Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs

Abstract

Human immunodeficiency virus type 1 (HIV-1) gene expression is modulated by both viral and cellular factors. A regulatory element in the HIV-1 long terminal repeat known as TAR, which extends from nucleotides ؊18 to ؉80, is critical for the activation of gene expression by the transactivator protein, Tat. RNA transcribed from TAR forms a stable stem-loop structure which serves as the binding site for both Tat and cellular factors. Although TAR RNA is critical for Tat activation, the role that TAR DNA plays in regulating HIV-1 gene expression is not clear. Several studies have demonstrated that TAR DNA can bind cellular proteins, such as UBP-1/LBP-1, which repress HIV-1 gene expression and other factors which are involved in the generation of short, nonprocessive transcripts. In an attempt to characterize additional cellular factors that bind to TAR DNA, a gt11 expression cloning strategy involving the use of a portion of TAR DNA extending from ؊18 to ؉28 to probe a HeLa cDNA library was used. We identified a cDNA, designated TAR DNA-binding protein (TDP-43), which encodes a cellular factor of 43 kDa that binds specifically to pyrimidine-rich motifs in TAR. Antibody to TDP-43 was used in gel retardation assays to demonstrate that endogenous TDP-43, present in HeLa nuclear extract, also bound to TAR DNA. Although TDP-43 bound strongly to double-stranded TAR DNA via its ribonucleoprotein protein-binding motifs, it did not bind to TAR RNA extending from ؉1 to ؉80. To determine the function of TDP-43 in regulating HIV-1 gene expression, in vitro transcription analysis was performed. TDP-43 repressed in vitro transcription from the HIV-1 long terminal repeat in both the presence and absence of Tat, but it did not repress transcription from other promoters such as the adenovirus major late promoter. In addition, transfection of a vector which expressed TDP-43 resulted in the repression of gene expression from an HIV-1 provirus. These results indicate that TDP-43 is capable of modulating both in vitro and in vivo HIV-1 gene expression by either altering or blocking the assembly of transcription complexes that are capable of responding to Tat.

TDP‐43 loss of function inhibits endosomal trafficking and alters trophic signaling in neurons

“…Enhanced VPS4B promoter activity upon TDP-43 knockdown suggests the transcriptional regulation of VPS4B by TDP-43. Chromatin immunoprecipitation shows that TDP-43 directly binds to a GT-rich region in the VPS4B promoter region in rat primary neurons and human brain, as shown before for TAR-DNA motif of HIV1 (Ou et al, 1995). Overexpression of VPS4B in neurons inhibits recycling endosome transport similar ◀ Figure 7.…”

Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4 + T Cell Line

“…3B) (14). Other DE genes at 24 hpi related to ribonucleoprotein biogenesis and RNA processing are also known to affect HIV-1 replication directly; these genes include TARDBP (TAR DNA-binding protein 43) whose protein binds the transactivation response (TAR) element of integrated HIV-1 DNA and represses HIV-1 transcription (15)(16)(17). Downregulation of HNRNPA1, TARDBP, and other related genes may therefore allow more efficient HIV-1 replication in SUP-T1 cells.…”

Parkin reverses TDP‐43‐induced cell death and failure of amino acid homeostasis

“…Parkin is an E3 ubiquitin ligase involved in protein degradation, while Park2 mutations result in loss of Parkin function, leading to autosomal recessive early onset Parkinson's disease (Kitada et al 1998;Lucking et al 2000;Shimura et al 2000;Cookson and Bandmann 2010). Transactivation response DNA-binding protein 43 (TDP-43) is a 414 amino acid protein with DNA/RNA binding protein properties (Ou et al 1995). TDP-43 binds to Park2 mRNA and regulates its expression (Polymenidou et al 2011).…”