title: Structural insights of post-translational modification sites in the proteome of Thermus thermophilus.
abstract: Phosphorylation and acetylation are the most prevalent post-translational modifications (PTMs) detected in not only eukaryotes but also bacteria. We performed phosphoproteome and acetylome analyses of proteins from an extremely thermophilic eubacterium Thermus thermophilus HB8, and identified numerous phosphorylation and acetylation sites. To facilitate the elucidation of the structural aspects of these PTM events, we mapped the PTM sites on the known tertiary structures for the respective proteins and their homologs. Wu et al. (Mol Cell Proteomics 12:2701-2713, 2013) recently reported phosphoproteome analysis of proteins from T. thermophilus HB27. Therefore, we assessed the structural characteristics of these phosphorylation and acetylation sites on the tertiary structures of the identified proteins or their homologs. Our study revealed that many of the identified phosphosites are in close proximity to bound ligands, i.e., the numbers of 'nearby' and 'peripheral' phosphorylation sites represent 56 % (48/86 sites) of total identified phosphorylation sites. In addition, approximately 60 % of all phosphosites exhibited <10 % accessible surface area of their side chains, suggesting some structural rearrangement is required for phosphoryl transfer by kinases. Our findings also indicate that phosphorylation of a residue occurs more frequently at a flexible region of the protein, whereas lysine acetylation occurs more frequently in an ordered structure.
authors.affiliation: Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan, rmasui@bio.sci.osaka-u.ac.jp.
authors.forename: Ryoji
authors.initials: R
authors.lastname: Masui
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Takahata
authors.forename: Masao
authors.initials: M
authors.lastname: Inoue
authors.forename: Yota
authors.initials: Y
authors.lastname: Iio
authors.forename: Hiroki
authors.initials: H
authors.lastname: Okanishi
authors.forename: Kwang
authors.initials: K
authors.lastname: Kim
authors.forename: Noriko
authors.initials: N
authors.lastname: Nakagawa
authors.forename: Kei
authors.initials: K
authors.lastname: Yura
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
mesh_terms: D000107:Acetylation; D000446:Aldehyde-Lyases / Q000378:metabolism; D000595:Amino Acid Sequence; D001219:Aspartate Aminotransferases / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D010748:Phosphopeptides / Q000032:analysis / Q000378:metabolism; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000032:analysis; D040901:Proteomics; D013329:Structure-Activity Relationship; D016963:Thermus thermophilus / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D010748:Phosphopeptides; D020543:Proteome; D001219:Aspartate Aminotransferases; D000446:Aldehyde-Lyases; C020019:deoxyribose-phosphate aldolase