Genome engineering . Week 10

Here is a list of 7 papers I would like you to take a gentle look at. What I want you to see is how different genomes were synthesized rather than dive into the science that the papers present. Just look for the general approaches. What you will see is an evolution of genome synthesis technology.

  1. 2000 First complete synthesis of a viral genome (the key thing to look at here is not so much the paper, which was a landmark accomplishment in hepatitis C virus biology, but the almost completely unnoticed synthesis of an ~8000 base pair copy of the a hepatitis C virus sub-genomic replicon. That information is tucked away in the references list at #9)

    Blight, K. J., A. A. Kolykhalov and C. M. Rice (2000). "Efficient initiation of HCV RNA replication in cell culture." Science 290(5498): 1972-1974.

  1. 2003 Rapid synthesis of a phage by genome synthesis. Viral genome synthesis that had previously taken years was now done in 2 weeks.

    Smith, H. O., C. A. Hutchison, 3rd, C. Pfannkoch and J. C. Venter (2003). "Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides." Proc Natl Acad Sci U S A 100(26): 15440-15445

  1. 2010 Construction of a bacterial cell with a chemically synthesized genome. This was not the first whole bacterial genome synthesized, but was the first time one was both synthesized and booted up.

    Gibson, D. G., J. I. Glass, C. Lartigue, V. N. Noskov, R. Y. Chuang, M. A. Algire, G. A. Benders, M. G. Montague, L. Ma, M. M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. Assad-Garcia, C. Andrews-Pfannkoch, E. A. Denisova, L. Young, Z. Q. Qi, T. H. Segall-Shapiro, C. H. Calvey, P. P. Parmar, C. A. Hutchison, 3rd, H. O. Smith and J. C. Venter (2010). "Creation of a bacterial cell controlled by a chemically synthesized genome." Science 329(5987): 52-56.

  1. 2014 Construction of a yeast cell with a synthetic natural yeast chromosome. While the Gibson paper presented construction of a whole bacterial genome cloned as a yeast artificial chromosome, this paper reports construction of a natural yeast chromosome and also is the first major paper about what will eventually be a yeast cell with a fully synthetic, reconstructed genome.

    Annaluru, N., H. Muller, L. A. Mitchell, S. Ramalingam, G. Stracquadanio, S. M. Richardson, J. S. Dymond, Z. Kuang, L. Z. Scheifele, E. M. Cooper, Y. Cai, K. Zeller, N. Agmon, J. S. Han, M. Hadjithomas, J. Tullman, K. Caravelli, K. Cirelli, Z. Guo, V. London, A. Yeluru, S. Murugan, K. Kandavelou, N. Agier, G. Fischer, K. Yang, J. A. Martin, M. Bilgel, P. Bohutski, K. M. Boulier, B. J. Capaldo, J. Chang, K. Charoen, W. J. Choi, P. Deng, J. E. DiCarlo, J. Doong, J. Dunn, J. I. Feinberg, C. Fernandez, C. E. Floria, D. Gladowski, P. Hadidi, I. Ishizuka, J. Jabbari, C. Y. Lau, P. A. Lee, S. Li, D. Lin, M. E. Linder, J. Ling, J. Liu, J. Liu, M. London, H. Ma, J. Mao, J. E. McDade, A. McMillan, A. M. Moore, W. C. Oh, Y. Ouyang, R. Patel, M. Paul, L. C. Paulsen, J. Qiu, A. Rhee, M. G. Rubashkin, I. Y. Soh, N. E. Sotuyo, V. Srinivas, A. Suarez, A. Wong, R. Wong, W. R. Xie, Y. Xu, A. T. Yu, R. Koszul, J. S. Bader, J. D. Boeke and S. Chandrasegaran (2014). "Total synthesis of a functional designer eukaryotic chromosome." Science 344(6179): 55-58.

  1. 2016 Construction of an E. coli strain whose genome uses only 57 codons. This project is a massive undertaking that is still in progress and represents a major change in the genetic code.

    Ostrov, N., M. Landon, M. Guell, G. Kuznetsov, J. Teramoto, N. Cervantes, M. Zhou, K. Singh, M. G. Napolitano, M. Moosburner, E. Shrock, B. W. Pruitt, N. Conway, D. B. Goodman, C. L. Gardner, G. Tyree, A. Gonzales, B. L. Wanner, J. E. Norville, M. J. Lajoie and G. M. Church (2016). "Design, synthesis, and testing toward a 57-codon genome." Science 353(6301): 819-822.

  1. 2019 Construction of a human artificial chromosome. Eventually, we may be able to construct chromosomes from higher eukaryotes. The paper gives you a look at the complexity of the process.

    Logsdon, G. A., C. W. Gambogi, M. A. Liskovykh, E. J. Barrey, V. Larionov, K. H. Miga, P. Heun and B. E. Black (2019). "Human Artificial Chromosomes that Bypass Centromeric DNA." Cell 178(3): 624-639 e619.

  1. 2021 A simple recipe to make SARS-CoV-2 virus. The technology here is simple. While getting this knowledge to coronavirus researchers can accelerate efforts to end the current pandemic, is publicizing this a good idea?

    Xie, X., K. G. Lokugamage, X. Zhang, M. N. Vu, A. E. Muruato, V. D. Menachery and P. Y. Shi (2021). "Engineering SARS-CoV-2 using a reverse genetic system." Nat Protoc 16(3): 1761-1784.