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Arabidopsis Thaliana Sang-Hoon Kim1, Claus-Peter Witte2 and Sangkee Rhee 1,3,*

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Arabidopsis Thaliana Sang-Hoon Kim1, Claus-Peter Witte2 and Sangkee Rhee 1,3,* Published online 8 December 2020 Nucleic Acids Research, 2021, Vol. 49, No. 1 491–503 doi: 10.1093/nar/gkaa1144 Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana Sang-Hoon Kim1, Claus-Peter Witte2 and Sangkee Rhee 1,3,* 1Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea, 2Department of Molecular Downloaded from https://academic.oup.com/nar/article/49/1/491/6027816 by Fachbereichsbibliothek user on 22 March 2021 Nutrition and Biochemistry of Plants, Leibniz University Hannover, Hannover, Germany and 3Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea Received June 24, 2020; Revised November 06, 2020; Editorial Decision November 06, 2020; Accepted November 10, 2020 ABSTRACT presently more than 140 known post-transcriptional modi- fications in RNAs. Specific enzymes are required forRNA RNA modifications can regulate the stability of modification. Enzymes introducing and removing modi- RNAs, mRNA–protein interactions, and translation fications are called writers and erasers, respectively, and efficiency. Pseudouridine is a prevalent RNA mod- the information stored in the modifications is interpreted ification, and its metabolic fate after RNA turnover via reader proteins (1–3). N6-Methylated adenine (m6A) was recently characterized in eukaryotes, in the plant and pseudouridine (), a C5-glycoside isomer of uridine Arabidopsis thaliana. Here, we present structural and (Figure 1A), are the most prevalent RNA modifications biochemical analyses of PSEUDOURIDINE KINASE (3,4). N6-Methylated adenine occurs mainly in messenger from Arabidopsis (AtPUKI), the enzyme catalyzing RNAs (mRNAs) and regulates for example mRNAs sta- the first step in pseudouridine degradation. AtPUKI, bility, accessibility to RNA-binding proteins, and transla- a member of the PfkB family of carbohydrate kinases, tion efficiency (3). By contrast, was first found in non- coding RNA, including transfer RNA (tRNA) and riboso- is a homodimeric ␣/␤ protein with a protruding small ␤ mal RNA (rRNA) (5), and only recently in mRNAs (6,7). -strand domain, which serves simultaneously as In Arabidopsis thaliana, there are 187 sites in rRNAs, 232 dimerization interface and dynamic substrate speci- sites in tRNAs, and more than 450 sites in mRNAs (8). ficity determinant. AtPUKI has a unique nucleoside plays a role in the folding of rRNAs and in the stabiliza- binding site specifying the binding of pseudourine, in tion of tRNA structures (9,10). In mRNA from yeast and particular at the nucleobase, by multiple hydrophilic human cells, pseudouridylation is regulated in response to interactions, of which one is mediated by a loop from changing cellular environments (6,7), and its presence alters the small ␤-strand domain of the adjacent monomer. translation (11). In plant mRNA, the role of pseudouridy- Conformational transition of the dimerized small ␤- lation is not yet clear. strand domains containing active site residues is re- Compared to the knowledge regarding the biogenesis quired for substrate specificity. These dynamic fea- and regulatory functions of RNA modifications, little is known about the metabolic fate of non-canonical nu- tures explain the higher catalytic efficiency for pseu- cleotides derived from the degradation of modified RNAs. douridine over uridine. Both substrates bind well Metabolic turnover of m6A- or -containing RNAs pro- (similar Km), but only pseudouridine is turned over duces the non-canonical nucleotides N6-methyl-adenosine efficiently. Our studies provide an example for struc- monophosphate (N6-mAMP) or pseudouridine monophos- tural and functional divergence in the PfkB family phate (MP) as products. Enzymes for the degradation and highlight how AtPUKI avoids futile uridine phos- of these modified nucleotides in eukaryotes have only re- phorylation which in vivo would disturb pyrimidine cently been discovered (12,13). In Arabidopsis plants and homeostasis. human cells, N6-mAMP deaminase hydrolyzes N6-mAMP, generating inosine monophosphate (IMP) (12), which is an intermediate of either purine nucleotide biosynthesis INTRODUCTION or catabolism (14,15). The N6-mAMP deaminase reac- RNA modifications play an important role in regulating the tion thus converts a non-canonical nucleotide into a nu- stability of various coding and non-coding RNAs, and in- cleotide occurring in general nucleotide metabolism. The fluence gene expression1 ( ,2). Across all organisms, there are elucidation of the structure of N6-mAMP deaminase from *To whom correspondence should be addressed. Tel: +82 2 880 4647; Fax: +82 2 873 3112; Email: [email protected] C The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] 492 Nucleic Acids Research, 2021, Vol. 49, No. 1 Downloaded from https://academic.oup.com/nar/article/49/1/491/6027816 by Fachbereichsbibliothek user on 22 March 2021 Figure 1. Reaction scheme of pseudouridine catabolism and sequence comparison of PUKI from different sources. (A)InArabidopsis thaliana, pseudouri- dine degradation requires two enzymatic reactions occurring in the peroxisome. PUKI phosphorylates pseudouridine with ATP as a phosphate donor to 5-MP, which is hydrolyzed into uracil and ribose 5-phosphate by PUMY. (B) The amino acid sequence of AtPUKI (At1g49350) is compared to that of other PUKI homologs from soybean (Glycine max), pepper (Capsicum annuum)rice(Oryza sativa), and a tobacco species (Nicotiana sylvestris). Highly conserved residues are shown in red and are boxed in blue, while strictly conserved residues are shown with a red background. Secondary structural ele- ments defined in unliganded AtPUKI are shown for the corresponding sequences. Residues or structural elements are indicated using the following color code: residues in the substrate pocket for pseudouridine, black circles; ADP-binding residues, gray triangles; putative catalytic residues, black asterisks; the nucleoside substrate-binding loop, green bar; the small ATP-binding loop (Gly239–Asn241), magenta bar; the large ATP-binding loop (Pro297–Gly308), light blue bar. This figure was prepared using ESPript48 ( ). Arabidopsis showed that this enzyme undergoes a ligand- The catabolic pathway for MP has recently been de- induced conformational change and identified the amino scribed in Arabidopsis (13). In this plant, a significant pro- acids in the active site that mediate the substrate speci- portion of RNA degradation seems to occur in the vac- ficity (16,17). The discovery of the in-vivo role of N6-mAMP uole (18,19), where breakdown of -containing RNA gen- deaminase has shown for the first time that eukaryotic erates MP (presumably 3-MP), which is then dephos- cells can catabolize non-canonical nucleotides released from phorylated to pseudouridine and exported to the cytosol modified nucleic acids. (13). For degradation, pseudouridine must reach the per- Nucleic Acids Research, 2021, Vol. 49, No. 1 493 oxisome. The catabolic pathway for pseudouridine in the coding sequence for an N-terminal (His)6-maltose bind- peroxisome consists of two enzymes: PSEUDOURIDINE ing protein (MBP) and the multiple cloning site. Later, we KINASE (PUKI), which phosphorylates pseudouridine to found that the (His)6-MBP tag could not be cleaved by 5-MP, and PSEUDOURIDINE MONOPHOSPHATE the TEV protease during purification. For a facile cleav- GLYCOSYLASE (PUMY), which hydrolyzes 5-MP pro- age of the tag, which is required for crystallization, addi- ducing uracil and ribose 5-phosphate (Figure 1A) (13). Both tional linkers coding for Gly-Gly-Gly-Ser (GGGS) were in- reaction products are intermediates of main metabolic path- serted, resulting in the N-terminal region of the AtPUKI ways. Uracil may be reincorporated into uridine monophos- fusion protein containing the sequence (H)6-MBP-GGGS- phate in a so-called salvage reaction or may enter pyrimi- GGGS-ENLYFQS (TEV protease cleavage site)–GGGS. dine ring catabolism (20, 21). Ribose 5-phosphate may be Escherichia coli BL21 (DE3) cells (Merck) transformed with Downloaded from https://academic.oup.com/nar/article/49/1/491/6027816 by Fachbereichsbibliothek user on 22 March 2021 activated to 5-phosphoribosyl 1-pyrophosphate needed for the resulting construct were cultured at 37◦C in Luria- phosphoribosyl transfer reactions or may enter the pentose Bertani medium until the absorbance at 600 nm reached phosphate pathway. PUKI and PUMY are required for the 0.6. Expression of AtPUKI was induced with 0.5 mM removal of pseudouridine. Malfunction of these enzymes isopropyl-␤-D-1-thiogalactopyranoside, followed by incu- causes massive accumulation of pseudouridine, resulting in bation at 12◦C for 40 h. Cells were collected by centrifuga- spurious formation of 5-MP catalyzed by cytosolic UMP tion and sonicated in buffer A (50 mM Tris–HCl at pH 8.0, kinases. Cytosolic 5-MP appears to be particularly toxic 300 mM NaCl, 2 mM dithiothreitol, and 5% [w/v] glycerol), and causes delayed seed germination and growth inhibition and the supernatant was obtained by centrifugation at 30 (13). 000 × gfor1hat4◦C. The fusion protein was purified using
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