Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage

Abstract

Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.

Goldilocks and RNA: Where Mg2+ concentration is just right

“…In sum, the effects of Mg 2+ on RNA persistence are expected to be pleomorphic, both protecting and degrading RNA. Folding is typically fast (28–32) compared to Mg 2+ -catalyzed cleavage (3, 5, 6), so cleavage operates over a fixed fold landscape.…”

“…RNA is especially fragile. In-line attack by 2'OH groups on adjacent phosphates catalyzes RNA cleavage (2)(3)(4) in reactions accelerated by divalent cations (5)(6)(7)(8). However, divalent cations also promote folding of RNAs (9-13), and are generally required for catalytic function of ribozymes (14)(15)(16), and for RNA biosynthesis (17), and RNA processing by protein enzymes (18).…”

In search of the RNA world on Mars

“…This is because some models predict reducing, circumneutral, and cool conditions throughout the Hadean (Charnay et al., 2017; Kadoya et al., 2020). Specifically, studies have demonstrated that Fe 2+ may have preceded life's transition to Mg 2+ due to its versatility in catalyzing polymerization (e.g., Jin et al., 2018), ribozyme folding (Athavale et al., 2012), translation (Petrov et al., 2015), and imparting novel catalytic activity (Guth‐Metzler et al., 2020; Hsiao et al., 2013; Okafor et al., 2017). It is therefore conceivable that Fe 2+ could have had a comparable influence on the stability, polymerization, and function of RNA on early Mars and should accordingly be discussed below.…”

A Conserved Gcn2-Gcn4 Axis Links Methionine Utilization and the Oxidative Stress Response in Cryptococcus neoformans

“…Since ascorbic acid can act as a pro-oxidant in addition to acting as an antioxidant, we considered that an increase in pro-oxidant activity could contribute to increased translation repression. A reaction between iron and ascorbic acid can generate hydrogen peroxide, increasing oxidative stress and leading to cleavage of the 25s rRNA in the 60s ribosomal subunit (Zinskie et al, 2018;Guth-Metzler et al, 2020;Kazmierczak-Barańska et al, 2020). If this reaction was occurring, it could explain the accumulation at the 40s peaks in the ascorbic acid polysome profiles.…”