Molecular organization of the 20S proteasome gene family from Arabidopsis thaliana (original) (raw)

Abstract

The 20S proteasome is the proteolytic complex in eukaryotes responsible for degrading short-lived and abnormal intracellular proteins, especially those targeted by ubiquitin conjugation. The 700-kD complex exists as a hollow cylinder comprising four stacked rings with the catalytic sites located in the lumen. The two outer rings and the two inner rings are composed of seven different alpha and beta polypeptides, respectively, giving an alpha7/beta7/beta7/alpha7 symmetric organization. Here we describe the molecular organization of the 20S proteasome from the plant Arabidopsis thaliana. From an analysis of a collection of cDNA and genomic clones, we identified a superfamily of 23 genes encoding all 14 of the Arabidopsis proteasome subunits, designated PAA-PAG and PBA-PBG for Proteasome Alpha and Beta subunits A-G, respectively. Four of the subunits likely are encoded by single genes, and the remaining subunits are encoded by families of at least 2 genes. Expression of the alpha and beta subunit genes appears to be coordinately regulated. Three of the nine Arabidopsis proteasome subunit genes tested, PAC1 (alpha3), PAE1 (alpha5) and PBC2 (beta3), could functionally replace their yeast orthologs, providing the first evidence for cross-species complementation of 20S subunit genes. Taken together, these results demonstrate that the 20S proteasome is structurally and functionally conserved among eukaryotes and suggest that the subunit arrangement of the Arabidopsis 20S proteasome is similar if not identical to that recently determined for the yeast complex.

Full Text

The Full Text of this article is available as a PDF (1.2 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arendt C. S., Hochstrasser M. Identification of the yeast 20S proteasome catalytic centers and subunit interactions required for active-site formation. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7156–7161. doi: 10.1073/pnas.94.14.7156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Callis J., Carpenter T., Sun C. W., Vierstra R. D. Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics. 1995 Feb;139(2):921–939. doi: 10.1093/genetics/139.2.921. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen P., Hochstrasser M. Autocatalytic subunit processing couples active site formation in the 20S proteasome to completion of assembly. Cell. 1996 Sep 20;86(6):961–972. doi: 10.1016/s0092-8674(00)80171-3. [DOI] [PubMed] [Google Scholar]
  4. Chen P., Hochstrasser M. Biogenesis, structure and function of the yeast 20S proteasome. EMBO J. 1995 Jun 1;14(11):2620–2630. doi: 10.1002/j.1460-2075.1995.tb07260.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen P., Johnson P., Sommer T., Jentsch S., Hochstrasser M. Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MAT alpha 2 repressor. Cell. 1993 Jul 30;74(2):357–369. doi: 10.1016/0092-8674(93)90426-q. [DOI] [PubMed] [Google Scholar]
  6. Coux O., Nothwang H. G., Silva Pereira I., Recillas Targa F., Bey F., Scherrer K. Phylogenic relationships of the amino acid sequences of prosome (proteasome, MCP) subunits. Mol Gen Genet. 1994 Dec 15;245(6):769–780. doi: 10.1007/BF00297284. [DOI] [PubMed] [Google Scholar]
  7. Coux O., Tanaka K., Goldberg A. L. Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem. 1996;65:801–847. doi: 10.1146/annurev.bi.65.070196.004101. [DOI] [PubMed] [Google Scholar]
  8. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Emori Y., Tsukahara T., Kawasaki H., Ishiura S., Sugita H., Suzuki K. Molecular cloning and functional analysis of three subunits of yeast proteasome. Mol Cell Biol. 1991 Jan;11(1):344–353. doi: 10.1128/mcb.11.1.344. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Enenkel C., Lehmann H., Kipper J., Gückel R., Hilt W., Wolf D. H. PRE3, highly homologous to the human major histocompatibility complex-linked LMP2 (RING12) gene, codes for a yeast proteasome subunit necessary for the peptidylglutamyl-peptide hydrolyzing activity. FEBS Lett. 1994 Mar 21;341(2-3):193–196. doi: 10.1016/0014-5793(94)80455-9. [DOI] [PubMed] [Google Scholar]
  11. Fu H., Sadis S., Rubin D. M., Glickman M., van Nocker S., Finley D., Vierstra R. D. Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1. J Biol Chem. 1998 Jan 23;273(4):1970–1981. doi: 10.1074/jbc.273.4.1970. [DOI] [PubMed] [Google Scholar]
  12. Fujinami K., Tanahashi N., Tanaka K., Ichihara A., Cejka Z., Baumeister W., Miyawaki M., Sato T., Nakagawa H. Purification and characterization of the 26 S proteasome from spinach leaves. J Biol Chem. 1994 Oct 14;269(41):25905–25910. [PubMed] [Google Scholar]
  13. Genschik P., Jamet E., Philipps G., Parmentier Y., Gigot C., Fleck J. Molecular characterization of a beta-type proteasome subunit from Arabidopsis thaliana co-expressed at a high level with an alpha-type proteasome subunit early in the cell cycle. Plant J. 1994 Oct;6(4):537–546. doi: 10.1046/j.1365-313x.1994.6040537.x. [DOI] [PubMed] [Google Scholar]
  14. Genschik P., Philipps G., Gigot C., Fleck J. Cloning and sequence analysis of a cDNA clone from Arabidopsis thaliana homologous to a proteasome alpha subunit from Drosophila. FEBS Lett. 1992 Sep 14;309(3):311–315. doi: 10.1016/0014-5793(92)80796-j. [DOI] [PubMed] [Google Scholar]
  15. Gietz R. D., Schiestl R. H., Willems A. R., Woods R. A. Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast. 1995 Apr 15;11(4):355–360. doi: 10.1002/yea.320110408. [DOI] [PubMed] [Google Scholar]
  16. Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
  17. Groll M., Ditzel L., Löwe J., Stock D., Bochtler M., Bartunik H. D., Huber R. Structure of 20S proteasome from yeast at 2.4 A resolution. Nature. 1997 Apr 3;386(6624):463–471. doi: 10.1038/386463a0. [DOI] [PubMed] [Google Scholar]
  18. Heinemeyer W., Fischer M., Krimmer T., Stachon U., Wolf D. H. The active sites of the eukaryotic 20 S proteasome and their involvement in subunit precursor processing. J Biol Chem. 1997 Oct 3;272(40):25200–25209. doi: 10.1074/jbc.272.40.25200. [DOI] [PubMed] [Google Scholar]
  19. Heinemeyer W., Gruhler A., Möhrle V., Mahé Y., Wolf D. H. PRE2, highly homologous to the human major histocompatibility complex-linked RING10 gene, codes for a yeast proteasome subunit necessary for chrymotryptic activity and degradation of ubiquitinated proteins. J Biol Chem. 1993 Mar 5;268(7):5115–5120. [PubMed] [Google Scholar]
  20. Heinemeyer W., Kleinschmidt J. A., Saidowsky J., Escher C., Wolf D. H. Proteinase yscE, the yeast proteasome/multicatalytic-multifunctional proteinase: mutants unravel its function in stress induced proteolysis and uncover its necessity for cell survival. EMBO J. 1991 Mar;10(3):555–562. doi: 10.1002/j.1460-2075.1991.tb07982.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hilt W., Enenkel C., Gruhler A., Singer T., Wolf D. H. The PRE4 gene codes for a subunit of the yeast proteasome necessary for peptidylglutamyl-peptide-hydrolyzing activity. Mutations link the proteasome to stress- and ubiquitin-dependent proteolysis. J Biol Chem. 1993 Feb 15;268(5):3479–3486. [PubMed] [Google Scholar]
  22. Jones M. E., Haire M. F., Kloetzel P. M., Mykles D. L., Schwartz L. M. Changes in the structure and function of the multicatalytic proteinase (proteasome) during programmed cell death in the intersegmental muscles of the hawkmoth, Manduca sexta. Dev Biol. 1995 Jun;169(2):436–447. doi: 10.1006/dbio.1995.1159. [DOI] [PubMed] [Google Scholar]
  23. Kremp A., Schliephacke M., Kull U., Schmid H. P. Prosomes exist in plant cells too. Exp Cell Res. 1986 Oct;166(2):553–557. doi: 10.1016/0014-4827(86)90500-8. [DOI] [PubMed] [Google Scholar]
  24. Kumatori A., Tanaka K., Inamura N., Sone S., Ogura T., Matsumoto T., Tachikawa T., Shin S., Ichihara A. Abnormally high expression of proteasomes in human leukemic cells. Proc Natl Acad Sci U S A. 1990 Sep;87(18):7071–7075. doi: 10.1073/pnas.87.18.7071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Löwe J., Stock D., Jap B., Zwickl P., Baumeister W., Huber R. Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. Science. 1995 Apr 28;268(5210):533–539. doi: 10.1126/science.7725097. [DOI] [PubMed] [Google Scholar]
  26. Maupin-Furlow J. A., Ferry J. G. A proteasome from the methanogenic archaeon Methanosarcina thermophila. J Biol Chem. 1995 Dec 1;270(48):28617–28622. doi: 10.1074/jbc.270.48.28617. [DOI] [PubMed] [Google Scholar]
  27. Rapp J. C., Baumgartner B. J., Mullet J. Quantitative analysis of transcription and RNA levels of 15 barley chloroplast genes. Transcription rates and mRNA levels vary over 300-fold; predicted mRNA stabilities vary 30-fold. J Biol Chem. 1992 Oct 25;267(30):21404–21411. [PubMed] [Google Scholar]
  28. Sawada M. T., Someno T., Hoshi M., Sawada H. Participation of 650-kDa protease (20 S proteasome) in starfish oocyte maturation. Dev Biol. 1992 Apr;150(2):414–418. doi: 10.1016/0012-1606(92)90252-c. [DOI] [PubMed] [Google Scholar]
  29. Schliephacke M., Kremp A., Schmid H. P., Köhler K., Kull U. Prosomes (proteasomes) of higher plants. Eur J Cell Biol. 1991 Jun;55(1):114–121. [PubMed] [Google Scholar]
  30. Schmidt M., Kloetzel P. M. Biogenesis of eukaryotic 20S proteasomes: the complex maturation pathway of a complex enzyme. FASEB J. 1997 Dec;11(14):1235–1243. doi: 10.1096/fasebj.11.14.9409542. [DOI] [PubMed] [Google Scholar]
  31. Schmidtke G., Kraft R., Kostka S., Henklein P., Frömmel C., Löwe J., Huber R., Kloetzel P. M., Schmidt M. Analysis of mammalian 20S proteasome biogenesis: the maturation of beta-subunits is an ordered two-step mechanism involving autocatalysis. EMBO J. 1996 Dec 16;15(24):6887–6898. [PMC free article] [PubMed] [Google Scholar]
  32. Seelig A., Multhaup G., Pesold-Hurt B., Beyreuther K., Kloetzel P. M. Drosophila proteasome Dm25 subunit substitutes the mouse MC3 subunit in hybrid proteasomes. The N-terminal domain is essential for subunit incorporation. J Biol Chem. 1993 Dec 5;268(34):25561–25567. [PubMed] [Google Scholar]
  33. Seemuller E., Lupas A., Baumeister W. Autocatalytic processing of the 20S proteasome. Nature. 1996 Aug 1;382(6590):468–471. doi: 10.1038/382468a0. [DOI] [PubMed] [Google Scholar]
  34. Seemüller E., Lupas A., Stock D., Löwe J., Huber R., Baumeister W. Proteasome from Thermoplasma acidophilum: a threonine protease. Science. 1995 Apr 28;268(5210):579–582. doi: 10.1126/science.7725107. [DOI] [PubMed] [Google Scholar]
  35. Shirley B. W., Goodman H. M. An Arabidopsis gene homologous to mammalian and insect genes encoding the largest proteasome subunit. Mol Gen Genet. 1993 Dec;241(5-6):586–594. doi: 10.1007/BF00279901. [DOI] [PubMed] [Google Scholar]
  36. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Skoda B., Malek L. Dry pea seed proteasome : purification and enzymic activities. Plant Physiol. 1992 Aug;99(4):1515–1519. doi: 10.1104/pp.99.4.1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Spence J., Sadis S., Haas A. L., Finley D. A ubiquitin mutant with specific defects in DNA repair and multiubiquitination. Mol Cell Biol. 1995 Mar;15(3):1265–1273. doi: 10.1128/mcb.15.3.1265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Sun C. W., Callis J. Independent modulation of Arabidopsis thaliana polyubiquitin mRNAs in different organs and in response to environmental changes. Plant J. 1997 May;11(5):1017–1027. doi: 10.1046/j.1365-313x.1997.11051017.x. [DOI] [PubMed] [Google Scholar]
  40. Tamura T., Nagy I., Lupas A., Lottspeich F., Cejka Z., Schoofs G., Tanaka K., De Mot R., Baumeister W. The first characterization of a eubacterial proteasome: the 20S complex of Rhodococcus. Curr Biol. 1995 Jul 1;5(7):766–774. doi: 10.1016/s0960-9822(95)00153-9. [DOI] [PubMed] [Google Scholar]
  41. Vierstra R. D. Proteolysis in plants: mechanisms and functions. Plant Mol Biol. 1996 Oct;32(1-2):275–302. doi: 10.1007/BF00039386. [DOI] [PubMed] [Google Scholar]