Skip to main content

Advertisement

SpringerLink
Log in

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

  • Published:
Journal of Structural and Functional Genomics

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11

Similar content being viewed by others

Abbreviations

ASA:

Accessible surface area

PTM:

Post-translational modification

References

  1. Cohen P (2000) The regulation of protein function by multisite phosphorylation: a 25 year update. Trends Biochem Sci 25:596–601

    Article  CAS  PubMed  Google Scholar 

  2. Deribe YL, Pawson T, Dikic I (2010) Post-translational modifications in signal integration. Nat Struct Mol Biol 17:666–672

    Article  CAS  PubMed  Google Scholar 

  3. Moses AM, Landry CR (2010) Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends Genet 26:462–467

    Article  CAS  PubMed  Google Scholar 

  4. Macek B, Mijakovic I (2011) Site-specific analysis of bacterial phosphoproteomes. Proteomics 11:3002–3011

    Article  CAS  PubMed  Google Scholar 

  5. Kobir A, Shi L, Boskovic A, Grangeasse C, Franjevic D, Mijakovic I (2011) Protein phosphorylation in bacterial signal transduction. Biochim Biophys Acta 1810:989–994

    Article  CAS  PubMed  Google Scholar 

  6. Garnak M, Reeves H (1979) Phosphorylation of isocitrate dehydrogenase of Escherichia coli. Science 203:1111–1112

    Article  CAS  PubMed  Google Scholar 

  7. Hubbard MJ, Cohen P (1993) On target with a new mechanism for the regulation of protein phosphorylation. Trends Biochem Sci 18:172–177

    Article  CAS  PubMed  Google Scholar 

  8. Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ (2002) Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J Biol Chem 277:39379–39387

    Article  CAS  PubMed  Google Scholar 

  9. Oshima T, Imahori K (1974) Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24:102–112

    Article  CAS  Google Scholar 

  10. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S (2000) Structural genomics projects in Japan. Nat Struct Biol 7:943–945

    Article  CAS  PubMed  Google Scholar 

  11. Cava F, Hidalgo A, Berenguer J (2009) Thermus thermophilus as biological model. Extremophiles 13:213–231

    Article  CAS  PubMed  Google Scholar 

  12. Okanishi H, Kim K, Masui R, Kuramitsu S (2013) Acetylome with structural mapping reveals the significance of lysine acetylation in Thermus thermophilus. J Proteome Res 12:3952–3968

    Article  CAS  PubMed  Google Scholar 

  13. Takahata Y, Inoue M, Kim K, Iio Y, Miyamoto M, Masui R, Ishihama Y, Kuramitsu S (2012) Close proximity of phosphorylation sites to ligand in the phosphoproteome of the extreme thermophile Thermus thermophilus HB8. Proteomics 12:1414–1430

    Article  CAS  PubMed  Google Scholar 

  14. Wu W, Liao J, Lin G, Lin M, Chang Y, Liang S, Yang F, Khoo K, Wu S (2013) Phosphoproteomic analysis reveals the effects of PilF phosphorylation on Type IV pilus and biofilm formation in Thermus thermophilus HB27. Mol Cell Proteomics 12:2701–2713

    Article  CAS  PubMed  Google Scholar 

  15. Shrake A, Rupley JA (1973) Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol 79:351–364

    Article  CAS  PubMed  Google Scholar 

  16. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 4:363–371

    Article  CAS  PubMed  Google Scholar 

  17. Lascu I, Gonin P (2000) The catalytic mechanism of nucleoside diphosphate kinases. J Bioenerg Biomembr 32:237–246

    Article  CAS  PubMed  Google Scholar 

  18. Ilag L, Videler H, McKay A, Sobott F, Fucini P, Nierhaus K, Robinson C (2005) Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria. Proc Natl Acad Sci USA 102:8192–8197

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Hu CW, Lin MH, Huang HC, Ku WC, Yi TH, Tsai CF, Chen YJ, Sugiyama N, Ishihama Y, Juan HF, Wu SH (2012) Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production. J Proteome Res 11:5362–5375

    Article  CAS  PubMed  Google Scholar 

  20. Costantini S, Colonna G, Facchiano AM (2006) Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun 342:441–451

    Article  CAS  PubMed  Google Scholar 

  21. Jiménez JL, Hegemann B, Hutchins JR, Peters JM, Durbin R (2007) A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol 8:R90

    Article  PubMed Central  PubMed  Google Scholar 

  22. Weinert BT, Iesmantavicius V, Wagner SA, Scholz C, Gummesson B, Beli P, Nystrom T, Choudhary C (2013) Acetyl-phosphate is a critical determinant of lysine acetylation in E. coli. Mol Cell 51:265–272

    Article  CAS  PubMed  Google Scholar 

  23. Wolfe AJ (2010) Physiologically relevant small phosphodonors link metabolism to signal transduction. Curr Opin Microbiol 13:204–209

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N (2004) Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability. Acta Crystallogr D Biol Crystallogr 60:1816–1823

    Article  PubMed  Google Scholar 

  25. Fushinobu S, Nishimasu H, Hattori D, Song HJ, Wakagi T (2011) Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature 478:538–541

    Article  CAS  PubMed  Google Scholar 

  26. Kuchta K, Knizewski L, Wyrwicz L, Rychlewski L, Ginalski K (2009) Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res 37:7701–7704

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D (2000) The crystal structure of human eukaryotic release factor eRF1—mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 100:311–321

    Article  CAS  PubMed  Google Scholar 

  28. Fontecave M, Ollagnier-de-Choudens S (2008) Iron-sulfur cluster biosynthesis in bacteria: mechanisms of cluster assembly and transfer. Arch Biochem Biophys 474:226–237

    Article  CAS  PubMed  Google Scholar 

  29. Wada K, Sumi N, Nagai R, Iwasaki K, Sato T, Suzuki K, Hasegawa Y, Kitaoka S, Minami Y, Outten FW, Takahashi Y, Fukuyama K (2009) Molecular dynamism of Fe–S cluster biosynthesis implicated by the structure of the SufC(2)–SufD(2) complex. J Mol Biol 387:245–258

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Fischer C, Geourjon C, Bourson C, Deutscher J (1996) Cloning and characterization of the Bacillus subtilis prkA gene encoding a novel serine protein kinase. Gene 168:55–60

    Article  CAS  PubMed  Google Scholar 

  31. Morita R, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R (2008) Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8. Proteins 73:259–264

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yoshio Takahata
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Masao Inoue
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yota Iio
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hiroki Okanishi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kwang Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Noriko Nakagawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Kei Yura
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Seiki Kuramitsu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ryoji Masui.

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

Keywords

Search

Navigation