-09-22
    Author
    Pertzev, AV
    Nicholson, AW
    Subject
    Base Pairing
    Base Sequence
    Catalysis
    Escherichia coli Proteins
    RNA Processing, Post-Transcriptional
    RNA, Bacterial
    Regulatory Sequences, Ribonucleic Acid
    Ribonuclease III
    Substrate Specificity
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5631
    
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    DOI
    10.1093/nar/gkl459
    Abstract
    Members of the ribonuclease III family are the primary agents of double-stranded (ds) RNA processing in prokaryotic and eukaryotic cells. Bacterial RNase III orthologs cleave their substrates in a highly site-specific manner, which is necessary for optimal RNA function or proper decay rates. The processing reactivities of Escherichia coli RNase III substrates are determined in part by the sequence content of two discrete double-helical elements, termed the distal box (db) and proximal box (pb). A minimal substrate of E.coli RNase III, μR1.1 RNA, was characterized and used to define the db and pb sequence requirements for reactivity and their involvement in cleavage site selection. The reactivities of μR1.1 RNA sequence variants were examined in assays of cleavage and binding in vitro. The ability of all examined substitutions in the db to inhibit cleavage by weakening RNase III binding indicates that the db is a positive determinant of RNase III recognition, with the canonical UA/UG sequence conferring optimal recognition. A similar analysis showed that the pb also functions as a positive recognition determinant. It also was shown that the ability of the GC or CG bp substitution at a specific position in the pb to inhibit RNase III binding is due to the purine 2-amino group, which acts as a minor groove recognition antideterminant. In contrast, a GC or CG bp at the pb position adjacent to the scissile bond can suppress cleavage without inhibiting binding, and thus act as a catalytic antideterminant. It is shown that a single pb+db 'set' is sufficient to specify a cleavage site, supporting the primary function of the two boxes as positive recognition determinants. The base pair sequence control of reactivity is discussed within the context of new structural information on a post-catalytic complex of a bacterial RNase III bound to the cleaved minimal substrate. © Copyright 2006 Oxford University Press.
    Citation to related work
    Oxford University Press (OUP)
    Has part
    Nucleic Acids Research
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5613
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