Advertisement

Solution structure of GSP13 from Bacillus subtilis exhibits an S1 domain related to cold shock proteins

  • Wenyu Yu
  • Jicheng Hu
  • Bingke Yu
  • Wei Xia
  • Changwen Jin
  • Bin XiaEmail author
NMR Structure Note

Abstract

GSP13 encoded by gene yugI is a σB-dependent general stress protein in Bacillus subtilis, which can be induced by heat shock, salt stress, ethanol stress, glucose starvation, oxidative stress and cold shock. Here we report the solution structure of GSP13 and it is the first structure of S1 domain containing protein in Bacillus subtilis. The structure of GSP13 mainly consists of a typical S1 domain along with a C-terminal 50-residue flexible tail, different from the other known S1 domain containing proteins. Comparison with other S1 domain structures reveals that GSP13 has a conserved RNA binding surface, and it may function similarly to cold shock proteins in response to cold stress.

Keywords

GSP GSP13 yugI S1 domain Cold shock protein 

Notes

Acknowledgments

All NMR experiments were carried out at the Beijing NMR Center. We thank Dr. Xiao-Dong Su for providing us the genome library of Bacillus subtilis. This research was supported by Grant 30125009 to BX from the National Science Foundation of China and grant 2006AA02A323 to CJ from the 863 Program.

References

  1. Antelmann H, Bernhardt J, Schmid R, Mach H, Völker U, Hecker M (1997) First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis. Electrophoresis 18:1451–1463CrossRefGoogle Scholar
  2. Bernhardt J, Völker U, Völker A, Antelmann H, Schmid R, Mach H, Hecker M (1997) Specific and general stress proteins in Bacillus subtilis—a two-deimensional protein electrophoresis study. Microbiology 143:999–1017CrossRefGoogle Scholar
  3. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG (1997) The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88:235–242CrossRefGoogle Scholar
  4. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302CrossRefGoogle Scholar
  5. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  6. Duggan BM, Legge GB, Dyson HJ, Wright PE (2001) SANE (Structure assisted NOE evaluation): an automated model-based approach for NOE assignment. J Biomol NMR 19:321–329CrossRefGoogle Scholar
  7. Haldenwang WG, Losick R (1980) Novel RNA polymerase sigma factor from Bacillus subtilis. Proc Natl Acad Sci USA 77:7000–7004CrossRefADSGoogle Scholar
  8. Hecker M, Pane-Farre J, Völker U (2007) SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria. Annu Rev Microbiol 61:215–236CrossRefGoogle Scholar
  9. Herrmann T, Guntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227CrossRefGoogle Scholar
  10. Johnson BA, Blevins RA (1994) NMRView: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614CrossRefGoogle Scholar
  11. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP (2008) Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J Mol Biol 377:1460–1473CrossRefGoogle Scholar
  12. Kaan T, Homuth G, Mader U, Bandow J, Schweder T (2002) Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology 148:3441–3455Google Scholar
  13. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14(51–55):29–32Google Scholar
  14. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486CrossRefGoogle Scholar
  15. Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 32:W590–594CrossRefGoogle Scholar
  16. Nanamiya H, Akanuma G, Natori Y, Murayama R, Kosono S, Kudo T, Kobayashi K, Ogasawara N, Park SM, Ochi K, Kawamura F (2004) Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Mol Microbiol 52:273–283CrossRefGoogle Scholar
  17. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 91:1–41zbMATHCrossRefADSGoogle Scholar
  18. Weber MH, Beckering CL, Marahiel MA (2001) Complementation of cold shock proteins by translation initiation factor IF1 in vivo. J Bacteriol 183:7381–7386CrossRefGoogle Scholar
  19. Xia B, Ke H, Inouye M (2001) Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli. Mol Microbiol 40:179–188CrossRefGoogle Scholar
  20. Yu W, Yu B, Hu J, Xia W, Jin C, Xia B (2008) 1H, 13C, and 15N resonance assignments of a general stress protein GSP13 from Bacillus subtilis. Biomolecular NMR Assignments 2:163–165CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Wenyu Yu
    • 1
  • Jicheng Hu
    • 1
  • Bingke Yu
    • 1
  • Wei Xia
    • 1
  • Changwen Jin
    • 1
    • 2
  • Bin Xia
    • 1
    • 2
    Email author
  1. 1.Beijing Nuclear Magnetic Resonance Center, College of Life SciencesPeking UniversityBeijingChina
  2. 2.College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina

Personalised recommendations