Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey

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Uus Saepuloh
Diah Iskandriati
Joko Pamungkas
Dedy Duryadi Solihin
Sela Septima Mariya
Dondin Sajuthi

Abstract

Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284–4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.

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How to Cite
Uus Saepuloh, Diah Iskandriati, Joko Pamungkas, Dedy Duryadi Solihin, Sela Septima Mariya, & Dondin Sajuthi. (2020). Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey. Tropical Life Sciences Research, 31(3), 47–61. https://doi.org/10.21315/tlsr2020.31.3.4
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References

Altschul S F, Madden T L, Schaffer A A, Zhang J, Zhang Z, Miller W and Lipman D J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25(17): 3389–3402. https://doi.org/10.1093/nar/25.17.3389

Boyer P L, Sarafianos S G, Arnold E and Hughes S H. (2000). Analysis of mutations at position 115 and 116 in the dNTPs binding site of HIV-1 reverse transcriptase. PNAS USA 97(7): 3056–3061. https://doi.org/10.1073/pnas.97.7.3056

Coté M L and Roth M J. (2008). Murine leukemia virus reverse transcriptase: Structural comparison with HIV-1 reverse transcriptase. Virus Research 134(1–2): 186–202. https://doi.org/10.1016/j.virusres.2008.01.001

Delano W L. (2002). PyMOL: An open-source molecular graphics tool. CCP4 Newsletter On Protein Crystallography 40: 82–92.

Ding J, Das K, Hsiou Y, Sarafianos SG, Clark A D Jr, Jacobo-Molina A, Tantillo C, Hughes S H and Arnold E. (1998). Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA templateprimer and an antibody Fab fragment at 2.8 A resolution. Journal of Molecular Biology 284(4): 1095–1111. https://doi.org/10.1006/jmbi.1998.2208

Gardner M B, Luciw P, Lerche N and Marx P. (1988). Nonhuman primate retrovirus isolates and AIDS. Advances Veterinary Sciences Comparative Medicine 32: 171–190. https://doi.org/10.1016/B978-0-12-039232-2.50011-6

Gille C and Frömmel C. (2001). STRAP: Editor for STRuctural Alignments of Proteins. Bioinformatics 17(4): 377–378. https://doi.org/10.1093/bioinformatics/17.4.377

Hall T A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. SymposiumSeries 41: 95–98.

Herschhorn A and Hizi A. (2010). Retroviral reverse transcriptase. Cell Molecular Life Science 67: 2717–2747. https://doi.org/10.1007/s00018-010-0346-2

Huang H, Chopra R, Verdine G L and Harrison S C. (1998). Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance. Science 282(5394): 1669–1675. https://doi.org/10.1126/science.282.5394.1669

Ilina T, LaBarge K, Sarafianos S G, Ishima R and Parniak M A. (2012). Inhibitors of HIV-1 reverse transcriptase-associated Ribonuclease H activity. Biology 1: 521–541. https://doi.org/10.3390/biology1030521

Iskandriati D, Saepuloh U, Mariya S, Grant R F, Solihin D D, Sajuthi D and Pamungkas J. (2010). Isolation and characterization of simian retrovirus type D from Macaca fascicularis and M. nemestrina in Indonesia. Microbiologi Indonesia 4(3): 132–136.

Kimura M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120. https://doi.org/10.1007/BF01731581

Lerche N W and Osborn K G. (2003). Simian retrovirus infections: Potential confounding variables in primate toxicology studies. Toxicology Pathology 31(Suppl.): 103–111. https://doi.org/10.1080/01926230390174977

Lerche N W. (2010). Simian retroviruses: Infection and disease-implications for immunotoxicology research in primates. Journal of Immunotoxicology 7(2): 93–101. https://doi.org/10.3109/15476911003657406

Li M D, Bronson D L, Lemke T D and Faras A J. (1995). Phylogenetic analysis of 55 retroelements on the basis of the nucleotide and product amino acid sequences of pol gene. Molecular Biology Evolution 12(4): 657–670.

Madeira F, Park Y M, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey A R N, Potter S C, Finn R D and Lopez R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research 47: W636–W641. https://doi.org/10.1093/nar/gkz268

Marracci G H, Kelley R D, Pilcher K Y, Crabtree L, Shiigi S M, Avery N, Leo G, Webb M C, Hallick L M and Axthelm M K. (1995). Simian AIDS type D serogroup 2 retrovirus: Isolation of an infectious molecular clone and sequence analyses of its envelope glycoprotein gene and 3' long terminal repeat. Journal of Virology 69(4): 2621–2628. https://doi.org/10.1128/JVI.69.4.2621-2628.1995

Marracci G H, Avery N A, Shiigi S M, Couch G, Palmer H, Pilcher K Y, Nichols H, Hallick L M, Axthelm M K and Machida C A. (1999). Molecular cloning and cell-specific growth characterization of polymorphic variants of type D serogroup 2 simian retroviruses. Virology 261(1): 43–58. https://doi.org/10.1006/viro.1999.9858

Marx P A, Maul D H and Osborne K G. (1984). Simian AIDS: Isolation of type D retrovirus and disease transmission. Science 223(4640): 1083–1086. https://doi.org/10.1126/science.6695196

Montiel N A. (2010). An updated review of simian betaretrovirus (SRV) in macaque hosts. Journal of Medical Primatology 39(5): 303–314. https://doi.org/10.1111/j.1600-0684.2010.00412.x

Roth T, Morningstar M L, Boyer P L, Hughes S H, Buckheit R W and Michejda C J. (1997). Synthesis and biological activity of novel non-nucleoside inhibitors of HIV-1 reverse transcriptase 2-Aryl-substituted benzimidazoles. Journal of Medical Chemistry 40(26): 4199–4207. https://doi.org/10.1021/jm970096g

Roy A, Kucukural A and Zhang Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocol 5: 725–738. https://doi.org/10.1038/nprot.2010.5

Sarafianos S G, Das K, Tantillo C, Arthur D, Clark J, Jianping D, Whitcomb J M, Boyer P L, Hughes S H and Arnold E. (2001). Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA: DNA. EMBO Journal 20(6): 1449–1461. https://doi.org/10.1093/emboj/20.6.1449

Sarafianos S G, Clark A D Jr, Das K, Tuske S, Birktoft J J, Ilankumaran P, Ramesha A R et al. (2002). Structures of HIV-1 reverse transcriptase with pre- and posttranslocation AZTMP-terminated DNA. EMBO Journal 21(23): 6614–6624. https://doi.org/10.1093/emboj/cdf637

Sarafianos S G, Marchand B, Das K, Himmel D, Parniak M A, Hughes S H and Arnold E. (2009). Structure and function of HIV-1 reverse transcriptase: Molecular mechanisms of polymerization and inhibition. Journal of Molecular Biology 385(3): 693–713. https://doi.org/10.1016/j.jmb.2008.10.071

Sharma P L, Nurpeisov V and Schinazi R F. (2005). Retrovirus reverse transcriptase containing a modified YXDD motif. Antiviral Chemical Chemotherapy 16(3): 169–182. https://doi.org/10.1177/095632020501600303

Tamura K, Stecher G, Peterson D, Filipski A and Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30(12): 2725–2729. https://doi.org/10.1093/molbev/mst197

Telesnitsky A and Goff S P. (1997). Reverse transcriptase and the generation of retroviral DNA. In: Coffin J M, Hughes S H and Varmus H E (eds.). Retroviruses. Plainview, NY: Cold Spring Harbor Laboratory Press, 121–160.

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B C, Remm M and Rozen S G. (2012). Primer3-new capabilities and interfaces. Nucleic Acids Research 40(15): e115. https://doi.org/10.1093/nar/gks596

Yang J, Yan R, Roy A, Xu D, Poisson J and Zhang Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods 12(1): 7–8. https://doi.org/10.1038/nmeth.3213

Zhang Y and Skolnick J. (2005). TM-alignment: A protein structure alignment algorithm based on the TM-score. Nucleic Acid Research 33(7): 2302–2309. https://doi.org/10.1093/nar/gki524

Zhang Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9(40). https://doi.org/10.1186/1471-2105-9-40