6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymes

Abstract

Since the 1980s, several small RNA motifs capable of chemical catalysis have been discovered. These small ribozymes, composed of between approximately 40 and 200 nucleotides, have been found to play vital roles in the replication of subviral and viral pathogens, gene regulation in prokaryotes, and have recently been discovered in noncoding eukaryotic RNAs. All of the known natural small ribozymes – the hairpin, hammerhead, hepatitis delta virus, Varkud satellite, and glmS ribozymes – catalyze the same self-cleavage reaction as RNAse A, resulting in two products, one bearing a 2′–3′ cyclic phosphate and the other a 5′-hydroxyl group. Although originally thought to be obligate metalloenzymes like the group I and II self-splicing introns, the small ribozymes are now known to support catalysis in a wide variety of cations that appear to be only indirectly involved in catalysis. Nevertheless, under physiologic conditions, metal ions are essential for the proper folding and function of the small ribozymes, the most effective of these being magnesium. Metal ions contribute to catalysis in the small ribozymes primarily by stabilizing the catalytically active conformation, but in some cases also by activating RNA functional groups for catalysis, directly participating in catalytic acid-base chemistry, and perhaps by neutralizing the developing negative charge of the transition state. Although interactions between the small ribozymes and cations are relatively nonspecific, ribozyme activity is quite sensitive to the types and concentrations of metal ions present in solution, suggesting a close evolutionary relationship between cellular metal ion homeostasis and cation requirements of catalytic RNAs, and perhaps RNA in general.

The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme

“…Structural and mechanistic studies first elucidated roles for metal ions in ribozymes 25,26 . More recently, nucleobases were shown to play key roles in the mechanisms of small ribozymes 27 .…”

Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA

“…Effect of metal ion on 3WJ structure confirmed by DNA packaging and viral assembly assay Divalent metal ions play a critical role in stabilizing the tertiary structure of RNA and in facilitating RNA functions (Carter and Holbrook 2002;Draper 2004;Scott 2007;Johnson-Buck et al 2011). The positively charged metal ions shield the negatively charged phosphate backbone of RNA, rendering the RNA tertiary structure more compact.…”

“…The positively charged metal ions shield the negatively charged phosphate backbone of RNA, rendering the RNA tertiary structure more compact. This interaction between metal ions and the RNA could lead either to the formation of a positively charged cloud around the RNA molecule or to site-specific binding (Draper 2004;Johnson-Buck et al 2011). The latter effect is often observed in various catalytic RNA structures (Cate et al , 1997Murray et al 1998;Kazantsev et al 2005Kazantsev et al , 2009Vicens and Cech 2006).…”

Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry

“…Ribozymes and riboswitches often require Mg 2+ ions for optimal activity. 69,70,76 One of the most striking examples of the interplay between magnesium and ribozyme is the RNase P ribozyme, where both high-affinity (∼0.2 mM) and low-affinity (∼3 mM) interactions are involved in catalysis. 77 Magnesium ions are believed to stabilize the transition state and neutralize charges to assist in substrate association.…”