Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

Nues, Rob W. van; Granneman, Sander; Kudla, Grzegorz; Sloan, Katherine E.; Chicken, Matthew; Tollervey, David; Watkins, Nicholas J.

doi:10.1038/emboj.2011.148

Cited by 61 publications

(117 citation statements)

References 34 publications

(52 reference statements)

Supporting

Mentioning

108

Contrasting

Order By: Relevance

“…The modified ASLs were PAGE purified and their homogeneity and identity were confirmed by anion exchange HPLC and ESI‐MS. Labelling of f 5 C‐RNA with 1‐ethyl‐2,3,3‐trimethylindoleninium‐5‐sulphonate (TMI) and analysis of primer extension stops on sequencing gels were performed as described (van Nues et al , 2011; Samanta et al , 2016). Ribosome binding assays were performed as described (Rezgui et al , 2013; see also Appendix Supplementary Methods).…”

Section: Methodsmentioning

confidence: 99%

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation

et al. 2016

View full text Add to dashboard Cite

Mitochondrial gene expression uses a non‐universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt‐)tRNAM et mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt‐tRNAM et to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m5C34 of mt‐tRNAM et to generate an f5C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m5C34 mt‐tRNA Met in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt‐tRNAM et function. Together, our data reveal how modifications in mt‐tRNAM et are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNAM et to recognise the different codons encoding methionine.

show abstract

Section: Methodsmentioning

confidence: 99%

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation

et al. 2016

View full text Add to dashboard Cite

show abstract

“…However, archaeal sRNPs containing sRNAs with mutated or absent conserved boxes have reduced in vitro methylation activity (Tran et al 2003). Although box C/D s(no)RNAs tolerate weak or atypical C9 or D9 boxes, especially in eukaryotes (Knox et al 2011;van Nues et al 2011), it is unknown how variant sRNAs function in vivo in Archaea. Taken together, reconstitution of box C/D sRNPs with any noncanonical sRNA (two-stranded, mutated in or lacking conserved sequences) causes substantial mono-sRNP assembly, revealing that the mono-sRNP is most often obtained following reconstitution with an atypical box C/D sRNA.…”

Section: Controversies In Box C/d Srnp Architecturementioning

confidence: 99%

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Bower-Phipps

Taylor²,

Wang³

et al. 2012

RNA

View full text Add to dashboard Cite

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 29-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species-Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus-indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

show abstract

“…Blasting A3717 in combination with surrounding bases within the snoRNA database resulted in two potential snoRNA guide hits, HBII-180B and U37, whose guides are complementary to this region and fulfill criteria for methylation at the fourth or fifth base of the rRNA complementary sequence. Although these two snoRNAs were previously noted to also methylate other positions within 28S, snoRNA-guided methylations of multiple targets is known to occur (van Nues et al 2011). As only a few novel sites of methylation in rRNAs in human have been characterized within recent years, this result argues that the RibOxi-seq method not only identifies known 2 ′ -OMe sites, but also allows the discovery of new ones.…”

Section: Key Principles Of Riboxi-seqmentioning

confidence: 99%

High-throughput and site-specific identification of 2′-O-methylation sites using ribose oxidation sequencing (RibOxi-seq)

Zhu

Pirnie

Carmichael

2017

RNA

View full text Add to dashboard Cite

Ribose methylation (2 ′ ′ ′ ′ ′ -O-methylation, 2 ′ ′ ′ ′ ′ -OMe) occurs at high frequencies in rRNAs and other small RNAs and is carried out using a shared mechanism across eukaryotes and archaea. As RNA modifications are important for ribosome maturation, and alterations in these modifications are associated with cellular defects and diseases, it is important to characterize the landscape of 2 ′ ′ ′ ′ ′ -Omethylation. Here we report the development of a highly sensitive and accurate method for ribose methylation detection using next-generation sequencing. A key feature of this method is the generation of RNA fragments with random 3 ′ ′ ′ ′ ′ -ends, followed by periodate oxidation of all molecules terminating in 2 ′ ′ ′ ′ ′ ,3 ′ ′ ′ ′ ′ -OH groups. This allows only RNAs harboring 2 ′ ′ ′ ′ ′ -OMe groups at their 3 ′ ′ ′ ′ ′ -ends to be sequenced. Although currently requiring microgram amounts of starting material, this method is robust for the analysis of rRNAs even at low sequencing depth.

show abstract

Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

Cited by 61 publications

References 34 publications

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation

The box C/D sRNP dimeric architecture is conserved across domain Archaea

High-throughput and site-specific identification of 2′-O-methylation sites using ribose oxidation sequencing (RibOxi-seq)

Contact Info

Product

Resources

About

Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

Cited by 61 publications

References 34 publications

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA Met to expand codon recognition in mitochondrial translation

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA Met to expand codon recognition in mitochondrial translation

The box C/D sRNP dimeric architecture is conserved across domain Archaea

High-throughput and site-specific identification of 2′-O-methylation sites using ribose oxidation sequencing (RibOxi-seq)

Contact Info

Product

Resources

About

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA ^Met to expand codon recognition in mitochondrial translation