A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains

Biochemical Journal

Volumn 435, Issue 1, 2011, Pages 167-174

  Schuhmann, Holger ^a   Mogg, Ulrike ^a   Adamska, Iwona ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Arabidopsis thaliana; Complex formation; DEG7; Degenerated protease domain; Serine protease; Taxonomic distribution

Indexed keywords

DEGRADATION OF PERIPLASMIC PROTEIN 7; PROTEINASE; RECOMBINANT PROTEIN; SERINE PROTEINASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGOMERIZATION; PLANT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; TAXONOMY; YEAST;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATOGRAPHY, GEL; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; HEAT-SHOCK PROTEINS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PDZ DOMAINS; PERIPLASMIC PROTEINS; PHYLOGENY; PROTEIN INTERACTION DOMAINS AND MOTIFS; RECOMBINANT PROTEINS; SERINE ENDOPEPTIDASES; TWO-HYBRID SYSTEM TECHNIQUES;

ARABIDOPSIS THALIANA;

EID: 79952852360     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20101613     Document Type: Article

References (42)

1. Kim, D. Y. and Kim, K. K. (2005) Structure and function of HtrA family proteins, the key players in protein quality control. J. Biochem. Mol. Biol. 38, 266-274
2. Clausen, T., Southan, C. and Ehrmann, M. (2002) The HtrA family of proteases: implications for protein composition and cell fate. Mol. Cell 10, 443-455 (Pubitemid 35284166)
3. Rawlings, N. D., Morton, F. R., Kok, C. Y., Kong, J. and Barrett, A. J. (2008) MEROPS: the peptidase database. Nucleic Acids Res. 36, D320-D325 (Pubitemid 351149743)
4. Helm, M., Luck, C., Prestele, J., Hierl, G., Huesgen, P. F., Fröhlich, T., Arnold, G. J., Adamska, I., Gorg, A., Lottspeich, F. and Gietl, C. (2007) Dual specificities of the glyoxysomal/peroxisomal processing protease Deg15 in higher plants. Proc. Natl. Acad. Sci. U.S.A. 104, 11501-1156
5. Schuhmann, H., Huesgen, P. F., Gietl, C. and Adamska, I. (2008) The DEG15 serine protease cleaves peroxisomal targeting signal 2-containing proteins in Arabidopsis thaliana . Plant Physiol. 148, 1847-1856 (Pubitemid 352847459)
6. Sun, X., Peng, L., Guo, J., Chi, W., Ma, J., Lu, C. and Zhang, L. (2007) Formation of DEG5 and DEG8 complexes and their involvement in the degradation of photodamaged photosystem II reaction center D1 protein in Arabidopsis. Plant Cell 19, 1347-1361 (Pubitemid 46941658)
7. Li, W., Srinivasula, S. M., Chai, J., Li, P., Wu, J. W., Zhang, Z., Alnemri, E. S. and Shi, Y. (2002) Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi. Nat. Struct. Biol. 9, 436-441
8. Wilken, C., Kitzing, K., Kurzbauer, R., Ehrmann, M. and Clausen, T. (2004) Crystal structure of the DegS stress sensor: how a PDZ domain recognizes misfolded protein and activates a protease. Cell 117, 483-494 (Pubitemid 38610233)
9. Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M. and Clausen, T. (2002) Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Nature 416, 455-459 (Pubitemid 34272883)
10. Jomaa, A., Damjanovic, D., Leong, V., Ghirlando, R., Iwanczyk, J. and Ortega, J. (2007) The inner cavity of Escherichia coli DegP protein is not essential for molecular chaperone and proteolytic activity. J. Bacteriol. 189, 706-716 (Pubitemid 46183845)
11. Kim, D. Y., Kim, D. R., Ha, S. C., Lokanath, N. K., Lee, C. J., Hwang, H. Y. and Kim, K. K. (2003) Crystal structure of the protease domain of a heat-shock protein HtrA from Thermotoga maritima . J. Biol. Chem. 278, 6543-6551
12. Krojer, T., Sawa, J., Schäfer, E., Saibil, H. R., Ehrmann, M. and Clausen, T. (2008) Structural basis for the regulated protease and chaperone function of DegP. Nature 453, 885-890 (Pubitemid 351832567)
13. Jiang, J., Zhang, X., Chen, Y., Wu, Y., Zhou, Z. H., Chang, Z. and Sui, S. F. (2008) Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins. Proc. Natl. Acad. Sci. U.S.A. 105, 11939-11944
14. E-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-σ factor. Genes Dev. 13, 2449-2461
15. E-dependent extracytoplasmic stress response. Genes Dev. 16, 2156-2168
16. Lipinska, B., Fayet, O., Baird, L. and Georgopoulos, C. (1989) Identification, characterization, and mapping of the Escherichia coli htrA gene, whose product is essential for bacterial growth only at elevated temperatures. J. Bacteriol. 171, 1574-1584 (Pubitemid 19080799)
17. Strauch, K. L., Johnson, K. and Beckwith, J. (1989) Characterization of degP , a gene required for proteolysis in the cell envelope and essential for growth of Escherichia coli at high temperature. J. Bacteriol. 171, 2689-2696
18. Verhagen, A. M., Silke, J., Ekert, P. G., Pakusch, M., Kaufmann, H., Connolly, L. M., Day, C. L., Tikoo, A., Burke, R., Wrobel, C. et al. (2002) HtrA2 promotes cell death through its serine protease activity and its ability to antagonize inhibitor of apoptosis proteins. J. Biol. Chem. 277, 445-454
19. Kurochkin, I. V., Mizuno, Y., Konagaya, A., Sakaki, Y., Schonbach, C. and Okazaki, Y. (2007) Novel peroxisomal protease Tysnd1 processes PTS1- and PTS2-containing enzymes involved in β-oxidation of fatty acids. EMBO J. 26, 835-845
20. Huesgen, P. F., Schuhmann, H. and Adamska, I. (2005) The family of Deg proteases in cyanobacteria and chloroplasts of higher plants. Physiol. Plant. 123, 413-420
21. Padmanabhan, N., Fichtner, L., Dickmanns, A., Ficner, R., Schulz, J. B. and Braus, G. H. (2009) The yeast HtrA orthologue Ynm3 is a protease with chaperone activity that aids survival under heat stress. Mol. Biol. Cell 20, 68-77
22. Fahrenkrog, B., Sauder, U. and Aebi, U. (2004) The S. cerevisiae HtrA-like protein Nma111p is a nuclear serine protease that mediates yeast apoptosis. J. Cell Sci. 117, 115-126 (Pubitemid 38072126)
23. Tong, F., Black, P. N., Bivins, L., Quackenbush, S., Ctrnacta, V. and DiRusso, C. C. (2006) Direct interaction of Saccharomyces cerevisiae Faa1p with the Omi/HtrA protease orthologue Ynm3p alters lipid homeostasis. Mol. Genet. Genomics 275, 330-343
24. Sun, X., Fu, T., Chen, N., Guo, J., Ma, J., Zou, M., Lu, C. and Zhang, L. (2010) The stromal chloroplast Deg7 protease participates in the repair of photosystem II after photoinhibition in Arabidopsis. Plant Physiol. 152, 1263-1273
25. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (Pubitemid 27359211)
26. Zdobnov, E. M. and Apweiler, R. (2001) InterProScan: an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 (Pubitemid 32970486)
27. Soding, J., Biegert, A. and Lupas, A. N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244-W248
28. Moretti, S., Armougom, F., Wallace, I. M., Higgins, D. G., Jongeneel, C. V. and Notredame, C. (2007) The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res. 35, W645-W648
29. Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J. F., Guindon, S., Lefort, V., Lescot, M. et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465-W469
30. Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M. Y., Pieper, U. and Sali, A. (2007) Comparative protein structure modeling using MODELLER. Curr. Protoc. Protein Sci. Chapter 2, Unit 29
31. Zhang, Y., Appleton, B. A., Wu, P., Wiesmann, C. and Sidhu, S. S. (2007) Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain. Protein Sci. 16, 1738-1750
32. Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn, Cold Spring Harbor Laboratory Press, Cold Spring Harbor
33. Yamada, K., Lim, J., Dale, J. M., Chen, H., Shinn, P., Palm, C. J., Southwick, A. M., Wu, H. C., Kim, C., Nguyen, M. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846 (Pubitemid 37339620)
34. Gietz, R. D. and Woods, R. A. (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350, 87-96
35. Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211-D215
36. Zeth, K. (2004) Structural analysis of DegS, a stress sensor of the bacterial periplasm. FEBS Lett. 569, 351-358
37. Wang, J., Hartling, J. A. and Flanagan, J. M. (1997) The structure of ClpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis. Cell 91, 447-456
38. Peltier, J. B., Ripoll, D. R., Friso, G., Rudella, A., Cai, Y., Ytterberg, J., Giacomelli, L., Pillardy, J. and van Wijk, K. J. (2004) Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J. Biol. Chem. 279, 4768-4781
39. Andersson, F. I., Tryggvesson, A., Sharon, M., Diemand, A. V., Classen, M., Best, C., Schmidt, R., Schelin, J., Stanne, T. M., Bukau, B. et al. (2009) Structure and function of a novel type of ATP-dependent Clp protease. J. Biol. Chem. 284, 13519-13532
40. Garcia-Lorenzo, M., Sjodin, A., Jansson, S. and Funk, C. (2006) Protease gene families in Populus and Arabidopsis. BMC Plant Biol. 6, 30
41. Gallastegui, N. and Groll, M. (2010) The 26S proteasome: assembly and function of a destructive machine. Trends Biochem. Sci. 35, 634-642
42. Groll, M., Bochtler, M., Brandstetter, H., Clausen, T. and Huber, R. (2005) Molecular machines for protein degradation. ChemBioChem 6, 222-256 (Pubitemid 40879733)