Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine

Young, Anthony P.; Bandarian, Vahe

doi:10.1016/j.cbpa.2013.05.035

Cited by 22 publications

(30 citation statements)

References 36 publications

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“…IPP and GPP were purchased from Isoprenoids. [4][5][6][7][8][9][10][11][12][13][14] C]IPP was purchased from PerkinElmer Life Sciences. HEK293T cell line was obtained from ATCC.…”

Section: Methodsmentioning

confidence: 99%

“…For example, radical SAM-dependent enzymes participate in the biosynthesis of herbicides, antibiotics, vitamins, co-factors such as biotin and thiamin, and various other natural products (2,(5)(6)(7)(8). They also function in the modification of ribosomal and transfer RNAs (9,10) and DNA repair (11) and in the post-translational modification of peptides and proteins (12)(13)(14). Sequence analyses indicate that there are potentially thousands of members of the radical SAM superfamily, but to date, relatively few of these enzymes have been isolated and characterized (15,16).…”

Section: Radical S-adenosyl-l-methionine-dependent (Sam)mentioning

confidence: 99%

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Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity?

Makins

Ghosh²,

Román‐Meléndez³

et al. 2016

Journal of Biological Chemistry

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Edited by Charles SamuelViperin is an endoplasmic reticulum-associated antiviral responsive protein that is highly up-regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-L-methionine (SAM) enzyme, but it is unknown whether viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS). Numerous enveloped viruses utilize cholesterol-rich lipid rafts to bud from the host cell membrane, and it is thought that by inhibiting FPPS activity (and therefore cholesterol synthesis), viperin retards viral budding from infected cells. We demonstrate that, consistent with this hypothesis, overexpression of viperin in human embryonic kidney cells reduces the intracellular rate of accumulation of FPPS but does not inhibit or inactivate FPPS. The endoplasmic reticulum-localizing, N-terminal amphipathic helix of viperin is specifically required for viperin to reduce cellular FPPS levels. However, although viperin reductively cleaves SAM to form 5-deoxyadenosine in a slow, uncoupled reaction characteristic of radical SAM enzymes, this cleavage reaction is independent of FPPS. Furthermore, mutation of key cysteinyl residues ligating the catalytic [Fe 4 S 4 ] cluster in the radical SAM domain, surprisingly, does not abolish the inhibitory activity of viperin against FPPS; indeed, some mutations potentiate viperin activity. These observations imply that viperin does not act as a radical SAM enzyme in regulating FPPS. Radical S-adenosyl-L-methionine-dependent (SAM)3 enzymes constitute a superfamily of enzymes that use SAM to generate free radicals (1-4). The superfamily is typified by a common CXXXCXXC motif, the cysteinyl residues of which coordinate a [Fe 4 S 4 ] cluster that is essential for radical generation. These enzymes catalyze a remarkably wide range of reactions involving an equally diverse set of substrates (2). For example, radical SAM-dependent enzymes participate in the biosynthesis of herbicides, antibiotics, vitamins, co-factors such as biotin and thiamin, and various other natural products (2, 5-8). They also function in the modification of ribosomal and transfer RNAs (9, 10) and DNA repair (11) and in the post-translational modification of peptides and proteins (12)(13)(14). Sequence analyses indicate that there are potentially thousands of members of the radical SAM superfamily, but to date, relatively few of these enzymes have been isolated and characterized (15, 16). Radical SAM enzymes were until recently thought to be confined to the microbial realm but intriguingly have now been identified in higher aerobic organisms, including plants and animals (3).Central to the mechanism of all radical SAM enzymes is the generation of a highly reactive 5Ј-deoxyadenosyl radical (Ado ⅐ ) (1,4,17). This is accomplished through one-electron reduction of SAM by the [Fe 4...

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“…IPP and GPP were purchased from Isoprenoids. [4][5][6][7][8][9][10][11][12][13][14] C]IPP was purchased from PerkinElmer Life Sciences. HEK293T cell line was obtained from ATCC.…”

Section: Methodsmentioning

confidence: 99%

Section: Radical S-adenosyl-l-methionine-dependent (Sam)mentioning

confidence: 99%

Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity?

Makins

Ghosh²,

Román‐Meléndez³

et al. 2016

Journal of Biological Chemistry

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“…Concerning the yW base and its derivatives, it is interesting to note its complex biosynthesis in which up to six molecules of S-adenosyl-methionine are involved in successive methylations catalyzed by different enzymes (Young and Bandarian 2013). Taken together, these observations suggest a strong link between the modification of tRNA and the cellular metabolic state.…”

Section: The State Of the Trna Population In The Cellmentioning

confidence: 97%

Protein folding and tRNA biology

2017

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Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

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“…A variant of this mechanism has been proposed in which pyruvate initially forms a Schiff base with a conserved and essential lysine (K41) upstream of the Radical-SAM cluster. 32,34 However, no evidence for such an adduct could be obtained either by UV-vis spectroscopy or by reductive trapping as commonly used for characterization of Schiff bases in PLP-containing enzymes. 35 On the contrary, preliminary Electron Paramagnetic Resonance (EPR) data obtained with the K41A mutant suggest that K41 is not at bonding distances of cluster II and rather plays an essential role in controlling the redox state of cluster II (T. Molle et al, to be published).…”

Section: Trna-4-demethylwyosine Synthase Tyw1mentioning

confidence: 99%