The Human Base Excision Repair Enzyme SMUG1 Directly Interacts with DKC1 and Contributes to RNA Quality Control

Abstract

Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that removes uracil and oxidised pyrimidines from DNA. We show that SMUG1 interacts with the pseudouridine synthase Dyskerin (DKC1) and colocalizes with DKC1 in nucleoli and Cajal bodies. As DKC1 functions in RNA processing, we tested whether SMUG1 excised modified bases in RNA and demonstrated that SMUG1 has activity on single-stranded RNA containing 5-hydroxymethyldeoxyuridine, but not pseudouridine, the nucleoside resulting from isomerization of uridine by DKC1. Moreover, SMUG1 associates with the 47S rRNA precursor processed by DKC1, and depletion of SMUG1 leads to a reduction in the levels of mature rRNA accompanied by an increase in polyadenylated rRNA. Depletion of SMUG1, and, in particular, the combined loss of SMUG1 and DKC1, leads to accumulation of 5-hydroxymethyluridine in rRNA. In conclusion, SMUG1 is a DKC1 interaction partner that contributes to rRNA quality control, partly by regulating 5-hydroxymethyluridine levels.

Nucleophosmin modulates stability, activity, and nucleolar accumulation of base excision repair proteins

“…The presence of DNA-repair proteins within nucleoli is well established (Moore et al ., 2011; Antoniali et al ., 2014). In fact, several BER proteins, including SMUG1, APE1, FEN1, XRCC1, aprataxin, and PARP1/2, have been reported to accumulate within nucleoli, where they may carry out functions that differ from their “canonical” roles in DNA repair (e.g., rRNA processing; Meder et al ., 2005; Becherel et al ., 2006; Guo et al ., 2008; Vascotto et al ., 2009, 2013; Rancourt and Satoh, 2009; Jobert et al ., 2013). To the best of our knowledge, this is the first report showing that a fraction of LigI and DNA polymerase δ catalytic subunit also accumulates within nucleoli in an NPM1-dependent manner, suggesting a prominent role for NPM1 in modulating nucleolar BER accumulation.…”

“…Nucleolar BER proteins have been suggested to exert functions related to rRNA quality control and cellular proliferation in addition to DNA repair (Guo et al ., 2008; Vascotto et al ., 2009; Jobert et al ., 2013). SMUG1 enzymatic activity, for instance, has been implicated in rRNA quality control mechanisms (Jobert et al ., 2013), whereas interfering with FEN1 nucleolar retention causes reduced survival (Guo et al ., 2008). We previously showed that impairment of nucleolar accumulation of APE1 reduces cell proliferation (Lirussi et al ., 2012).…”

Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression?

“…Actually, the major focus is on APE1, SMUG1 and PARP1, as prototypical examples [17,59,[62][63][64]. In this review, in particular, we highlight current knowledge of APE1 in controlling RNA metabolism.…”

Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair

“…These observations demonstrate that APE1 regulates a previously unappreciated 'quality control' mechanism for nucleolar rRNA (Vascotto et al 2009). The observation that SMUG1 DNA glycosylase is also able to metabolize base-oxidized rRNA within the nucleolus (Jobert et al 2013), and D r a f t 26 that several other BER proteins are targeted to the nucleolus via NPM1 ) and may regulate rRNA transcription and/or repair (Aas et al 2003), suggest that NPM1 may be responsible for the redeployment of canonical BER proteins into a novel nucleolar rRNA quality control pathway.…”