Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions.

Area of Science:

• * Molecular Biology
• * RNA Structure and Function
• * Bioinformatics

Background:

• * Complex RNA folding relies on recurrent structural motifs, including the T-loop.
• * T-loops are found in various RNAs, but their interacting receptors are not fully understood.
• * Flavin mononucleotide (FMN) and cobalamin (Cbl) riboswitches utilize T-loop receptor motifs.

Purpose of the Study:

• * To investigate T-loop/T-loop receptor (TL/TLR) interactions in Cbl riboswitches.
• * To identify sequence signatures and context-dependent functional constraints of TL/TLR motifs.
• * To compare TL/TLR interactions across different riboswitch subclasses.

Main Methods:

• * Employed a cell-based genetic screen using randomized nucleotide libraries.
• * Utilized the env8 class-II Cbl riboswitch as a host for T-loop receptors.
• * Performed bioinformatic analysis and phylogenetic comparisons.

Main Results:

• * Functional sequence space for TL/TLR interactions in Cbl riboswitches is more restricted than anticipated.
• * Identified distinct sequence signatures for different T-loop receptor motifs.
• * Demonstrated context-dependent TL/TLR interactions within the riboswitch subclass.

Conclusions:

• * TL/TLR interactions are highly context-dependent, particularly within riboswitches.
• * Sequence signatures provide insights into the evolution and function of these RNA motifs.
• * Nucleobase-mediated long-range interactions in riboswitches are distinct from those in other RNAs.