RESEARCH NEWS & VIEWS of variations in the difference of climatic phenomena correctly. 180° sea-level atmospheric pressure By linking cooling in the tropical between the Icelandic low-pressure Pacific with trends in atmospheric cirsystem (Icelandic low) and the culation and regional Arctic warming, Azores high-pressure system (Azores Ding and colleagues highlight the comhigh), and is most pronounced durplexity of processes involved in regional ing boreal winter. In the positive climate change. Even remote climatic phase of the NAO, there is a considfluctuations can have a substantial erable difference in pressure between impact. Improving the representathese two systems, with both the Icetion of such teleconnections in cli90° W 90° E landic low and the Azores high being mate models should therefore remain intensified. In the negative phase, the a high priority for climate scientists. two pressure zones are weakened and The authors also note the importance the difference between them is less. of natural internal climate variability The NAO is linked to changes in for present and near-future regional the intensity and location of the North Arctic climate. But as greenhouse-gas Atlantic jet stream and storm track, concentrations are likely to increase in and to large-scale temperature and the future, it is only a question of time precipitation variations over Europe, before external forcing dominates 0° Greenland and North America. It is regional Arctic warming. ■ –0.3 0.3 0.5 0.7 0.9 an intrinsic atmospheric phenomSurface-temperature change (°C) enon, but fluctuations in sea surface Jürgen Bader is at the Max Planck temperature (SST) can also affect it. In Figure 1 | Trend in annual mean surface temperature. The graphic Institute for Meteorology, 20146 fact, it can be influenced by both vari- shows the observed change per decade of annual mean surface and Hamburg, Germany, and at Uni ations in local North Atlantic SST and near-surface temperature for the period 1979–2012, based on the Climate, Uni Research & the Bjerknes remote SST in the tropics5. Changes in ERA-interim climate data set. The most marked warming has occurred Centre for Climate Research, Bergen, tropical SSTs lead to changes in con- in northeastern Canada, Greenland and north Siberia. (Adapted from Norway. Extended Data Fig. 1 of ref. 4.) vection throughout the lowest portion e-mail: [email protected] of the atmosphere (the troposphere) at low latitudes, which in turn excite large-scale Arctic warming. Two plausible reasons for this 1. Graversen, R. G., Mauritsen, T., Tjernström, M., Källén, E. & Svensson, G. Nature 451, 53–56 atmospheric waves called Rossby waves. These failure are worth mentioning. First, the recent (2008). waves can propagate to mid- and high latitudes cooling in the tropical Pacific can probably be 2. Screen, J. A. & Simmonds, I. Nature 464, 1334–1337 and affect the NAO. attributed to intrinsic variability of the climate (2010). In their study, Ding et al. demonstrate that system6, because it is not simulated by coupled 3. Shindell, D. & Faluvegi, G. Nature Geosci. 2, 294–300 (2009). Rossby waves and the NAO are involved in climate simulations that incorporate observed regional Arctic warming. Their finding that changes in the concentration of greenhouse 4. Ding, Q. et al. Nature 509, 209–212 (2014). 5. Hoerling, M. P., Hurrell, J. W. & Xu, T. Science 292, the Arctic warming in northeastern Canada gases and aerosols. Second, despite continued 90–92 (2001). and Greenland since 1979 is strongly driven improvements to climate models, it is still a 6. Kosaka, Y. & Xie, S.-P. Nature 501, 403–407 (2013). by cooling in the tropical Pacific is supported challenge to simulate the influence of remote by observational data indicating that warming in these two regions is not limited to the surface but also extends to the upper troposphere. SY N TH ETI C B I OLOGY The authors argue that it is unlikely that decadal temperature changes in the upper Arctic troposphere are locally forced by variations in surface temperature. They suggest instead that warming at the surface and in the troposphere are the result of atmospheric-circulation changes in the high troposphere, and that these changes are remotely forced. Specifically, Ding et al. show that the recent warming in One aim of synthetic biology is to generate complex synthetic organisms. northeastern Canada and Greenland is asso- Now, a stage in this process has been achieved in yeast cells — an entire yeast ciated with a negative NAO phase driven by chromosome has been converted to a synthetic sequence in a stepwise manner. Rossby-wave activity caused by SST cooling in the tropical Pacific. These results are confirmed by modelling D A N I E L G . G I B S O N & J . C R A I G V E N T E R cells. Indeed, in 2010, the entire genome of experiments. The authors demonstrate that the bacterium Mycoplasma mycoides was an atmospheric general circulation model biological cell is much like a computer replaced with a rewritten synthetic genome, forced by the observed tropical SST can simu— the genome can be thought of as generating the first synthetic cell1. Now, in a late the connection between tropical Pacific the software that encodes the cell’s paper published in Science, Annaluru et al.2 SST cooling and regional Arctic tropospheric instructions, and the cellular machinery as describe how they have begun rewriting the warming. However, they also show that cou- the hardware that interprets and runs the genome of a more complex organism, that pled ocean–atmosphere climate models used software. Advances in DNA technology of the yeast species Saccharomyces cerevisiae. in the fifth assessment report of the Intergov- have made it possible for scientists to act as The researchers report the design and genernmental Panel on Climate Change fail to biological ‘software engineers’, program- eration of a functional, synthetic chromoreproduce the observed regional pattern of ming new biological ‘operating systems’ into some in this yeast, a milestone that they have
Construction of a yeast chromosome
A
1 6 8 | NAT U R E | VO L 5 0 9 | 8 M AY 2 0 1 4
© 2014 Macmillan Publishers Limited. All rights reserved
NEWS & VIEWS RESEARCH had in their sights for almost ten years. A quote by the theoretical physicist Richard Feynman, “What I cannot create, I do not understand”, has inspired synthetic biologists around the world. But this does not necessarily mean that what can be created is understood. There is an enormous gap between our ability to build DNA and our understanding of the instructions it encodes. The production of a synthetic chromosome in yeast (the first such achievement in a eukaryote — the class of organisms comprising plants, animals and fungi) represents a step towards closing that gap. Generation of synthetic versions of widely used model organisms such as S. cerevisiae will enable scientists to investigate the requirements of life in eukaryotes, because synthetic organisms can be easily manipulated. The process began at the computer, where Annaluru and colleagues downloaded the publicly available DNA sequence of a S. cere visiae chromosome (chromosome III). Next, they designed genetic changes, which can be thought of as software edits, with the aim of introducing specific alterations into the chromosome. These edits included the deletion of dispensable DNA sequences; the incorporation of unique sequences to enable the researchers to differentiate between natural and engineered DNA; and the replacement of one particular region of DNA that terminates gene transcription with another that performs the same task. In addition, the authors flanked each nonessential gene with DNA sequences designed to cause deletion of the flanked genes on a given signal. This flanking allows the size of the chromosome to be reduced, a feature designed to help determine the smallest cohorts of genes required to perform a given function or necessary for survival under a particular growth condition. This information is crucial if we are to write biological software in a more predictable fashion, thus ensuring that cells can be engineered to reliably carry out the tasks they have been programmed to perform. To generate the synthetic chromosome, Annaluru and co-workers broke down their designer DNA sequence into overlapping stretches of 70 nucleotides, which were chemically synthesized in parallel. Students in the Build-a-Genome course at Johns Hopkins University in Baltimore, Maryland, stitched together these DNA stretches into constructs approximately 3 kilobases long, using established DNA-assembly methods3–6. Next, the original chromosome sequence was systematically replaced with the synthetic DNA in vivo, by introducing up to 12 overlapping 3-kb synthetic fragments at a time into the yeast cell, in 11 successive rounds of integration.
BEYOND DIVISIONS
The future of synthetic biology nature.com/synbio
a
b Nucleus
Yeast chromosome
Genome transplantation Integration
Synthetic yeast DNA
Synthetic bacterial genome Yeast cell
Bacterial cell
Yeast-cell nucleus
Figure 1 | Building synthetic genomes. a, To generate a synthetic bacterial cell, the entire synthetic bacterial genome is assembled in a yeast cell. In this setting, the bacterial genome is inactive because the yeast cell lacks the proteins required to turn on bacterial genes. After synthesis is complete, the synthetic genome is transferred to a compatible bacterial host cell, where it is activated and produces a synthetic cell. b, By contrast, Annaluru et al.2 have generated a synthetic yeast chromosome within the yeast cell itself. To do this, they replaced the natural chromosome with chunks of synthetic DNA in a stepwise manner.
The product of this work is a yeast strain that contains an extensively engineered chromosome III, and that grows just as well as the original strain. The 273-kb designer chromosome contains more than 50,000 sequence alterations, and is 14% shorter than the natural sequence. This work is important because it begins to address unanswered questions about how genome design can be used to manipulate the rules of biology in a eukaryotic model. For example, can superfluous DNA between genes be removed? Can unnecessary genetic code be altered? So far, the sequence alterations made by Annaluru and colleagues have not reduced the fitness of the yeast, which bodes well for future modifications. If two or more genes perform a similar function, can one be deleted? Which combinations of the 5,000 yeast genes that are thought to be dispensable can be simultaneously removed? The authors have already begun cataloguing genes that can be simultaneously deleted without adversely affecting the fitness of the yeast. Answering these fundamental questions is a goal that the synthetic-yeast group shares with efforts to recode the genome of the bacterium Escherichia coli7, and with current research programmes1,8 that aim to understand better how to build bacterial genomes containing only the genes necessary to sustain life. Two bacterial genomes have previously been chemically synthesized — the 583-kb genome of Mycoplasma genitalium4 and the 1,078-kb M. mycoides genome1 — and so synthesis of a chromosome of 273 kb is not in itself unusual. The genomes of both M. genitalium and M. mycoides were assembled and propagated in yeast, acting as an extra chromosome. Like incompatible Macintosh software in a Windows computer, synthetic bacterial genomes are unable to ‘boot up’ in yeastcell machinery, and so cannot produce selfreplicating bacterial cells in this setting. In a process called genome transplantation9,10, the complete bacterial genome must be moved to a bacterial host with compatible
hardware, converting the recipient cell into a new, synthetic species (Fig. 1a). By contrast, Annaluru et al. gradually converted the natural yeast chromosome into a fully functional designer chromosome within their target species, the yeast cell itself (Fig. 1b). In comparison to the completely synthetic M. mycoides cell1, chromosome III accounts for less than 3% of the yeast genome. Now the question is: can these design rules be successfully applied across the entire yeast genome? The scientists attempting to generate synthetic yeast cells still have a long way to go before they make a fully reprogrammed yeast genome. However, by demonstrating the success of their design principles and assembling an international team of scientists to build the remaining 15 chromosomes, Annaluru and colleagues have laid the groundwork for making this happen in the near future. Advances such as these are of interest to the entire field of synthetic biology. Each innovation not only enhances our general understanding of biology, but also creates a framework on which we can build and expand, allowing us to work towards the goal of basing our economy on synthetic biology — a development that will have a positive impact on all of society. ■ Daniel G. Gibson and J. Craig Venter are at the J. Craig Venter Institute, La Jolla, California 92037, USA, and at Synthetic Genomics, La Jolla. e-mail: [email protected] 1. Gibson, D. G. et al. Science 329, 52–56 (2010). 2. Annaluru, N. et al. Science 344, 55–58 (2014). 3. Gibson, D. G. et al. Proc. Natl Acad. Sci. USA 105, 20404–20409 (2008). 4. Gibson, D. G. et al. Science 319, 1215–1220 (2008). 5. Gibson, D. G. et al. Nature Methods 6, 343–345 (2009). 6. Annaluru, N. et al. Methods Mol. Biol. 852, 77–95 (2012). 7. Isaacs, F. J. et al. Science 333, 348–353 (2011). 8. Glass, J. I., Hutchison, C. A. III, Smith, H. O. & Venter, J. C. Mol. Syst. Biol. 5, 330 (2009). 9. Lartigue, C. et al. Science 325, 1693–1696 (2009). 10. Lartigue, C. et al. Science 317, 632–638 (2007). 8 M AY 2 0 1 4 | VO L 5 0 9 | NAT U R E | 1 6 9
© 2014 Macmillan Publishers Limited. All rights reserved
Construction of a yeast chromosome
A
1 6 8 | NAT U R E | VO L 5 0 9 | 8 M AY 2 0 1 4
© 2014 Macmillan Publishers Limited. All rights reserved
NEWS & VIEWS RESEARCH had in their sights for almost ten years. A quote by the theoretical physicist Richard Feynman, “What I cannot create, I do not understand”, has inspired synthetic biologists around the world. But this does not necessarily mean that what can be created is understood. There is an enormous gap between our ability to build DNA and our understanding of the instructions it encodes. The production of a synthetic chromosome in yeast (the first such achievement in a eukaryote — the class of organisms comprising plants, animals and fungi) represents a step towards closing that gap. Generation of synthetic versions of widely used model organisms such as S. cerevisiae will enable scientists to investigate the requirements of life in eukaryotes, because synthetic organisms can be easily manipulated. The process began at the computer, where Annaluru and colleagues downloaded the publicly available DNA sequence of a S. cere visiae chromosome (chromosome III). Next, they designed genetic changes, which can be thought of as software edits, with the aim of introducing specific alterations into the chromosome. These edits included the deletion of dispensable DNA sequences; the incorporation of unique sequences to enable the researchers to differentiate between natural and engineered DNA; and the replacement of one particular region of DNA that terminates gene transcription with another that performs the same task. In addition, the authors flanked each nonessential gene with DNA sequences designed to cause deletion of the flanked genes on a given signal. This flanking allows the size of the chromosome to be reduced, a feature designed to help determine the smallest cohorts of genes required to perform a given function or necessary for survival under a particular growth condition. This information is crucial if we are to write biological software in a more predictable fashion, thus ensuring that cells can be engineered to reliably carry out the tasks they have been programmed to perform. To generate the synthetic chromosome, Annaluru and co-workers broke down their designer DNA sequence into overlapping stretches of 70 nucleotides, which were chemically synthesized in parallel. Students in the Build-a-Genome course at Johns Hopkins University in Baltimore, Maryland, stitched together these DNA stretches into constructs approximately 3 kilobases long, using established DNA-assembly methods3–6. Next, the original chromosome sequence was systematically replaced with the synthetic DNA in vivo, by introducing up to 12 overlapping 3-kb synthetic fragments at a time into the yeast cell, in 11 successive rounds of integration.
BEYOND DIVISIONS
The future of synthetic biology nature.com/synbio
a
b Nucleus
Yeast chromosome
Genome transplantation Integration
Synthetic yeast DNA
Synthetic bacterial genome Yeast cell
Bacterial cell
Yeast-cell nucleus
Figure 1 | Building synthetic genomes. a, To generate a synthetic bacterial cell, the entire synthetic bacterial genome is assembled in a yeast cell. In this setting, the bacterial genome is inactive because the yeast cell lacks the proteins required to turn on bacterial genes. After synthesis is complete, the synthetic genome is transferred to a compatible bacterial host cell, where it is activated and produces a synthetic cell. b, By contrast, Annaluru et al.2 have generated a synthetic yeast chromosome within the yeast cell itself. To do this, they replaced the natural chromosome with chunks of synthetic DNA in a stepwise manner.
The product of this work is a yeast strain that contains an extensively engineered chromosome III, and that grows just as well as the original strain. The 273-kb designer chromosome contains more than 50,000 sequence alterations, and is 14% shorter than the natural sequence. This work is important because it begins to address unanswered questions about how genome design can be used to manipulate the rules of biology in a eukaryotic model. For example, can superfluous DNA between genes be removed? Can unnecessary genetic code be altered? So far, the sequence alterations made by Annaluru and colleagues have not reduced the fitness of the yeast, which bodes well for future modifications. If two or more genes perform a similar function, can one be deleted? Which combinations of the 5,000 yeast genes that are thought to be dispensable can be simultaneously removed? The authors have already begun cataloguing genes that can be simultaneously deleted without adversely affecting the fitness of the yeast. Answering these fundamental questions is a goal that the synthetic-yeast group shares with efforts to recode the genome of the bacterium Escherichia coli7, and with current research programmes1,8 that aim to understand better how to build bacterial genomes containing only the genes necessary to sustain life. Two bacterial genomes have previously been chemically synthesized — the 583-kb genome of Mycoplasma genitalium4 and the 1,078-kb M. mycoides genome1 — and so synthesis of a chromosome of 273 kb is not in itself unusual. The genomes of both M. genitalium and M. mycoides were assembled and propagated in yeast, acting as an extra chromosome. Like incompatible Macintosh software in a Windows computer, synthetic bacterial genomes are unable to ‘boot up’ in yeastcell machinery, and so cannot produce selfreplicating bacterial cells in this setting. In a process called genome transplantation9,10, the complete bacterial genome must be moved to a bacterial host with compatible
hardware, converting the recipient cell into a new, synthetic species (Fig. 1a). By contrast, Annaluru et al. gradually converted the natural yeast chromosome into a fully functional designer chromosome within their target species, the yeast cell itself (Fig. 1b). In comparison to the completely synthetic M. mycoides cell1, chromosome III accounts for less than 3% of the yeast genome. Now the question is: can these design rules be successfully applied across the entire yeast genome? The scientists attempting to generate synthetic yeast cells still have a long way to go before they make a fully reprogrammed yeast genome. However, by demonstrating the success of their design principles and assembling an international team of scientists to build the remaining 15 chromosomes, Annaluru and colleagues have laid the groundwork for making this happen in the near future. Advances such as these are of interest to the entire field of synthetic biology. Each innovation not only enhances our general understanding of biology, but also creates a framework on which we can build and expand, allowing us to work towards the goal of basing our economy on synthetic biology — a development that will have a positive impact on all of society. ■ Daniel G. Gibson and J. Craig Venter are at the J. Craig Venter Institute, La Jolla, California 92037, USA, and at Synthetic Genomics, La Jolla. e-mail: [email protected] 1. Gibson, D. G. et al. Science 329, 52–56 (2010). 2. Annaluru, N. et al. Science 344, 55–58 (2014). 3. Gibson, D. G. et al. Proc. Natl Acad. Sci. USA 105, 20404–20409 (2008). 4. Gibson, D. G. et al. Science 319, 1215–1220 (2008). 5. Gibson, D. G. et al. Nature Methods 6, 343–345 (2009). 6. Annaluru, N. et al. Methods Mol. Biol. 852, 77–95 (2012). 7. Isaacs, F. J. et al. Science 333, 348–353 (2011). 8. Glass, J. I., Hutchison, C. A. III, Smith, H. O. & Venter, J. C. Mol. Syst. Biol. 5, 330 (2009). 9. Lartigue, C. et al. Science 325, 1693–1696 (2009). 10. Lartigue, C. et al. Science 317, 632–638 (2007). 8 M AY 2 0 1 4 | VO L 5 0 9 | NAT U R E | 1 6 9
© 2014 Macmillan Publishers Limited. All rights reserved
