Duplication and familial promiscuity within the proteasome lid and COP9 signalosome kin complexes

Plant Science

Volumn 203-204, Issue , 2013, Pages 89-97

  Serino, Giovanna ^a   Pick, Elah ^b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF HAIFA   (Israel)

Author keywords

Arabidopsis thaliana; COP9 signalosome; EIF3; PCI complexes; Proteasome lid; Saccharomyces cerevisiae

Indexed keywords

ATP DEPENDENT 26S PROTEASE; COP9 SIGNALOSOME; MULTIPROTEIN COMPLEX; PEPTIDE HYDROLASE; PROTEASOME; UBIQUITIN PROTEIN LIGASE; VEGETABLE PROTEIN;

ARABIDOPSIS; BIOLOGICAL MODEL; GENE DUPLICATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT; REVIEW;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; MODELS, GENETIC; MULTIPROTEIN COMPLEXES; PEPTIDE HYDROLASES; PHYLOGENY; PLANT PROTEINS; PLANTS; PROTEASOME ENDOPEPTIDASE COMPLEX; UBIQUITIN-PROTEIN LIGASES;

EID: 84873652229     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2012.12.018     Document Type: Review

References (73)

1. Pick E., Hofmann K., Glickman M.H. PCI complexes: beyond the proteasome, CSN, and eIF3 Troika. Mol. Cell 2009, 35:260-264.
2. Ellisdon A.M., Stewart M. Structural biology of the PCI-protein fold. Bioarchitecture 2012, 2.
3. Enchev R.I., Schreiber A., Beuron F., Morris E.P. Structural insights into the COP9 signalosome and its common architecture with the 26S proteasome lid and eIF3. Structure 2010, 18:518-527.
4. Pick E., Pintard L. In the land of the rising sun with the COP9 signalosome and related zomes. Symposium on the COP9 signalosome, proteasome and eIF3. EMBO Rep. 2009, 10:343-348.
5. Scheel H., Hofmann K. Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes. BMC Bioinformatics 2005, 6:71.
6. Dessau M., et al. The Arabidopsis COP9 signalosome subunit 7 is a model PCI domain protein with subdomains involved in COP9 signalosome assembly. Plant Cell 2008, 20:2815-2834.
7. Enchev R.I., et al. Structural basis for a reciprocal regulation between SCF and CSN. Cell Rep. 2012, 2:616-627.
8. Lyapina S., et al. Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome. Science 2001, 292:1382-1385.
9. Schwechheimer C., et al. Interactions of the COP9 signalosome with the E3 ubiquitin ligase SCFTIRI in mediating auxin response. Science 2001, 292:1379-1382.
10. Glickman M.H., et al. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell 1998, 94:615-623.
11. Cope G.A., et al. Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from cul1. Science 2002, 298:608-611.
12. +, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem. 2002, 3:28.
13. Verma R., et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 2002, 298:611-615.
14. Pick E., et al. The minimal deneddylase core of the COP9 signalosome excludes the Csn6 MPN(-) domain. PLoS ONE 2012, 7:e43980.
15. Sanches M., Alves B.S., Zanchin N.I., Guimaraes B.G. The crystal structure of the human Mov34 MPN domain reveals a metal-free dimer. J. Mol. Biol. 2007, 370:846-855.
16. Zhang H., et al. The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6. FEBS Lett. 2012, 586:1147-1153.
17. Kotiguda G.G., et al. The organization of a CSN5-containing subcomplex of the COP9 signalosome. J. Biol. Chem. 2012, 287:42031-42041.
18. Finley D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu. Rev. Biochem. 2009, 78:477-513.
19. Wei N., Deng X.W. The COP9 signalosome. Annu. Rev. Cell Dev. Biol. 2003, 19:261-286.
20. Sonnhammer E.L., Koonin E.V. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 2002, 18:619-620.
21. Conant G.C., Wolfe K.H. Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 2008, 9:938-950.
22. Yang P., et al. Purification of the Arabidopsis 26S proteasome: biochemical and molecular analyses revealed the presence of multiple isoforms. J. Biol. Chem. 2004, 279:6401-6413.
23. Book A.J., et al. Affinity purification of the Arabidopsis 26S proteasome reveals a diverse array of plant proteolytic complexes. J. Biol. Chem. 2010, 285:25554-25569.
24. Gusmaroli G., Feng S., Deng X.W. The Arabidopsis CSN5A and CSN5B subunits are present in distinct COP9 signalosome complexes, and mutations in their JAMM domains exhibit differential dominant negative effects on development. Plant Cell 2004, 16:2984-3001.
25. Gusmaroli G., Figueroa P., Serino G., Deng X.W. Role of the MPN subunits in COP9 signalosome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3-based E3 ligases. Plant Cell 2007, 19:564-581.
26. Huang W., et al. The proteolytic function of the Arabidopsis 26S proteasome is required for specifying leaf adaxial identity. Plant Cell 2006, 18:2479-2492.
27. Dohmann E.M., Kuhnle C., Schwechheimer C. Loss of the constitutive photomorphogenic9 signalosome subunit 5 is sufficient to cause the cop/det/fus mutant phenotype in Arabidopsis. Plant Cell 2005, 17:1967-1978.
28. Book A.J., et al. The RPN5 subunit of the 26s proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis. Plant Cell 2009, 21:460-478.
29. Belote J.M., Zhong L. Duplicated proteasome subunit genes in Drosophila and their roles in spermatogenesis. Heredity (Edinb.) 2009, 103:23-31.
30. Murata S., et al. Regulation of CD8+ T cell development by thymus-specific proteasomes. Science 2007, 316:1349-1353.
31. Shalev A., et al. Saccharomyces cerevisiae protein Pci8p and human protein eIF3e/Int-6 interact with the eIF3 core complex by binding to cognate eIF3b subunits. J. Biol. Chem. 2001, 276:34948-34957.
32. Sha Z., et al. Isolation of the Schizosaccharomyces pombe proteasome subunit Rpn7 and a structure-function study of the proteasome-COP9-initiation factor domain. J. Biol. Chem. 2007, 282:32414-32423.
33. Yu Z., et al. Dual function of Rpn5 in two PCI complexes, the 26S proteasome and COP9 signalosome. Mol. Biol. Cell 2011, 22:911-920.
34. Kellis M., Birren B.W., Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624.
35. Yen H.C., Chang E.C. INT6 - a link between the proteasome and tumorigenesis. Cell Cycle 2003, 2:81-83.
36. Yen H.C., Espiritu C., Chang E.C. Rpn5 is a conserved proteasome subunit and required for proper proteasome localization and assembly. J. Biol. Chem. 2003, 278:30669-30676.
37. Dunand-Sauthier I., et al. Sum1, a component of the fission yeast eIF3 translation initiation complex, is rapidly relocalized during environmental stress and interacts with components of the 26S proteasome. Mol. Biol. Cell 2002, 13:1626-1640.
38. Karniol B., et al. The Arabidopsis homologue of an eIF3 complex subunit associates with the COP9 complex. FEBS Lett. 1998, 439:173-179.
39. Kim T.H., Kim B.H., Yahalom A., Chamovitz D.A., von Arnim A.G. Translational regulation via 5' mRNA leader sequences revealed by mutational analysis of the Arabidopsis translation initiation factor subunit eIF3h. Plant Cell 2004, 16:3341-3356.
40. Paz-Aviram T., Yahalom A., Chamovitz D.A. Arabidopsis eIF3e interacts with subunits of the ribosome, COP9 signalosome and proteasome. Plant Signal. Behav. 2008, 3:409-411.
41. Yahalom A., et al. Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation. Plant J. 2008, 53:300-311.
42. Halimi Y., et al. COP9 signalosome subunit 7 from Arabidopsis interacts with and regulates the small subunit of ribonucleotide reductase (RNR2). Plant Mol. Biol. 2011, 77:77-89.
43. Kwok S.F., Staub J.M., Deng X.W. Characterization of two subunits of Arabidopsis 19S proteasome regulatory complex and its possible interaction with the COP9 complex. J. Mol. Biol. 1999, 285:85-95.
44. Bennett E.J., Rush J., Gygi S.P., Harper J.W. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 2010, 143:951-965.
45. Sowa M.E., Bennett E.J., Gygi S.P., Harper J.W. Defining the human deubiquitinating enzyme interaction landscape. Cell 2009, 138:389-403.
46. Luke-Glaser S., et al. CIF-1, a shared subunit of the COP9/signalosome and eukaryotic initiation factor 3 complexes, regulates MEL-26 levels in the Caenorhabditis elegans embryo. Mol. Cell. Biol. 2007, 27:4526-4540.
47. Huang X., et al. Consequences of COP9 signalosome and 26S proteasome interaction. FEBS J. 2005, 272:3909-3917.
48. Zhou C., et al. PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes. BMC Biol. 2005, 3:14.
49. Chamovitz D.A. Revisiting the COP9 signalosome as a transcriptional regulator. EMBO Rep. 2009, 10:352-358.
50. Chamovitz D.A., et al. The COP9 complex, a novel multisubunit nuclear regulator involved in light control of a plant developmental switch. Cell 1996, 86:115-121.
51. Fukumoto A., Tomoda K., Kubota M., Kato J.Y., Yoneda-Kato N. Small Jab1-containing subcomplex is regulated in an anchorage- and cell cycle-dependent manner, which is abrogated by ras transformation. FEBS Lett. 2005, 579:1047-1054.
52. Tomoda K., et al. The Jab1/COP9 signalosome subcomplex is a downstream mediator of Bcr-Abl kinase activity and facilitates cell-cycle progression. Blood 2005, 105:775-783.
53. Sharon M., et al. Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure 2009, 17:31-40.
54. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
55. Dereeper A., et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008, 36:W465-W469.
56. Chevenet F., Brun C., Banuls A.L., Jacq B., Christen R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 2006, 7:439.
57. Peng Z., Serino G., Deng X.W. A role of Arabidopsis COP9 signalosome in multifaceted developmental processes revealed by the characterization of its subunit 3. Development 2001, 128:4277-4288.
58. Serino G., et al. Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome. Plant Cell 1999, 11:1967-1980.
59. Serino G., et al. Characterization of the last subunit of the Arabidopsis COP9 signalosome: implications for the overall structure and origin of the complex. Plant Cell 2003, 15:719-731.
60. Staub J.M., Wei N., Deng X.W. Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis. Plant Cell 1996, 8:2047-2056.
61. Karniol B., Malec P., Chamovitz D.A. Arabidopsis FUSCA5 encodes a novel phosphoprotein that is a component of the COP9 complex. Plant Cell 1999, 11:839-848.
62. Kurepa J., Toh E.A., Smalle J.A. 26S proteasome regulatory particle mutants have increased oxidative stress tolerance. Plant J. 2008, 53:102-114.
63. Kurepa J., et al. Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs. Plant Physiol. 2009, 150:178-189.
64. Smalle J., et al. Cytokinin growth responses in Arabidopsis involve the 26S proteasome subunit RPN12. Plant Cell 2002, 14:17-32.
65. Jain V., Kaiser W., Huber S.C. Cytokinin inhibits the proteasome-mediated degradation of carbonylated proteins in Arabidopsis leaves. Plant Cell Physiol. 2008, 49:843-852.
66. Sonoda Y., et al. Regulation of leaf organ size by the Arabidopsis RPT2a 19S proteasome subunit. Plant J. 2009, 60:68-78.
67. Ueda M., et al. Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b. Plant Cell Physiol. 2011, 52:1628-1640.
68. Sakamoto T., et al. Arabidopsis thaliana 26S proteasome subunits RPT2a and RPT5a are crucial for zinc deficiency-tolerance. Biosci. Biotechnol. Biochem. 2011, 75:561-567.
69. Brenner E.D., Feinberg P., Runko S., Coruzzi G.M. A mutation in the proteosomal regulatory particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA. Plant Mol. Biol. 2009, 70:523-533.
70. Gallois J.L., et al. The Arabidopsis proteasome RPT5 subunits are essential for gametophyte development and show accession-dependent redundancy. Plant Cell 2009, 21:442-459.
71. Wang S., Kurepa J., Smalle J.A. The Arabidopsis 26S proteasome subunit RPN1a is required for optimal plant growth and stress responses. Plant Cell Physiol. 2009, 50:1721-1725.
72. Brukhin V., Gheyselinck J., Gagliardini V., Genschik P., Grossniklaus U. The RPN1 subunit of the 26S proteasome in Arabidopsis is essential for embryogenesis. Plant Cell 2005, 17:2723-2737.
73. Smalle J., et al. The pleiotropic role of the 26S proteasome subunit RPN10 in Arabidopsis growth and development supports a substrate-specific function in abscisic acid signaling. Plant Cell 2003, 15:965-980.