Chapter 53
Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing
Thomas W. Schoenfeld,
Nick Hermersmann,
Mike Moser, Darby Renneckar, Vinay Dhodda, David Mead,
Thomas W. Schoenfeld
Lucigen Corporation, Middleton, Wisconsin, USA
Search for more papers by this authorNick Hermersmann
Lucigen Corporation, Middleton, Wisconsin, USA
Search for more papers by this authorThomas W. Schoenfeld,
Nick Hermersmann,
Mike Moser, Darby Renneckar, Vinay Dhodda, David Mead,
Thomas W. Schoenfeld
Lucigen Corporation, Middleton, Wisconsin, USA
Search for more papers by this authorNick Hermersmann
Lucigen Corporation, Middleton, Wisconsin, USA
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorFirst published: 16 September 2011
Summary
This chapter contains sections titled:
-
Introduction
-
Methods
-
Results and Discussion
-
Prospects
-
References
REFERENCES
- Ando T, Monroe SS, Noel JS, Glass RI. 1997. A one-tube method of reverse transcription-PCR to efficiently amplify a 3-kilobase region from the RNA polymerase gene to the poly(A) tail of small round-structured viruses (Norwalk-like viruses). J. Clin. Microbiol. 35: 570–577.
- Andraos N, Tabor S, Richardson CC. 2004. The highly processive DNA polymerase of bacteriophage T5. Role of the unique N and C termini. J. Biol. Chem. 279: 50609–50618.
- Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4: e368.
- Babon JJ, McKenzie M, Cotton RG. 2003. The use of resolvases T4 endonuclease VII and T7 endonuclease I in mutation detection. Mol. Biotechnol. 23: 73–81.
- Bae E, Phillips GN Jr. 2004. Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases. J. Biol. Chem. 279: 28202–28208.
- Bakhanashvili M, Hizi A. 1993. The fidelity of the reverse transcriptases of human immunodeficiency viruses and murine leukemia virus, exhibited by the mispair extension frequencies, is sequence dependent and enzyme related. FEBS Lett. 319: 201–205.
- Barry ER, Bell SD. 2006. DNA replication in the archaea. Microbiol. Biol. Rev. 70: 876–887.
-
Beese LS, Steitz TA. 1991. Structural basis for the 3 –5 exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10: 25–33.
10.1002/j.1460-2075.1991.tb07917.x Google Scholar
- Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K, Wommack KE. 2007. Metagenomic characterization of Chesapeake Bay virioplankton. Appl. Environ. Microbiol. 73(23): 7629–7641.
- Besemer J, Borodovsky M. 2005. GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33: W451–4.
- Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, et al. 1989. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264: 8935–8940.
- Blanco L, Lazaro JM, de Vega M, Bonnin A, Salas M. 1994. Terminal protein-primed DNA amplification. Proc. Natl. Acad. Sci. USA 91: 12198–12202.
- Blom N, Hansen J, Blaas D, Brunak S. 1996. Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Protein Sci. 5: 2203–2216.
- Blondal T, Hjorleifsdottir SH, Fridjonsson OF, Aevarsson A, Skirnisdottir S, et al. 2003. Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1. Nucleic Acids Res. 31: 7247–7254.
- Bowman RR, Hu WS, Pathak VK. 1998. Relative rates of retroviral reverse transcriptase template switching during RNA- and DNA-dependent DNA synthesis. J. Virol. 72: 5198–5206.
- Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, et al. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99: 14250–14255.
- Breitbart M, Wegley L, Leeds S, Schoenfeld T, Rohwer F. 2004. Phage community dynamics in hot springs. Appl. Environ. Microbiol. 70: 1633–1640.
- Brincat JL, Pfeiffer JK, Telesnitsky A. 2002. RNase H activity is required for high-frequency repeat deletion during Moloney murine leukemia virus replication. J. Virol. 76: 88–95.
- Burns DP, Temin HM. 1994. High rates of frameshift mutations within homo-oligomeric runs during a single cycle of retroviral replication. J. Virol. 68: 4196–4203.
- Bustin SA, Mueller R. 2005. Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin. Sci. (Lond.) 109: 365–379.
- Chandler DP, Wagnon CA, Bolton H Jr. 1998. Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR. Appl. Environ. Microbiol. 64: 669–677.
- Chumakov KM. 1994. Reverse transcriptase can inhibit PCR and stimulate primer–dimer formation. PCR Methods Appl. 4: 62–64.
- Compton J. 1991. Nucleic acid sequence-based amplification. Nature 350: 91–92.
- Creighton S, Huang MM, Cai H, Arnheim N, Goodman MF. 1992. Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini. J. Biol. Chem. 267: 2633–2639.
- Dean FB, Nelson JR, Giesler TL, Lasken RS. 2001. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11: 1095–1099.
- Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, et al. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99: 5261–5266.
- Desiere F, Lucchini S, Bruttin A, Zwahlen M, Brussow H. 1997. A highly conserved DNA replication module from Streptococcus thermophilus phages is similar in sequence and topology to a module from Lactococcus lactis phages. Virology 234: 372–382.
- Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452: 629–632.
- Dionne I, Bell SD. 2005. Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Biochem. J. 387: 859–863.
- Fehlmann C, Krapf R, Solioz M. 1993. Reverse transcriptase can block polymerase chain reaction. Clin. Chem. 39: 368–369.
- Galibert F, Mandart E, Fitoussi F, Tiollais P, Charnay P. 1979. Nucleotide sequence of the hepatitis B virus genome (subtype ayw) cloned in E. coli. Nature 281: 646–650.
- Ghadessy FJ, Ong JL, Holliger P. 2001. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl. Acad. Sci. USA 98: 4552–4557.
- Giver L, Gershenson A, Freskgard PO, Arnold FH. 1998. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA 95: 12809–12813.
- Goff SP. 1990. Retroviral reverse transcriptase: Synthesis, structure, and function. J. Acquir. Immune. Defic. Syndr. 3: 817–831.
- Griffiths E, Gupta RS. 2004. Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int. Microbiol. 7: 41–52.
- Guatelli JC, Whitfield KM, Kwoh DY, Barringer KJ, Richman DD, et al. 1990. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA 87: 7797.
- Haft DH, Selengut J, Mongodin EF, Nelson KE. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1: e60.
- Halvas EK, Svarovskaia ES, Pathak VK. 2000. Development of an in vivo assay to identify structural determinants in murine leukemia virus reverse transcriptase important for fidelity. J. Virol. 74: 312–319.
- Hamdan SM, Richardson CC. 2009. Motors, switches, and contacts in the replisome. Annu. Rev. Biochem. 78: 205–243.
- Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, et al. 2006. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2: e92.
- Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D. 2009. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 4: e4169.
- Hjorleifsdottir S, Hreggvidsson GO, Fridjonsson OH, Aevarsson A, Kristjansson JK. 2003. Nucleic acid encoding DNA polymerase of bacteriophage RM 378 U PTO.
- Hogrefe HH, Cline J, Lovejoy AE, Nielson KB. 2001. DNA polymerases from hyperthermophiles. Methods Enzymol. 334: 91–116.
- Jaatinen ST, Happonen LJ, Laurinmaki P, Butcher SJ, Bamford DH. 2008. Biochemical and structural characterisation of membrane-containing icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus. Virology 379: 10–19.
- Johnson A, O’Donnell M. 2005. Cellular DNA replicases: Components and dynamics at the replication fork. Annu. Rev. Biochem. 74: 283–315.
- Kahler M, Antranikian G. 2000. Cloning and characterization of a family B DNA polymerase from the hyperthermophilic crenarchaeon Pyrobaculum islandicum. J. Bacteriol. 182: 655–663.
- Karam JD, Konigsberg WH. 2000. DNA polymerase of the T4-related bacteriophages. Prog. Nucleic Acid. Res. Mol. Biol. 64: 65–96.
- Kim Y, Eom SH, Wang J, Lee DS, Suh SW, et al. 1995. Crystal structure of Thermus aquaticus DNA polymerase. Nature 376: 612–616.
- Komoda Y, Hijikata M, Tanji Y, Hirowatari Y, Mizushima H, et al. 1994. Processing of hepatitis C viral polyprotein in Escherichia coli. Gene 145: 221–226.
- Konnick EQ, Williams SM, Ashwood ER, Hillyard DR. 2005. Evaluation of the COBAS hepatitis C virus (HCV) TaqMan analytespecific reagent assay and comparison to the COBAS Amplicor HCV Monitor V2.0 and Versant HCV bDNA 3.0 assays. J. Clin. Microbiol. 43: 2133–2140.
- Koonin EV. 2006. Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases. Biol. Direct. 1: 39.
- Kornberg A, Baker TA. 1992. DNA Replication 2. 187–189.
- Kotewicz ML, Sampson CM, D'Alessio JM, Gerard GF. 1988. Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity. Nucleic Acids Res. 16: 265–277.
- Kulpa D, Topping R, Telesnitsky A. 1997. Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors. EMBO J. 16: 856–865.
- Lehman IR, Boehmer PE. 1999. Replication of herpes simplex virus DNA. J. Biol. Chem. 274: 28059–28062.
- Leplae R, Hebrant A, Wodak SJ, Toussaint A. 2004. ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Res. 32: D45–D49.
- Levesque-Sergerie JP, Duquette M, Thibault C, Delbecchi L, Bissonnette N. 2007. Detection limits of several commercial reverse transcriptase enzymes: Impact on the low- and high-abundance transcript levels assessed by quantitative RT-PCR. BMC Mol. Biol. 8: 93.
- Liss B. 2002. Improved quantitative real-time RT-PCR for expression profiling of individual cells. Nucleic Acids Res. 30: e89.
- Liu D, Graber JH. 2006. Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. BMC Bioinformatics 7: 77.
- Lloyd RE. 2006. Translational control by viral proteinases. Virus Res. 119: 76–88.
- Lucchini S, Desiere F, Brussow H. 1999. Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J. Virol. 73: 8647–8656.
- Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, et al. 1991. High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108: 1–6.
- Mardis ER. 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9: 387–402.
- Matsushita I, Yanase H. 2009. The genomic structure of thermus bacteriophage {phi}IN93. J. Biochem. 146: 775–785.
- Mbisa JL, Nikolenko GN and Pathak VK. 2005. Mutations in the RNase H primer grip domain of murine leukemia virus reverse transcriptase decrease efficiency and accuracy of plus-strand DNA transfer. J. Virol. 79: 419–427.
- McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, et al. 2008. Metagenomic analysis of lysogeny in Tampa Bay: Implications for prophage gene expression. PLoS ONE 3: e3263.
- Merkens LS, Bryan SK, Moses RE. 1995. Inactivation of the 5′ –3 exonuclease of Thermus aquaticus DNA polymerase. Biochim. Biophys. Acta 1264: 243–248.
- Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, et al. 2008. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18: 571–584.
- Myers TW, Gelfand DH. 1991. Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30: 7661–7666.
- Naryshkina T, Liu J, Florens L, Swanson SK, Pavlov AR, et al. 2006. Thermus thermophilus bacteriophage phiYS40 genome and proteomic characterization of virions. J. Mol. Biol. 364: 667–677.
- Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, et al. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28: E63.
- Oshima T, Sakaki Y, Wakayama N, Watanabe K? Ohashi Z. 1976. Biochemical studies on an extreme thermophile Thermus thermophilus: Thermal stabilities of cell constituents and a bacteriophage. Experientia Suppl. 26: 317–331.
- Pathak VK, Temin HM. 1990. Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: Substitutions, frameshifts, and hypermutations. Proc. Natl. Acad. Sci. USA 87: 6019–6023.
- Pederson DM, Welsh LC, Marvin DA, Sampson M, Perham RN, et al. 2001. The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus. J. Mol. Biol. 309: 401–421.
- Peng X, Basta T, Haring M, Garrett RA, Prangishvili D. 2007. Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms. Virology 364: 237–243.
- Perler FB, Kumar S, Kong H. 1996. Thermostable DNA polymerases. Adv. Protein Chem. 48: 377–435.
- Perrino FW, Preston BD, Sandell LL, Loeb LA. 1989. Extension of mismatched 3 termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 86: 8343–8347.
- Prangishvili D, Garrett RA. 2005. Viruses of hyperthermophilic Crenarchaea. Trends Microbiol. 13: 535–542.
- Pulsinelli GA, Temin HM. 1991. Characterization of large deletions occurring during a single round of retrovirus vector replication: Novel deletion mechanism involving errors in strand transfer. J. Virol. 65: 4786–4797.
- Reeve MA, Fuller CW. 1995. A novel thermostable polymerase for DNA sequencing. Nature 376: 796–797.
- Ricchetti M, Buc H. 1990. Reverse transcriptases and genomic variability: The accuracy of DNA replication is enzyme specific and sequence dependent. EMBO J. 9: 1583–1593.
- Roberts JA, Bell SD, White MF. 2003. An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA. Mol. Microbiol. 48: 361–371.
- Roberts JD, Preston BD, Johnston LA, Soni A, Loeb LA, et al. 1989. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol. Cell Biol. 9: 469–476.
- Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, et al. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491.
- Sakaki Y, Oshima T. 1975. Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8. J. Virol. 15: 1449–1453.
- Schonfeld T. Unpublished results.
- Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, et al. 2008. Assembly of viral metagenomes from yellowstone hot springs. Appl. Environ. Microbiol. 74: 4164–4174.
- Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, et al. 2010. Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol. 18: 20–29.
- Sellner LN, Coelen RJ, Mackenzie JS. 1992. Reverse transcriptase inhibits Taq polymerase activity. Nucleic Acids Res. 20: 1487–1490.
- Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135–45.
- Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, Wommack KE. 2008. Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Res. Microbiol. 159(5): 349–357.
- Stanitsa ES, Arps L, Traktman P. 2006. Vaccinia virus uracil DNA glycosylase interacts with the A20 protein to form a heterodimeric processivity factor for the viral DNA polymerase. J. Biol. Chem. 281: 3439–3451.
- Suslov O, Steindler DA. 2005. PCR inhibition by reverse transcriptase leads to an overestimation of amplification efficiency. Nucleic Acids Res. 33: e181.
- Suttle CA. 2007. Marine viruses—Major players in the global ecosystem. Nat. Rev. Microbiol. 5: 801–812.
- Suzan-Monti M, La Scola B, Raoult D. 2006. Genomic and evolutionary aspects of Mimivirus. Virus Res. 117: 145–155.
- Svarovskaia ES, Delviks KA, Hwang CK, Pathak VK. 2000. Structural determinants of murine leukemia virus reverse transcriptase that affect the frequency of template switching. J. Virol. 74: 7171–7178.
- Tabor S, Richardson CC. 1987. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. USA 84: 4767–4771.
- Tabor S, Richardson CC. 1995. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Proc. Natl. Acad. Sci. USA 92: 6339–6343.
- Tabor S, Huber HE, Richardson CC. 1987. Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J. Biol. Chem. 262: 16212–16223.
- Taube R, Avidan O, Hizi A. 1997. The fidelity of misinsertion and mispair extension throughout DNA synthesis exhibited by mutants of the reverse transcriptase of human immunodeficiency virus type 2 resistant to nucleoside analogs. Eur. J. Biochem. 250: 106–114.
- Temin HM. 1993. Retrovirus variation and reverse transcription: Abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci USA 90: 6900–6903.
- Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
- Trakselis MA, Mayer MU, Ishmael FT, Roccasecca RM, Benkovic SJ. 2001. Dynamic protein interactions in the bacteriophage T4 repli-some. Trends Biochem. Sci. 26: 566–572.
- Vincent M, Xu Y, Kong H. 2004. Helicase-dependent isothermal DNA amplification. EMBO Rep. 5: 795–800.
- Voigt CA, Mayo SL, Arnold FH, Wang ZG. 2001. Computationally focusing the directed evolution of proteins. J. Cell Biochem. Suppl. 37: 58–63.
- Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, et al. 2008. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3: e3839.
- Weaver CA, Gordon DF, Kemper B. 1981. Introduction by molecular cloning of artifactual inverted sequences at the 5′ terminus of the sense strand of bovine parathyroid hormone cDNA. Proc Natl Acad Sci USA 78: 4073–4077.
- Wommack KE, Bhavsar J, Ravel J. 2008. Metagenomics: read length matters. Appl. Environ. Microbiol. 74(5): 1453–1463.
- Yu MX, Slater MR, Ackermann HW. 2006. Isolation and characterization of Thermus bacteriophages. Arc, Virol. 151: 663–679.
