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Structural insights of post-translational modification sites in the proteome of Thermus thermophilus

Journal of Structural and Functional Genomics volume 15, pages 137–151 (2014)Cite this article

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.

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Abbreviations

ASA:

Accessible surface area

PTM:

Post-translational modification

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Acknowledgments

This research was supported in part by Grant-in-Aid for Challenging Exploratory Research 25650008 (to RM). KY was supported by Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.

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Authors and Affiliations

  1. Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan

    Ryoji Masui, Masao Inoue, Yota Iio, Hiroki Okanishi, Kwang Kim, Noriko Nakagawa & Seiki Kuramitsu

  2. Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Yoshio Takahata & Seiki Kuramitsu

  3. Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan

    Kei Yura

  4. Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan

    Kei Yura

  5. National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan

    Kei Yura

Authors
  1. Ryoji Masui
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  2. Yoshio Takahata
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  3. Masao Inoue
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  4. Yota Iio
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  5. Hiroki Okanishi
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  6. Kwang Kim
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  7. Noriko Nakagawa
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  8. Kei Yura
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  9. Seiki Kuramitsu
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Correspondence to Ryoji Masui.

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Masui, R., Takahata, Y., Inoue, M. et al. Structural insights of post-translational modification sites in the proteome of Thermus thermophilus . J Struct Funct Genomics 15, 137–151 (2014). https://doi.org/10.1007/s10969-013-9169-3

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  • DOI: https://doi.org/10.1007/s10969-013-9169-3

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