Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology

P Dvořák, PI Nikel, J Damborský, V de Lorenzo - Biotechnology advances, 2017 - Elsevier
Elimination or mitigation of the toxic effects of chemical waste released to the environment
by industrial and urban activities relies largely on the catalytic activities of microorganisms …

Metabolic pathway balancing and its role in the production of biofuels and chemicals

JA Jones, ÖD Toparlak, MAG Koffas - Current opinion in biotechnology, 2015 - Elsevier
Highlights•Rational and modern approaches for metabolic pathway engineering.•Tailor-
made cell factories for biofuel and value-added chemical production.•Synthetic and systems …

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

PLH Vo, C Ronda, SE Klompe, EE Chen, C Acree… - Nature …, 2021 - nature.com
Existing technologies for site-specific integration of kilobase-sized DNA sequences in
bacteria are limited by low efficiency, a reliance on recombination, the need for multiple …

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

A Gupta, IMB Reizman, CR Reisch, KLJ Prather - Nature biotechnology, 2017 - nature.com
Metabolic engineering of microorganisms to produce desirable products on an industrial
scale can result in unbalanced cellular metabolic networks that reduce productivity and …

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

L Cui, A Vigouroux, F Rousset, H Varet… - Nature …, 2018 - nature.com
High-throughput CRISPR-Cas9 screens have recently emerged as powerful tools to
decipher gene functions and genetic interactions. Here we use a genome-wide library of …

Acoustic biosensors for ultrasound imaging of enzyme activity

A Lakshmanan, Z Jin, SP Nety, DP Sawyer… - Nature chemical …, 2020 - nature.com
Visualizing biomolecular and cellular processes inside intact living organisms is a major
goal of chemical biology. However, existing molecular biosensors, based primarily on …

Consequences of Cas9 cleavage in the chromosome of Escherichia coli

L Cui, D Bikard - Nucleic acids research, 2016 - academic.oup.com
The RNA-guided Cas9 nuclease from CRISPR-Cas systems has emerged as a powerful
biotechnological tool. The specificity of Cas9 can be reprogrammed to cleave desired …

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

W Jiang, X Zhao, T Gabrieli, C Lou, Y Ebenstein… - Nature …, 2015 - nature.com
The cloning of long DNA segments, especially those containing large gene clusters, is of
particular importance to synthetic and chemical biology efforts for engineering organisms …

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

F Rousset, L Cui, E Siouve, C Becavin… - PLoS …, 2018 - journals.plos.org
High-throughput genetic screens are powerful methods to identify genes linked to a given
phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be …

[HTML][HTML] Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome

KN Lam, P Spanogiannopoulos, P Soto-Perez… - Cell Reports, 2021 - cell.com
Mechanistic insights into the role of the human microbiome in the predisposition to and
treatment of disease are limited by the lack of methods to precisely add or remove microbial …