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The 2OGD Superfamily: Emerging Functions in Plant Epigenetics and Hormone Metabolism

2018; Elsevier BV; Volume: 11; Issue: 10 Linguagem: Inglês

10.1016/j.molp.2018.09.002

1674-2052

Riad Nadi, Eduardo Mateo‐Bonmatí, Lucía Juan-Vicente, José Luis Micol,

Photosynthetic Processes and Mechanisms

The 2-oxoglutarate and Fe (II)-dependent dioxygenase (2OGD) superfamily includes oxidative enzymes with an active site containing two histidines and (in most cases) one aspartic or glutamic acid residue. This conserved motif is termed the 2-His-1-carboxylate facial triad, chelates iron, and is housed within a double-stranded β-helix fold, also known as the DSBH, jelly-roll, cupin, or Jumonji C fold (Martinez and Hausinger, 2015Martinez S. Hausinger R.P. Catalytic mechanisms of Fe(II)- and 2-oxoglutarate-dependent oxygenases.J. Biol. Chem. 2015; 290: 20702-20711Crossref PubMed Scopus (243) Google Scholar). The reactions catalyzed by 2OGDs (also called 2ODDs, 2ODOs, and 2OGXs) include but are not limited to demethylation, demethylenation, hydroxylation, halogenation, desaturation, ring cleavage, ring closure, and epimerization (Farrow and Facchini, 2014Farrow S.C. Facchini P.J. Functional diversity of 2-oxoglutarate/Fe(II)-dependent dioxygenases in plant metabolism.Front. Plant Sci. 2014; 5: 524Crossref PubMed Scopus (104) Google Scholar). The list of plant 2OGDs is long and growing; for example, the Arabidopsis thaliana (hereafter, Arabidopsis) genome contains more than 150 genes encoding proteins containing a 2OGD domain. These Arabidopsis proteins can be classified into the DOXA, DOXB, DOXC (Kawai et al., 2014Kawai Y. Ono E. Mizutani M. Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants.Plant J. 2014; 78: 328-343Crossref PubMed Scopus (210) Google Scholar), and JMJ groups, which include 14, 14, 102, and 21 proteins, respectively. DOXA proteins are homologs of Escherichia coli alpha-ketoglutarate-dependent dioxygenase (AlkB), a DNA repair enzyme that reverses the N1-methyladenine (m1A) and N3-methylcytosine (m3C) lesions caused by alkylating agents. Nine AlkB homologs (ALKBHs) have been found in mammals, and their substrates include DNA (m1A and m3C), RNA (m6A, the most abundant RNA methylation mark), and proteins (methylated lysine). Two Arabidopsis DOXAs, the close paralogs ALKBH9B and ALKBH10B, have been recently found to demethylate m6A in RNA (Figure 1A). ALKBH9B is the first plant RNA demethylase described that demethylates m6A marks of specific foreign RNAs. ALKBH9B physically interacts with the coat protein of Alfalfa mosaic virus (AMV), thereby regulating its capacity for infection. AMV-infected alkbh9b Arabidopsis mutants exhibit reduced systemic infection and lower levels of viral RNA, which was found to be hypermethylated. In addition, ALKBH9B demethylates single-stranded AMV RNA in vitro (Martínez-Pérez et al., 2017Martínez-Pérez M. Aparicio F. López-Gresa M.P. Bellés J.M. Sánchez-Navarro J.A. Pallás V. Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs.Proc. Natl. Acad. Sci. USA. 2017; 114: 10755-10760Crossref PubMed Scopus (151) Google Scholar). ALKBH10B demethylates endogenous mRNAs in Arabidopsis. The alkbh10b mutant flowers late due to instability of mRNAs from genes regulating flowering time. ALKBH10B reduces the m6A methylation of FLOWERING LOCUS T, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3), and SPL9 mRNAs, increasing their stability and capacity to trigger the floral transition (Duan et al., 2017Duan H.C. Wei L.H. Zhang C. Wang Y. Chen L. Lu Z. Chen P.R. He C. Jia G. ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition.Plant Cell. 2017; 29: 2995-3011Crossref PubMed Scopus (157) Google Scholar). Proteins of the DOXB clade have a subtype of the 2OGD domain, the prolyl 4-hydroxylase (P4Hc) domain. Animal P4H proteins play a key role in the biosynthesis of collagen, the main structural component of the extracellular space in many tissues. Some plant P4Hs catalyze post-translational modifications of cell wall hydroxyproline-rich O-glycoproteins, such as extensins, which are structurally similar to collagen. Arabidopsis P4H2, P4H5, and P4H13 participate in extensin hydroxylation (Figure 1B), which is required for proper cell wall architecture and thus root hair tip growth (Velasquez et al., 2015Velasquez S.M. Ricardi M.M. Poulsen C.P. Oikawa A. Dilokpimol A. Halim A. Mangano S. Denita Juarez S.P. Marzol E. Salgado Salter J.D. et al.Complex regulation of prolyl-4-hydroxylases impacts root hair expansion.Mol. Plant. 2015; 8: 734-746Abstract Full Text Full Text PDF PubMed Scopus (45) Google Scholar). The recently discovered CUPULIFORMIS (CP) family includes five proteins already annotated as 2OGDs with a P4Hc: INCURVATA11 (ICU11), and CP2 to CP5. The icu11 mutants have hyponastic leaves and early flowering, traits that they share with mutants affected in genes encoding some components of the epigenetic machinery, such as CURLY LEAF (CLF), a Polycomb-group (PcG) gene. The cp2 mutants are indistinguishable from wild type, but the icu11 cp2 double mutants exhibit a severe, post-embryonic lethal phenotype reminiscent of single mutants carrying alleles of the PcG genes EMBRYONIC FLOWER 1 (EMF1) and EMF2. The icu11 mutants have ectopic and heterochronic derepression of hundreds of genes, and in at least some of these genes, histone methylation and acetylation are altered, suggesting that ICU11 and CP2 act redundantly as epigenetic repressors through histone modification but not DNA methylation. Unlike P4H2, P4H5, and P4H13, which localize to the secretory pathway, ICU11 and CP2 are nucleoplasmic proteins (Mateo-Bonmatí et al., 2018Mateo-Bonmatí E. Esteve-Bruna D. Juan-Vicente L. Nadi R. Candela H. Lozano F.M. Ponce M.R. Pérez-Pérez J.M. Micol J.L. INCURVATA11 and CUPULIFORMIS2 are redundant genes that encode epigenetic machinery components in Arabidopsis.Plant Cell. 2018; 30: 1596-1616Crossref PubMed Scopus (11) Google Scholar). The Jumonji C (JmjC) domain-containing (JMJ) proteins function in the demethylation by hydroxylation of lysine residues in histones (Figure 1C). Mutations in Arabidopsis JMJ genes affect reproductive development and plant immunity. For example, flowering time is modulated by JMJ27, which demethylates H3K9me1/2 in vitro and in vivo, and directly or indirectly removes H3K9me2 methyl marks from the promoters of major flowering time genes, including FLOWERING LOCUS C, which encodes a repressor of flowering (Dutta et al., 2017Dutta A. Choudhary P. Caruana J. Raina R. JMJ27, an Arabidopsis H3K9 histone demethylase, modulates defense against Pseudomonas syringae and flowering time.Plant J. 2017; 91: 1015-1028Crossref PubMed Scopus (46) Google Scholar). Different to the direct histone demethylase activity of other JMJs, JMJ24 indirectly demethylates H3K9me2. JMJ24 has a 2OGD domain that has lost demethylating activity but is able to bind H3, and also a RING domain, which is shared by many ubiquitin ligases. JMJ24 prevents DNA methylation in the CHG context, destabilizing the DNA methyltransferase CHROMOMETHYLASE3 (CMT3). Through its RING motif, JMJ24 ubiquitinates CMT3, tagging it for degradation. Hence, CHG but not CG or CHH methylation increased in the jmj24 mutant as a consequence of excess CMT3 function. Given the positive feedback loop between CHG methylation and H3K9me2, JMJ24 apparently regulates the presence of H3K9me2 by controlling CHG methylation (Deng et al., 2016Deng S. Jang I.C. Su L. Xu J. Chua N.H. JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in Arabidopsis.Genes Dev. 2016; 30: 251-256Crossref PubMed Scopus (17) Google Scholar, Kabelitz et al., 2016Kabelitz T. Brzezinka K. Friedrich T. Górka M. Graf A. Kappel C. Bäurle I. A JUMONJI protein with E3 ligase and histone H3 binding activities affects transposon silencing in Arabidopsis.Plant Physiol. 2016; 171: 344-358Crossref PubMed Scopus (14) Google Scholar). DOXCs are the largest and most functionally diverse class of 2OGDs. These enzymes act in plant metabolism, including biosynthesis and/or catabolism of lignans, isoprenoids, flavonoids, glucosinolates, alkaloids, and coumarins. DOXCs play important roles in ethylene, gibberellin, auxin, and salicylic acid homeostasis (Kawai et al., 2014Kawai Y. Ono E. Mizutani M. Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants.Plant J. 2014; 78: 328-343Crossref PubMed Scopus (210) Google Scholar). The terpenoid strigolactones, which optimize plant growth and development and promote soil microbe interactions, were recently added to this list of hormones. Carlactone (CL) is a common precursor to all strigolactones. Treatments modifying auxin levels and mutations that alter strigolactone homeostasis change the expression levels of MORE AXILLARY GROWTH 3 (MAX3) and MAX4, which encode enzymes required for CL biosynthesis. Wild-type plants treated with an auxin transport inhibitor, decapitated, or decapitated and treated with auxin were subjected to transcriptomic analysis, together with the max mutants. Some genes were found coexpressed with MAX3, and study of the mutant alleles of these genes identified LATERAL BRANCHING OXIDOREDUCTASE (LBO) as a DOXC protein that oxidizes methyl carlactonoate (MeCLA) to render an unidentified strigolactone-like compound (Figure 1D). The lbo mutants exhibit increased shoot branching, a phenotype associated with strigolactone depletion (Brewer et al., 2016Brewer P.B. Yoneyama K. Filardo F. Meyers E. Scaffidi A. Frickey T. Akiyama K. Seto Y. Dun E.A. Cremer J.E. et al.LATERAL BRANCHING OXIDOREDUCTASE acts in the final stages of strigolactone biosynthesis in Arabidopsis.Proc. Natl. Acad. Sci. USA. 2016; 113: 6301-6306Crossref PubMed Scopus (146) Google Scholar). Auxin controls many aspects of plant growth and development. The optimal concentration of indole-3-acetic acid (IAA), the major form of active auxin, is regulated by mechanisms including its degradation and reversible conjugation. Arabidopsis DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1) is a DOXC protein recently shown to be the major regulator of auxin degradation; DAO1 oxidizes IAA to the inactive 2-oxoindole-3-acetic acid (oxIAA) (Figure 1E). IAA levels in the dao1 mutants were only mildly affected, in spite of the strong variations in the concentration of oxIAA and IAA conjugates shown by these mutants. DAO1 seems to act redundantly with GH3 IAA-conjugating enzymes to maintain optimal IAA concentrations (Porco et al., 2016Porco S. Pěncik A. Rashed A. Voß U. Casanova-Sáez R. Bishopp A. Golebiowska A. Bhosale R. Swarup R. Swarup K. et al.Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis.Proc. Natl. Acad. Sci. USA. 2016; 113: 11016-11021Crossref PubMed Scopus (115) Google Scholar, Zhang et al., 2016Zhang J. Lin J.E. Harris C. Pereira F.C.M. Wu F. Blakeslee J.J. Peer W.A. DAO1 catalyzes temporal and tissue-specific oxidative inactivation of auxin in Arabidopsis thaliana.Proc. Natl. Acad. Sci. USA. 2016; 113: 11010-11015Crossref PubMed Scopus (88) Google Scholar). The lipid-derived hormone jasmonic acid (JA) plays a key role activating defense responses to pathogen attack or wounding. Most JA responses require JA activation to form the conjugate jasmonoyl-isoleucine (JA-Ile). The DOXC paralogs JASMONATE-INDUCED OXYGENASE 1 (JOX1) to JOX4, also named JASMONIC ACID OXIDASES (JAOs), have been recently found to hydroxylate JA to 12-hydroxy-JA (12-OH-JA) (Figure 1F). The jao2 mutants display permanent defense expression in the absence of stress, and strongly increased resistance against subsequent fungal infection. At least three of the JOX/JAO paralogs hydroxylate JA into 12-OH-JA in vitro. JAO2/JOX2 defines a metabolic diversion mechanism that contributes to maintain JA-Ile-dependent responses repressed in wild-type plants (Caarls et al., 2017Caarls L. Elberse J. Awwanah M. Ludwig N.R. de Vries M. Zeilmaker T. Van Wees S.C.M. Schuurink R.C. Van den Ackerveken G. Arabidopsis JASMONATE-INDUCED OXYGENASES down-regulate plant immunity by hydroxylation and inactivation of the hormone jasmonic acid.Proc. Natl. Acad. Sci. USA. 2017; 114: 6388-6393Crossref PubMed Scopus (91) Google Scholar, Smirnova et al., 2017Smirnova E. Marquis V. Poirier L. Aubert Y. Zumsteg J. Ménard R. Miesch L. Heitz T. Jasmonic acid oxidase 2 hydroxylates jasmonic acid and represses basal defense and resistance responses against Botrytis cinerea infection.Mol. Plant. 2017; 10: 1159-1173Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). Members of the large and ancient 2OGD superfamily participate in post-translational and epigenetic processes, as well as in metabolic pathways. In plants, the functions of most 2OGDs remain uncharacterized. Some enzymatic activities of the recently described plant 2OGDs mentioned above were somewhat predictable from their homologs across kingdoms, such as those of ALKBHs and JMJs in demethylating nucleic acids and histones, respectively. By contrast, the CP proteins play a role completely unexpected for the DOXB class, because they behave as components of the epigenetic machinery instead of participating in post-translational modification of cell wall proteins. In addition, the roles of the LBO, DAO1, and JAO/JOX DOXC genes in strigolactone biosynthesis, auxin and JA-Ile down-regulation, respectively, were also somewhat unexpected; identification of these genes has allowed the discovery of missing metabolic pathway steps. Phylogenetic analyses have eased functional studies of gene families. The full-length sequences of the 2OGD superfamily members, however, show low identities and similarities, which hinder their reliable clustering and the study of their evolutionary relationships. Combinations of phylogenetic, transcriptomic, and forward and reverse genetic analyses have proven to be useful for 2OGD functional studies, and have shown that in some cases, jointly clustered members of a clade may have divergent and/or additional roles, as seen for the CP family of DOXBs or JMJ24. Functional redundancy is a major limitation for the functional analysis of the members of large gene families, as shown by the icu11 and cp2 mutants—and to a lesser extent, the jao/jox mutants—mentioned here. Re-examination of some clades of the 2OGD superfamily using approaches to overcome the genetic redundancy may uncover novel functions, which may involve domains or motifs other than the 2OGD domain in these proteins. Although some JMJ proteins contain domains additional to the JmjC domain, such as JmjN, zinc finger, tudor, and PHD finger domains, this does not seem to be the case for the remaining 2OGDs. As already shown for some gene families, CRISPR-based technologies may be used to simultaneously inactivate groups of 2OGD paralogs, producing plants homozygous for multiple mutations. These technologies also provide ways to modify genes in vivo for the production of tagged but fully functional proteins, allowing fast purification of protein complexes and the identification of protein interactors on a large scale. These experimental approaches will speed up the unraveling of novel 2OGD catalytic activities in already known or yet unknown pathways. Plant metabolism is estimated to produce hundreds of thousands of compounds. Kawai et al., 2014Kawai Y. Ono E. Mizutani M. Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants.Plant J. 2014; 78: 328-343Crossref PubMed Scopus (210) Google Scholar noted that the number of DOXA and DOXB proteins is similar in all the plant taxa they studied, whereas 31 of the 57 DOXC-class clades they defined were found only in a single species. This indicates that 2OGDs are at least partially responsible for the diversification of plant metabolites. Thus, further searches for novel members of this superfamily probably will reveal novel biosynthetic pathways. This work was supported by grants from the Ministerio de Economía, Industria y Competitividad of Spain (BIO2014-53063-P) and the Generalitat Valenciana (PROMETEOII/2014/006) to J.L.M.