Literature DB >> 25849635

Quantifying cellular capacity identifies gene expression designs with reduced burden.

Francesca Ceroni1, Rhys Algar1, Guy-Bart Stan1, Tom Ellis1.   

Abstract

Heterologous gene expression can be a significant burden for cells. Here we describe an in vivo monitor that tracks changes in the capacity of Escherichia coli in real time and can be used to assay the burden imposed by synthetic constructs and their parts. We identify construct designs with reduced burden that predictably outperformed less efficient designs, despite having equivalent output.

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Year:  2015        PMID: 25849635     DOI: 10.1038/nmeth.3339

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  43 in total

1.  Design of the linkers which effectively separate domains of a bifunctional fusion protein.

Authors:  R Arai; H Ueda; A Kitayama; N Kamiya; T Nagamune
Journal:  Protein Eng       Date:  2001-08

2.  Interdependence of cell growth and gene expression: origins and consequences.

Authors:  Matthew Scott; Carl W Gunderson; Eduard M Mateescu; Zhongge Zhang; Terence Hwa
Journal:  Science       Date:  2010-11-19       Impact factor: 47.728

3.  Causes and effects of N-terminal codon bias in bacterial genes.

Authors:  Daniel B Goodman; George M Church; Sriram Kosuri
Journal:  Science       Date:  2013-09-26       Impact factor: 47.728

4.  Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels.

Authors:  J Vind; M A Sørensen; M D Rasmussen; S Pedersen
Journal:  J Mol Biol       Date:  1993-06-05       Impact factor: 5.469

5.  Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate.

Authors:  Javier Carrera; Guillermo Rodrigo; Vijai Singh; Boris Kirov; Alfonso Jaramillo
Journal:  Biotechnol J       Date:  2011-06-16       Impact factor: 4.677

Review 6.  Synthetic biology--putting engineering into biology.

Authors:  Matthias Heinemann; Sven Panke
Journal:  Bioinformatics       Date:  2006-09-05       Impact factor: 6.937

Review 7.  Synonymous but not the same: the causes and consequences of codon bias.

Authors:  Joshua B Plotkin; Grzegorz Kudla
Journal:  Nat Rev Genet       Date:  2010-11-23       Impact factor: 53.242

Review 8.  Effects of genetic variation on the E. coli host-circuit interface.

Authors:  Stefano Cardinale; Marcin Pawel Joachimiak; Adam Paul Arkin
Journal:  Cell Rep       Date:  2013-07-18       Impact factor: 9.423

9.  The role of codon selection in regulation of translation efficiency deduced from synthetic libraries.

Authors:  Sivan Navon; Yitzhak Pilpel
Journal:  Genome Biol       Date:  2011-02-01       Impact factor: 13.583

10.  Dissecting specific and global transcriptional regulation of bacterial gene expression.

Authors:  Luca Gerosa; Karl Kochanowski; Matthias Heinemann; Uwe Sauer
Journal:  Mol Syst Biol       Date:  2013-04-16       Impact factor: 11.429

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  122 in total

Review 1.  Predictive biology: modelling, understanding and harnessing microbial complexity.

Authors:  Allison J Lopatkin; James J Collins
Journal:  Nat Rev Microbiol       Date:  2020-05-29       Impact factor: 60.633

2.  Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law.

Authors:  M Carbonell-Ballestero; E Garcia-Ramallo; R Montañez; C Rodriguez-Caso; J Macía
Journal:  Nucleic Acids Res       Date:  2015-12-09       Impact factor: 16.971

3.  Modelling and measuring intracellular competition for finite resources during gene expression.

Authors:  Renana Sabi; Tamir Tuller
Journal:  J R Soc Interface       Date:  2019-05-31       Impact factor: 4.118

4.  A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks.

Authors:  Andras Gyorgy
Journal:  Methods Mol Biol       Date:  2021

5.  Prediction of Cellular Burden with Host-Circuit Models.

Authors:  Evangelos-Marios Nikolados; Andrea Y Weiße; Diego A Oyarzún
Journal:  Methods Mol Biol       Date:  2021

Review 6.  Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Authors:  Bryan A Bartley; Kyung Kim; J Kyle Medley; Herbert M Sauro
Journal:  Biophys J       Date:  2017-03-28       Impact factor: 4.033

7.  Engineering Sensors for Gene Expression Burden.

Authors:  Alice Boo; Francesca Ceroni
Journal:  Methods Mol Biol       Date:  2021

8.  The paths of mortality: how understanding the biology of aging can help explain systems behavior of single cells.

Authors:  Matthew M Crane; Matt Kaeberlein
Journal:  Curr Opin Syst Biol       Date:  2017-12-06

Review 9.  Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.

Authors:  Xinyun Cao; Joshua J Hamilton; Ophelia S Venturelli
Journal:  Biochemistry       Date:  2018-11-20       Impact factor: 3.162

10.  Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli.

Authors:  Bradley Walters Biggs; Chin Giaw Lim; Kristen Sagliani; Smriti Shankar; Gregory Stephanopoulos; Marjan De Mey; Parayil Kumaran Ajikumar
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-07       Impact factor: 11.205

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