The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme

Shraddha Sharma; Santosh K. Patnaik; Robert T. Taggart; Bora E. Baysal

doi:10.1038/srep39100

journal article Open Access Dec 15, 2016

The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme

Shraddha Sharma Santosh K. Patnaik

Robert T. Taggart Bora E. Baysal

Scientific Reports Vol. 6 No. 1 · Springer Science and Business Media LLC

View at Publisher Save 10.1038/srep39100

Abstract

AbstractAPOBEC3G is a cytidine deaminase with two homologous domains and restricts retroelements and HIV-1. APOBEC3G deaminates single-stranded DNAs via its C-terminal domain, whereas the N-terminal domain is considered non-catalytic. Although APOBEC3G is known to bind RNAs, APOBEC3G-mediated RNA editing has not been observed. We recently discovered RNA editing by the single-domain enzyme APOBEC3A in innate immune cells. To determine if APOBEC3G is capable of RNA editing, we transiently expressed APOBEC3G in the HEK293T cell line and performed transcriptome-wide RNA sequencing. We show that APOBEC3G causes site-specific C-to-U editing of mRNAs from over 600 genes. The edited cytidines are often flanked by inverted repeats, but are largely distinct from those deaminated by APOBEC3A. We verified protein-recoding RNA editing of selected genes including several that are known to be involved in HIV-1 infectivity. APOBEC3G co-purifies with highly edited mRNA substrates. We find that conserved catalytic residues in both cytidine deaminase domains are required for RNA editing. Our findings demonstrate the novel RNA editing function of APOBEC3G and suggest a role for the N-terminal domain in RNA editing.

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References

59

[1]

Wedekind, J. E., Dance, G. S., Sowden, M. P. & Smith, H. C. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends in Genetics 19, 207–216 (2003). 10.1016/s0168-9525(03)00054-4

[2]

LaRue, R. S. et al. Guidelines for naming nonprimate APOBEC3 genes and proteins. J. Virol. 83, 494–497 (2009). 10.1128/jvi.01976-08

[3]

Smith, H. C., Bennett, R. P., Kizilyer, A., McDougall, W. M. & Prohaska, K. M. Functions and regulation of the APOBEC family of proteins (Seminars in cell & developmental biology Ser. 23, Elsevier, 2012). 10.1016/j.semcdb.2011.10.004

[4]

Conticello, S. G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 9, 229 (2008). 10.1186/gb-2008-9-6-229

[5]

Sheehy, A. M., Gaddis, N. C., Choi, J. D. & Malim, M. H. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418, 646–650 (2002). 10.1038/nature00939

[6]

APOBECs and virus restriction

Reuben S. Harris, Jaquelin P. Dudley

Virology 2015 10.1016/j.virol.2015.03.012

[7]

Refsland, E. W. & Harris, R. S. In Intrinsic Immunity 1–27 (Springer, 2013). 10.1007/978-3-642-37765-5_1

[8]

Apolonia, L. et al. Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1. PLoS Pathog 11, e1004609 (2015). 10.1371/journal.ppat.1004609

[9]

Bogerd, H. P. & Cullen, B. R. Single-stranded RNA facilitates nucleocapsid: APOBEC3G complex formation. RNA 14, 1228–1236 (2008). 10.1261/rna.964708

[10]

Svarovskaia, E. S. et al. Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs. J. Biol. Chem. 279, 35822–35828 (2004). 10.1074/jbc.m405761200

[11]

Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts

Bastien Mangeat, Priscilla Turelli, Gersende Caron et al.

Nature 2003 10.1038/nature01709

[12]

The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA

Hong Zhang, Bin Yang, Roger J. Pomerantz et al.

Nature 2003 10.1038/nature01707

[13]

Langlois, M. A., Beale, R. C., Conticello, S. G. & Neuberger, M. S. Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities. Nucleic Acids Res. 33, 1913–1923 (2005). 10.1093/nar/gki343

[14]

Harjes, S. et al. Impact of H216 on the DNA binding and catalytic activities of the HIV restriction factor APOBEC3G. J. Virol. 87, 7008–7014 (2013). 10.1128/jvi.03173-12

[15]

Iwatani, Y. et al. Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G. Nucleic Acids Res. 35, 7096–7108 (2007). 10.1093/nar/gkm750

[16]

Newman, E. N. et al. Antiviral function of APOBEC3G can be dissociated from cytidine deaminase activity. Current Biology 15, 166–170 (2005). 10.1016/j.cub.2004.12.068

[17]

Bishop, K. N., Verma, M., Kim, E., Wolinsky, S. M. & Malim, M. H. APOBEC3G inhibits elongation of HIV-1 reverse transcripts. PLoS Pathog 4, e1000231 (2008). 10.1371/journal.ppat.1000231

[18]

Esnault, C., Millet, J., Schwartz, O. & Heidmann, T. Dual inhibitory effects of APOBEC family proteins on retrotransposition of mammalian endogenous retroviruses. Nucleic Acids Res. 34, 1522–1531 (2006). 10.1093/nar/gkl054

[19]

Chiu, Y. L. et al. High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition. Proc. Natl. Acad. Sci. USA 103, 15588–15593 (2006). 10.1073/pnas.0604524103

[20]

Hulme, A. E., Bogerd, H. P., Cullen, B. R. & Moran, J. V. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 390, 199–205 (2007). 10.1016/j.gene.2006.08.032

[21]

Bishop, K. N. et al. Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Current biology 14, 1392–1396 (2004). 10.1016/j.cub.2004.06.057

[22]

Takeda, E. et al. Mouse APOBEC3 restricts friend leukemia virus infection and pathogenesis in vivo. J. Virol. 82, 10998–11008 (2008). 10.1128/jvi.01311-08

[23]

Low, A. et al. Enhanced replication and pathogenesis of Moloney murine leukemia virus in mice defective in the murine APOBEC3 gene. Virology 385, 455–463 (2009). 10.1016/j.virol.2008.11.051

[24]

Prohaska, K. M., Bennett, R. P., Salter, J. D. & Smith, H. C. The multifaceted roles of RNA binding in APOBEC cytidine deaminase functions. Wiley Interdisciplinary Reviews: RNA 5, 493–508 (2014). 10.1002/wrna.1226

[25]

McDougall, W. M., Okany, C. & Smith, H. C. Deaminase activity on single-stranded DNA (ssDNA) occurs in vitro when APOBEC3G cytidine deaminase forms homotetramers and higher-order complexes. J. Biol. Chem. 286, 30655–30661 (2011). 10.1074/jbc.m111.269506

[26]

Navarro, F. et al. Complementary function of the two catalytic domains of APOBEC3G. Virology 333, 374–386 (2005). 10.1016/j.virol.2005.01.011

[27]

Iwatani, Y., Takeuchi, H., Strebel, K. & Levin, J. G. Biochemical activities of highly purified, catalytically active human APOBEC3G: correlation with antiviral effect. J. Virol. 80, 5992–6002 (2006). 10.1128/jvi.02680-05

[28]

DNA Deamination Mediates Innate Immunity to Retroviral Infection

Reuben S Harris, Kate N Bishop, Ann M Sheehy et al.

Cell 2003 10.1016/s0092-8674(03)00423-9

[29]

Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10, 1247–1253 (2002). 10.1016/s1097-2765(02)00742-6

[30]

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages

Shraddha Sharma, Santosh K. Patnaik, R. Thomas Taggart et al.

Nature Communications 10.1038/ncomms7881

[31]

Sharma, S., Patnaik, S. K., Kemer, Z. & Baysal, B. E. Transient overexpression of exogenous APOBEC3A causes C-to-U RNA editing of thousands of genes. RNA biology 00–00 (2016). 10.1080/15476286.2016.1184387

[32]

Mariani, R. et al. Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell 114, 21–31 (2003). 10.1016/s0092-8674(03)00515-4

[33]

Bulliard, Y. et al. Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition. J. Virol. 83, 12611–12621 (2009). 10.1128/jvi.01491-09

[34]

Huthoff, H., Autore, F., Gallois-Montbrun, S., Fraternali, F. & Malim, M. H. RNA-dependent oligomerization of APOBEC3G is required for restriction of HIV-1. PLoS Pathog 5, e1000330 (2009). 10.1371/journal.ppat.1000330

[35]

Belanger, K., Savoie, M., Rosales Gerpe, M. C., Couture, J. F. & Langlois, M. A. Binding of RNA by APOBEC3G controls deamination-independent restriction of retroviruses. Nucleic Acids Res. 41, 7438–7452 (2013). 10.1093/nar/gkt527

[36]

Polevoda, B., McDougall, W. M., Bennett, R. P., Salter, J. D. & Smith, H. C. Structural and functional assessment of APOBEC3G macromolecular complexes. Methods (2016). 10.1016/j.ymeth.2016.03.006

[37]

Huthoff, H. & Malim, M. H. Identification of amino acid residues in APOBEC3G required for regulation by human immunodeficiency virus type 1 Vif and Virion encapsidation. J. Virol. 81, 3807–3815 (2007). 10.1128/jvi.02795-06

[38]

Martin, K. L., Johnson, M. & D’Aquila, R. T. APOBEC3G complexes decrease human immunodeficiency virus type 1 production. J. Virol. 85, 9314–9326 (2011). 10.1128/jvi.00273-11

[39]

Ancient Adaptive Evolution of the Primate Antiviral DNA-Editing Enzyme APOBEC3G

Sara L Sawyer, Michael Emerman, Harmit S Malik

PLOS Biology 2004 10.1371/journal.pbio.0020275

[40]

Zhang, J. & Webb, D. M. Rapid evolution of primate antiviral enzyme APOBEC3G. Hum. Mol. Genet. 13, 1785–1791 (2004). 10.1093/hmg/ddh183

[41]

Gerber, A. P. & Keller, W. RNA editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem. Sci. 26, 376–384 (2001). 10.1016/s0968-0004(01)01827-8

[42]

Lu, X. et al. Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA. J. Biol. Chem. 290, 4010–4021 (2015). 10.1074/jbc.m114.624262

[43]

Shandilya, S. M. et al. Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure 18, 28–38 (2010). 10.1016/j.str.2009.10.016

[44]

Furukawa, A. et al. Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. EMBO J. 28, 440–451 (2009). 10.1038/emboj.2008.290

[45]

Kouno, T. et al. Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nature structural & molecular biology 22, 485–491 (2015). 10.1038/nsmb.3033

[46]

Bennett, R. P., Salter, J. D., Liu, X., Wedekind, J. E. & Smith, H. C. APOBEC3G subunits self-associate via the C-terminal deaminase domain. J. Biol. Chem. 283, 33329–33336 (2008). 10.1074/jbc.m803726200

[47]

Feng, Y. & Chelico, L. Intensity of deoxycytidine deamination of HIV-1 proviral DNA by the retroviral restriction factor APOBEC3G is mediated by the noncatalytic domain. J. Biol. Chem. 286, 11415–11426 (2011). 10.1074/jbc.m110.199604

[48]

Chelico, L., Prochnow, C., Erie, D. A., Chen, X. S. & Goodman, M. F. Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G. J. Biol. Chem. 285, 16195–16205 (2010). 10.1074/jbc.m110.107987

[49]

Leiros, I., Secundo, F., Zambonelli, C., Servi, S. & Hough, E. The first crystal structure of a phospholipase D. Structure 8, 655–667 (2000). 10.1016/s0969-2126(00)00150-7

[50]

Davies, D. R., Interthal, H., Champoux, J. J. & Hol, W. G. The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1. Structure 10, 237–248 (2002). 10.1016/s0969-2126(02)00707-4

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Published: Dec 15, 2016
Vol/Issue: 6(1)
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Shraddha Sharma, Santosh K. Patnaik, Robert T. Taggart, et al. (2016). The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme. Scientific Reports, 6(1). https://doi.org/10.1038/srep39100

The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme

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