UvA-DARE (Digital Academic Repository) Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms Hammoudi, V.; Vlachakis, G.; Schranz, M.E.; van den Burg, H.A. DOI 10.1111/nph.13911 Publication date 2016 Document Version Final published version Published in New Phytologist Link to publication Citation for published version (APA): Hammoudi, V., Vlachakis, G., Schranz, M. E., & van den Burg, H. A. (2016). Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms. New Phytologist, 211(1), 172-185. https://doi.org/10.1111/nph.13911 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:30 Sep 2021 Research Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms Valentin Hammoudi1, Georgios Vlachakis1, M. Eric Schranz2 and Harrold A. van den Burg1 1Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1089 XH, Amsterdam, the Netherlands; 2Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands Summary Author for correspondence: The ubiquitin-like modifier (UBL) SUMO (Small Ubiquitin-Like Modifier) regulates protein Harrold van den Burg function. Structural rather than sequence homology typifies UBL families. However, individual Tel: +31 20 5257797 UBL types, such as SUMO, show remarkable sequence conservation. Selection pressure also Email: [email protected] operates at the SUMO gene copy number, as increased SUMO levels activate immunity and Received: 8 November 2015 alter flowering time in Arabidopsis. Accepted: 10 January 2016 We show how, despite this selection pressure, the SUMO family has diversified into eight paralogues in Arabidopsis. Relationships between the paralogues were investigated using New Phytologist (2016) 211: 172–185 genome collinearity and gene tree analysis. We show that palaeopolyploidy followed by doi: 10.1111/nph.13911 tandem duplications allowed expansion and then diversification of the SUMO genes. For example, Arabidopsis SUMO5 evolved from the pan-eudicot palaeohexaploidy event Key words: evolution, immunity, (gamma), which yielded three SUMO copies. Two gamma copies were preserved as neofunctionalization, palaeoploidy, archetype SUMOs, suggesting subfunctionalization, whereas the third copy served as a paralogue, protein modification, SUMO, hotspot for SUMO diversification. ubiquitin-like modifier. The Brassicaceae-specific alpha duplication then caused the duplication of one archetype gamma copy, which, by subfunctionalization, allowed the retention of both SUMO1 and SUMO2. The other archetype gamma copy was simultaneously pseudogenized (SUMO4/6). A tandem duplication of SUMO2 subsequently yielded SUMO3 in the Brassicaceae crown group. SUMO3 potentially neofunctionalized in Arabidopsis, but it is lost in many Brassi- caceae. Our advanced methodology allows the study of the birth and fixation of other par- alogues in plants. Introduction regulation, chromatin remodelling, DNA repair and DNA replication (Miller et al., 2010b, 2013; Flotho & Melchior, Post-translational modifications (PTMs) set a reversible mark on 2013). SUMO is translated as a precursor that undergoes C- proteins, altering their function (van der Veen & Ploegh, 2012). terminal processing by SUMO proteases (also known as ubiq- The first polypeptide that was discovered to act as a PTM was uitin-like proteases or ULPs). The processing exposes a C- ubiquitin (Ub), a highly conserved 76-residue polypeptide. Ub terminal diglycine (diGly) motif essential for conjugation. and ubiquitin-like modifiers (UBLs) are typified by their b-grasp Mature SUMO is conjugated to substrates via the E1 SUMO fold, which generates a highly stable tertiary structure resistant to Activating Enzyme dimer (SAE1/2) and the E2 SUMO Con- environmental perturbations, such as heat (Burroughs et al., jugating Enzyme (SCE1) (Saracco et al., 2007; Castano-Miquel 2012; Vierstra, 2012; Callis, 2014). There is limited sequence et al., 2013). On conjugation (SUMOylation), an isopeptide identity between UBL types, yet remarkable sequence conserva- bond is formed between the carboxyl terminus of mature tion is seen for individual UBL types across eukaryotes. For SUMO and the acceptor lysine (Lys) side chain. SUMOylation example, Ub is 96% identical between plants, yeast and mam- is an essential process, with mutations causing embryonic mals (Vierstra, 2003). lethality in mice and the model plant Arabidopsis (Arabidopsis A prominent UBL type is the Small Ubiquitin-Like Modi- thaliana) (Saracco et al., 2007; Wang et al., 2014). E3 ligases fier (SUMO), which is conserved across eukaryotes (Miura & can promote SUMOylation (Flotho & Melchior, 2013). In Hasegawa, 2010; Flotho & Melchior, 2013; Jentsch & Arabidopsis, two E3 ligases have been characterized. Loss of Psakhye, 2013). Its conjugation is primarily associated with the E3 ligase SIZ1 (SAP AND MIZ 1) causes dwarfism, early nuclear processes, such as nucleocytoplasmic transport, gene flowering, altered responses to abiotic stresses and activation of 172 New Phytologist (2016) 211: 172–185 Ó 2016 The Authors www.newphytologist.com New Phytologist Ó 2016 New Phytologist Trust This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. New Phytologist Research 173 plant immunity (Miura & Hasegawa, 2010; Park et al., 2011). The overexpression of tagged AtSUMO1 or AtSUMO2 vari- By contrast, the E3 ligase High Ploidy2 (HPY2/MMS21) ants causes the activation of plant immunity, reduced rosette size represses endocycle onset in meristems (Huang et al., 2009; and altered flowering time (Budhiraja et al., 2009; Van den Burg Ishida et al., 2009, 2012). SUMO conjugation is reversible et al., 2010). This suggests that enhanced SUMO levels caused and ULPs catalyse de-conjugation. Plant ULPs form at least by gene duplication of the archetype SUMOs potentially result in four subgroups that are conserved across angiosperms and a fitness cost in plants. A key question is how novel SUMO par- function non-redundantly (Conti et al., 2008; Novatchkova alogues have emerged with this evolutionary penalty. Here, we et al., 2012). report how the plant SUMO family has expanded and diversified In many eukaryotes, such as budding yeast (Saccharomyces in plants, focusing on Brassicaceae (a eudicot family) and Poaceae cerevisiae), fruit fly (Drosophila melanogaster) and the worm (a monocot family). Caenorhabditis elegans, SUMO is encoded by a single-copy gene The genome evolution of flowering plants has been massively (Flotho & Melchior, 2013). Yet, mammals and Arabidopsis shaped by palaeoploidy events (Van de Peer et al., 2009). For express up to four paralogues. The mammalian paralogues have example, one of the largest clades of angiosperms, eudicots, is functionally diversified, modifying distinct but overlapping pro- characterized by an ancient whole-genome triplication (hereafter tein subsets (Citro & Chiocca, 2013). At the sequence level, the called WGT At-c) that predates the split of the eudicot clades mammalian SUMO2 and SUMO3 are very similar (97% Asterids, Caryophyllales and Rosids (Tang et al., 2008; Dohm sequence identity), whereas SUMO1 only shares 47% sequence et al., 2014). Numerous gene duplicates and duplication blocks identity with SUMO2/3. Functionally, the mammalian have been retained from this pan-eudicot WGT across extant SUMO2/3 can form SUMO chains that target their substrates eudicots. Subsequently, two additional whole-genome duplica- for degradation, whereas SUMO1 cannot (Hay, 2013). SUMO1 tions (WGDs) (At-b (88–81 million yr ago (Ma)) and At-a and SUMO2/3 also interact with different proteins non- (47 Ma)) occurred in the Brassicales lineage, which comprises the covalently, as they prefer slightly different SUMO interaction family Brassicaceae (Vision et al., 2000; Hohmann et al., 2015). motifs (SIMs) in their partners (Hecker et al., 2006; Ghisletti These three palaeopolyploidy events would already have given et al., 2007; Meulmeester et al., 2008). Interestingly, the mam- rise to 12 gene copies in Arabidopsis for any SUMO copy present malian SUMO2 is essential for embryonic development, whereas in the ancestral species that underwent At-c. Importantly, exten- SUMO3 is dispensable (Wang et al., 2014). This functional dif- sive genome synteny remains from these polyploidy events, both ference between SUMO2 and SUMO3 appears to be caused by between