Application of Mammalian Nudix Enzymes to Capped RNA Analysis
Abstract
:1. Introduction
2. Diversity of 5′ RNA Cap Structures—Natural Caps
Cap Structure | RNA Type | Cell Type | Ref. |
---|---|---|---|
m7GpppN1 m7Gpppm2′ON1 m7Gpppm6,2′OA m7Gpppm2′ON12′ON2 | mRNA | Eukaryotic | [8,19,20] |
m32,2,7GpppN | snRNA (U1, U2, U4, U5), snoRNA primary miRNA (pri-miRNA) selenoprotein encoded transcripts, junD, dhx9 and tgs1 mRNA | Eukaryotic HPFs (human foreskin fibroblasts) HEK293, OSCA-40 canine osteosarcoma, HEK293FT | [20] [34] [22,23,24] |
CH3pppN 5′-gamma-methyl (tri)phosphate cap | U6 and 7SK snRNAs | Eukaryotic | [35,36] |
(CH3)2pN Alfa-dimethyl-phosphate cap | Precursor RNA of miR-145 (pre-miR-145) | MCF-7 and MDA-MB-231 breast cancer cells | [21] |
m7GpppA(G) m22,7GpppA(G) m32,2,7GpppA(G) | pre-tRNA | S. cerevisiae HeLa | [25] |
m7GpppA(G) mGpppC GpppG, GpppA m32,2,7Gp, m22,7Gp, m22,2Gp m1Gp, m2Gp, mCp | Fraction of short RNAs (~20–200 nt), obtained from total RNA preparation | THP-1 (acute monocyte leukemia cell line) | [26] |
NAD+ (5′ nicotinamide-adenine dinucleotide cap) | mRNA Intronic snoRNA mRNA | S. cerevisiae HEK293T Human (CCRF-SB cell line), mouse (C57BL/6 tissues), S.cervisiae | [28] [29] [37] |
FAD | mRNA | Human (CCRF-SB cell line), mouse (C57BL/6 tissues), S.cervisiae | [37] |
dpCoA | Mouse liver RNA | Mouse liver RNA | [32] |
AppppA | RNA (>200 nt) | HEK293T RBL-2H3 (rat basophilic leukemia cells) | [33] |
UDP-GlcNAc UDP-Glc | mRNA | Human (CCRF-SB cell line), mouse (C57BL/6 tissues), S.cervisiae | [37] |
3. Diversity of Synthetic Cap Structures
4. NUDIX Protein Family
5. RNA Decapping with Mammalian Nudt2, Nudt5, Nudt12, Nudt16, and Dcp2
Dcp2 | Nudt16 | Nudt12 | Nudt2 | |
---|---|---|---|---|
m7GpppN | + [105] | |||
m7GpppNm | + [105] | |||
m7GpppG | + [92,105,120,136] | +/− [92,93,120] | + [116,130] | + [116] |
m7GpppA | + [105] | − [120] | ||
m7GpppGm | + [105] | +/− [120] | ||
m7GpppAm | + [105] | − [120] | ||
m7Gpppm6Am | + [105,107] − [19] (transcript dependent) | |||
m7GpppAmGm | + [103] | |||
m7Gpppbn6AmG | + [107] | |||
GpppG | − [14] | + [92,93,120] | + [116,130] | + [33,116] |
GpppA | + [120] | + [33] | ||
ApppA | + [33] | |||
ApppG | − [33] | |||
GppppG | + [33] | |||
GppppA | + [33] | |||
AppppA | + [33] | |||
AppppG | + [33] | |||
m27,3′OGpppG | + [58,89,136] | − [92,93,120] | ||
m27,2′OGpppG | + [38] | |||
m27,2′OGppppG | + [136] | |||
m27,2′-OGppCH2ppG | − [136] | |||
m27,2′-OGppCCl2ppG | − [136] | |||
m27,2′-OGppCF2ppG | − [136] | |||
m27,2′-OGpp-tz-C2H4OppG | − [64] | |||
m27,2′-OGppp-tz-C2H4OpG | + [64] | |||
m27,2′OGppNHpN | − [56] | |||
m27,3′OGppCH2pN | − [56,58] | |||
m27,2′OGppSpG (D1) | −/+ [38] | |||
m27,2′OGppSpG (D2) | −/+ [38] | |||
m27,2′OGppBH3pG (D2) | − [38] | |||
bn2m7GpppG | + [92] | −/+ [92] | ||
bn2m7GppSpG | − [93] | |||
bn2m27,3′OGpppG | + [89] | |||
bn2m27,2′OGpppG | + [89] | |||
bn2m7GppppG | + [93] | |||
bn2m7GpppAmG | − [93] | |||
(4-Cl-bn)2m7GpppG | + [92] | −/+ [92] | ||
(4-Cl-bn)2m7GppppG | + [93] | |||
(4-Cl-bn)2m7GpppAmG | − [93] | |||
(4-OCH3-bn)2m7GpppG | + [92] | −/+ [92] | ||
(4-OCH3-bn)2m27,3′OGpppN | + [89] | |||
(4-di(OCH3-bn)-tz)2m7GpppG | + [92] | − [92] | ||
(4-di(OCH3-bn)-tz-CH2)2m7GpppG | − [93] | |||
(4-di(OCH3-bn)-tz-(CH2)2)2m7GpppG | +/− [93] | |||
(4-di(OCH3-bn)-tz-(CH2)4)2m7GpppG | − [93] | |||
(4-bn-isx)2m7GpppG | + [92] | −/+ [92] | ||
(4-CH3-th)2m7GpppG | + [92] | −/+ [92] | ||
2′-O/3′-O-(FAM-L6N)-m7GpppG | + [77] | + [77] | ||
m32,2,7GpppG | + [120,129] | + [130] | ||
m32,2,7GpppA | −/+ [121] |
6. Other RNA Decapping Enzymes
7. Discussion
8. Conclusions
Funding
Conflicts of Interest
References
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NAD Cap | FAD Cap | dpCoA Cap | UDP-GlcNAc Cap | |
---|---|---|---|---|
Nudt16 | + | + | + | |
Nudt12 | + | + | ||
Nudt5 | + | |||
Nudt2 | + | + |
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Lukaszewicz, M. Application of Mammalian Nudix Enzymes to Capped RNA Analysis. Pharmaceuticals 2024, 17, 1195. https://doi.org/10.3390/ph17091195
Lukaszewicz M. Application of Mammalian Nudix Enzymes to Capped RNA Analysis. Pharmaceuticals. 2024; 17(9):1195. https://doi.org/10.3390/ph17091195
Chicago/Turabian StyleLukaszewicz, Maciej. 2024. "Application of Mammalian Nudix Enzymes to Capped RNA Analysis" Pharmaceuticals 17, no. 9: 1195. https://doi.org/10.3390/ph17091195