in this issue

Focus on synthetic biology

This issue of Nature Biotechnology surveys the field of synthetic biology, its commercial applications and the legal, regulatory and ethical challenges that it poses to science and society. Although any new emerging technology has its share of hype, synthetic biology seems to have had more than its fair share. On p. 1071, we ask 20 experts their views on how this field should be defined; the range and diversity of responses is illuminating. The related field of biohacking or garage biologya grassroots movement in which amateur biologists and enthusiasts use recombinant technology outside of the traditional laboratory settingis also investigated [News Feature, p. 1077]. Such developments are not without potential implications for regulatory oversight and the risk of misuse [Commentary, p. 1109], although it remains unclear how many amateur biologists there are. What is clear is that the engagement of younger scientists in such events as the International Genetically Engineered Machines (iGEM) competition is invigorating the field with new researchers, driving adoption of the concept of programmable biology and helping to build a scientific community oriented to open sharing of standardized component parts [Commentary, p. 1099]. For this momentum to be sustained, however, it will be important to encourage both academic institutions and corporations to adopt new open intellectual property paradigms and desist from patenting individual DNA parts, the restrictive licensing of which could slow the creation of more-complex circuits, which are likely to prove useful [Commentary, p. 1095; Patents, p. 1127]. Already, the corporate world is finding ways of applying these technologies, even at this early stage. On p. 1091, Carlson provides his perspective on how the economics of synthetic biology are likely to develop in the coming years. One area currently receiving particular attention is the use of synthetic biology in generating organisms capable of producing alternative fuels [News Feature, p. 1074]. Several other approaches are also attracting commercial interest, including the recoding of genes to generate proteins with enhanced properties. But much of the work for generating medicines and industrial chemicals appears to be plain metabolic engineering dressed up under a new name [Feature, p. 1112]. What is clear is that the potential of these new technologies to radically alter the genetic component of organisms not only raises ethical disquiet concerning their use and misuse but also might negatively influence public perception of the field [Commentary, p. 1103]. Even so, as Kaebnick argues on p. 1106, different personal moral objections do not necessarily provide justification for a rethink of the current regulatory system. In 2002, the first de novo synthesis of a whole viral genome in the absence of a natural template prompted a substantial public backlash and numerous calls for more stringent regulatory oversight. In the intervening years, however, synthetic virology has yielded several beneficial applications in vaccine attenuation and archaevirology [Review, p. 1172]. Progress in assembling larger and larger pieces of DNA into genes and genomes in viruses and cells, together with ways of generating sequence diversity on a genome scale, is summarized on p. 1151. Rapid advances have also been made in generating more complex genetic circuits, and one of the pioneers in this field provides a perspective on the challenges going forward [Perspective, p. 1139]. Perhaps the ultimate goal in the field, though, is the creation of a chassis organism with a minimal genome onto which different circuits encoding traits of interest could be superimposed [Editorial, p. 1059]. On p. 1121, J. Craig Venter provides an assessment of the progress his group has made in achieving that aim. LD, MF, BH & AM

2009 Nature America, Inc. All rights reserved.

Prolonging half-life in plasma

Rapid clearance from the circulation frequently complicates therapeutic use of proteins and peptides. This is commonly addressed by either chemical conjugation to polyethylene glycol (PEG) or genetic fusion to long-lived proteins such as albumin, immunoglobulins or immunoglobulin-derived fragments. Even so, PEGylation can be costly and often generates a heterogeneous endproduct, whereas use of certain protein fusion partners is restricted to mammalian cells and can complicate tight control over plasma
Written by Laura DeFrancesco, Markus Elsner, Michael Francisco, Peter Hare, Brady Huggett, Craig Mak, Andrew Marshall & Lisa Melton

half-life for indications when an extended residence time in the circulation is undesirable. Stemmer and colleagues demonstrate that genetic fusion of a long unstructured, ~850-amino-acid polypeptide offers a general strategy to extend peptide or protein half-life in vivo in a tunable manner. This polypeptide, named XTEN, comprises only six types of amino acid that were selected with the intention of minimizing immunogenicity and optimizing ease of manufacture. Half-life can be tuned by controlling the length and/or composition of the attached sequence. As fusion of XTEN to the peptide drug exenatide is estimated to extend its half-life ~60-fold in humans without loss of function in a mouse model of diabetes, this strategy could provide a therapeutic with monthly, rather than daily, dosing frequency. In contrast, appending a truncated XTEN sequence to glucagon provides a more moderate half-life extension in the range suitable for treatment of nocturnal hypoglycemia. [Letters, p. 1186] PH

nature biotechnology volume 27 number 12 december 2009

IN ThIS ISSUE

Photosynthetic biofuel production

New sources of low-emission fuels are needed to replace fossil fuels. Liao and colleagues show that the cyanobacterium Synechococcus elongatus can be engineered to photosynthetically produce isobutyraldehyde and isobutanol directly from CO2 and water. The production of isobutyraldehyde is advantageous because its high vapor pressure makes it possible to remove it directly from the culture medium during production. Isobutyraldehyde can be used as a precursor for a large range of chemicals. It can also be converted to isobutanol, which is considered to be a promising biofuel, either biologically or by chemical catalysis. In their laboratory-scale experiments, Liao and colleagues achieve isobutyraldehyde yields that are superior to those of current technologies that harvest photosynthetic biomass or directly produce ethanol or hydrogen. The synthesis of isobutanol by S. elongatus is less efficient, but still comparable to the current algae-based biodiesel production and superior to cellulosic ethanol production. [Letters, p. 1177; News and Views p. 1128] ME

experimental assay of the effects has played a starring role. Shendure and colleagues describe a modern take on the classic technique of saturation mutagenesis to determine promoter function. They first synthesize thousands of single-base and two-base mutants of bacterial and mammalian promoters on custom-designed oligonucleotide microarrays. After cleavage from the array, the promoter variants are transcribed in vitro and the promoters strength is quantified by high-throughput sequencing of barcode sequences embedded in the mRNA transcripts. The technology enables for the first time an exhaustive survey of promoter variation at single-base resolution, data that could prove invaluable for choosing promoters for use in synthetic genetic circuits or for better understanding the growing cadre of regulatory regions that are being discovered by genome sequencing. [Brief Communications, p. 1173] CM

measuring alternative lengthening of telomeres

Each round of replication leaves eukaryotic chromosomes slightly shorter than before. Actively dividing cells maintain the specialized end-structures of the chromosomes, the telomeres, either by expressing an enzyme called telomerase or by a less well-defined mechanism called alternative lengthening of telomeres (ALT). Whereas the more common telomerase pathway has emerged as a promising anti-cancer target, specific ALT inhibitors are yet to be described, mainly because there is no means to easily measure ALT activity. Reddel and colleagues have now developed a rapid, specific and sensitive ALT assay that is based on the detection of so-called C-circles, partially single-stranded telomeric (CCCTAA)n DNA circles, by rolling circle amplification. The authors demonstrate the specificity by measuring the presence of C-circles in a wide range of human cells with and without ALT activity and by the expression of known ALT-inhibitory proteins in cells. They also show that their assay can detect C-circles in blood samples of individuals with ALT-positive tumors, suggesting possible clinical applications of their assay. [Letters, p. 1181] ME

2009 Nature America, Inc. All rights reserved.

Synthetic promoter bashing

Shendure and colleagues demonstrate the extraordinary power afforded by technologies for writing and reading the genetic code on a massive scale. In tracing the common conceptual threads that tie early genetic experiments to the wealth of mechanistic insights available today, painstaking mutagenesisoften base-by-base manipulationfollowed by

Patent roundup
Life Technologies in Carlsbad, California, and its subsidiary Applied Biosystems have filed a patent infringement lawsuit against San Diego-based Illumina), and subsidiary Solexa, which promptly responded with a countersuit. [News, p. 1069] LM The US Supreme Courts 2007 decision in KSR v. Teleflex gave courts a new test to determine an inventions obviousness. In this issue, Wang analyzes US Federal Circuit decisions pre- and post-KSR to shows its effects on biotech inventions. [Patent Article, p. 1125] MF Recent patent applications in synthetic biology. [New patents, p. 1127] MF

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Chimeric-mouse tumor models Normalized, label-free protein quantification Allosteric regulation of phosphodiesterase 4 Predicting functions of Plasmodium falciparum genes

volume 27 number 12 december 2009 nature biotechnology