title: Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation.
abstract: The higher plant Arabidopsis (Arabidopsis thaliana) has eight genes potentially coding for small ubiquitin-related modifier (SUMO) proteins. However, two well-expressed isoforms differ from fungal and animal consensus in a conserved glutamine (Gln) residue situated four residues from the carboxyl terminus. We tested deviations in this position in the background of SUMO1, the isoform with the highest expression level, and found that changes do not prevent conjugation to substrate proteins in vivo. Replacement of this conserved Gln by alanine resulted in a protein that was less readily removed from a substrate by SUMO protease EARLY IN SHORT DAYS4 in an in vitro reaction and apparently led to higher levels of SUMO conjugates when expressed in vivo. We used the SUMO1 variant with the Gln-to-alanine substitution, as well as SUMO3 and SUMO5 (which carry methionine and leucine, respectively, at this position), to enrich in vivo substrates. Identification of the most abundant proteins contained in these fractions indicated that they are involved in DNA-related, or in RNA-dependent, processes, such as regulation of chromatin structure, splicing, or translation. The majority of the identified bona fide substrates contain predicted sumoylation sites. A subset of the proteins was expressed in Escherichia coli and could be sumoylated in vitro.
authors.affiliation: Department of Plant Developmental Biology , Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
authors.forename: Ruchika
authors.initials: R
authors.lastname: Budhiraja
authors.forename: Rebecca
authors.initials: R
authors.lastname: Hermkes
authors.forename: Stefan
authors.initials: S
authors.lastname: Müller
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmidt
authors.forename: Thomas
authors.initials: T
authors.lastname: Colby
authors.forename: Kishore
authors.initials: K
authors.lastname: Panigrahi
authors.forename: George
authors.initials: G
authors.lastname: Coupland
authors.forename: Andreas
authors.initials: A
authors.lastname: Bachmair
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry; D002843:Chromatin / Q000378:metabolism*; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009154:Mutation; D020033:Protein Isoforms / Q000737:chemistry / Q000378:metabolism; D018749:RNA, Plant / Q000378:metabolism*; D025841:Small Ubiquitin-Related Modifier Proteins / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D020033:Protein Isoforms; D018749:RNA, Plant; D025841:Small Ubiquitin-Related Modifier Proteins