Literature DB >> 26752768

Predictable tuning of protein expression in bacteria.

Mads T Bonde1, Margit Pedersen1, Michael S Klausen1, Sheila I Jensen1, Tune Wulff1, Scott Harrison1, Alex T Nielsen1, Markus J Herrgård1, Morten O A Sommer1.   

Abstract

We comprehensively assessed the contribution of the Shine-Dalgarno sequence to protein expression and used the data to develop EMOPEC (Empirical Model and Oligos for Protein Expression Changes; http://emopec.biosustain.dtu.dk). EMOPEC is a free tool that makes it possible to modulate the expression level of any Escherichia coli gene by changing only a few bases. Measured protein levels for 91% of our designed sequences were within twofold of the desired target level.

Entities:  

Mesh：

Substances：

Year:  2016        PMID： 26752768     DOI： 10.1038/nmeth.3727

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


  33 in total

1.  Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein.

Authors:  Nathan C Shaner; Robert E Campbell; Paul A Steinbach; Ben N G Giepmans; Amy E Palmer; Roger Y Tsien
Journal:  Nat Biotechnol       Date:  2004-11-21       Impact factor: 54.908

2.  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

3.  The ribosome binding site calculator.

Authors:  Howard M Salis
Journal:  Methods Enzymol       Date:  2011       Impact factor: 1.600

4.  Quantitative estimation of activity and quality for collections of functional genetic elements.

Authors:  Vivek K Mutalik; Joao C Guimaraes; Guillaume Cambray; Quynh-Anh Mai; Marc Juul Christoffersen; Lance Martin; Ayumi Yu; Colin Lam; Cesar Rodriguez; Gaymon Bennett; Jay D Keasling; Drew Endy; Adam P Arkin
Journal:  Nat Methods       Date:  2013-03-10       Impact factor: 28.547

5.  A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion.

Authors:  Morten O A Sommer; George M Church; Gautam Dantas
Journal:  Mol Syst Biol       Date:  2010-04-13       Impact factor: 11.429

6.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

7.  Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips.

Authors:  Juri Rappsilber; Matthias Mann; Yasushi Ishihama
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

8.  Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant.

Authors:  P P Cherepanov; W Wackernagel
Journal:  Gene       Date:  1995-05-26       Impact factor: 3.688

9.  ViennaRNA Package 2.0.

Authors:  Ronny Lorenz; Stephan H Bernhart; Christian Höner Zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal:  Algorithms Mol Biol       Date:  2011-11-24       Impact factor: 1.405

10.  Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria.

Authors:  Iman Farasat; Manish Kushwaha; Jason Collens; Michael Easterbrook; Matthew Guido; Howard M Salis
Journal:  Mol Syst Biol       Date:  2014-06-21       Impact factor: 11.429
View more
  34 in total

Review 1.  Compartmentalized partnered replication for the directed evolution of genetic parts and circuits.

Authors:  Zhanar Abil; Jared W Ellefson; Jimmy D Gollihar; Ella Watkins; Andrew D Ellington
Journal:  Nat Protoc       Date:  2017-11-09       Impact factor: 13.491

Review 2.  Recent advances in genetic engineering tools based on synthetic biology.

Authors:  Jun Ren; Jingyu Lee; Dokyun Na
Journal:  J Microbiol       Date:  2020-01-02       Impact factor: 3.422

3.  Improved sgRNA design in bacteria via genome-wide activity profiling.

Authors:  Jiahui Guo; Tianmin Wang; Changge Guan; Bing Liu; Cheng Luo; Zhen Xie; Chong Zhang; Xin-Hui Xing
Journal:  Nucleic Acids Res       Date:  2018-08-21       Impact factor: 16.971

4.  QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity.

Authors:  Goro Terai; Kiyoshi Asai
Journal:  Nucleic Acids Res       Date:  2022-07-22       Impact factor: 19.160

Review 5.  The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.

Authors:  Jin-Der Wen; Syue-Ting Kuo; Hsin-Hung David Chou
Journal:  RNA Biol       Date:  2020-12-21       Impact factor: 4.652

Review 6.  Prospects of microbial cell factories developed through systems metabolic engineering.

Authors:  Martin Gustavsson; Sang Yup Lee
Journal:  Microb Biotechnol       Date:  2016-07-20       Impact factor: 5.813

Review 7.  High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives.

Authors:  Baolei Jia; Che Ok Jeon
Journal:  Open Biol       Date:  2016-08       Impact factor: 6.411

Review 8.  Quality Control of Orphaned Proteins.

Authors:  Szymon Juszkiewicz; Ramanujan S Hegde
Journal:  Mol Cell       Date:  2018-08-02       Impact factor: 17.970

Review 9.  Learning the Regulatory Code of Gene Expression.

Authors:  Jan Zrimec; Filip Buric; Mariia Kokina; Victor Garcia; Aleksej Zelezniak
Journal:  Front Mol Biosci       Date:  2021-06-10

10.  Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability.

Authors:  Nikolay Martyushenko; Sigurd Hagen Johansen; Cheol-Min Ghim; Eivind Almaas
Journal:  BMC Syst Biol       Date:  2016-06-06
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.