Synthetic Biology at Nature Methods

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Apr 24, 2014
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Since its launch, Nature Methods has seen many papers that have influenced the Synthetic Biology community. As a supplement to our May Focus on Synthetic Biology we take a nostalgic trip through the highlights of our papers in this area for different aspects of synthetic biology.

Cloning
In 2007 Stephen Elledge and Mamie Li developed SLIC (sequence and ligation-independent cloning) a strategy that uses homologous recombination to assembly many DNA fragments in vitro in a single reaction. Later the same year Mitsuhiro Itaya and colleagues also used homologous recombination in their bottom up assembly to unite larger DNA pieces to genomes of ~ 140kb size.

In 2009 Daniel Gibson and colleagues presented their one-pot enzymatic reaction that successfully assembled genomes 100s of kilobases and has since been dubbed ‘Gibson Assembly’. The method reached fame on Youtube when the Cambridge iGEM team for 2010 created a music video showing how Gibson Assembly saves frustrated scientists:

Gene and genome synthesis
In 2007, to improve error-free DNA synthesis, Duhee Bang and George Church developed circular assembly amplification that eliminated error-containing oligonucleotides from the assembly. A few years later Jay Shendure and colleagues introduced their dial-out PCR to retrieve desired DNA molecules from a library for gene assembly.

For an in depth review on the topic of DNA synthesis, error correction and gene assembly visit Sriram Kosuri and George Church’s review in our Focus issue.

In 2010, on the heels of their breakthrough with Mycoplasma mycoides JCVI-syn1.0 – the first chemically synthesized bacterial genome (Gibson D, et al Science 329, 2010) ­- Gibson et al. published the chemical synthesis of the mouse mitochondrial genome in our pages. They adapted Gibson Assembly to begin at the oligonucleotide level to rapidly make larger fragments that were then combined into the desired genome, exclusively in vitro. Once synthesized a bacterial genome might need to be further modified, but to do so in an organism other than E. coli proved challenging. In 2013 Bogumil Karas et al, showed that whole genomes, as large as 1.8 megabases can be directly transferred from bacteria to yeast where genetic manipulation is routine.

In our current Focus issue Gibson reviews the state of the art in genome assembly techniques , compares strategies and discusses what the future may hold.

Genome modification
To quickly generate large libraries of promoters in targeted regions of a bacterial chromosome George Church and colleagues presented coselection MAGE (multiplex automated genome engineering) in 2012. The increasingly popular CRISPR system can also rapidly edit genomes with few off-target effects when Cas9 is used as a nickase as William Skarnes and colleagues showed earlier this year.

Gene activation can be tuned by targeting transcription factors via the CRISPR-Cas9 system as Charles Gersbach demonstrated in 2013.

Circuit design
To ease construction of complex circuits Adam Arkin and colleagues adapted known translational regulators to control transcriptional elongation in 2012. A bit later the same year Jim Collins and colleagues showed that an iterative plug-and-play method makes use of a large repository of genetic components when designing circuits. This year Jeff Tabor and colleagues showed how gene circuit dynamics can be controlled with light. On April 28 Douglas Densmore and his team introduced Raven , software that calculates assembly plans for complex circuits.

Parts characterization
To be successful in any of the above applications one needs reliable and well characterized parts. Last year Drew Endy, Adam Arkin and colleagues presented a method to quantify the performance of genetic elements and in a companion paper they introduced a library of standardized transcription and translation initiation elements available through biofab.

Towards the end of 2013 Christopher Voigt and colleagues expanded the designer’s toolbox with over 500 well characterized transcriptional terminators. Robert Landick discussed how these ‘better stop signs’ as he termed them provide insight into the mechanism of termination.

UPDATE: There is now a joint special on Synthetic Biology at nature.com/synbio with articles from Nature, Nature Reviews Microbiology and Nature Methods.

Enjoy reading. The papers mentioned above are listed below in chronological order.

References:

Mamie Z Li & Stephen J Elledge
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
Nature Methods 4, 251-256 (2007) doi:10.1038/nmeth1010

Mitsuhiro Itaya, Kyoko Fujita, Azusa Kuroki & Kenji Tsuge
Bottom-up genome assembly using the Bacillus subtilis genome vector
Nature Methods 5, 41-43 (2008) doi:10.1038/nmeth1143

Duhee Bang & George M Church
Gene synthesis by circular assembly amplification
Nature Methods 5, 37–39 (2008) doi:10.1038/nmeth1136

Daniel G Gibson, Lei Young, Ray-Yuan Chuang, J Craig Venter, Clyde A Hutchison III & Hamilton O Smith
Enzymatic assembly of DNA molecules up to several hundred kilobases
Nature Methods 6, 343-345 (2009) doi:10.1038/nmeth.1318

Daniel G Gibson, Hamilton O Smith, Clyde A Hutchison III, J Craig Venter & Chuck Merryman
Chemical synthesis of the mouse mitochondrial genome
Nature Methods 7, 901–903 (2010) doi:10.1038/nmeth.1515

Harris H Wang, Hwangbeom Kim, Le Cong, Jaehwan Jeong, Duhee Bang & George M Church
Genome-scale promoter engineering by coselection MAGE
Nature Methods 9, 591–593 (2012) doi:10.1038/nmeth.1971

Jerrod J Schwartz, Choli Lee & Jay Shendure
Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules
Nature Methods 9, 913–915 (2012) doi:10.1038/nmeth.2137

Chang C Liu, Lei Qi, Julius B Lucks, Thomas H Segall-Shapiro, Denise Wang, Vivek K Mutalik & Adam P Arkin
An adaptor from translational to transcriptional control enables predictable assembly of complex regulation
Nature Methods 9, 1088–1094 (2012) doi:10.1038/nmeth.2184

Kevin D Litcofsky, Raffi B Afeyan, Russell J Krom, Ahmad S Khalil & James J Collins
Iterative plug-and-play methodology for constructing and modifying synthetic gene networks
Nature Methods 9, 1077–1080 (2012) doi:10.1038/nmeth.2205

Bogumil J Karas et al.
Direct transfer of whole genomes from bacteria to yeast
Nature Methods 10, 410–412 (2013) doi:10.1038/nmeth.2433

Pablo Perez-Pinera et al.
RNA-guided gene activation by CRISPR-Cas9–based transcription factors
Nature Methods 10, 973–976 (2013) doi:10.1038/nmeth.2600

Vivek K Mutalik et al.
Quantitative estimation of activity and quality for collections of functional genetic elements
Nature Methods 10, 347–353 (2013) doi:10.1038/nmeth.2403

Vivek K Mutalik et al.
Precise and reliable gene expression via standard transcription and translation initiation elements
Nature Methods 10, 354–360 (2013) doi:10.1038/nmeth.2404

Ying-Ja Chen et al.
Characterization of 582 natural and synthetic terminators and quantification of their design constraints
Nature Methods 10, 659–664 (2013) doi:10.1038/nmeth.2515

Rachel Anne Mooney & Robert Landick
Building a better stop sign: understanding the signals that terminate transcription
Nature Methods 10, 618–619 (2013) doi:10.1038/nmeth.2527

Bin Shen et al.
Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects
Nature Methods 11, 399–402 (2014) doi:10.1038/nmeth.2857

Evan J Olson, Lucas A Hartsough, Brian P Landry, Raghav Shroff & Jeffrey J Tabor
Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals
Nature Methods (2014) doi:10.1038/nmeth.2884

James Attwater & Philipp Holliger
A synthetic approach to abiogenesis
Nature Methods 11, 495–498 (2014) doi:10.1038/nmeth.2893

Sriram Kosuri & George M Church
Large-scale de novo DNA synthesis: technologies and applications
Nature Methods 11, 499–507 (2014) doi:10.1038/nmeth.2918

Daniel G Gibson
Programming biological operating systems: genome design, assembly and activation
Nature Methods 11, 521–526 (2014) doi:10.1038/nmeth.2894

Jennifer Brophy & Christopher Voigt
Principles of genetic circuit design
Nature Methods 11, 508–520 (2014) doi:10.1038/nmeth.2926

Evan Appleton, Jenhan Tao, Traci Haddock & Douglas Densmore
Interactive assembly algorithms for molecular cloning
Nature Methods (2014) doi:10.1038/nmeth.2939

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Nicole Rusk

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