A proteomic study of the Arabidopsis nuclear matrix

Journal of Cellular Biochemistry

Volumn 90, Issue 2, 2003, Pages 361-378

  Calikowski, Tomasz T ^a,c   Meulia, Tea ^b   Meier, Iris ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

Arabidopsis; Mass spectrometry; Nuclear matrix; Nucleolus; Proteomics

Indexed keywords

DNA; FIBRILLARIN; HISTONE DEACETYLASE; NUCLEOLIN; NUCLEOPROTEIN; RNA;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CELL NUCLEUS; CELL NUCLEUS MATRIX; CHROMATIN; CONFOCAL MICROSCOPY; ELECTRON MICROSCOPY; EUKARYOTE; MASS SPECTROMETRY; NUCLEOLUS; NUCLEOTIDE SEQUENCE; PLANT; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL FRACTIONATION; CELL NUCLEUS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; MASS SPECTROMETRY; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON; NUCLEAR MATRIX; PROTEOMICS;

ANIMALIA; ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA;

EID: 0141529726     PISSN: 07302312     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcb.10624     Document Type: Article

References (67)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment tool. J Mol Biol 215:403-410.
2. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. 2002. Directed proteomic analysis of the human nucleolus. Curr Biol 12:1-11.
3. Barneche F, Steinmetz F, Echeverria M. 2000. Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana. J Biol Chem 275: 27212-27220.
4. Belgrader P, Siegel AJ, Berezney R. 1991. A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. J Cell Sci 98:281-291.
5. Berezney R. 1984. Organization and functions of the nuclear matrix. In: Hnilica LS, editor. Chromosomal nonhistone proteins. Vol. IV. Boca Raton, FL: CRC Press. pp 119-180.
6. Berezney R, Coffey DS. 1974. Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410-1417.
7. Berezney R, Coffey DS. 1977. Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J Cell Biol 73:616-637.
8. Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J. 1995. The nuclear matrix: A structural milieu for genomic function. Int Rev Cytol 162A:1-65.
9. Bjerling P, Silverstein RA, Thon G, Caudy A, Grewal S, Ekwall K. 2002. Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Mol Cell Biol 22:2170-2181.
10. Brasch K. 1982. Fine structure and localization of the nuclear matrix in situ. Exp Cell Res 140:161-171.
11. Brogna S, Sato TA, Rosbash M. 2002. Ribosome components are associated with sites of transcription. Mol Cell 10:93-104.
12. Brown JW, Echeverria M, Qu LH. 2003. Plant snoRNAs: Functional evolution and new modes of gene expression. Trends Plant Sci 8:42-49.
13. Chen D, Huang S. 2001. Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells. J Cell Biol 153:169-176.
14. Chen HK, Pai CY, Huang JY, Yeh NH. 1999. Human Nopp140, which interacts with RNA polymerase I: Implications for rRNA gene transcription and nucleolar structural organization. Mol Cell Biol 19:8536-8546.
15. Chi-Ham CL, Keaton MA, Cannon GC, And Heinhorst S. 2002. The DNA-compacting protein DCP68 from soybean chloroplasts is ferrodoxin:sulfite reductase and co-localizes with the organellar nucleoid. Plant Mol Biol 49: 621-631.
16. Cokol M, Nair R, Rost B. 2000. Finding nuclear localization signals. EMBO Rep 1:411-415.
17. Davie JR. 1996. Histone modifications, chromatin structure, and the nuclear matrix. J Cell Biochem 62:149-157.
18. Dickinson LA, Kohwi-Shigematsu T. 1995. Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol 15:456-465.
19. Dreger M, Bengtsson L, Schoneberg T, Otto H, Hucho F. 2001. Nuclear envelope proteomics: Novel integral membrane proteins of the inner nuclear membrane. Proc Natl Acad Sci USA 98:11943-11948.
20. Fatica A, Tollervey D. 2002. Making ribosomes. Curr Opin Cell Biol 14:313-318.
21. Fawcet DW. 1966. An atlas of fine structure: The cell, its organelles and inclusions. Philadelphia: W.B. Saunders Co.
22. Filipowicz W, Pogacic V. 2000. Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol 14:319-327.
23. Gerner C, Holzmann K, Grimm R, Sauermann G. 1998. Similarity between nuclear matrix proteins of various cells revealed by an improved isolation method. J Cell Biochem 71:363-374.
24. Gerner C, Holzmann K, Meissner M, Goetzmann J, Grimm R, Sauermann G. 1999. Reassembling proteins and chaperones in human nuclear matrix protein fractions. J Cell Biochem 74:145-151.
25. Gerner C, Gotzmann J, Froehwein U, Schamberger C, Ellinger A, Sauermann G. 2002. Proteome analysis of nuclear matrix proteins during apoptotic chromatin condensation. Cell Death Differentiation 9:671-681.
26. Gindullis F, Meier I. 1999. Matrix attachment region binding protein MFP1 is located in discrete domains at the nuclear envelope. Plant Cell 11:1117-1128.
27. Ginisty H, Amalric F, Bouvet P. 1998. Nucleolin functions in the first step of ribosomal RNA processing. EMBO J 17:1476-1486.
28. Ginisty H, Sicard H, Roger B, Bouvet P. 1999. Structure and functions of nucleolin. J Cell Sci 112:761-772.
29. Hall G, Jr., Allen GC, Loer DS, Thompson WF, Spiker S. 1991. Nuclear scaffolds and scaffold-attachment regions in higher plants. Proc Natl Acad Sci USA 88:9320-9324.
30. Hancock R. 2000. A new look at the nuclear matrix. Chromosoma 109:219-225.
31. Hatton D, Gray JC. 1999. Two MAR DNA-binding proteins of the pea nuclear matrix identify a new class of DNA-binding proteins. Plant J 18:417-429.
32. Hirschler-Laszkiewicz I, Cavanaugh A, Hu Q, Catania J, Avantaggiati ML, Rothblum LI. 2001. The role of acetylation in rDNA transcription. Nucleic Acids Res 29:4114-4124.
33. Holzmann K, Gerner C, Poltl A, Schafer R, Obrist P, Ensinger C, Grimm R, Sauermann G. 2000. A human common nuclear matrix protein homologous to eukaryotic translation initiation factor 4A. Biochem Biophys Res Commun 267:339-344.
34. Iborra FJ, Jackson DA, Cook PR. 2001. Coupled transcription and translation within nuclei of mammalian cells. Science 293:1139-1142.
35. Lin BL, Wang JS, Liu HC, Chen RW, Meyer Y, Barakat A, Delseny M. 2001. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress Chaperones 6:201-208.
36. Lothstein L, Arensdorf HP, Chung S-Y, Walker BW, Wooley JC, LeSturgeon WM. 1985. General organization of protein in HeLa 40S nuclear ribonucleoprotein particles. J Cell Biol 100:1570-1581.
37. Lusser A, Brosch G, Loidl A, Haas H, Loidl P. 1997. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277:88-91.
38. Lydersen BK, Petijohn DE. 1980. Human-specific nuclear protein that associates with the polar region of the mitotic apparatus: Distribution in a human/hamster hybrid cells. Cell 22:489-499.
39. Martelli AM, Manzoli L, Rubbini S, Billi AM, Bareggi R, Cocco L. 1995. The protein composition of Friend cell nuclear matrix stabilized by various treatments. Different recovery of nucleolar proteins B23 and C23 and nuclear lamins. Biol Cell 83:15-22.
40. Martelli AM, Falcieri E, Zweyer M, Bortul R, Tabellini G, Cappellini A, Cocco L, Manzoli L. 2002. The controversial nuclear matrix: A balanced point of view. Histol Histopathol 17:1193-1205.
41. Martin M, Garcia-Fernandez LF, Diaz de la Espina SM, Noaillac-Depeyre J, Gas N, Javier Medina F. 1992. Identification and localization of a nucleolin homologue in onion nucleoli. Exp Cell Res 199:74-84.
42. Minguez A, Moreno Diaz de la Espina S. 1996. In situ localization of nucleolin in the plant nucleolar matrix. Exp Cell Res 222:171-178.
43. Mirkovitch J, Mirault ME, Laemmli UK. 1984. Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold. Cell 39:223-232.
44. Nakai K, Kanehisa M. 1992. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14:897-911.
45. Nickerson JA. 2001. Experimental observations of a nuclear matrix. J Cell Sci 114:463-474.
46. Nickerson JA, Krockmalnic G, He DC, Penman S. 1990. Immunolocalization in three dimensions: Immunogold staining of cytoskeletal and nuclear matrix proteins in resinless electron microscopy sections. Proc Natl Acad Sci USA 87:2259-2263.
47. Nickerson JA, Krockmalnic G, Wan KM, Penman S. 1997. The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus. Proc Natl Acad Sci USA 94:4446-4450.
48. Niewmierzycka A, Clarke S. 1999. S-adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein argininemethyltransferase. J Biol Chem 274:814-824.
49. Pai CY, Chen HK, Shen HL, Yeh NH. 1995. Cell-cycle-dependent alterations of a highly phosphorylated nucleolar protein p130 are associated with nucleologenesis. J Cell Sci 108:1911-1920.
50. Pederson T. 1998. Thinking about a nuclear matrix. J Mol Biol 277:147-159.
51. Pederson T. 2000. Half a century of "the nuclear matrix." Mol Biol Cell 11:799-805.
52. Penman S. 1995. Rethinking cell structure. Proc Natl Acad Sci USA 92:525-527.
53. Pih KT, Yi MJ, Liang YS, Shin BJ, Cho MJ, Hwang I, Son D. 2000. Molecular cloning and targeting of a fibrillarin homolog from arabidopsis. Plant Phys 123:51-58.
54. Pouchelet M, St-Pierre E, Bibor-Hardy V, Simard R. 1983. Localization of the 70,000 dalton heat-induced protein in the nuclear matrix of BHK cells. Exp Cell Res 149:451-459.
55. Rose A, Gindullis F, Meier I. 2003. A novel alpha-helical protein, specific to and highly conserved in plants, is associated with the nuclear matrix fraction. J Exp Botany 54:1-9.
56. Scherl A, Couté Y, Déon C, Callé A, Kindbieter K, Sanchez J-C, Greco A, Hochstrasser D, Diaz J-J. 2002. Functional proteomic analysis of human nucleolus. Mol Biol Cell 13:4100-4109.
57. Smetana K, Steele WJ, Busch H. 1966. A ribonucleoprotein network. Exp Cell Res 31:198-201.
58. Spiker S, Thompson WT. 1996. Nuclear matrix attachment regions and transgene expression in plants. Plant Physiol 110:15-21.
59. Tabor CW, Tabor H. 1984. Methionine adenosyltransferase (S-adenosylmethionine synthase) and S-adenosylmethione decarboxylase. Adv Enzymol 56:251-282.
60. Tan J-H, Wooley JC, LeSturgeon WM. 2000. Nuclear matrix-like filaments and fibrogranular complexes form through the rearrangement of specific nuclear ribonucleoproteins. Mol Biol Cell 11:1547-1554.
61. van Holde KE. 1989. Chromatin. New York: Springer.
62. Venema J, Tollervey D. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311.
63. Washburn MP, Wolters D, Yates JR III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247.
64. Westendorf JJ, Zaidi SK, Cascino JE, Kahler R, van Wijnen AJ, Lian JB, Yoshida M, Stein GS, Li X. 2002. Runx2 (Cbfa1, AML-3) interacts with histone deacetylase 6 and represses the p21(CIP1/WAF1) promoter. Mol Cell Biol 22:7982-7992.
65. Willsie JK, Clegg JS. 2002. Small heat shock protein p26 associates with nuclear lamins and HSP70 in nuclei and nuclear matrix fractions from stressed cells. J Cell Biochem 84:601-614.
66. Yu W, Moreno Diaz de la Espina S. 1999. The plant nucleoskeleton: Ultrastructural organization and identification of NuMA homologues in the nuclear matrix and mitotic spindle of plant cells. Exp Cell Res 246:516-526.
67. Zimmer C, von Gabain A, Henics T. 2001. Analysis of sequence-specific binding of RNA to Hsp70 and its various homologs indicates the involvement of N- and C-terminal interactions. RNA 7:1628-1637.