Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison

Abstract

SummaryThe conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.

Arabidopsis PIAL1 and 2 Promote SUMO Chain Formation as E4-Type SUMO Ligases and Are Involved in Stress Responses and Sulfur Metabolism

“…One striking difference between them is the presence of an insertion consisting of seven repeats of 23 amino acids in PIAL1, but not in PIAL2 (Supplemental Figure 3C). PIAL1 and 2 have potential orthologs in other plants, although some plants have only a single gene, as opposed to the two representatives in Arabidopsis (Novatchkova et al, 2012). Using the SP-RING sequence for alignment, Figure 1C shows a phylogenetic tree, indicating that plants encode three classes of SP-RING containing SUMO ligases.…”

“…Sumoylation, the conjugation of the small ubiquitin-related modifier (SUMO) to substrate proteins, is an essential posttranslational modification in plants (reviewed in Novatchkova et al, 2004Novatchkova et al, , 2012Castro et al, 2012;Mazur and van den Burg, 2012;Flotho and Melchior, 2013;Jentsch and Psakhye, 2013;. SUMO activating enzyme (SAE) catalyzes activation of the SUMO carboxyl terminus by formation of a thioester and SUMO transfer to a SUMO conjugating enzyme (SCE).…”

Characterization of The Interaction Between RIN13 (RPM1-Interacting13) and Sumo Proteins in Arabidopsis Thaliana

“…In vitro experiment showed that yeast SUMO and human SUMO1 was able to form chains using Lys7, Lys16 and Lys 17 (Col- one active gene for SUMO-E2 (SCE) in A. thaliana, substrate specificity was usually determined by specific E3 ligase or a certain motif within the target proteins. Covalent modification by SUMO requires consensus motif of ψKXD/E (ψ, hydrophobic amino acid; K, lysine; X, any amino acid, D, aspartic acid; E, glutamic acid), while non-covalent binding of SUMO usually determined by SIM (SUMO-interacting Motif) or SBM (SUMObinding Motif) (Novatchkova et al, 2012;Park et al, 2011). Gene expression pattern of RIN13 and RIL1…”

“…A. thaliana has one pseudogene and one active gene (AtSCE1a; At3g57870) for SUMO E2 enzyme (Novatchkova et al, 2012). To identify potential target proteins for SUMOylation in A. thaliana, a yeast two-hybrid screening using an Arabidopsis SUMO E2 enzyme, AtSCE1a, as the bait was conducted.…”

“…Many of the core components of SUMOylation have been identified in Arabidopsis thaliana (Lois, Lima, & Chua, 2003;Novatchkova, Tomanov, Hofmann, Stuible, & Bachmair, 2012) such as ubiquitin, has emerged as a common and important mechanism for regulating protein function. Small ubiquitin-like modifier (SUMO.…”