Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding

2021 ◽  
pp. 106589
Author(s):  
Preethi Parameswaran ◽  
Yashaswina Arora ◽  
Rajesh Patidar ◽  
Nihar Ranjan
Keyword(s):  
Intercalative Binding ◽  
A Site ◽  
Site Recognition

scholarly journals A Pentatricopeptide Repeat Protein Is a Site Recognition Factor in Chloroplast RNA Editing

2006 ◽  
Vol 281 (49) ◽  
pp. 37661-37667 ◽  
Author(s):  
Kenji Okuda ◽  
Takahiro Nakamura ◽  
Mamoru Sugita ◽  
Toshiyuki Shimizu ◽  
Toshiharu Shikanai
Keyword(s):  
Rna Editing ◽  
Pentatricopeptide Repeat ◽  
Repeat Protein ◽  
Pentatricopeptide Repeat Protein ◽  
Chloroplast Rna ◽  
A Site ◽  
Site Recognition

scholarly journals RNA structure is a critical determinant of poly(A) site recognition by cleavage and polyadenylation specificity factor.

1996 ◽  
Vol 16 (9) ◽  
pp. 4942-4951 ◽  
Author(s):  
B R Graveley ◽  
E S Fleming ◽  
G M Gilmartin
Keyword(s):  
Human Immunodeficiency Virus ◽  
Rna Structure ◽  
Critical Determinant ◽  
Immunodeficiency Virus ◽  
Cleavage And Polyadenylation ◽  
Specificity Factor ◽  
A Site ◽  
Site Recognition

Sequence conservation among mammalian poly(A) sites is limited to the sequence AAUAAA, coupled with an amorphous downstream U- or GU-rich region. Since these sequences may also occur within the coding region of mRNAs, additional information must be required to define authentic poly(A) sites. Several poly(A) sites have been shown to contain sequences outside the core elements that enhance the efficiency of 3' processing in vivo and in vitro. The human immunodeficiency virus type 1, equine infectious anemia virus, and adenovirus L1 3' processing enhancers have been shown to promote the binding of cleavage and polyadenylation specificity factor (CPSF), the factor responsible for recognition of AAUAAA, to the pre-mRNA, thereby facilitating the assembly of a stable 3' processing complex. We have used in vitro selection to examine the mechanism by which the human immunodeficiency virus type 1 3' processing enhancer promotes the interaction of CPSF with the AAUAAA hexamer. Surprisingly, RNAs selected for efficient polyadenylation were related by structure rather than sequence. Therefore, in the absence of extensive sequence conservation, our results strongly suggest that RNA structure is a critical determinant of poly(A) site recognition by CPSF and may play a key role in poly(A) site definition.

scholarly journals Getting in the Loop: New Insights into the Mechanism of Poly(A) Site Recognition

Structure ◽  
2011 ◽  
Vol 19 (3) ◽  
pp. 279-281
Author(s):  
Brenton R. Graveley
Keyword(s):  
A Site ◽  
Site Recognition

scholarly journals Nonsense suppression position effect implicates poly(A)-binding protein in the regulation of translation termination

2019 ◽  
Author(s):  
Chan Wu ◽  
Bijoyita Roy ◽  
Feng He ◽  
Allan Jacobson
Keyword(s):  
Translation Termination ◽  
Binding Protein ◽  
Position Effect ◽  
Critical Role ◽  
Yeast Cells ◽  
Nonsense Suppression ◽  
Regulation Of Translation ◽  
Nonsense Codon ◽  
A Site ◽  
Site Recognition

SUMMARYReadthrough of translation termination codons, also known as nonsense suppression, is a relatively inefficient process mediated by ribosomal A site recognition and insertion of near-cognate tRNAs. Multiple factors influence readthrough efficiency, including nonsense codon specificity and context. To determine whether nonsense codon position in a gene influences the extent of readthrough, we generated a series of LUC nonsense alleles and quantitated both readthrough and termination efficiencies at each nonsense codon in yeast cells lacking nonsense-mediated mRNA decay (NMD) activity. Readthrough efficiency for premature termination codons (PTCs) manifested a marked dependence on PTC proximity to the mRNA 3’-end, decreasing progressively across the LUC ORF but increasing with 3’-UTR lengthening. These effects were eliminated, and translation termination efficiency decreased considerably, in cells harboring pab1 mutations. Our results support a critical role for poly(A)-binding protein in the regulation of translation termination and suggest that inefficient termination is the trigger for NMD.

scholarly journals Crystal Structure of a Human Cleavage Factor CFIm25/CFIm68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping

Structure ◽  
2011 ◽  
Vol 19 (3) ◽  
pp. 368-377 ◽  
Author(s):  
Qin Yang ◽  
Molly Coseno ◽  
Gregory M. Gilmartin ◽  
Sylvie Doublié
Keyword(s):  
Crystal Structure ◽  
A Site ◽  
Rna Complex ◽  
Site Recognition ◽  
Insight Into

scholarly journals Site-Specific Insertion of IS492 in Pseudoalteromonas atlantica

2009 ◽  
Vol 191 (20) ◽  
pp. 6408-6414 ◽  
Author(s):  
Brian P. Higgins ◽  
Adam C. Popkowski ◽  
Peter R. Caruana ◽  
Anna C. Karls
Keyword(s):  
Extracellular Polysaccharide ◽  
Structural Features ◽  
Target Site ◽  
Recombination Mechanism ◽  
Site Specific ◽  
Precise Excision ◽  
Pseudoalteromonas Atlantica ◽  
A Site ◽  
Site Recognition

ABSTRACT Reversible insertion of IS492 at a site within epsG on the Pseudoalteromonas atlantica chromosome controls peripheral extracellular polysaccharide production and biofilm formation by P. atlantica. High-frequency precise excision of IS492 from epsG requires 5 and 7 bp of flanking DNA, suggesting that IS492 transposition involves a site-specific recombination mechanism. The site specificity of IS492 insertion was examined in P. atlantica and shown to be specific for a 7-bp target, 5′-CTTGTTA-3′. Characterization of numerous insertion events at the target site in epsG indicated that insertion is also orientation specific. The frequency of IS492 insertion at the epsG target site (2.7 × 10−7/cell/generation), determined by quantitative PCR, is 4 to 5 orders of magnitude lower than the frequency of IS492 precise excision from the same site. Comparison of insertion sites for IS492 and the highly related ISPtu2 from Pseudoalteromonas tunicata suggests DNA sequence and/or structural features that may contribute to site recognition and recombination by the transposase of IS492.

Sign in / Sign up

Export Citation Format

Share Document