A proteomic study of TAR-RNA binding protein (TRBP)-associated factors
© Chi et al; licensee BioMed Central Ltd. 2011
Received: 27 January 2011
Accepted: 25 February 2011
Published: 25 February 2011
The human TAR RNA-binding protein, TRBP, was first identified and cloned based on its high affinity binding to the small hairpin trans-activation responsive (TAR) RNA of HIV-1. TRBP has more recently been found to be a constituent of the RNA-induced silencing complex (RISC) serving as a Dicer co-factor in the processing of the ~70 nucleotide pre-microRNAs(miRNAs) to 21-25 nucleotide mature miRNAs.
Using co-immunoprecipitation and protein-identification by mass spectrometry, we characterized intracellular proteins that complex with TRBP. These interacting proteins include those that have been described to act in protein synthesis, RNA modifications and processing, DNA transcription, and cell proliferation.
Our findings provide a proteome of factors that may cooperate with TRBP in activities such as miRNA processing and in RNA interference by the RISC complex.
TAR-RNA binding protein 2
RNA-induced silencing complex
trans-activation responsive element.
MicroRNAs (miRNAs) are important regulators of cellular development, differentiation, proliferation, apoptosis, metabolism, and oncogenesis [1–4]. Cellular miRNAs have also been proposed to function in restricting virus infection of cells [5–11]. The biogenesis of miRNAs in eukaryotic cells has been reviewed extensively elsewhere [12, 13]. In brief, RNA polymerase II transcribed primary microRNA transcripts (pri-miRNA) are processed by Drosha in the nucleus to pre-miRNA precursors which are then processed by Dicer in the cytoplasm to mature miRNAs. In analyzing miRNA processing, it was noted that a cellular protein, TAR RNA-binding protein TRBP, binds directly to Dicer [14–17] and is important to the activity of miRNA-mediated RNA-silencing. Moreover, a TRBP-Ago2 composed RNA-induced silencing complex (RISC) has been shown to be needed for optimal miRNA-guided post-transcriptional silencing .
TRBP contains two double-stranded RNA binding domains (RBD)  and was originally characterized and cloned based on its high affinity binding to the HIV-1 small hairpin leader RNA, TAR [19–21]. Consistent with the notion of miRNA-mediated restriction of viral infection in mammalian cells, loss of TRBP activity through its sequestration by TAR RNA resulted in the enhanced replication of HIV-1 in human cells . To date, TRBP is considered to act inside cells through at least three different mechanisms: it can promote the translation of TAR RNA-containing viral RNAs ; it can directly bind and inhibit the interferon (IFN)-induced double-stranded RNA (dsRNA)-activated protein kinase R (PKR) ; and as mentioned above, it can be a Dicer co-factor in the miRNA/siRNA RNAi pathway. To gain additional insight into TRBP function, we sought to identify human cellular factors that associate with TRBP. Here, using co-immunoprecipitation (co-IP) and protein-identification by mass spectrometry, we report proteins in a TRBP-proteome.
Functional categories of the TRBP-associated complex
ABCF1, EEF1A2, EIF2AK2, EIF2S1, PTBP1, RPL3, RPL4, RPL5, RPL6, RPL7, RPL9, RPL11, RPL15, RPL18, RPL21, RPL22, RPL24, RPL30, RPL32, RPL34, RPL35, RPL18A, RPL23A, RPL27A, RPL29 (includes EG:6159), RPL31 (includes EG:6160), RPL7A (includes EG:6130), RPS2, RPS5, RPS6, RPS9, RPS10, RPS11, RPS17 (includes EG:6218), RPS3A
RNA Post-Transcriptional Modification
DDX17, DDX54, EFTUD2, HNRPAB, HNRPC, HNRPUL1, PABPC1, PRPF8, PTBP1, SFRS1, SNRPD1, SNRPD3, SYNCRIP, U2AF1
Cellular Growth and Proliferation
AKAP13, ATP5B, ATP5F1, CCT2, DBN1, DCD, DNAJA3, EIF2AK2, GLTSCR2, HMGA1, HNRPA1, HNRPAB, HNRPC, HNRPF, HNRPM, PHB (includes EG:5245), PPP1R9B, PRPF8, PRPF19, RAP1B, RPS3A, RSL1D1, SART1, SFRS1, TOP1, XRN2
BASP1, BTF3, CDC5L, CHD4, CSDA, DDX5, DEK, EIF2S1, GTF3C1, GTF3C3, GTF3C4, HMGA1, HNRPAB, IGHMBP2, PARP1, PHB (includes EG:5245), RBM39, RPL6, SOX21, TARBP2, TOP1, TOP2A
DDX5, DIDO1, DNAJA3, EEF1A2, EIF2AK2, EIF2S1, GNL3, HIST1H1C, HMGA1, HNRPA1, HNRPC, HSPA1B, PARP1, PHB (includes EG:5245), PPP1R9B, PRPF19, RBBP4, RPLP0 (includes EG:6175), RPS3A, SLC2A1, TOP1, TOP2A
DNA Replication, Recombination, and Repair
CDC5L, HMGA1, HSPA1B, IGHMBP2, PARP1, PRPF19, TOP1, TOP2A
CDC5L, EIF2AK2, GNL3, HMGA1, NOL1, PARP1, PES1, PHB (includes EG:5245), PPP1R9B, PRMT5, RPL5, RPL11, RPL23, TOP2A
RPL5, RPL11, RPL23, AKAP13, ASPH, DNAJA3, HMGA1, HSPA1B, PES1, PRMT5, RPS3A
Skeletal and Muscular Disorders
RPL5, RPL11, RPL23
AKAP13, ASPH, DNAJA3, HMGA1, HSPA1B, PES1, PRMT5, RPS3A
Cellular Function and Maintenance/Connective Tissue Development and Function
AKAP13, EIF2AK2, HMGA1, PARP1, SFRS1
Although previous reports implicated TRBP as active primarily in the cytoplasm, our mass spectrometry results (Additional file 2. Supplementary Materials and Methods) identified several TRBP-interacting nuclear factors which are known to participate in processes including RNA splicing, cellular growth and proliferation and gene transcription (Figure 2, Table 1; and Additional file 1, Table S1). For example, EFTUD2, HNRPC, PRPF8, PTBP1, SFRS1, SYNCRIP, SNRPD1, SNRPD3 and U2AF1 are components of the small nuclear ribonucleoprotein (snRNPs) that are involved in splicing of pre-mRNAs. Related to gene transcription, TRBP-associated proteins include those found to be active in RNA polymerase II- and III-dependent transcription (Additional file 1, Table S1). Additionally, a TRBP-associated factor, Sox21, is a HMG-box transcription factor that acts in a complex array of repressive and activating transcriptional processes in embryonic stem cells . The transcription co-activator HMGA1 was also identified in our proteomic data (Table 1). Whether TRBP participates in the determination of pluripotency through Sox21 requires further study.
Recently, TRBP truncating mutations were found in human cancers with microsatellite instability . Evidence exists which supports the notion that impaired miRNA processing and destabilization of the DICER1 protein are correlated with tumorigenesis . Because TRBP is known to interact with Dicer and to be involved in mRNA processing, how TRBP and TRBP-interacting proteins contribute to oncogenesis merits future investigation. The current TRBP proteome provides a starting point for initiating those explorations. Our study describes the TRBP-proteome in HeLa cells. Although TRBP was originally identified as the HIV-1 TAR RNA-binding protein, its more recently characterized function in microRNA biogenesis and RISC-activity is widely conserved in all cell types (e.g. epithelial, hematopoietic, mesenchymal cells etc...). Thus, a HeLa-like TRBP-proteome is likely to be found in all types of human cells. We realize that systematic functional validation of the currently identified TRBP proteome will be necessary in order to clarify the biological relevance of each factor. Indeed, some of the TRBP-interacting proteins are being currently characterized.
Work in the KTJ laboratory was supported in part by NIAID/NIH intramural funds and by the Intramural AIDS Targeted Anti-viral Program (IATAP).
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