ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida

Characterizing the portability of phage-encoded homologous recombination proteins

(2021) Gabriel T. Filsinger et al.   Nature Chemical Biology

A navigation guide of synthetic biology tools for Pseudomonas putida

(2021) Maria Martin-Pascual et al.   BIOTECHNOLOGY ADVANCES

Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a

(2020) Sjoerd C A Creutzburg et al.   NUCLEIC ACIDS RESEARCH

Recombineering for Genetic Engineering of Natural Product Biosynthetic Pathways

(2020) Muhammad Nazeer Abbasi et al.   TRENDS IN BIOTECHNOLOGY

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

(2020) Christos Batianis et al.   Microbial Biotechnology

An engineered ScCas9 with broad PAM range and high specificity and activity

(2020) Pranam Chatterjee et al.   NATURE BIOTECHNOLOGY

Improved bacterial recombineering by parallelized protein discovery

(2020) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Safeguards for Safety-by-design: So Close Yet So Far

(2020) Enrique Asin-Garcia et al.   TRENDS IN BIOTECHNOLOGY

SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards

(2020) Stamatios G. Damalas et al.   Microbial Biotechnology

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

(2020) Patricia Calero et al.   Nature Communications

A RAGE Based Strategy for the Genome Engineering of the Human Respiratory Pathogen Mycoplasma pneumoniae

(2020) Luis Garcia-Morales et al.   ACS Synthetic Biology

Accelerated genome engineering of Pseudomonas putida by I-Sce I―mediated recombination and CRISPR-Cas9 counterselection

(2019) Nicolas T. Wirth et al.   Microbial Biotechnology

A rapid and versatile tool for genomic engineering in Lactococcus lactis

(2019) Tingting Guo et al.   Microbial Cell Factories

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

Defining the core essential genome of Pseudomonas aeruginosa

(2019) Bradley E. Poulsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis of Recoded Bacterial Genomes toward Bespoke Biocatalysis

(2019) Pablo I. Nikel   TRENDS IN BIOTECHNOLOGY

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

(2019) Tomas Aparicio et al.   ENVIRONMENTAL MICROBIOLOGY

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans -metabolism

(2018) Pablo I. Nikel et al.   METABOLIC ENGINEERING

Efficient and Scalable Precision Genome Editing in Staphylococcus aureus through Conditional Recombineering and CRISPR/Cas9-Mediated Counterselection

(2018) Kelsi Penewit et al.   mBio

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

(2018) Patricia Calero et al.   Microbial Biotechnology

Improved Thermotolerance of Genome-Reduced Pseudomonas putida EM42 Enables Effective Functioning of the PL /c I857 System

(2018) Tomás Aparicio et al.   Biotechnology Journal

Crystal structure of the Redβ C-terminal domain in complex with λ Exonuclease reveals an unexpected homology with λ Orf and an interaction with Escherichia coli single stranded DNA binding protein

(2018) Brian J Caldwell et al.   NUCLEIC ACIDS RESEARCH

Minimal PAM specificity of a highly similar SpCas9 ortholog

(2018) Pranam Chatterjee et al.   Science Advances

Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA

(2017) Yu Heng Lau et al.   NUCLEIC ACIDS RESEARCH

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

CRISPR/Cas9-Based Counterselection Boosts Recombineering Efficiency in Pseudomonas putida

(2017) Tomás Aparicio et al.   Biotechnology Journal

Analysis of RecA-independent recombination events between short direct repeats related to a genomic island and to a plasmid in Escherichia coli K12

(2017) María F. Azpiroz et al.   PeerJ

A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

(2017) Deirdre E. Ricaurte et al.   Microbial Biotechnology

CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency

(2017) Dongdong Zhao et al.   Scientific Reports

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

(2016) Eugeni Belda et al.   ENVIRONMENTAL MICROBIOLOGY

Defining synonymous codon compression schemes by genome recoding

(2016) Kaihang Wang et al.   NATURE

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness

(2016) Miguel Angel Martínez et al.   TRENDS IN MICROBIOLOGY

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements

(2016) Natalie Jing Ma et al.   Cell Systems

Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species

(2016) Ming Song et al.   Scientific Reports

A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35

(2015) Zhaopeng Sun et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

CRISPR-Based Technologies and the Future of Food Science

(2015) Kurt Selle et al.   JOURNAL OF FOOD SCIENCE

Recoded organisms engineered to depend on synthetic amino acids

(2015) Alexis J. Rovner et al.   NATURE

Biocontainment of genetically modified organisms by synthetic protein design

(2015) Daniel J. Mandell et al.   NATURE

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination

(2015) Gur Pines et al.   ACS Synthetic Biology

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

(2014) Gürkan Korkmaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA

(2014) Ryan R Gallagher et al.   Nature Protocols

Total Synthesis of a Functional Designer Eukaryotic Chromosome

(2014) N. Annaluru et al.   SCIENCE

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

(2013) Stephan Binder et al.   NUCLEIC ACIDS RESEARCH

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

Industrial biotechnology of Pseudomonas putida and related species

(2012) Ignacio Poblete-Castro et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Stop codons in bacteria are not selectively equivalent

(2012) Inna S Povolotskaya et al.   Biology Direct

CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection

(2012) David Bikard et al.   Cell Host & Microbe

High efficiency recombineering in lactic acid bacteria

(2012) Jan-Peter van Pijkeren et al.   NUCLEIC ACIDS RESEARCH

Reprogramming the genetic code

(2011) Jason W Chin   EMBO JOURNAL

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

(2011) P. Sobetzko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Identification of conditionally essential genes for growth ofPseudomonas putidaKT2440 on minimal medium through the screening of a genome-wide mutant library

(2010) M. Antonia Molina-Henares et al.   ENVIRONMENTAL MICROBIOLOGY

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

High-resolution DNA melting analysis: advancements and limitations

(2008) Carl T. Wittwer   HUMAN MUTATION

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology