DDX3, Cofactors, and RNA Export
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KeywordsRubella Virus Innate Antiviral Immunity Stress Granule Formation DDX3 Protein Nuclear Export Factor
RNA helicases are enzymes that bind to RNA, hydrolyze ATP in an RNA-binding-dependent manner, and separate two annealed RNA duplex strands. Based on sequencing data, there are approximately 85 deduced RNA helicases in the human genome. They have been postulated to have many different functions inside cells. DDX3 is a DEAD (Asp-Glu-Ala-Asp) box RNA helicase protein. There are two forms of the protein. DDX3X is encoded on the X chromosome at position Xp11.3-p11.23 while DDX3Y is located at Yq11. The X-encoded protein and the Y-encoded protein are 91 % identical. The DDX3 helicase has attributed roles in pre-mRNA splicing, RNA export, and translation of mRNAs, among other functions.
Organization of DDX3 Protein
There are five superfamilies of helicases, SF1–5 (Kwong et al. 2005). DDX3 is a member of the SF2 family of helicases. Helicases are operationally defined by whether they can bind single- or double-stranded nucleic acids, unwind RNA or DNA, or both, in either 5′ to 3′ or 3′ to 5′ directions. They generally, albeit not invariably, contain certain conserved signature motifs (Kwong et al. 2005). The two major superfamilies of helicases, SF1 and SF2, share at least seven conserved protein motifs. These include domains that specify for nucleic acid binding, ATP hydrolysis, and core helicase activity. The conserved motifs in DDX3 and the demonstration of its RNA unwinding activity have been previously outlined (Yedavalli et al. 2004).
Pleiotropic Functions Attributed to DDX3
Several different functions have been attributed to DDX3. For example, it has been reported that DDX3 has a cell proliferative function through enhancing the translation of cyclin E1 (Lai et al. 2010) and that DDX3 can influence the progression of some cancers through increasing the expressing of the SNAIL transcription factor (Sun et al. 2011). On the other hand, DDX3 has also been reported to act as a tumor suppressor through its transcriptional upregulation of p21waf1/cip1 (Chao et al. 2006), and in settings of environmental insult, DDX3 was reported to inhibit eIF4e (eukaryotic initiation factor 4E), leading to a repression of translation accompanied by an increase in stress granule formation (Shih et al. 2012). DDX3’s inhibitory effect on eIF4e-mediated translation appears to correlate with its described tumor-suppressing function, but interestingly, these activities apparently do not require intact ATPase or helicase functions (Shih et al. 2008). DDX3 also has been reported to play roles in neuronal RNA granules and RNA transport (Kanai et al. 2004), in spliceosomes and RNA splicing (Zhou et al. 2002), in innate antiviral immunity to virus infections (Schroder 2011), as well as in interactions with HCV (Ariumi et al. 2007; Angus et al. 2010) and HIV (Yedavalli et al. 2004; Chen et al. 2012).
Interactions of DDX3 with HIV
Several viruses encode RNA helicases. Herpes virus UL5 and UL9, alphavirus nsP2, rubella virus p70, SARS coronavirus nsp13, hepatitis E virus ORF1, and flavivirus NS3 are some examples of virus-encoded helicases (Jeang and Yedavalli 2006). HIV-1 does not encode an RNA helicase, but there is growing evidence that it interacts with several RNA helicases for replication (Chen et al. 2012). First, cDNA microarray analyses have found that the expression of RNA helicases DHX9, DDX11, DDX18, DDX21, and DDX24 are changed in human cells by HIV-1 infection (Krishnan and Zeichner 2004). Second, a recent mass spectrometric proteomic study found that HIV-1 Gag complexes with DHX9, DDX18, DDX21, DDX24, HIV-1 Vpr interact with DDX20, and Env gp120 binds DDX6 (Jager et al. 2012). In a separate study, Rev, in the presence of RNA, was reported to bind DDX1, DDX3, DDX5, DHX9, DDX17, DDX24, DHX36, and DDX47 (Naji et al. 2012); and DDX24 and DHX30 were described to be involved in Rev-influenced packaging of HIV-1 RNA (Ma et al. 2008; Zhou et al. 2008a).
The role of DDX3 in HIV-1 biology was first broached by Yedavalli et al. (2004). They reported that DDX3 is a nucleocytoplasmic shuttling protein that binds CRM1 (see CRM1), a nuclear export factor, and also that DDX3 is involved in the egress from the nucleus of Rev/RRE-dependent unspliced and partially spliced HIV-1 RNAs (see HIV-1 Rev Expression and Functions) (Yedavalli et al. 2004). Another RNA helicase, DDX1, was found to also provide a similar nuclear-to-cytoplasmic transport of HIV-1 RNAs (Fang et al. 2004). However, among all the RNA helicases postulated to be important for HIV-1, in three recent siRNA-based genome-wide screens for HIV-1 dependency factors, DDX3 was the only RNA helicase found in all three studies to be required for HIV-1 propagation in human cells (Brass et al. 2008; Konig et al. 2008; Zhou et al. 2008b). In addition to DDX3’s role in HIV-1 RNA transport, there is emerging evidence that DDX3 can also contribute to the translation of viral RNAs (Liu et al. 2011; Lee et al. 2008). More investigation is needed to parse the mechanistic distinctions between DDX3 activity needed for RNA transport versus RNA translation.
Extant data suggest that the DDX3 RNA helicase plays roles in cell proliferation, tumor progression, and virus infection of human cells. Above, the contributions of DDX3 to several pathological processes are outlined, arguing that this helicase could be an important drug target. It is thus encouraging that progress has been made in the development of small molecule compounds that target DDX3 (see Cellular Cofactors of HIV as Drug Targets) (Yedavalli et al. 2008; Maga et al. 2011; Radi et al. 2012). Going forward, these candidates should help investigators to further dissect the mechanism(s) and function(s) of DDX3.
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