Abstract
The proteins of rat liver cytoplasm, nuclear washes, matrix, membrane, heterogeneous nuclear (hn)RNA proteins and chromatin were examined by two-dimensional gel electrophoresis. The inclusion in the gels of six common protein standards of carefully selected molecular weight and isoelectric point allowed us to clearly follow the distribution of specific proteins during nuclear extraction. In the nuclear washes and chromatin, we observed five classes of proteins: (a) Exclusively cytoplasmic proteins, present in the first saline-EDTA wash but rapidly disappearing from subsequent washes; (b) ubiquitous proteins of 75,000, 68,000, 57,000, and 43,000 mol wt, the latter being actin, found in the cytoplasm, all nuclear washes and the final chromatin pellet; (c) proteins of 94,000, 25,000, and 20,500 mol wt specific to the nuclear washes; (d) proteins present in the nuclear washes and final chromatin, represented by species at 62,000, 55,000, 54,000, and 48,000 mol wt, primarily derived from the nuclear matrix; and (e) two proteins of 68,000 mol wt present only in the final chromatin. The major 65,000- 75,000-mol wt proteins seen by one-dimensional gel electrophoresis of nuclear matrix were very heterogeneous and contained a major acidic, an intermediate, and a basic group. A single 68,000-mol wt polypeptide constituted the majority of the membrane-lamina fraction, consistent with immunological studies indicating that a distinct subset of matrix proteins occurs, associated with heterochromatin, at the periphery of the nucleus. Actin was the second major nuclear membrane-lamina protein. Two polypeptides at 36,000 and 34,000 mol wt constituted 60% of the hnRNP. Approximately 80% of the mass of the nonhistone chromosomal proteins (NHP) from unwashed nuclei is contributed by nuclear matrix and hnRNPs, and essentially the same patterns were seen with chromatin NHP. The concept of NHP being a distinct set of DNA- bound proteins is unnecessarily limiting. Many are derived from the nuclear matrix or hnRNp particles and vary in the degree to which they share different intracellular compartments.
Full Text
The Full Text of this article is available as a PDF (2.4 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aaronson R. P., Blobel G. Isolation of nuclear pore complexes in association with a lamina. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1007–1011. doi: 10.1073/pnas.72.3.1007. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Adolph K. W., Cheng S. M., Laemmli U. K. Role of nonhistone proteins in metaphase chromosome structure. Cell. 1977 Nov;12(3):805–816. doi: 10.1016/0092-8674(77)90279-3. [DOI] [PubMed] [Google Scholar]
- Adolphs K. W., Cheng S. M., Paulson J. R., Laemmli U. K. Isolation of a protein scaffold from mitotic HeLa cell chromosomes. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4937–4941. doi: 10.1073/pnas.74.11.4937. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Anderson L., Anderson N. G. High resolution two-dimensional electrophoresis of human plasma proteins. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5421–5425. doi: 10.1073/pnas.74.12.5421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Augenlicht L. H., Lipkin M. Appearance of rapidly labeled, high molecular weight RNA in nuclear ribonucleoprotein. Release from chromatin and association with protein. J Biol Chem. 1976 May 10;251(9):2592–2599. [PubMed] [Google Scholar]
- BULL H. B., BREESE K., FERGUSON G. L., SWENSON C. A. THE PH OF UREA SOLUTIONS. Arch Biochem Biophys. 1964 Feb;104:297–304. doi: 10.1016/s0003-9861(64)80017-5. [DOI] [PubMed] [Google Scholar]
- Barrieux A., Ingraham H. A., Nystul S., Rosenfeld M. G. Characterization of the association of specific proteins with messenger ribonucleic acid. Biochemistry. 1976 Aug 10;15(16):3523–3528. doi: 10.1021/bi00661a020. [DOI] [PubMed] [Google Scholar]
- Berezney R., Coffey D. S. Identification of a nuclear protein matrix. Biochem Biophys Res Commun. 1974 Oct 23;60(4):1410–1417. doi: 10.1016/0006-291x(74)90355-6. [DOI] [PubMed] [Google Scholar]
- Berezney R., Coffey D. S. Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J Cell Biol. 1977 Jun;73(3):616–637. doi: 10.1083/jcb.73.3.616. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Berezney R., Coffey D. S. Nuclear protein matrix: association with newly synthesized DNA. Science. 1975 Jul 25;189(4199):291–293. doi: 10.1126/science.1145202. [DOI] [PubMed] [Google Scholar]
- Beyer A. L., Christensen M. E., Walker B. W., LeStourgeon W. M. Identification and characterization of the packaging proteins of core 40S hnRNP particles. Cell. 1977 May;11(1):127–138. doi: 10.1016/0092-8674(77)90323-3. [DOI] [PubMed] [Google Scholar]
- Bhorjee J. S., Pederson T. Chromatin: its isolation from cultured mammalian cells with particular reference to contamination by nuclear ribnucleoprotein particles. Biochemistry. 1973 Jul 3;12(14):2766–2773. doi: 10.1021/bi00738a033. [DOI] [PubMed] [Google Scholar]
- Blobel G. A protein of molecular weight 78,000 bound to the polyadenylate region of eukaryotic messenger RNAs. Proc Natl Acad Sci U S A. 1973 Mar;70(3):924–928. doi: 10.1073/pnas.70.3.924. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bornens M., Kasper C. B. Fractionation and partial characterization of proteins of the bileaflet nuclear membrane from rat liver. J Biol Chem. 1973 Jan 25;248(2):571–579. [PubMed] [Google Scholar]
- Brunel C., Lelay M. N. Two-dimensional analysis of proteins associated with heterogenous nuclear RNA in various animal cell lines. Eur J Biochem. 1979 Sep;99(2):273–283. doi: 10.1111/j.1432-1033.1979.tb13254.x. [DOI] [PubMed] [Google Scholar]
- Clark T. G., Merriam R. W. Diffusible and bound actin nuclei of Xenopus laevis oocytes. Cell. 1977 Dec;12(4):883–891. doi: 10.1016/0092-8674(77)90152-0. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Cohen L. W. Two-dimensional gel electrophoresis of 125I-labeled surface proteins of human fibroblasts. Biochim Biophys Acta. 1979 May 23;578(1):61–67. doi: 10.1016/0005-2795(79)90113-2. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Harris D. C. Nuclear proteins. I. Electrophoretic comparison of mouse nucleoli, heterochromatin, euchromatin and contractile proteins. Exp Cell Res. 1975 Nov;96(1):161–179. doi: 10.1016/s0014-4827(75)80049-8. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Harris D. C. Nuclear proteins. II. Similarity of nonhistone proteins in nuclear sap and chromatin, and essential absence of contractile proteins from mouse liver nuclei. J Cell Biol. 1976 Aug;70(2 Pt 1):440–452. doi: 10.1083/jcb.70.2.440. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Comings D. E. Mechanisms of chromosome banding and implications for chromosome structure. Annu Rev Genet. 1978;12:25–46. doi: 10.1146/annurev.ge.12.120178.000325. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Okada T. A. Nuclear proteins. III. The fibrillar nature of the nuclear matrix. Exp Cell Res. 1976 Dec;103(2):341–360. doi: 10.1016/0014-4827(76)90271-8. [DOI] [PubMed] [Google Scholar]
- Comings D. E. Pc 1 Duarte, a common polymorphism of a human brain protein, and its relationship to depressive disease and multiple sclerosis. Nature. 1979 Jan 4;277(5691):28–32. doi: 10.1038/277028a0. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Peters K. E. Triple-spot proteins in two-dimensional gel electrophoresis. Am J Hum Genet. 1979 May;31(3):311–314. [PMC free article] [PubMed] [Google Scholar]
- Comings D. E., Tack L. C. Similarities in the cytoplasmic proteins of different organs and species examined by SDS gel electrophoresis. Exp Cell Res. 1972 Nov;75(1):73–78. doi: 10.1016/0014-4827(72)90521-6. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Tack L. O. Non-histone proteins. The effect of nuclear washes and comparison of metaphase and interphase chromatin. Exp Cell Res. 1973 Nov;82(1):175–191. doi: 10.1016/0014-4827(73)90260-7. [DOI] [PubMed] [Google Scholar]
- Comings D. E., Wallack A. S. DNA-binding properties of nuclear matrix proteins. J Cell Sci. 1978 Dec;34:233–246. doi: 10.1242/jcs.34.1.233. [DOI] [PubMed] [Google Scholar]
- Conner B. J., Comings D. E. Nuclear proteins. V. Studies of histone-binding proteins from mouse liver by affinity chromatography. Biochim Biophys Acta. 1978 Jan 25;532(1):122–136. doi: 10.1016/0005-2795(78)90455-5. [DOI] [PubMed] [Google Scholar]
- Douvas A. S., Harrington C. A., Bonner J. Major nonhistone proteins of rat liver chromatin: preliminary identification of myosin, actin, tubulin, and tropomyosin. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3902–3906. doi: 10.1073/pnas.72.10.3902. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Elgin S. C., Weintraub H. Chromosomal proteins and chromatin structure. Annu Rev Biochem. 1975;44:725–774. doi: 10.1146/annurev.bi.44.070175.003453. [DOI] [PubMed] [Google Scholar]
- Ely S., D'Arcy A., Jost E. Interaction of antibodies against nuclear envelope-associated proteins from rat liver nuclei with rodent and human cells. Exp Cell Res. 1978 Oct 15;116(2):325–331. doi: 10.1016/0014-4827(78)90455-x. [DOI] [PubMed] [Google Scholar]
- Faiferman I., Pogo A. O. Isolation of a nuclear ribonucleoprotein network that contains heterogeneous RNA and is bound to the nuclear envelope. Biochemistry. 1975 Aug 26;14(17):3808–3816. doi: 10.1021/bi00688a013. [DOI] [PubMed] [Google Scholar]
- Fujitani H., Holoubek V. Similarity of the 0.35 M NaCl soluble nuclear proteins and the nonhistone chromosomal proteins. Biochem Biophys Res Commun. 1973 Oct 15;54(4):1300–1305. doi: 10.1016/0006-291x(73)91129-7. [DOI] [PubMed] [Google Scholar]
- Garrard W. T., Pearson W. R., Wake S. K., Bonner J. Stoichiometry of chromatin proteins. Biochem Biophys Res Commun. 1974 May 7;58(1):50–57. doi: 10.1016/0006-291x(74)90889-4. [DOI] [PubMed] [Google Scholar]
- Garrels J. I., Gibson W. Identification and characterization of multiple forms of actin. Cell. 1976 Dec;9(4 Pt 2):793–805. doi: 10.1016/0092-8674(76)90142-2. [DOI] [PubMed] [Google Scholar]
- Gerace L., Blum A., Blobel G. Immunocytochemical localization of the major polypeptides of the nuclear pore complex-lamina fraction. Interphase and mitotic distribution. J Cell Biol. 1978 Nov;79(2 Pt 1):546–566. doi: 10.1083/jcb.79.2.546. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goodwin G. H., Johns E. W. Isolation and characterisation of two calf-thymus chromatin non-histone proteins with high contents of acidic and basic amino acids. Eur J Biochem. 1973 Dec 3;40(1):215–219. doi: 10.1111/j.1432-1033.1973.tb03188.x. [DOI] [PubMed] [Google Scholar]
- Goodwin G. H., Sanders C., Johns E. W. A new group of chromatin-associated proteins with a high content of acidic and basic amino acids. Eur J Biochem. 1973 Sep 21;38(1):14–19. doi: 10.1111/j.1432-1033.1973.tb03026.x. [DOI] [PubMed] [Google Scholar]
- Hedrick J. L., Smith A. J. Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis. Arch Biochem Biophys. 1968 Jul;126(1):155–164. doi: 10.1016/0003-9861(68)90569-9. [DOI] [PubMed] [Google Scholar]
- Heinrich P. C., Gross V., Northemann W., Scheurlen M. Structure and function of nuclear ribonucleoprotein complexes. Rev Physiol Biochem Pharmacol. 1978;81:101–134. doi: 10.1007/BFb0034092. [DOI] [PubMed] [Google Scholar]
- Herman R., Weymouth L., Penman S. Heterogeneous nuclear RNA-protein fibers in chromatin-depleted nuclei. J Cell Biol. 1978 Sep;78(3):663–674. doi: 10.1083/jcb.78.3.663. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hodge L. D., Mancini P., Davis F. M., Heywood P. Nuclear matrix of HeLa S3 cells. Polypeptide composition during adenovirus infection and in phases of the cell cycle. J Cell Biol. 1977 Jan;72(1):194–208. doi: 10.1083/jcb.72.1.194. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jockusch B. M., Becker M., Hindennach I., Jockusch H. Slime mould actin: homology to vertebrate actin and presence in the nucleus. Exp Cell Res. 1974 Dec;89(2):241–246. doi: 10.1016/0014-4827(74)90787-3. [DOI] [PubMed] [Google Scholar]
- Karn J., Vidali G., Boffa L. C., Allfrey V. G. Characterization of the non-histone nuclear proteins associated with rapidly labeled heterogeneous nuclear RNA. J Biol Chem. 1977 Oct 25;252(20):7307–7322. [PubMed] [Google Scholar]
- Kostraba N. C., Montagna R. A., Wang T. Y. Study of the loosely bound non-histone chromatin proteins. Stimulation of deoxyribonucleic acid-templated ribonucleic acid synthesis by a specific deoxyribonucleic acid-binding phosphoprotein fraction. J Biol Chem. 1975 Feb 25;250(4):1548–1555. [PubMed] [Google Scholar]
- Krohne G., Franke W. W., Scheer U. The major polypeptides of the nuclear pore complex. Exp Cell Res. 1978 Oct 1;116(1):85–102. doi: 10.1016/0014-4827(78)90067-8. [DOI] [PubMed] [Google Scholar]
- LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
- Laemmli U. K., Cheng S. M., Adolph K. W., Paulson J. R., Brown J. A., Baumbach W. R. Metaphase chromosome structure: the role of nonhistone proteins. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):351–360. doi: 10.1101/sqb.1978.042.01.036. [DOI] [PubMed] [Google Scholar]
- Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
- Lazarides E., Lindberg U. Actin is the naturally occurring inhibitor of deoxyribonuclease I. Proc Natl Acad Sci U S A. 1974 Dec;71(12):4742–4746. doi: 10.1073/pnas.71.12.4742. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lestourgeon W. M., Forer A., Yang Y. Z., Bertram J. S., Pusch H. P. Contractile proteins. Major components of nuclear and chromosome non-histone proteins. Biochim Biophys Acta. 1975 Feb 27;379(2):529–552. [PubMed] [Google Scholar]
- Liew C. C., Chan P. K. Identification of nonhistone chromatin proteins in chromatin subunits. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3458–3462. doi: 10.1073/pnas.73.10.3458. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Long B. H., Huang C. Y., Pogo A. O. Isolation and characterization of the nuclear matrix in Friend erythroleukemia cells: chromatin and hnRNA interactions with the nuclear matrix. Cell. 1979 Dec;18(4):1079–1090. doi: 10.1016/0092-8674(79)90221-6. [DOI] [PubMed] [Google Scholar]
- MacGillivray A. J., Rickwood D. The heterogeneity of mouse-chromatin nonhistone proteins as evidenced by two-dimensional polyacrylamide-gel electrophoresis and ion-exchange chromatography. Eur J Biochem. 1974 Jan 3;41(1):181–190. doi: 10.1111/j.1432-1033.1974.tb03258.x. [DOI] [PubMed] [Google Scholar]
- Martin T., Billings P., Levey A., Ozarslan S., Quinlan T., Swift H., Urbas L. Some properties of RNA:protein complexes from the nucleus of eukaryotic cells. Cold Spring Harb Symp Quant Biol. 1974;38:921–932. doi: 10.1101/sqb.1974.038.01.094. [DOI] [PubMed] [Google Scholar]
- Miller O. L., Jr, Hamkalo B. A. Visualization of RNA synthesis on chromosomes. Int Rev Cytol. 1972;33:1–25. doi: 10.1016/s0074-7696(08)61446-1. [DOI] [PubMed] [Google Scholar]
- Miller T. E., Huang C. Y., Pogo A. O. Rat liver nuclear skeleton and ribonucleoprotein complexes containing HnRNA. J Cell Biol. 1978 Mar;76(3):675–691. doi: 10.1083/jcb.76.3.675. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Northemann W., Gross V., Scheurlen M., Heinrich P. C. Studies on the preparation and properties of ribonucleoprotein particles from rat liver nuclei. Biochim Biophys Acta. 1978 Jul 24;519(2):406–417. doi: 10.1016/0005-2787(78)90094-1. [DOI] [PubMed] [Google Scholar]
- O'Farrell P. H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PMC free article] [PubMed] [Google Scholar]
- O'Farrell P. Z., Goodman H. M., O'Farrell P. H. High resolution two-dimensional electrophoresis of basic as well as acidic proteins. Cell. 1977 Dec;12(4):1133–1141. doi: 10.1016/0092-8674(77)90176-3. [DOI] [PubMed] [Google Scholar]
- O'Malley B. W., Means A. R. Female steroid hormones and target cell nuclei. Science. 1974 Feb 15;183(4125):610–620. doi: 10.1126/science.183.4125.610. [DOI] [PubMed] [Google Scholar]
- Okada T. A., Comings D. E. Higher order structure of chromosomes. Chromosoma. 1979 Apr 5;72(1):1–14. doi: 10.1007/BF00286426. [DOI] [PubMed] [Google Scholar]
- Pagoulatos G. N., Yaniv M. High resolution two-dimensional electrophoresis of proteins bound to heterogeneous nuclear RNA. FEBS Lett. 1977 Feb 15;74(1):115–120. doi: 10.1016/0014-5793(77)80766-7. [DOI] [PubMed] [Google Scholar]
- Pederson T. Gene activation in eukaryotes: are nuclear acidic proteins the cause or the effect? Proc Natl Acad Sci U S A. 1974 Mar;71(3):617–621. doi: 10.1073/pnas.71.3.617. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Peterson J. L., McConkey E. H. Non-histone chromosomal proteins from HeLa cells. A survey by high resolution, two-dimensional electrophoresis. J Biol Chem. 1976 Jan 25;251(2):548–554. [PubMed] [Google Scholar]
- Prestayko A. W., Crane P. M., Busch H. Phosphorylation and DNA binding of nuclear rat liver proteins soluble at low ionic strength. Biochemistry. 1976 Jan 27;15(2):414–421. doi: 10.1021/bi00647a027. [DOI] [PubMed] [Google Scholar]
- Samarina O. P., Lukanidin E. M., Molnar J., Georgiev G. P. Structural organization of nuclear complexes containing DNA-like RNA. J Mol Biol. 1968 Apr 14;33(1):251–263. doi: 10.1016/0022-2836(68)90292-1. [DOI] [PubMed] [Google Scholar]
- Sanger J. W. Presence of actin during chromosomal movement. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2451–2455. doi: 10.1073/pnas.72.6.2451. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Scheer U., Kartenbeck J., Trendelenburg M. F., Stadler J., Franke W. W. Experimental disintegration of the nuclear envelope. Evidence for pore-connecting fibrils. J Cell Biol. 1976 Apr;69(1):1–18. doi: 10.1083/jcb.69.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schwartz H., Darnell J. E. The association of protein with the polyadenylic acid of HeLa cell messenger RNA: evidence for a "transport" role of a 75,000 molecular weight polypeptide. J Mol Biol. 1976 Jul 15;104(4):833–851. doi: 10.1016/0022-2836(76)90185-6. [DOI] [PubMed] [Google Scholar]
- Shapiro A. L., Viñuela E., Maizel J. V., Jr Molecular weight estimation of polypeptide chains by electrophoresis in SDS-polyacrylamide gels. Biochem Biophys Res Commun. 1967 Sep 7;28(5):815–820. doi: 10.1016/0006-291x(67)90391-9. [DOI] [PubMed] [Google Scholar]
- Stevenin J., Gattoni R., Gallinaro-Matringe H., Jacob M. Nuclear ribonucleoprotein particles contain specific proteins and unspecific non-histone nuclear proteins. Eur J Biochem. 1978 Mar 15;84(2):541–549. doi: 10.1111/j.1432-1033.1978.tb12197.x. [DOI] [PubMed] [Google Scholar]
- Suria D., Liew C. C. Characterization of proteins associated with nuclear ribonucleoprotein particles by two-dimensional polyacrylamide gel electrophoresis. Can J Biochem. 1979 Jan;57(1):32–42. doi: 10.1139/o79-004. [DOI] [PubMed] [Google Scholar]
- Tata J. R., Baker B. Sub-nuclear fractionation. II. Intranuclear compartmentation of transcription in vivo and in vitro. Exp Cell Res. 1974 Jan;83(1):125–138. doi: 10.1016/0014-4827(74)90695-8. [DOI] [PubMed] [Google Scholar]
- Ui N. Isoelectric points and conformation of proteins. I. Effect of urea on the behavior of some proteins in isoelectric focusing. Biochim Biophys Acta. 1971 Mar 23;229(3):567–581. [PubMed] [Google Scholar]
- Whalen R. G., Butler-Browne G. S., Gros F. Protein synthesis and actin heterogeneity in calf muscle cells in culture. Proc Natl Acad Sci U S A. 1976 Jun;73(6):2018–2022. doi: 10.1073/pnas.73.6.2018. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wilhelm J. A., Groves C. M., Hnilica L. S. Lack of major cytoplasmic protein contamination of rat liver nuclear chromatin. Experientia. 1972 May 15;28(5):514–516. doi: 10.1007/BF01931850. [DOI] [PubMed] [Google Scholar]
- Wunderlich F., Herlan G. Reversibly contractile nuclear matrix. Its isolation, structure, and composition. J Cell Biol. 1977 May;73(2):271–278. doi: 10.1083/jcb.73.2.271. [DOI] [PMC free article] [PubMed] [Google Scholar]
