tertiary interaction
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2020 ◽  
Author(s):  
Conner J. Langeberg ◽  
Madeline E. Sherlock ◽  
Andrea MacFadden ◽  
Jeffrey S. Kieft

ABSTRACTStructured RNA elements are common in the genomes of RNA viruses, often playing critical roles during viral infection. Some RNA elements use forms of tRNA mimicry, but the diverse ways this mimicry can be achieved are poorly understood. Histidine-accepting tRNA-like structures (TLSHis) are examples found at the 3′ termini of some positive-sense single-stranded RNA (+ssRNA) viruses where they interact with several host proteins, induce histidylation of the RNA genome, and facilitate several processes important for infection, to include replication. As only five TLSHis examples had been reported, we explored the possible larger phylogenetic distribution and diversity of this TLS class using bioinformatic approaches. We identified many new examples of TLSHis, yielding a rigorous consensus sequence and secondary structure model that we validated by chemical probing of representative TLSHis RNAs. We confirmed new examples as authentic TLSHis by demonstrating their ability to be histidylated in vitro, then used mutational analyses to verify a tertiary interaction that is likely analogous to the D- and T-loop interaction found in canonical tRNAs. These results expand our understanding of how diverse RNA sequences achieve tRNA-like structures and functions in the context of viral RNA genomes and lay the groundwork for high-resolution structural studies of tRNA mimicry by histidine-accepting TLSs.


2018 ◽  
Vol 46 (17) ◽  
pp. 9094-9105 ◽  
Author(s):  
Jacob T Polaski ◽  
Otto A Kletzien ◽  
Lea K Drogalis ◽  
Robert T Batey

2017 ◽  
Vol 292 (34) ◽  
pp. 13934-13946 ◽  
Author(s):  
Mi Zhou ◽  
Meng Wang ◽  
Ling Xue ◽  
Zhi Lin ◽  
Qiufen He ◽  
...  

Cell ◽  
2012 ◽  
Vol 149 (2) ◽  
pp. 348-357 ◽  
Author(s):  
Reza Behrouzi ◽  
Joon Ho Roh ◽  
Duncan Kilburn ◽  
R.M. Briber ◽  
Sarah A. Woodson

2011 ◽  
Vol 73 (3-4) ◽  
pp. 221-229 ◽  
Author(s):  
Rei Ohmori ◽  
Hirohide Saito ◽  
Yoshiya Ikawa ◽  
Yoshihiko Fujita ◽  
Tan Inoue

2011 ◽  
Vol 92 (10) ◽  
pp. 2310-2319 ◽  
Author(s):  
Bhupendra Verma ◽  
Anand Ponnuswamy ◽  
Sivakumar Vadivel Gnanasundram ◽  
Saumitra Das

We have investigated the possible role of a conserved cis-acting element, the cryptic AUG, present in the 5′ UTR of coxsackievirus B3 (CVB3 ) RNA. CVB3 5′ UTR contains multiple AUG codons upstream of the initiator AUG, which are not used for the initiation of translation. The 48S ribosomal assembly takes place upstream of the cryptic AUG. We show here that mutation in the cryptic AUG results in reduced efficiency of translation mediated by the CVB3 IRES; mutation also reduces the interaction of mutant IRES with a well characterized IRES trans-acting factor, the human La protein. Furthermore, partial silencing of the La gene showed a decrease in IRES activity in the case of both the wild-type and mutant. We have demonstrated here that the interaction of the 48S ribosomal complex with mutant RNA was weaker compared with wild-type RNA by ribosome assembly analysis. We have also investigated by chemical and enzymic modifications the possible alteration in secondary structure in the mutant RNA. Results suggest that the secondary structure of mutant RNA was only marginally altered. Additionally, we have demonstrated by generating compensatory and non-specific mutations the specific function of the cryptic AUG in internal initiation. Results suggest that the effect of the cryptic AUG is specific and translation could not be rescued. However, a possibility of tertiary interaction of the cryptic AUG with other cis-acting elements cannot be ruled out. Taken together, it appears that the integrity of the cryptic AUG is important for efficient translation initiation by the CVB3 IRES RNA.


2010 ◽  
Vol 402 (1) ◽  
pp. 154-164 ◽  
Author(s):  
Adelaine K.W. Leung ◽  
Christian Kambach ◽  
Yasushi Kondo ◽  
Martin Kampmann ◽  
Martin Jinek ◽  
...  

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