title: Integrating reductive and synthetic approaches in biology using man-made cell-like compartments.
abstract: We propose 'integrated synthetic genetics' as a novel methodology that integrates reductive and synthetic approaches used in life science research. Integrated synthetic genetics enables determinations of sets of genes required for the functioning of any biological subsystem. This method utilizes artificial cell-like compartments, including a randomly introduced whole gene library, strictly defined components for in vitro transcription and translation and a reporter that fluoresces 'only when a particular function of a target biological subsystem is active.' The set of genes necessary for the target biological subsystem can be identified by isolating fluorescent artificial cells and multiplex next-generation sequencing of genes included in these cells. The importance of this methodology is that screening for the set of genes involved in a subsystem and reconstructing the entire subsystem can be done simultaneously. This methodology can be applied to any biological subsystem of any species and may remarkably accelerate life science research.
authors.affiliation: 1] Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan [2] Japan Society for the Promotion of Science, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Aoki
authors.affiliation: Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Saito
authors.affiliation: Genome Network Analysis Support Facility, Division of Genomics Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Ri-ichiroh
authors.initials: R
authors.lastname: Manabe
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
authors.affiliation: Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Yamaguchi
authors.affiliation: Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Eiichi
authors.initials: E
authors.lastname: Tamiya
mesh_terms: D058045:Artificial Cells / Q000737:chemistry* / Q000166:cytology; D002451:Cell Compartmentation; D014176:Protein Biosynthesis; D058615:Synthetic Biology; D014158:Transcription, Genetic
references.citation: Nucleic Acids Res. 2007;35(15):e97
references.pmid: 17670798
references.citation: Proc Natl Acad Sci U S A. 1988 Apr;85(8):2603-7
references.pmid: 3128790
references.citation: Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17669-74
references.pmid: 15591347
references.citation: Bioinformatics. 2004 Nov 22;20(17):3246-8
references.pmid: 15180930
references.citation: DNA Res. 2005;12(5):291-9
references.pmid: 16769691
references.citation: Nat Commun. 2013;4:2494
references.pmid: 24088711
references.citation: Langmuir. 2009 Sep 15;25(18):10439-43
references.pmid: 19670878
references.citation: Methods. 2005 Jul;36(3):299-304
references.pmid: 16076456
references.citation: Anal Chem. 2012 Jun 5;84(11):5017-24
references.pmid: 22519524
references.citation: Nat Biotechnol. 1998 Jul;16(7):652-6
references.pmid: 9661199
references.citation: Semin Cancer Biol. 2013 Aug;23(4):286-92
references.pmid: 23792107
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4201-6
references.pmid: 19251648
references.citation: Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16796-801
references.pmid: 24082135
references.citation: Bioinformatics. 2004 Jun 12;20(9):1453-4
references.pmid: 14871861
references.citation: J Biosci Bioeng. 2001;92(6):590-3
references.pmid: 16233152
references.citation: Anal Biochem. 2006 Oct 1;357(1):128-36
references.pmid: 16889743
references.citation: Semin Cancer Biol. 2013 Aug;23(4):279-85
references.pmid: 23791722
references.citation: Nat Biotechnol. 2001 Aug;19(8):751-5
references.pmid: 11479568
references.citation: Nat Methods. 2012 Mar 04;9(4):357-9
references.pmid: 22388286