PXD000184

PXD000184 is an original dataset announced via ProteomeXchange.

Title	Acetylome of Thermus thermophilus HB8
Description	Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes.  Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved.  Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in Thermus thermophilus HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation.  To further characterize functional significance, we successfully mapped 113 acetylation sites on their 54 authentic and 59 homologous protein structures.  The acetylation in the majority of proteins occurs in ordered structures and the sites were situated near the negatively charged glutamic acid residues. In addition, 59 of 103 acetylations were located within considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surface, demonstrating the physiological significances of the acetylations. Finally, we further summarized 22 critical acetylation sites related to Schiff-base formation, ligand binding, protein-RNA and protein-protein interaction. The structural information of 113 acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins. Data processing, bioinformatics: MS and MS/MS spectral data were processed by DataAnalysis 4.0 software (Bruker Daltonics).  The peak lists containing m/z of precursor ions with that of their product ions were generated by the Compound-Auto MS(n) option of the DataAnalysis 4.0 software. Fifty non-deconvoluted peaks over the intensity threshold 150 and charge deconvoluted peaks in each MS/MS spectrum were exported into peak list files. The spectra were searched against our in-house T. thermophilus HB8 database, containing 2,238 protein sequence entries from the complete genome sequence using Mascot search engine (version 2.3; Matrix Science, London, UK).  The acetylated peptides were identified using a mass tolerance of ±0.05 Da for precursor and product ions and allowed a maximum of 6 mis-cleavage sites for trypsin. The carbamidomethylation of cysteine was selected as a fixed modification. The oxidation of methionine, deamidation of asparagine and glutamine, acetylation of lysine and acetylation of protein N-terminus were selected as variable modifications.  Only peptides in the confidence range of 99% probability (P value < 0.01) in Mascot ion score were assumed to be identified.
HostingRepository	PRIDE
AnnounceDate	2020-01-22
AnnouncementXML	Submission_2020-01-21_23:40:31.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000184
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kwang Kim
SpeciesList	scientific name: Thermus thermophilus; NCBI TaxID: 274;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	instrument model; Bruker Daltonics micrOTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-18 04:12:47	ID requested
⏵ 1	2020-01-21 23:40:32	announced

Okanishi H, Kim K, Masui R, Kuramitsu S, Acetylome with structural mapping reveals the significance of lysine acetylation in Thermus thermophilus. J Proteome Res, 12(9):3952-68(2013) [pubmed]

submitter keyword: acetylome, anti-acetyllysine antibody, LC-MS/MS, T.thermophilus

Seiki Kuramitsu
contact affiliation	Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
contact email	kwangkim@bio.sci.osaka-u.ac.jp
lab head
Kwang Kim
contact affiliation	Dept. of Biological Sciences
contact email	kimkwang@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000184
     1. Label: PRIDE project
     2. Name: Acetylome of Thermus thermophilus HB8