pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31

Kotar, Anita; Ma, Sicong; Keane, Sarah C.

doi:10.1016/j.bpc.2022.106763

Cited by 12 publications

(7 citation statements)

References 68 publications

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“…S2 ). To guide assignments of the FL pre-miR-31 RNA, we combined our previously reported chemical shift assignments for fragments BottomA and BottomB ( 36 ) with chemical shift assignments for two additional oligo fragments, TopA ( SI Appendix , Fig. S3 ) and Top ( SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Base pair mismatches are a common feature within the helical stem of pre-miRNAs ( 36 , 44 ). Studies on fly Dicer-1 suggest that while the length of the pre-miRNA helical stem is important, the presence of mismatches does not significantly affect Dicer processing ( 16 ).…”

Section: Resultsmentioning

confidence: 99%

“…S19 ). We previously investigated the pH-dependence of the C18•A54 mismatch and found that A54 is partially protonated at physiological pH, suggesting the potential formation of a C•A + base pair near neutral pH ( 36 ). We were therefore interested in testing whether mutations that replaced the mismatch with a canonical U-A or C-G base pair (C18U and A54G, respectively) affected the processing by Dicer–TRBP ( SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

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Structure of pre-miR-31 reveals an active role in Dicer–TRBP complex processing

Ma,

Kotar,

Hall

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer–TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer–TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer–TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer–TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Structure of pre-miR-31 reveals an active role in Dicer–TRBP complex processing

Ma,

Kotar,

Hall

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…The temperature was moved to the target value, and the system was allowed to equilibrate for one minute before a measurement was taken. Thermal melting data was fit to a two-state model with sloping baselines ( 32 ) (Equation 1 ) in Prism 9. All RNAs tested exhibited reversible thermal melting profiles.…”

Section: Methodsmentioning

confidence: 99%

Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome

Nissley

Penev

Watson

et al. 2023

Nucleic Acids Research

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The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3′-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.

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“…Instead, in many cases, the factor determining where a substrate is cleaved and which counting rule is used depends upon the structural features of the RNA substrate. Indeed, recent studies have identified pH-dependent impacts on Dicer-mediated processing of select miRNAs with nucleotide base mismatches and base flipping-induced structural arrangements within the RNA stem region leading to different cleavage sites. − These studies also suggest that the cleavage reactions performed by the RNase IIIA and IIIB domains may not occur simultaneously. , As a result, two separate counting rules could be used to determine the cleavage sites for the 5P and 3P strands . This cleavage versatility can act as an additional mechanism that Dicer uses to distinguish between RNA substrates, as well as determine strand selection during RISC assembly.…”

Section: Platform-paz-connector Domainmentioning

confidence: 99%