Identification of nuclear matrix proteins tightly bound to soluble simian virus 40 chromosomes

Nuclear matrix proteins (defined as the nuclear proteins which were highly enriched in an insoluble fraction following extraction of lipids, loosely bound proteins, and nucleic acids) from mock- and SV40-infected cells were identified by two-dimensional polyacrylamide gel electrophoresis, consisting of nonequilibrium pH gradients in the first dimension and sodium dodecyl sulfate gel electrophoresis in the second dimension. The proteins identified in the mock-infected nuclear matrix included M1 (molecular weight, 71K), M2 (69K) M3 (58K), M4 (50K), M5 (49K), M6 (36K), M7 (36K), and M8 (31K), while the nuclear matrix from SV40-infected cells included, in addition to all these proteins, VP-1 (45K), VP-1' (44K), VP-3 (25K), V1 (36K), V2 (35K), and V3 (35K). Except for M7 all of these proteins sedimented with SV40 chromosomes isolated and partially purified by glycerol gradient sedimentation at low ionic strength, and only M6 and M8 were removed from the SV40 chromosomes during more extensive purification of the SV40 chromosomes by subsequent sedimentation at high ionic strength (0.5 M NaCl). When the structures of the SV40 chromosomes were destroyed by digestion with DNAase I, these tightly bound proteins no longer sedimented to the position of SV40 chromosomes. Further subfractionation of SV40 chromosomes indicated that the proteins M1 to M4 were preferentially associated with the nonreplicating SV40 chromosomes, whereas M5 was associated with encapsidating SV40 chromosomes and virions.