Literature DB >> 20192780

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

Caleb J Bashor1, Andrew A Horwitz, Sergio G Peisajovich, Wendell A Lim.   

Abstract

The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems.

Entities:  

Mesh:

Year:  2010        PMID: 20192780      PMCID: PMC2965450          DOI: 10.1146/annurev.biophys.050708.133652

Source DB:  PubMed          Journal:  Annu Rev Biophys        ISSN: 1936-122X            Impact factor:   12.981


  69 in total

1.  Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms.

Authors:  Sang-Hyun Park; Ali Zarrinpar; Wendell A Lim
Journal:  Science       Date:  2003-01-02       Impact factor: 47.728

Review 2.  Reconstruction of genetic circuits.

Authors:  David Sprinzak; Michael B Elowitz
Journal:  Nature       Date:  2005-11-24       Impact factor: 49.962

3.  Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene.

Authors:  Benjamin Prud'homme; Nicolas Gompel; Antonis Rokas; Victoria A Kassner; Thomas M Williams; Shu-Dan Yeh; John R True; Sean B Carroll
Journal:  Nature       Date:  2006-04-20       Impact factor: 49.962

Review 4.  Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.

Authors:  Roby P Bhattacharyya; Attila Reményi; Brian J Yeh; Wendell A Lim
Journal:  Annu Rev Biochem       Date:  2006       Impact factor: 23.643

Review 5.  The second wave of synthetic biology: from modules to systems.

Authors:  Priscilla E M Purnick; Ron Weiss
Journal:  Nat Rev Mol Cell Biol       Date:  2009-06       Impact factor: 94.444

Review 6.  Nonproteolytic functions of ubiquitin in cell signaling.

Authors:  Zhijian J Chen; Lijun J Sun
Journal:  Mol Cell       Date:  2009-02-13       Impact factor: 17.970

7.  A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene.

Authors:  R Brent; M Ptashne
Journal:  Nature       Date:  1984 Dec 13-19       Impact factor: 49.962

Review 8.  Ubiquitin-binding domains.

Authors:  James H Hurley; Sangho Lee; Gali Prag
Journal:  Biochem J       Date:  2006-11-01       Impact factor: 3.857

9.  Synthesis of methyl halides from biomass using engineered microbes.

Authors:  Travis S Bayer; Daniel M Widmaier; Karsten Temme; Ethan A Mirsky; Daniel V Santi; Christopher A Voigt
Journal:  J Am Chem Soc       Date:  2009-05-13       Impact factor: 15.419

10.  An engineered epigenetic transgene switch in mammalian cells.

Authors:  Beat P Kramer; Alessandro Usseglio Viretta; Marie Daoud-El-Baba; Dominique Aubel; Wilfried Weber; Martin Fussenegger
Journal:  Nat Biotechnol       Date:  2004-06-06       Impact factor: 54.908

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  67 in total

Review 1.  Synthetic biology with surgical precision: targeted reengineering of signaling proteins.

Authors:  Vsevolod V Gurevich; Eugenia V Gurevich
Journal:  Cell Signal       Date:  2012-06-01       Impact factor: 4.315

2.  The Levinthal paradox of the interactome.

Authors:  Peter Tompa; George D Rose
Journal:  Protein Sci       Date:  2011-11-09       Impact factor: 6.725

3.  Distributed biological computation with multicellular engineered networks.

Authors:  Sergi Regot; Javier Macia; Núria Conde; Kentaro Furukawa; Jimmy Kjellén; Tom Peeters; Stefan Hohmann; Eulàlia de Nadal; Francesc Posas; Ricard Solé
Journal:  Nature       Date:  2010-12-08       Impact factor: 49.962

4.  Build life to understand it.

Authors:  Michael Elowitz; Wendell A Lim
Journal:  Nature       Date:  2010-12-16       Impact factor: 49.962

5.  Design principles for robust oscillatory behavior.

Authors:  Sebastian M Castillo-Hair; Elizabeth R Villota; Alberto M Coronado
Journal:  Syst Synth Biol       Date:  2015-08-05

Review 6.  Genetic design automation: engineering fantasy or scientific renewal?

Authors:  Matthew W Lux; Brian W Bramlett; David A Ball; Jean Peccoud
Journal:  Trends Biotechnol       Date:  2011-10-14       Impact factor: 19.536

7.  Ultrasensitivity by molecular titration in spatially propagating enzymatic reactions.

Authors:  Sergey N Semenov; Albert J Markvoort; Wouter B L Gevers; Aigars Piruska; Tom F A de Greef; Wilhelm T S Huck
Journal:  Biophys J       Date:  2013-08-20       Impact factor: 4.033

8.  Ultrasensitivity of the Bacillus subtilis sporulation decision.

Authors:  Jatin Narula; Seram N Devi; Masaya Fujita; Oleg A Igoshin
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-19       Impact factor: 11.205

9.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

10.  Controlling enzymatic action in living cells with a kinase-inducible bimolecular switch.

Authors:  Vedangi Sample; Qiang Ni; Sohum Mehta; Takanari Inoue; Jin Zhang
Journal:  ACS Chem Biol       Date:  2012-10-26       Impact factor: 5.100

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