Alternate RNA Structures

Abstract

RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.

Figure 1.

(A) The monomeric and dimeric states of the human immunodeficiency virus 1 (HIV-1) 5′ leader. Transcripts with ^cap2G or ^cap3G favor the monomeric form, whereas transcripts with ^cap1G favor the dimeric form, largely because of the dissolution or formation of the C58-G104 base pair, respectively. (B) Sampling of alternate conformations by the metastasis-associated lung adenocarcinoma transcript 1 long noncoding RNA (MALAT1 lncRNA). The RNA shows increased dynamics of the upper hairpin structure on N⁶-methyladenosine (m⁶A)-modification, as indicated by the dotted lines, allowing for increased sampling of the protein-binding conformation (lavender oval). The star indicates the location for the potential m⁶A modification.

Figure 2.

(A) Mutually exclusive splicing in the 14-3-3ξ mRNA is controlled by three structures that differ in their base-pairing pattern: Intronic element a (IEa) forms base pairs with either IE1 or IE2 or neither. (B) The HIV-1 Rev response element (RRE) partitions into two equally populated structures with either four or five stem loops (SLs). (C) The HIV-1 transactivation response (TAR) element has two “excited” states that differ from the “ground” state (GS). Excited state 1 (ES1) maintains the same overall stem architecture but differs in tertiary interactions at the apical loop, whereas ES2 shows reshuffled base pairs, resulting in a large-scale repairing of the TAR secondary structure. (D) The stem II region on the spliceosome U2 small nuclear RNA (snRNA) can transition between two alternate conformations that each serve a different role in the process of splicing.

Figure 3.

(A) The murine leukemia virus (MLV) readthrough RNA pseudoknot is partitioned into two alternate structures, depending on the protonation state. The inactive structure is unprotonated, with stem 2 stacked on top of stem 1. The active structure is protonated at the loop 1 adenine, forming a triple-base interaction that causes a bend at the junction, which allows for tertiary interactions to be formed between loop 2 and stem 1. (B) The U5–primer-binding site (PBS) of MLV exchanges between two conformations, one of which is bound by the nucleocapsid (NC). NC binding frees select nucleotides in the PBS and polyadenylation signal (PAS) regions for access by the appropriate complementary regions on the transfer RNA (tRNA; not pictured), to anneal and form the reverse transcription initiation complex. (C) The 16S ribosomal RNA (rRNA) samples many conformations including native and non-native forms. Protein binding simultaneously reduces conformational sampling and enriches the native forms.

Figure 4.

(A) The Escherichia coli thiamine pyrophosphate (TPP) thiC riboswitch has two conformations, ligand-bound (OFF) and ligand-free (ON). The ribosome-binding site (RBS) and the AUG start codon are sequestered in the ligand-bound state and exposed in the ligand-free state, respectively. (B) The Bacillus cereus fluoride riboswitch has apo and holo conformations with highly similar structures. The apo conformation can transiently access a short-lived excited state (apo ES) in which a highly conserved reverse Hoogsteen “linchpin” base pair is broken, enabling strand invasion and leading to formation of the terminator stem. (C) The Neurospora crassa TPP NMT1 riboswitch regulates the expression of alternate upstream open reading frames (ORFs) by using alternate base-pairing involving residues in the P4 and P5 stems to change the formation of the lariat. (D) The Vibrio vulnificus adenine add riboswitch operates using a three-state mechanism rather than canonical two-state mechanism, allowing it to maintain its ligand concentration dependence at temperatures ranging from 37°C to 10°C. The apoA conformation is similar to the holo conformation, whereas apoB differs significantly.