Matrin CYP, an SR-rich Cyclophilin That Associates with the Nuclear Matrix and Splicing Factors

Abstract

We report the identification and cloning of a nuclear matrix protein termed matrin cyclophilin or matrin CYP. The derived sequence of matrin cyp encodes a protein of 752 amino acids with a predicted mass of 88 kDa. A 172-residue stretch at the amino terminus shows high identity with the ubiquitous family of cyclophilins. Clustered throughout the carboxyl half of the protein are a series of serine-arginine (SR) repeats that are a characteristic feature of many RNA splicing factors. Antibodies raised against matrin CYP recognize a 106-kDa antigen that is detected in isolated nuclei and quantitatively subfractionates in the nuclear matrix. Laser scanning confocal microscopy localizes most of the anti-matrin CYP-specific antigen within the nucleus in a pattern of large bright speckles that co-localize with splicing factors and diffuse nucleoplasmic staining. A strikingly similar pattern of staining is observed in cells extracted for in situ nuclear matrices. A fusion protein containing the cyclophilin domain of matrin CYP exhibits cyclosporin A (CsA)-sensitive, peptidylprolyl cis-trans-isomerase activity that is characteristic of native cyclophilins. Although total rat liver nuclei contains predominantly CsA-resistant PPIase activity, the corresponding activity in the nuclear matrix is largely CsA-sensitive.The many functions associated with the cell nucleus are temporally and spatially regulated. Nuclear proteins and nucleic acids are often partitioned into functional domains (1). Examples include the nucleoli, heterochromatin, DNA replication sites (2, 3), and transcription domains (4, 5). In addition, a number of other domains have been identified that may also perform specific functions, such as the nuclear speckles (1, 6) and coiled (7) and promyelocytic leukemia (8 -10) bodies. Determining which molecules comprise these structures and how these molecules interact will lead to a greater understanding of the mechanisms responsible for their diverse functions and the role of nuclear architecture in these processes.The proteins and nucleic acids in the cell nucleus that resist solubilization by high salt extraction, nuclease digestion, and detergent solubilization constitute a structure termed the nuclear matrix (11,12). The isolated nuclear matrix has been shown to maintain a structure similar to and containing many of the functional properties associated with the nucleus (13).Several major proteins of the internal nuclear matrix have been identified by immunological methods and termed the nuclear matrins (14). The nuclear matrins include previously characterized proteins such as human RNP 1 A, human nRNP B (15), the nucleolar protein, B23/numatrin (14, 16), the hyperphosphorylated form of RNA pol II LS (17, 18), numerous SR-related proteins (19), and a 125-kDa acidic protein, termed matrin 3 (20). A recent study has confirmed the RNP nature of many of the major nuclear matrix proteins (21).Here we present results on the isolation of a cDNA that encodes an 88-kDa protein with a cyclophilin domain at the amino ter...

Interactions of Arabidopsis RS Domain Containing Cyclophilins with SR Proteins and U1 and U11 Small Nuclear Ribonucleoprotein-specific Proteins Suggest Their Involvement in Pre-mRNA Splicing

“…This domain organization is similar to the recently described large nucleus-localized cyclophilins from human (18,19), rat (20), and Drosophila (21). We have demonstrated here that Arabidopsis RS domain-containing cyclophilins, CypRS64 and CypRS92, interact with a subset of Arabidopsis SR proteins and with U1 and U11 snRNPspecific proteins U1-70K and U11-35K, respectively.…”

“…CypRS64 is a nucleoplasmic protein; however, in transiently transformed protoplasts it accumulates in nuclear bodies of unknown origin, although cells showing speckled/diffuse nuclear localization pattern were also observed. In contrast, human SRcyp and its rat ortholog matrinCYP localized to nuclear speckles where they co-localized with SC35 and U1-70K proteins, respectively (19,20). Interestingly, upon co-expression with its interacting partners, CypRS64 re-localized form nuclear bodies into speckles, subnuclear compartments in which SR proteins and snRNPs are found as well (reviewed in Refs.…”

“…Data base searches with CypRS64 and CypRS92 revealed high sequence similarity with the human protein SRCyp (18,19), its rat ortholog matrinCYP (20), and Drosophila Moca-cyp, which was isolated as an interacting partner of the transcriptional regulator p300/CBP (21). Sequence similarity between metazoan and Arabidopsis proteins is particularly high in the PPIase domain, with 52% identity and 64% similarity (Fig.…”

Immunophilins and Parvulins. Superfamily of Peptidyl Prolyl Isomerases in Arabidopsis

“…The highly charged domain is also rich in Ser-Arg (SR repeats), a feature of many RNA splicing factors (Zahler et al, 1992;Neugebauer et al, 1995). Matrin cyclophilin, the mammalian homolog of AtCYP95, is shown to associate with the nuclear matrix and splicing factors (Mortillaro and Berezney, 1998). Another Arabidopsis multiple domain cyclophilin, AtCYP63, has a domain structure similar to AtCYP95.…”

AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II

“…Human SRcyp has been identified as an interacting partner of the RNA polymerase II C-terminal domain (CTD) and the SR protein-specific kinase Clk/Sty (Nestel et al 1996;Bourquin et al 1997). Its rat and Drosophila homologs have been identified as components of the nuclear matrix (Mortillaro and Berezney 1998) and an interacting partner of the transcriptional regulator p300/CBP (Cavarec et al 2002), respectively. Arabidopsis CypRS64 and CypRS92 are likewise nuclear proteins interacting with SR and snRNP-specific proteins.…”