The hottest tech news in last week were from Google: open source VP8 at WebM, Android Froyo with 2x-5x speed increase for mobile phone, Google TV - when TV meets web, web meets TV
The hottest science news in last week is from J. Craig Venter Institute: they created the first self-replicating synthetic bacterial cell, after their success in synthesizing a small virus in 2003
HERE IT IS!
"A defining moment in the history of biology and biotechnology" - Mark Bedau
"It represents an important technical milestone in the new field of synthetic genomics" - Jef Boeke
"That's a pretty amazing accomplishment" - Anthony Forster
"There are great challenges ahead before genetic engineers can mix, match, and fully design an organism's genome from scratch" - Paul Keim
Published Online May 20, 2010
Science DOI: 10.1126/science.1190719Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Daniel G. Gibson,1 John I. Glass,1 Carole Lartigue,1 Vladimir N. Noskov,1 Ray-Yuan Chuang,1 Mikkel A. Algire,1 Gwynedd A. Benders,2 Michael G. Montague,1 Li Ma,1 Monzia M. Moodie,1 Chuck Merryman,1 Sanjay Vashee,1 Radha Krishnakumar,1 Nacyra Assad-Garcia,1 Cynthia Andrews-Pfannkoch,1 Evgeniya A. Denisova,1 Lei Young,1 Zhi-Qing Qi,1 Thomas H. Segall-Shapiro,1 Christopher H. Calvey,1 Prashanth P. Parmar,1 Clyde A. Hutchison, III,2 Hamilton O. Smith,2 J. Craig Venter1,2,*We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.
1 The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
2 The J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA.* To whom correspondence should be addressed. E-mail: jcventer@jcvi.org
Interesting notes taken from the comment and the Science paper
- "... the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations."
- "... Like computer programmers debugging faulty software, they systematically transplanted combinations of synthetic and natural DNA, finally homing in on a single-base mistake in the synthetic genome. The error delayed the project 3 months."
- This was accomplished through a combination of in vitro enzymatic methods and in vivo recombination in Saccharomyces cerevisiae. The whole synthetic genome (582,970 bp) was stably grown as a yeast centromeric plasmid (YCp)
- We needed to improve methods for extracting intact chromosomes from yeast. We also needed to learn how to transplant these genomes into a recipient bacterial cell to establish a cell controlled only by a synthetic genome.
- We were able to overcome this restriction barrier by methylating the donor DNA with purified methylases or crude M. mycoides or M. capricolum extracts, or by simply disrupting the recipient cell’s restriction system (8).
- These watermark sequences encode unique identifiers while limiting their translation into peptides.
- To aid in the building process, DNA cassettes and assembly intermediates were designed to contain Not I restriction sites at their termini, and recombined in the presence of vector elements to allow for growth and selection in yeast (7) (11).
- All of the first-stage intermediates were sequenced. Nineteen out of 111 assemblies contained errors. Alternate clones were selected, sequence-verified, and moved on to the next assembly stage (11).
- In general, 25% or more of the clones screened contained all of the amplicons expected for a complete assembly.
- To further enrich for the eleven circular assembly intermediates, ~200 ng samples of each assembly were pooled and mixed with molten agarose. As the agarose solidifies, the fibers thread through and topologically "trap" circular DNA (15). Untrapped linear DNA can then be electrophoresed out of the agarose plug, thus enriching for the trapped circular molecules.
- Our success was thwarted for many weeks by a single base pair deletion in the essential gene dnaA. One wrong base out of over one million in an essential gene rendered the genome inactive,
- As synthetic genomic applications expand, we anticipate that this work will continue to raise philosophical issues that have broad societal and ethical implications. We encourage the continued discourse.
“人造生命”诞生了吗？——方舟子的最新评论文章
http://blog.sina.com.cn/s/blog_474068790100jmbw.html
个人以为，他低估了这个研究的价值。这篇文章证明了化学合成的真核基因组包涵了所有的信息，毕竟生物合成的时候有各种修饰上去，而化学合成的仅仅是单纯的ATGC。再者，单单这个技术活就很令人佩服了的！
Here is the missing F1000 review http://f1000biology.com/article/id/3346969/evaluation
Simon Zeller and Bernhard Schmid
University of Zurich, Switzerland
With this paper, Craig Venter's lab group fulfil their promise to create a self-replicating bacterial cell, controlled by a synthetic genome. For the first time, a complete 1.08Mbp genome of Mycoplasma mycoides has been synthesized and successfully transplanted into M. capricolum recipient cells. This breakthrough might promote research in the field of synthetic biology and at the same time initiate ethical discussions about life itself.
Only a few years after synthesizing the first synthetic genome and transplanting the first genomes from one species into another, researchers were able to combine these steps. Firstly, a digitalized genome of a small bacterium, M. mycoides, was 'designed' and assembled using E. coli and later yeast cells. Before the pieces of DNA were fused into a single chromosome, a number of proofreading steps were necessary. Semi-synthetic genomes, which included pieces of the final genome, were produced and tested for functionality. Among other problems, a single point mutation seemed to cause much hardship since it inactivated the whole genome. Only after these problems were overcome could the genome pieces be assembled in yeast cells. Bacterial genomes grown in yeast are unmethylated and not protected from the restriction system of bacterial cells. It was therefore necessary to methylate the synthetic DNA and to disrupt the recipient cells' restriction system. Finally, the synthetic genome could be inserted successfully into M. capricolum recipient cells. Phenotypic examinations, cultivation tests and genome sequencing ('watermarks') were used to demonstrate self-replication and the absence of the original DNA. There seems to be some controversy of whether or not these organisms can be called 'synthetic life' since only the genome and not the whole cell was created from scratch. Either way, this work can be seen as 'proof of concept' and might initiate interesting scientific and philosophical discussions.
----
Junjie U Guo and Hongjun Song
Johns Hopkins University School of Medicine, USA
This milestone work by Venter and colleagues reports their successful chemical synthesis and assembly of a bacterial genome which drives the first self-replicable 'synthetic life'.
Creating synthetic life forms has been the central challenge of synthetic biology. Although scientists have been able to modify and engineer genomes on small scales for decades, engineering of a mega-base-scale genome has been a daunting task. Venter and colleagues have previously succeeded in transplanting the genome from one Mycoplasma strain to a different recipient strain to produce viable cells {1}. Building on their earlier efforts in the synthesis and assembly of the smaller Mycoplasma genitalium genome (0.58Mbp) {2,3}, here they demonstrated for the first time the computer-assisted design, chemical synthesis, assembly, and successful transplantation of a synthetic genome that highly resembles the natural M. mycoides genome (1.1Mbp) into M. capricolum recipient cells -- in which the restriction system had been disrupted -- and created viable M. mycoides-like cells. As a proof of principle, this study opens many doors of possibilities for a better understanding of genome functions by re-designing and implementing new functions on a genome scale. It also points out the technical difficulties in handling large amounts of genetic material and the importance of quality control at each assembly step. One would expect to see in the future how multi-chromosomal genomes can be transplanted and, more importantly, the elimination of the need for natural recipient cells to create fully synthetic life.
References: {1} Lartigue et al. Science 2009, 325:1693-6 [PMID:19696314]. {2} Gibson et al. Science 2008, 319:1215-20 [PMID:18218864]. {3} Gibson et al. Proc Natl Acad Sci U S A 2008, 105:20404-9 [PMID:19073939].