By overexpressing various A3 and AID members in cell culture experiments

By overexpressing various A3 and AID members in cell culture experiments (Bogerd et al., 2006b; Chiu et al., 2006; BMS-214662 msds Kinomoto et al., 2007; MacDuff et al., 2009; Muckenfuss et al., 2006; Stenglein and Harris, 2006). Restriction did not correlate with A3 localization to the nuclear compartment, where L1 reverse transcription occurs (Stenglein and Harris, 2006). In all of these instances, the inhibition of transposition occurred without detectable G-to-A mutation, suggesting that the major mechanism of inhibition may be BAY 11-7083 chemical information linked to the strong RNA-binding activity of these enzymes. Consistent with this idea, AID overexpression inhibited production of L1 ORF1 [equivalent to Gag capsid proteins (Metzner et al., 2012)]. However, a recent study blocked uracil DNA repair and observed some L1 G-to-A mutation (Richardson et al., 2014). Thus, similar to other examples discussed earlier, the mechanism of L1 and Alu restriction by A3 family members may involve both deaminase-dependent and -independent activities. However, a major drawback to the aforementioned studies is a dependence on A3/AID overexpression and L1/Alu transposition from a reporter plasmid inserted into chromosomal DNA. Only two studies have attempted to address the impact of endogenous A3 enzymes on transposition. One study depleted endogenous A3B in both HeLa and human embryonic stem cell lines and observed a significant 3 to 5-fold increase in L1 transposition from a transfected reporter plasmid (Wissing et al., 2011). The second study reported an inverse correlation between L1 mobility in primates and expression levels of endogenous A3B and PiWi proteins (Marchetto et al., 2013). Thus, more work will be necessary to establish the precise mechanisms and the identities of the A3 family members that are most relevant to suppressing the transposition of L1 and Alu elements. Endogenous retroviruses are also substrates for restriction and hypermutation by A3 family members. Like exogenous viruses, but unlike L1/Alu elements, these parasites require terminal long-terminal repeats (LTRs) for reverse transcription and gene expression, most ofVirology. Author manuscript; available in PMC 2016 May 01.Harris and DudleyPagewhich are inactive (Bannert and Kurth, 2004). Initial studies demonstrated that mouse intracisternal A particles (IAPs) and MusD elements are susceptible to restriction and hypermutation by overexpressed A3 enzymes (Bogerd et al., 2006a; Esnault et al., 2005; Esnault et al., 2006). Interestingly, the inhibition and hypermutation of LTR-dependent elements is also observed by overexpressing A3 enzymes in heterologous systems, as evidenced by suppression of Ty1 element replication in yeast (Dutko et al., 2005; Schumacher et al., 2005). These studies suggest that at least one aspect of the restriction mechanism does not require additional mammalian proteins as cofactors. Although most mechanistic studies have been performed in model systems, bioinformatics approaches have revealed that significant fractions of some, but not all, endogenous retroviruses have been rendered inactive by a G-to-A hypermutation mechanism, most likely mediated by A3 enzymes based on hallmark signatures (Anwar et al., 2013; Jern and Coffin, 2008; Jern et al., 2007; Lee et al., 2008).Author Manuscript Author Manuscript Author Manuscript Author ManuscriptDNA viruses and the APOBEC familyAlthough the vast majority of information about APOBEC inhibition of viruses pertains to retroviruses and retroelements,.By overexpressing various A3 and AID members in cell culture experiments (Bogerd et al., 2006b; Chiu et al., 2006; Kinomoto et al., 2007; MacDuff et al., 2009; Muckenfuss et al., 2006; Stenglein and Harris, 2006). Restriction did not correlate with A3 localization to the nuclear compartment, where L1 reverse transcription occurs (Stenglein and Harris, 2006). In all of these instances, the inhibition of transposition occurred without detectable G-to-A mutation, suggesting that the major mechanism of inhibition may be linked to the strong RNA-binding activity of these enzymes. Consistent with this idea, AID overexpression inhibited production of L1 ORF1 [equivalent to Gag capsid proteins (Metzner et al., 2012)]. However, a recent study blocked uracil DNA repair and observed some L1 G-to-A mutation (Richardson et al., 2014). Thus, similar to other examples discussed earlier, the mechanism of L1 and Alu restriction by A3 family members may involve both deaminase-dependent and -independent activities. However, a major drawback to the aforementioned studies is a dependence on A3/AID overexpression and L1/Alu transposition from a reporter plasmid inserted into chromosomal DNA. Only two studies have attempted to address the impact of endogenous A3 enzymes on transposition. One study depleted endogenous A3B in both HeLa and human embryonic stem cell lines and observed a significant 3 to 5-fold increase in L1 transposition from a transfected reporter plasmid (Wissing et al., 2011). The second study reported an inverse correlation between L1 mobility in primates and expression levels of endogenous A3B and PiWi proteins (Marchetto et al., 2013). Thus, more work will be necessary to establish the precise mechanisms and the identities of the A3 family members that are most relevant to suppressing the transposition of L1 and Alu elements. Endogenous retroviruses are also substrates for restriction and hypermutation by A3 family members. Like exogenous viruses, but unlike L1/Alu elements, these parasites require terminal long-terminal repeats (LTRs) for reverse transcription and gene expression, most ofVirology. Author manuscript; available in PMC 2016 May 01.Harris and DudleyPagewhich are inactive (Bannert and Kurth, 2004). Initial studies demonstrated that mouse intracisternal A particles (IAPs) and MusD elements are susceptible to restriction and hypermutation by overexpressed A3 enzymes (Bogerd et al., 2006a; Esnault et al., 2005; Esnault et al., 2006). Interestingly, the inhibition and hypermutation of LTR-dependent elements is also observed by overexpressing A3 enzymes in heterologous systems, as evidenced by suppression of Ty1 element replication in yeast (Dutko et al., 2005; Schumacher et al., 2005). These studies suggest that at least one aspect of the restriction mechanism does not require additional mammalian proteins as cofactors. Although most mechanistic studies have been performed in model systems, bioinformatics approaches have revealed that significant fractions of some, but not all, endogenous retroviruses have been rendered inactive by a G-to-A hypermutation mechanism, most likely mediated by A3 enzymes based on hallmark signatures (Anwar et al., 2013; Jern and Coffin, 2008; Jern et al., 2007; Lee et al., 2008).Author Manuscript Author Manuscript Author Manuscript Author ManuscriptDNA viruses and the APOBEC familyAlthough the vast majority of information about APOBEC inhibition of viruses pertains to retroviruses and retroelements,.