Origin and Evolution of Peptide-Modifying Dioxygenases and Identification of the Wybutosine Hydroxylase/Hydroperoxidase Lakshminarayan M
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Published online 27 April 2010 Nucleic Acids Research, 2010, Vol. 38, No. 16 5261–5279 doi:10.1093/nar/gkq265 Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase Lakshminarayan M. Iyer, Saraswathi Abhiman, Robson F. de Souza and L. Aravind* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Received February 26, 2010; Revised March 26, 2010; Accepted March 30, 2010 ABSTRACT eukaryotic enzymes. The specificity of wybutosine Unlike classical 2-oxoglutarate and iron-dependent hydroxylase/peroxidase probably relates to the dioxygenases, which include several nucleic acid structural similarity of the modified moiety to the modifiers, the structurally similar jumonji-related ancestral amino acid substrate of this superfamily. dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative INTRODUCTION genomics methods, we predict that a family of RNAs, especially transfer RNAs (tRNA), show diverse jumonji-related enzymes catalyzes wybutosine hy- post-translational modifications of bases. To date, at droxylation/peroxidation at position 37 of eukaryotic least 90 distinct modifications have been described (1,2). tRNAPhe. Identification of this enzyme raised ques- These include simple substitutions (e.g. deamination of tions regarding the emergence of protein- and adenosine to inosine), addition of small functional nucleic acid-modifying activities among jumonji- groups to bases (such as a methyl group in related domains. We addressed these with a 1-methylguanosine) and chemical transformations result- natural classification of DSBH domains and recon- ing in large complex bases (such as threonyl structed the precursor of the dioxygenases as a carbamoyladenosine, queuosine and wyosine and their further derivatives). A veritable biochemical menagerie sugar-binding domain. This precursor gave rise to of enzymes catalyzing these modifications has become sugar epimerases and metal-binding sugar isomer- apparent over the past 15 years through a combination ases. The sugar isomerase active site was exapted of computational and experimental studies (1). The cata- for catalysis of oxygenation, with a radiation of lytic mechanisms and phyletic distributions of these these enzymes in bacteria, probably due to enzymes have greatly contributed to our understanding impetus from the primary oxygenation event in of novel biochemical reactions and the evolutionary sig- Earth’s history. 2-Oxoglutarate-dependent versions nificance of RNA modifications, respectively. However, appear to have further expanded with rise of the lacunae remain in terms of candidate enzymes and tricarboxylic acid cycle. We identify previously reaction mechanisms responsible for several of the more under-appreciated aspects of their active site and complex modifications. Modified bases are particularly multiple independent innovations of 2-oxoacid- prevalent at position 37 of tRNA, which is adjacent to the anticodon, and is known to stabilize mRNA–tRNA binding basic residues among these superfamilies. pairing and maintenance of reading frame (1,3). An im- We show that double-stranded b-helix dioxygenases portant complex base derived from guanosine is diversified extensively in biosynthesis and modifica- wybutosine (yW) present at position 37 of tRNAPhe in tion of halogenated siderophores, antibiotics, eukaryotes. Precursors of yW, such as wyosine and its peptide secondary metabolites and glycine-rich derivatives, are detected in the same position in collagen-like proteins in bacteria. Jumonji-related tRNAPhe in archaea (4–6). In contrast, bacteria contain domains diversified into three distinct lineages in an adenosine at position 37 of tRNAPhe and may show a bacterial secondary metabolism systems and completely different modification at this position such as these were precursors of the three major clades of isopentenyladenosine and its derivatives (7). Biochemical *To whom correspondence should be addressed. Tel: +1 301 594 2445; Fax: +1 301 480 9241; Email: [email protected] Published by Oxford University Press 2010. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 5262 Nucleic Acids Research, 2010, Vol. 38, No. 16 studies in Saccharomyces cerevisiae have identified five group of proteins, frequently termed cupins, are also proteins, Trm5, Tyw1, Tyw2, Tyw3 and Tyw4, in the bio- known to share a similar DSBH fold with the above two synthetic pathway that convert a guanosine to yW superfamilies. These are typified by the non-catalytic (Figure 1; 8). Orthologs of some of these enzymes, such sugar-binding domain of the bacterial transcription as Trm5, Tyw1, Tyw2 and Tyw3 are also present in factor AraC, the plant seed-storage proteins and archaea, which synthesize yW precursors such as enzymes such as the oxalate oxidase and sugar 4-demethylwyosine and its archaeal-specific derivatives epimerases/isomerases (e.g. RmlC, mannose-6-phosphate (5,6,9,10). This suggests that the basic pathway for yW isomerase and glucose-6-phosphate isomerase; 25). In the biosynthesis was already present in the common literature, there is rampant confusion in the nomenclature archaeo-eukaryotic ancestor, and was further elaborated of these proteins with different overlapping groups termed in eukaryotes. Though yW is an ancestral modification, it cupins, JmjC or 2OGFeDO without a regard for their shows considerable variation in its distribution across eu- biochemistry (i.e. dependence on 2-oxoglutarate, or con- karyotes. A particularly prevalent variant of yW is its figuration of active site residues) or an objective analysis hydroxy or hydroperoxide derivative that is observed in of their actual evolutionary relationships. This has several eukaryotes like animals (including humans) and hindered an evaluation of the emergence of multiple fungi such as Geotrichum candidum (6,11,12). Despite the nucleic acid- and protein-modifying activities among complete characterization of the yW pathway in yeast, the these enzymes—e.g. questions pertaining to how many enzyme/s catalyzing the hydroxylation or peroxidation of these biopolymer-modifying activities emerged step resulting in hydroxywybutosine and/or hydroperoxy- convergently as opposed to divergently and from what wybutosine has evaded detection (6). kind of precursors. Hence, we undertook a systematic Using sensitive computational analysis, we have higher order classification of the catalytic and small- recently described several novel nucleic acid-modifying molecule-binding DSBH fold proteins and objectively enzymes that were predicted to catalyze hydroxylation of defined major evolutionary radiations within them. This bases (13). Most of these belong to the clade of classical provided a new understanding of the major catalytic in- 2-oxoglutarate and iron-dependent dioxygenases novations within the fold. We also clarified relationships (2OGFeDO) with the double-stranded b-helix fold within the jumonji-related superfamily and the higher (DSBH), which includes numerous enzymes acting on order relationship of this superfamily to other members diverse substrates such as: amino acids and proteins (e.g. of this fold. We present evidence that enzymes belonging EGL-9, prolyl and lysyl hydroxylases), small molecules to all the distinct superfamilies of the DSBH fold under- (e.g. clavaminate synthase, isopenicillin synthase and went major radiations within a previously unappreciated plant leukoanthocyanin hydroxylases), antibiotic precur- array of bacterial biosynthetic systems that are involved in sors (e.g. halogenases in syringomycin and coronamic synthesis of hydroxylated and halogenated peptide– acid) and bases in RNA and DNA (such as the derived secondary metabolites. Based on this, we DNA-repair protein AlkB, TET/JBP and thymine-7- propose that peptide-modifying activities are likely to be hydroxylases; 14–19). Subsequent experimental studies the ancestral feature of the jumonji-related superfamily. on some of the enzymes we identified have confirmed Three distinct lineages of jumonji-like enzymes emerged that indeed some of these mediate the hydroxylation of in bacteria within the context of these biosynthetic bases in DNA such as 5-methylcytosine, while others systems and were transferred to eukaryotes, where they were predicted to perform similar modifications in RNA radiated further to acquire protein and RNA-modifying (13,20). Yet, none of these newly identified enzymes specificities. showed the phyletic patterns or other contextual features that made them candidates for the yW hydroxylase/ peroxidase. MATERIALS AND METHODS Hence, we undertook a new computational study of the yW biosynthesis pathway and identified an enzyme which Structure similarity searches were conducted using the belongs to a structurally related but distinct superfamily FSSP program (26), and structural alignments were of dioxygenases, the jumonji-related (JOR/JmjC) made using the MUSTANG program (27). Protein struc- dioxygenases (21–23), as the yW hydroxylase/peroxidase. tures were visualized and manipulated using the This identification provided us with a molecular marker to Swiss-PDB (28) and PyMol programs (http://www infer the diversity of the position 37 of tRNAPhe