title: Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes.
abstract: We describe an integrated workflow for proteogenomic analysis and global profiling of posttranslational modifications (PTMs) in prokaryotes and use the model cyanobacterium Synechococcus sp. PCC 7002 (hereafter Synechococcus 7002) as a test case. We found more than 20 different kinds of PTMs, and a holistic view of PTM events in this organism grown under different conditions was obtained without specific enrichment strategies. Among 3,186 predicted protein-coding genes, 2,938 gene products (>92%) were identified. We also identified 118 previously unidentified proteins and corrected 38 predicted gene-coding regions in the Synechococcus 7002 genome. This systematic analysis not only provides comprehensive information on protein profiles and the diversity of PTMs in Synechococcus 7002 but also provides some insights into photosynthetic pathways in cyanobacteria. The entire proteogenomics pipeline is applicable to any sequenced prokaryotic organism, and we suggest that it should become a standard part of genome annotation projects.
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Ming-kun
authors.initials: MK
authors.lastname: Yang
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Yao-hua
authors.initials: YH
authors.lastname: Yang
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Jia
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Yan
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Qian
authors.initials: Q
authors.lastname: Xiong
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and gefeng@ihb.ac.cn litao@ihb.ac.cn.
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and gefeng@ihb.ac.cn litao@ihb.ac.cn.
authors.forename: Feng
authors.initials: F
authors.lastname: Ge
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802.
authors.forename: Donald A
authors.initials: DA
authors.lastname: Bryant
authors.affiliation: Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.
authors.forename: Jin-dong
authors.initials: JD
authors.lastname: Zhao
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial / Q000502:physiology*; D011499:Protein Processing, Post-Translational / Q000502:physiology*; D040901:Proteomics; D046940:Synechococcus / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins
keywords: Synechococcus; cyanobacteria; photosynthesis; post-translational modifications; proteogenomics