scholarly journals Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase

2021 ◽  
Author(s):  
Timothy A. Coulther ◽  
Moritz Pott ◽  
Cathleen Zeymer ◽  
Donald Hilvert ◽  
Mary Jo Ondrechen
Keyword(s):  
Laboratory Evolution ◽  
Electrostatic Coupling

scholarly journals Engineering improved ethylene production: Leveraging systems Biology and adaptive laboratory evolution

2021 ◽  
Author(s):  
Sophie Vaud ◽  
Nicole Pearcy ◽  
Marko Hanževački ◽  
Alexander M.W. Van Hagen ◽  
Salah Abdelrazig ◽  
...  
Keyword(s):  
Systems Biology ◽  
Ethylene Production ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution

scholarly journals Sense codon reassignment enables viral resistance and encoded polymer synthesis

Science ◽  
2021 ◽  
Vol 372 (6546) ◽  
pp. 1057-1062
Author(s):  
Wesley E. Robertson ◽  
Louise F. H. Funke ◽  
Daniel de la Torre ◽  
Julius Fredens ◽  
Thomas S. Elliott ◽  
...  
Keyword(s):  
Stop Codon ◽  
Synonymous Codon ◽  
Viral Resistance ◽  
Release Factor ◽  
Codon Reassignment ◽  
Efficient Synthesis ◽  
Noncanonical Amino Acids ◽  
Laboratory Evolution ◽  
Transfer Rnas ◽  
Sense Codon

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)—making their cognate codons unreadable—might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.

Adaptive laboratory evolution of the fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for improved solvent tolerance

2021 ◽  
Author(s):  
Vaibhav Srivastava ◽  
Ruth Amanna ◽  
Stephen J.L. Rowden ◽  
Shinjinee Sengupta ◽  
Swati Madhu ◽  
...  
Keyword(s):  
Synechococcus Elongatus ◽  
Solvent Tolerance ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution ◽  
Fast Growing

scholarly journals Adaptive Laboratory Evolution of Cupriavidus necator H16 for Carbon Co-Utilization with Glycerol

2019 ◽  
Vol 20 (22) ◽  
pp. 5737 ◽  
Author(s):  
Miriam González-Villanueva ◽  
Hemanshi Galaiya ◽  
Paul Staniland ◽  
Jessica Staniland ◽  
Ian Savill ◽  
...  
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Carbon Sources ◽  
Strain Engineering ◽  
Cupriavidus Necator ◽  
Superior Performance ◽  
Wild Type ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution ◽  
Cupriavidus Necator H16

Cupriavidus necator H16 is a non-pathogenic Gram-negative betaproteobacterium that can utilize a broad range of renewable heterotrophic resources to produce chemicals ranging from polyhydroxybutyrate (biopolymer) to alcohols, alkanes, and alkenes. However, C. necator H16 utilizes carbon sources to different efficiency, for example its growth in glycerol is 11.4 times slower than a favorable substrate like gluconate. This work used adaptive laboratory evolution to enhance the glycerol assimilation in C. necator H16 and identified a variant (v6C6) that can co-utilize gluconate and glycerol. The v6C6 variant has a specific growth rate in glycerol 9.5 times faster than the wild-type strain and grows faster in mixed gluconate–glycerol carbon sources compared to gluconate alone. It also accumulated more PHB when cultivated in glycerol medium compared to gluconate medium while the inverse is true for the wild-type strain. Through genome sequencing and expression studies, glycerol kinase was identified as the key enzyme for its improved glycerol utilization. The superior performance of v6C6 in assimilating pure glycerol was extended to crude glycerol (sweetwater) from an industrial fat splitting process. These results highlight the robustness of adaptive laboratory evolution for strain engineering and the versatility and potential of C. necator H16 for industrial waste glycerol valorization.

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling

2005 ◽  
Vol 1 (6) ◽  
pp. 1176-1184 ◽  
Author(s):  
Teodoro Laino ◽  
Fawzi Mohamed ◽  
Alessandro Laio ◽  
Michele Parrinello
Keyword(s):  
Real Space ◽  
Electrostatic Coupling

scholarly journals Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting

2016 ◽  
Vol 29 (9) ◽  
pp. 355-366 ◽  
Author(s):  
Richard Obexer ◽  
Moritz Pott ◽  
Cathleen Zeymer ◽  
Andrew D. Griffiths ◽  
Donald Hilvert
Keyword(s):  
Laboratory Evolution ◽  
Droplet Sorting
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