Molecular Biotechnology. Bernard R. Glick
in a dense array on a solid surface, have enabled rapid and inexpensive acquisition of genome sequences. Hundreds of millions of short nucleotide reads can be acquired simultaneously (massive parallelization) and assembled into contigs. Using these approaches, the genome sequences of thousands of organisms from all domains of life, including the metagenomes of entire communities of microorganisms in an environmental sample, have been completed or are in progress. The next steps are to annotate the sequence features and to determine the functions of the genes encoded in the genomes by investigating patterns of transcription (transcriptomics), protein synthesis (proteomics), and small-molecule production (metabolomics) using a variety of techniques such as DNA and protein microarray analysis, RNA sequencing, 2D PAGE, mass spectrometry, and NMR. Comparison of genome sequences can reveal the genetic basis of a disease, the mechanism of pathogenicity of a microbe, or the evolutionary relationships among organisms, while transcript, protein, and metabolite profiles can identify biomarkers for diagnosis and treatment of disease.
REFERENCES
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456:53−59.
Bondy-Denomy J, and Davidson AR. 2014. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol. 22:218−225.
Brasch, MA, Hartley JL, Vidal M. 2004. ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res. 14:2001−9.
Cello J, Paul PV, Wimmer E. 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 297:1016−18.
Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H. 2008. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods. 5:69−74.
Cohen SN, Chang ACY, Boyer HW, Helling RB. 1973. Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA. 70:3240–44.
Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, Hsu PD, Wu XB, Jiang WY, Marraffini LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science. 339:819−23.
Czar MJ, Anderson JC, Bader JS, Peccoud J. 2008. Gene synthesis demystified. Trends Biotechnol. 27:63−72.
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science. 323:133−38.
Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL. 1993. Multiplexed biochemical assays with biological chips. Nature. 364:555−56.
Formstecher E, Aresta S, Collura V, Hamburger A, Meil A, Trehin A, Reverdy C, Betin V, Maire S, Brun C, et al. 2005. Protein interaction mapping: a Drosophila case study. Genome Res. 15:376−84.
Gibson DG. 2014. Programming biological operating systems: genome design, assembly and activation. Nat Methods. 11:521−26.
Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, et al. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 319:1215–20.
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma l, Mododie MM, et al. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science. 329:52–6.
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods. 6:343−45.
Haab BB. 2006. Applications of antibody array platforms. Curr Opin Biotechnol. 17:415−21.
Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 68:669−85.
Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M. 2007. Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci USA. 104:17494−9.
International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409:860–921.
Itakura K, Rossi JJ, Wallace RB. 1984. Synthesis and use of synthetic oligonucleotides. Annu Rev Biochem. 53:323–56.
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA. 98:4569–74.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 337:816–21.
Ju J, Kim DH, Bi L, Meng Q, Bai X, Li Z, Li X, Marma MS, Shi S, Wu J, et al. 2006. Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci USA. 103:19635−40.
Köcher T, Superti-Furga G. 2007. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods. 4:807−15.
Lederer SL, Walters KA, Proll S, Paeper B, Robinzon S, Boix L, Fausto N, Bruix J, Katze MG. 2006. Distinct cellular responses differentiating alcohol- and hepatitis C virus-induced liver cirrhosis. Virol. J. 3:98.
Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. 2003. Zero-mode waveguides for single-molecule analysis at high concentrations. Science. 299:682−6.
Li Y. 2011. The tandem affinity purification technology: an overview. Biotechnol Lett. 33:1487–99.
Mali P, Yang LH, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. 2013. RNA-guided human genome engineering via Cas9. Science. 339:823−6.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437:376−80.
Martin JA, Wang Z. 2011. Next-generation transcriptome assembly. Nat Rev Genet. 12:671–82.
Maxam AM, Gilbert W. 1977. A new method for sequencing DNA. Proc Natl Acad Sci USA. 74:560–4.
Mertz JE, Davis RW. 1972. Cleavage of DNA by R1 restriction endonuclease generates cohesive ends. Proc Natl Acad Sci USA. 69:3370–4.
Mirete S, Mora-Ruiz MR, Lamprecht-Grandío M, de Figueras CG, Rosselló-Móra R, González-Pastor JE. 2015. Salt resistant genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment. Front Microbiol. 6:1121.
Mullis KB, Faloona FA, Scharf SJ, Saiki RK, Horn GT, Erlich HA. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp Quant Biol. 51:263–73.
Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, et al. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science. 314:1113–8.
Parrish JR, Gulyas KD, Finley RL, Jr. 2006. Yeast two-hybrid contributions to interactome mapping. Curr Opin Biotechnol. 17:387–93.
Roberts RJ. 2005. How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci USA. 102:5905–8.
Rothberg JM, Leamon JH. 2008. The development and impact of 454 sequencing. Nat Biotechnol. 26:1117−24.
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, et al. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5:e77.
Saiki RK, Gelfand DH, Stoffel S, Scharf S, Higuchi R, Horn GT, Mullis KB, Erlich HA. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:487–91.
Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl