Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture

Retrovirology

Miguel Angel Martinez¹  Bonaventura Clotet¹  Cristina Andres¹  Maria Nevot¹  Gloria Martrus¹ 

[1] Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona 08916, Spain

关键词: Evolution;    Attenuation;    HIV;    Codon-pair bias;   

Others  :  1209096
DOI  :  10.1186/1742-4690-10-78

 received in 2013-06-04, accepted in 2013-07-18,  发布年份 2013

【 摘 要 】

Background

Human immunodeficiency virus type 1 (HIV-1) has a biased nucleotide composition different from human genes. This raises the question of how evolution has chosen the nucleotide sequence of HIV-1 that is observed today, or to what extent the actual encoding contributes to virus replication capacity, evolvability and pathogenesis. Here, we applied the previously described synthetic attenuated virus engineering (SAVE) approach to HIV-1.

Results

Using synonymous codon pairs, we rationally recoded and codon pair–optimized and deoptimized different moieties of the HIV-1 gag and pol genes. Deoptimized viruses had significantly lower viral replication capacity in MT-4 and peripheral blood mononuclear cells (PBMCs). Varying degrees of ex vivo attenuation were obtained, depending upon both the specific deoptimized region and the number of deoptimized codons. A protease optimized virus carrying 38 synonymous mutations was not attenuated and displayed a replication capacity similar to that of the wild-type virus in MT-4 cells and PBMCs. Although attenuation is based on several tens of nucleotide changes, deoptimized HIV-1 reverted to wild-type virulence after serial passages in MT-4 cells. Remarkably, no reversion was observed in the optimized virus.

Conclusion

These data demonstrate that SAVE is a useful strategy to phenotypically affect the replicative properties of HIV-1.

【 授权许可】

   
2013 Martrus et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Burns CC, Shaw J, Campagnoli R, Jorba J, Vincent A, Quay J, Kew O: Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. J Virol 2006, 80:3259-3272.
• [2]Mueller S, Papamichail D, Coleman JR, Skiena S, Wimmer E: Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J Virol 2006, 80:9687-9696.
• [3]Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S: Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320:1784-1787.
• [4]van der Kuyl AC, Berkhout B: The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology 2012, 9:92. BioMed Central Full Text
• [5]Berkhout B, van Hemert FJ: The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins. Nucleic Acids Res 1994, 22:1705-1711.
• [6]Haas J, Park EC, Seed B: Codon usage limitation in the expression of HIV-1 envelope glycoprotein. Curr Biol 1996, 6:315-324.
• [7]Keating CP, Hill MK, Hawkes DJ, Smyth RP, Isel C, Le SY, Palmenberg AC, Marshall JA, Marquet R, Nabel GJ, Mak J: The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA. Nucleic Acids Res 2009, 37:945-956.
• [8]Li M, Kao E, Gao X, Sandig H, Limmer K, Pavon-Eternod M, Jones TE, Landry S, Pan T, Weitzman MD, David M: Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature 2012, 491:125-128.
• [9]Cuevas JM, Domingo-Calap P, Sanjuan R: The fitness effects of synonymous mutations in DNA and RNA viruses. Mol Biol Evol 2012, 29:17-20.
• [10]Nevot M, Martrus G, Clotet B, Martinez MA: RNA interference as a tool for exploring HIV-1 robustness. J Mol Biol 2011, 413:84-96.
• [11]Mueller S, Coleman JR, Papamichail D, Ward CB, Nimnual A, Futcher B, Skiena S, Wimmer E: Live attenuated influenza virus vaccines by computer-aided rational design. Nat Biotechnol 2010, 28:723-726.
• [12]Gutman GA, Hatfield GW: Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci USA 1989, 86:3699-3703.
• [13]Plotkin JB, Kudla G: Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 2011, 12:32-42.
• [14]Buchan JR, Aucott LS, Stansfield I: tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res 2006, 34:1015-1027.
• [15]Karn J, Stoltzfus CM: Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression. Cold Spring Harb Perspect Med 2012, 2:a006916.
• [16]Chamond N, Locker N, Sargueil B: The different pathways of HIV genomic RNA translation. Biochem Soc Trans 2010, 38:1548-1552.
• [17]Martinez-Picado J, Wrin T, Frost SD, Clotet B, Ruiz L, Brown AJ, Petropoulos CJ, Parkin NT: Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1. J Virol 2005, 79:5907-5913.
• [18]Kimchi-Sarfaty C: A ‘silent’ polymorphism in the MDR1 gene changes substrate specificity (vol 315, pg 525, 2007). Science 2007, 318:1382-1383.
• [19]Sanjuan R, Borderia AV: Interplay between RNA structure and protein evolution in HIV-1. Mol Biol Evol 2011, 28:1333-1338.
• [20]Kypr J, Mrazek J, Reich J: Nucleotide composition bias and CpG dinucleotide content in the genomes of HIV and HTLV 1/2. Biochim Biophys Acta 1989, 1009:280-282.
• [21]Sitaraman V, Hearing P, Ward CB, Gnatenko DV, Wimmer E, Mueller S, Skiena S, Bahou WF: Computationally designed adeno-associated virus (AAV) Rep 78 is efficiently maintained within an adenovirus vector. Proc Natl Acad Sci USA 2011, 108:14294-14299.
• [22]Song Y, Liu Y, Ward CB, Mueller S, Futcher B, Skiena S, Paul AV, Wimmer E: Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design. Proc Natl Acad Sci USA 2012, 109:14301-14307.
• [23]Lauring AS, Acevedo A, Cooper SB, Andino R: Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus. Cell Host Microbe 2012, 12:623-632.
• [24]Lauring AS, Frydman J, Andino R: The role of mutational robustness in RNA virus evolution. Nat Rev Microbiol 2013, 11:327-336.
• [25]Martinez-Picado J, Martinez MA: HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res 2008, 134:104-123.
• [26]Parera M, Clotet B, Martinez MA: Genetic screen for monitoring severe acute respiratory syndrome coronavirus 3C-like protease. J Virol 2004, 78:14057-14061.
• [27]Capel E, Martrus G, Parera M, Clotet B, Martinez MA: Evolution of the human immunodeficiency virus type 1 protease: Effects on viral replication capacity and protease robustness. J Gen Virol 2012, 93:2625-2634.
• [28]Kisic M, Matamoros T, Nevot M, Mendieta J, Martinez-Picado J, Martinez MA, Menendez-Arias L: Thymidine analogue excision and discrimination modulated by mutational complexes including single amino acid deletions of Asp-67 or Thr-69 in HIV-1 reverse transcriptase. J Biol Chem 2011, 286:20615-20624.
• [29]Maschera B, Furfine E, Blair ED: Analysis of resistance to human immunodeficiency virus type 1 protease inhibitors by using matched bacterial expression and proviral infection vectors. J Virol 1995, 69:5431-5436.
• [30]Miura T, Brockman MA, Brumme ZL, Brumme CJ, Pereyra F, Trocha A, Block BL, Schneidewind A, Allen TM, Heckerman D, Walker BD: HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol 2009, 83:140-149.
• [31]Pauwels R, Balzarini J, Baba M, Snoeck R, Schols D, Herdewijn P, Desmyter J, De Clercq E: Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds. J Virol Methods 1988, 20:309-321.
• [32]Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415.
• [33]Wright F: The ‘effective number of codons’ used in a gene. Gene 1990, 87:23-29.
• [34]DA L, Pinto RM, Bosch A, Musto H, Cristina J: A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus. Virus Res 2011, 157:19-24.
• [35]Betancor G, Puertas MC, Nevot M, Garriga C, Martinez MA, Martinez-Picado J, Menendez-Arias L: Mechanisms involved in the selection of HIV-1 reverse transcriptase thumb subdomain polymorphisms associated with nucleoside analogue therapy failure. Antimicrob Agents Chemother 2010, 54:4799-4811.
• [36]Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) Method. Methods 2001, 25:402-408.
• [37]Fernandez G, Clotet B, Martinez MA: Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. J Virol 2007, 81:2485-2496.