Genome‐scale engineering for systems and synthetic biology

KM Esvelt, HH Wang - Molecular systems biology, 2013 - embopress.org
Genome‐modification technologies enable the rational engineering and perturbation of
biological systems. Historically, these methods have been limited to gene insertions or …

Biosynthetic pathway and metabolic engineering of succinic acid

X Liu, G Zhao, S Sun, C Fan, X Feng… - … in Bioengineering and …, 2022 - frontiersin.org
Succinic acid, a dicarboxylic acid produced as an intermediate of the tricarboxylic acid (TCA)
cycle, is one of the most important platform chemicals for the production of various high …

A periplasmic phospholipase that maintains outer membrane lipid asymmetry in Pseudomonas aeruginosa

RL Guest, MJ Lee, W Wang… - Proceedings of the …, 2023 - National Acad Sciences
The outer membrane of Gram-negative bacteria is unique in both structure and function. The
surface-exposed outer leaflet is composed of lipopolysaccharide, while the inner leaflet is …

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

MH Larson, LA Gilbert, X Wang, WA Lim… - Nature protocols, 2013 - nature.com
Sequence-specific control of gene expression on a genome-wide scale is an important
approach for understanding gene functions and for engineering genetic regulatory systems …

Protein interaction networks revealed by proteome coevolution

Q Cong, I Anishchenko, S Ovchinnikov, D Baker - Science, 2019 - science.org
Residue-residue coevolution has been observed across a number of protein-protein
interfaces, but the extent of residue coevolution between protein families on the whole …

Genomically recoded organisms expand biological functions

MJ Lajoie, AJ Rovner, DB Goodman, HR Aerni… - science, 2013 - science.org
We describe the construction and characterization of a genomically recoded organism
(GRO). We replaced all known UAG stop codons in Escherichia coli MG1655 with …

Mechanistic links between cellular trade-offs, gene expression, and growth

AY Weiße, DA Oyarzún, V Danos… - Proceedings of the …, 2015 - National Acad Sciences
Intracellular processes rarely work in isolation but continually interact with the rest of the cell.
In microbes, for example, we now know that gene expression across the whole genome …

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

A Espah Borujeni, AS Channarasappa… - Nucleic acids …, 2014 - academic.oup.com
The ribosome's interactions with mRNA govern its translation rate and the effects of post-
transcriptional regulation. Long, structured 5′ untranslated regions (5′ UTRs) are …

The molecular diversity of adaptive convergence

O Tenaillon, A Rodríguez-Verdugo, RL Gaut… - Science, 2012 - science.org
To estimate the number and diversity of beneficial mutations, we experimentally evolved 115
populations of Escherichia coli to 42.2° C for 2000 generations and sequenced one genome …

Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a phloem-feeding insect

GM Bennett, NA Moran - Genome biology and evolution, 2013 - academic.oup.com
Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning
nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets …