Quality control of chemically damaged RNA

Abstract

The "central dogma" of molecular biology describes how information contained in DNA is transformed into RNA and finally into proteins. In order for proteins to maintain their functionality in both the parent cell and subsequent generations, it is essential that the information encoded in DNA and RNA remains unaltered. DNA and RNA are constantly exposed to damaging agents, which can modify nucleic acids and change the information they encode. While much is known about how cells respond to damaged DNA, the importance of protecting RNA has only become appreciated over the past decade. Modification of the nucleobase through oxidation and alkylation has long been known to affect its base-pairing properties during DNA replication. Similarly, recent studies have begun to highlight some of the unwanted consequences of chemical damage on mRNA decoding during translation. Oxidation and alkylation of mRNA appear to have drastic effects on the speed and fidelity of protein synthesis. As some mRNAs can persist for days in certain tissues, it is not surprising that it has recently emerged that mRNA-surveillance and RNA-repair pathways have evolved to clear or correct damaged mRNA.

Keywords: 8-Oxoguanosine; Alkylation; O6-Methylguanosine; Oxidation; RNA damage; RNA surveillance; Ribosome; Translation.

Fig. 1

Targets of oxidative and alkylative damage on RNA. a Structures of the four RNA nucleobases with location of common oxidation sites marked (red arrows). Damage at these positions produces 8-oxo-7,8-dihydroadenosine, 8-oxo-7,8-dihydroguanosine, 5-hydroxycytosine, and 5-hydroxyuracil, respectively. Most of the nitrogen and oxygen atoms of the nucleobase are susceptible to alkylative damage (blue arrows). b The phosphodiester backbone and 2′-OH of the ribose are also targets for alkylation (blue arrows)

Fig. 2

Damaged nucleobases exhibit altered base pairing. After oxidation, guanosine can still pair with cytosine, but is more likely to adopt a syn conformation and pair with adenosine (top). Aklylation of guanosine allows for efficient base pairing with uracil (bottom)

Fig. 3

RNA damage affects cellular fitness through multiple mechanisms. Damage to mRNA, rRNA, or tRNA could lead to failed peptide synthesis by miscoding, stalling, or mRNA turnover. Damage to rRNA could cause defects in ribosomal assembly or crosslinking with ribosomal proteins. tRNA damage may cause aminoacylation defects, potentially leading to production of miscoded proteins

Fig. 4

Model for No-go decay in response to stalling by a damaged mRNA. a Translating ribosome stalls with a damaged codon in the A-site. b Ribosome rescue factors, Dom34p and Hbs1p in yeast, are recruited to the stalled ribosome, and mRNA is endonucleolytically cleaved. c The resulting 3′-fragment is degraded by the 5′–3′ exonuclease Xrn1p, whereas the 5′-fragment is degraded through the action of the cytoplasmic exosome in a 3′–5′ direction