title: Initial description of the developing soybean seed protein Lys-N(ε)-acetylome.
abstract: Characterization of the myriad protein posttranslational modifications (PTM) is a key aspect of proteome profiling. While there have been previous studies of the developing soybean seed phospho-proteome, herein we present the first analysis of non-histone lysine-N(Ɛ)-acetylation in this system. In recent years there have been reports that lysine acetylation is widespread, affecting thousands of proteins in diverse species from bacteria to mammals. Recently preliminary descriptions of the protein lysine acetylome from the plants Arabidopsis thaliana and Vitis vinifera have been reported. Using a combination of immunoenrichment and mass spectrometry-based techniques, we have identified over 400 sites of lysine acetylation in 245 proteins from developing soybean (Glycine max (L.) Merr., cv. Jack) seeds, which substantially increases the number of known plant N(Ɛ)-lysine-acetylation sites. Results of functional annotation indicate acetyl-proteins are involved with a host of cellular activities. In addition to histones, and other proteins involved in RNA synthesis and processing, acetyl-proteins participate in signaling, protein folding, and a plethora of metabolic processes. Results from in silico localization indicate that lysine-acetylated proteins are present in all major subcellular compartments. In toto, our results establish developing soybean seeds as a physiologically distinct addendum to Arabidopsis thaliana seedlings for functional analysis of protein Lys-N(Ɛ)-acetylation.
  
  
  CONCLUSIONS
  Several modes of peptide fragmentation and database search algorithms are incorporated to identify, for the first time, sites of lysine acetylation on a plethora of proteins from developing soybean seeds. The contributions of distinct techniques to achieve increased coverage of the lysine acetylome are compared, providing insight to their respective benefits. Acetyl-proteins and specific acetylation sites are characterized, revealing intriguing similarities as well as differences with those previously identified in other plant and non-plant species.
authors.affiliation: Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA. Electronic address: colin.smithhammond@mail.missouri.edu.
authors.forename: Colin L
authors.initials: CL
authors.lastname: Smith-Hammond
authors.affiliation: Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA. Electronic address: knsty4@mail.missouri.edu.
authors.forename: Kirby N
authors.initials: KN
authors.lastname: Swatek
authors.affiliation: Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO, USA. Electronic address: mark.johnston@ars.usda.gov.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Johnston
authors.affiliation: Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA. Electronic address: thelenj@missouri.edu.
authors.forename: Jay J
authors.initials: JJ
authors.lastname: Thelen
authors.affiliation: Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO, USA. Electronic address: jan.miernyk@ars.usda.gov.
authors.forename: Ján A
authors.initials: JA
authors.lastname: Miernyk
mesh_terms: D000107:Acetylation; D010940:Plant Proteins / Q000378:metabolism*; D011499:Protein Processing, Post-Translational / Q000502:physiology*; D020543:Proteome / Q000378:metabolism*; D012639:Seeds / Q000378:metabolism*; D013025:Glycine max / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Collision-induced dissociation (CID); Data-dependent decision tree; Electron transfer dissociation (ETD); Glycine max; Lysine acetylation