1,780
Views
12
CrossRef citations to date
0
Altmetric
Point-of-View

RNA capping by mitochondrial and multi-subunit RNA polymerases

ORCID Icon, & ORCID Icon
Pages 292-297 | Received 14 Feb 2018, Accepted 14 Mar 2018, Published online: 25 Apr 2018

References

  • Cahova H, Winz ML, Hofer K, et al. NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature. 2015;519(7543):374–377. doi:10.1038/nature14020. PMID:25533955
  • Kowtoniuk WE, Shen Y, Heemstra JM, et al. A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc Natl Acad Sci U S A. 2009;106(19):7768–7773. doi:10.1073/pnas.0900528106. PMID:19416889; PMCID:PMC2674394.
  • Chen YG, Kowtoniuk WE, Agarwal I, et al. LC/MS analysis of cellular RNA reveals NAD-linked RNA. Nat Chem Biol. 2009;5(12):879–881. doi:10.1038/nchembio.235. PMID:19820715; PMCID:PMC2842606.
  • Walters RW, Matheny T, Mizoue LS, et al. Identification of NAD+ capped mRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2017;114(3):480–485. doi:10.1073/pnas.1619369114. PMID:28031484; PMCID:PMC5255579
  • Jiao X, Doamekpor SK, Bird JG, et al. 5' End Nicotinamide Adenine Dinucleotide cap in human cells promotes RNA decay through DXO-mediated deNADding. Cell. 2017;168(6):1015–1027 e10. doi:10.1016/j.cell.2017.02.019. PMID:28283058; PMCID:PMC5371429
  • Malygin AG, Shemyakin MF. Adenosine, NAD and FAD can initiate template-dependent RNA synthesis catalyzed by Escherichia coli RNA polymerase. FEBS Lett. 1979;102(1):51–54. doi:10.1016/0014-5793(79)80926-6. PMID:222618
  • Bird JG, Zhang Y, Tian Y, et al. The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA. Nature. 2016;535(7612):444–447. doi:10.1038/nature18622. PMID:27383794; PMCID:PMC4961592
  • Julius C, Yuzenkova Y. Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors. Nucleic Acids Res. 2017;45(14):8282–8290. doi:10.1093/nar/gkx452. PMID:28531287; PMCID:PMC5737558
  • Bennett BD, Kimball EH, Gao M, et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009;5(8):593–599. doi:10.1038/nchembio.186. PMID:19561621; PMCID:PMC2754216
  • Kulbachinskiy A, Mustaev A. Region 3.2 of the sigma subunit contributes to the binding of the 3'-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiation. J Biol Chem. 2006;281(27):18273–18276. doi:10.1074/jbc.C600060200. PMID:16690607
  • Frick DN, Bessman MJ. Cloning, purification, and properties of a novel NADH pyrophosphatase. Evidence for a nucleotide pyrophosphatase catalytic domain in MutT-like enzymes. J Biol Chem. 1995;270(4):1529–1534. doi:10.1074/jbc.270.4.1529. PMID:7829480
  • Zhang D, Liu Y, Wang Q, et al. Structural basis of prokaryotic NAD-RNA decapping by NudC. Cell Res. 2016;26(9):1062–1066. doi:10.1038/cr.2016.98. PMID:27561816; PMCID:PMC5034116
  • Hofer K, Li S, Abele F, et al. Structure and function of the bacterial decapping enzyme NudC. Nat Chem Biol. 2016;12(9):730–734. doi:10.1038/nchembio.2132. PMID:27428510; PMCID:PMC5003112
  • van Nues RW, Castro-Roa D, Yuzenkova Y, et al. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate. Nucleic Acids Res. 2016;44(6):2577–2592. doi:10.1093/nar/gkv1302. PMID:26609136; PMCID:PMC4824073
  • Deana A, Celesnik H, Belasco JG. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature. 2008;451(7176):355–358. doi:10.1038/nature06475. PMID:18202662
  • McLennan AG. The Nudix hydrolase superfamily. Cell Mol Life Sci. 2006;63(2):123–143. doi:10.1007/s00018-005-5386-7. PMID:16378245
  • Stein LR, Imai S. The dynamic regulation of NAD metabolism in mitochondria. Trends Endocrinol Metabol. 2012;23(9):420–428. doi:10.1016/j.tem.2012.06.005. PMID:22819213; PMCID:PMC3683958
  • Wanrooij PH, Uhler JP, Simonsson T, et al. G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation. Proc Natl Acad Sci U S A. 2010;107(37):16072–16077. doi:10.1073/pnas.1006026107. PMID:20798345; PMCID:PMC2941323
  • Veening JW, Stewart EJ, Berngruber TW, et al. Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci U S A. 2008;105(11):4393–4398. doi:10.1073/pnas.0700463105. PMID:18326026; PMCID:PMC2393751.
  • Fozo EM. New type I toxin-antitoxin families from “wild” and laboratory strains of E. coli: Ibs-Sib, ShoB-OhsC and Zor-Orz. RNA Biol. 2012;9(12):1504–1512. doi:10.4161/rna.22568. PMID:23182878
  • Melnyk AH, Wong A, Kassen R. The fitness costs of antibiotic resistance mutations. Evol Appl. 2015;8(3):273–283. doi:10.1111/eva.12196. PMID:25861385; PMCID:PMC4380921
  • Chen H, Shiroguchi K, Ge H, et al. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol. 2015;11(5):808. doi:10.15252/msb.20159000. PMID:25964259; PMCID:PMC4461401
  • Gaspari M, Falkenberg M, Larsson NG, et al. The mitochondrial RNA polymerase contributes critically to promoter specificity in mammalian cells. EMBO J. 2004;23(23):4606–4614. doi:10.1038/sj.emboj.7600465. PMID:15526033; PMCID:PMC533051