Editing Mycoplasma genitalium (section)

==Synthetic genome==
On 6 October 2007, [[Craig Venter]] announced that a team of scientists led by Nobel laureate [[Hamilton O. Smith|Hamilton Smith]] at the J. Craig Venter Institute had successfully constructed [[synthetic DNA]] with which they planned to make the first synthetic genome. Reporting in ''[[The Guardian]]'', Venter said that they had stitched together a DNA strand containing 381 genes, consisting of 580,000 base pairs, based on the genome of ''M. genitalium''.<ref>{{cite news |last1=Pilkington |first1=Ed |title=I am creating artificial life, declares US gene pioneer |url=https://www.theguardian.com/science/2007/oct/06/genetics.climatechange |access-date=9 August 2014 |work=The Guardian |publisher=Guardian News and Media Limited |date=6 October 2007 |archive-date=28 May 2010 |archive-url=https://web.archive.org/web/20100528172927/http://www.guardian.co.uk/science/2007/oct/06/genetics.climatechange |url-status=live }}</ref> On 24 January 2008, they announced the successful creation of a synthetic bacterium, which they named ''Mycoplasma genitalium'' JCVI-1.0 (the name of the strain indicating J. Craig Venter Institute with its specimen number).<ref>{{cite web |last1=Kowalski |first1=Heather |title=Venter Institute Scientists Create First Synthetic Bacterial Genome |url=http://www.jcvi.org/cms/research/projects/synthetic-bacterial-genome/press-release/ |publisher=J. Craig Venter Institute |access-date=9 August 2014 |archive-date=11 July 2015 |archive-url=https://web.archive.org/web/20150711044023/http://www.jcvi.org/cms/research/projects/synthetic-bacterial-genome/press-release/ |url-status=dead }}</ref> They synthesised and assembled the complete 582,970-base pair genome of the bacterium. The final stages of synthesis involved cloning the DNA into the bacterium ''[[Escherichia coli|E. coli]]'' for nucleotide production and sequencing. This produced large fragments of approximately 144,000 base pairs or 1/4th of the whole genome. Finally, the products were cloned inside the yeast ''[[Saccharomyces cerevisiae]]'' to synthesize the 580,000 base pairs.<ref>{{cite journal |last1=Gibson |first1=D. G. |last2=Benders |first2=G. A. |last3=Andrews-Pfannkoch |first3=C. |last4=Denisova |first4=E. A. |last5=Baden-Tillson |first5=H. |last6=Zaveri |first6=J. |last7=Stockwell |first7=T. B. |last8=Brownley |first8=A. |last9=Thomas |first9=D. W.|last10=Algire|first10=M. A. |last11=Merryman |first11=C. |last12=Young |first12=L. |last13=Noskov |first13=V. N. |last14=Glass |first14=J. I. |last15=Venter |first15=J. C. |last16=Hutchison |first16=C. A. |last17=Smith |first17=H. O. |title=Complete Chemical Synthesis, Assembly, and Cloning of a ''Mycoplasma genitalium'' Genome |journal=Science |year=2008 |volume=319 |issue=5867 |pages=1215–1220 |doi=10.1126/science.1151721 |pmid=18218864 |bibcode=2008Sci...319.1215G |s2cid=8190996}}</ref><ref>{{cite news |first=Philip |last=Ball |title=Genome stitched together by hand |url=http://www.nature.com/news/2008/080124/full/news.2008.522.html |work=Nature News |date=2008-01-24 |doi=10.1038/news.2008.522 |access-date=25 January 2008 |archive-date=21 October 2020 |archive-url=https://web.archive.org/web/20201021002756/https://www.nature.com/news/2008/080124/full/news.2008.522.html |url-status=live }}</ref> The molecular size of the synthetic bacterial genome is 360,110 [[Unified atomic mass unit|kilodaltons]] (kDa). Printed in 10-point font, the letters of the genome cover 147 pages.<ref>{{cite web |title=Scientists Create First Synthetic Bacterial Genome -- Largest Chemically Defined Structure Synthesized In The Lab |url=https://www.sciencedaily.com/releases/2008/01/080124175924.htm |work=ScienceDaily |access-date=9 August 2014 |date=24 January 2008 |archive-date=10 August 2014 |archive-url=https://web.archive.org/web/20140810181302/http://www.sciencedaily.com/releases/2008/01/080124175924.htm |url-status=live }}</ref>

On 20 July 2012, [[Stanford University]] and the J. Craig Venter Institute announced successful simulation of the complete life cycle of a ''Mycoplasma genitalium'' cell, in the journal ''[[Cell (journal)|Cell]]''.<ref>{{cite journal |last1=Karr |first1=Jonathan R. |last2=Sanghvi |first2=Jayodita C. |last3=Macklin |first3=Derek N. |last4=Gutschow |first4=Miriam V. |last5=Jacobs |first5=Jared M. |last6=Bolival |first6=Benjamin |last7=Assad-Garcia |first7=Nacyra |last8=Glass |first8=John I. |last9=Covert |first9=Markus W. |title=A Whole-Cell Computational Model Predicts Phenotype from Genotype |journal=Cell |year=2010 |volume=150 |issue=2 |pages=389–401 |doi=10.1016/j.cell.2012.05.044 |pmid=22817898 |pmc=3413483}}</ref> The entire organism is modeled in terms of its molecular components, integrating all cellular processes into a single model. Using object oriented programming to model the interactions of 28 categories of molecules, including DNA, RNA, proteins, and metabolites, and running on a 128 computer Linux cluster, the simulation takes 10 hours for a single ''M. genitalium'' cell to divide once—about the same time the actual cell takes—and generates half a gigabyte of data.<ref>{{cite news |title=In First, Software Emulates Lifespan of Entire Organism |date=20 July 2012 |newspaper=[[The New York Times]] |access-date=2012-07-20 |url=https://www.nytimes.com/2012/07/21/science/in-a-first-an-entire-organism-is-simulated-by-software.html |archive-date=4 December 2016 |archive-url=https://web.archive.org/web/20161204042711/http://www.nytimes.com/2012/07/21/science/in-a-first-an-entire-organism-is-simulated-by-software.html?_r=3 |url-status=live }}</ref>