Genetic toolkits for engineering Rhodococcus species with versatile applications

Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA

(2021) Divya Singhi et al.   MICROBIOLOGY-SGM

Engineering Tools for the Development of Recombinant Lactic Acid Bacteria

(2020) Sung Won Cho et al.   Biotechnology Journal

Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis

(2020) Sarah Thorwall et al.   Nature Chemical Biology

Development of a Rhodococcus opacus Cell Factory for Valorizing Lignin to Muconate

(2020) Chenggu Cai et al.   ACS Sustainable Chemistry & Engineering

Mechanism of the oxidative stress‐mediated increase in lipid accumulation by the bacterium, R. opacus PD630: Experimental analysis and genome‐scale metabolic modeling

(2020) Archanaa Sundararaghavan et al.   BIOTECHNOLOGY AND BIOENGINEERING

Synthetic promoter design in Escherichia coli based on a deep generative network

(2020) Ye Wang et al.   NUCLEIC ACIDS RESEARCH

Developing an endogenous quorum-sensing based CRISPRi circuit for autonomous and tunable dynamic regulation of multiple targets in Streptomyces

(2020) Jinzhong Tian et al.   NUCLEIC ACIDS RESEARCH

Biotechnology of Rhodococcus for the production of valuable compounds

(2020) Martina Cappelletti et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A deep learning approach to programmable RNA switches

(2020) Nicolaas M. Angenent-Mari et al.   Nature Communications

Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering

(2019) Kyeong Rok Choi et al.   TRENDS IN BIOTECHNOLOGY

Systematic evasion of the restriction-modification barrier in bacteria

(2019) Christopher D. Johnston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism‐Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining

(2019) Shangxian Xie et al.   Advanced Science

Engineering of an oleaginous bacterium for the production of fatty acids and fuels

(2019) Hye Mi Kim et al.   Nature Chemical Biology

Construction of genetic logic gates based on the T7 RNA polymerase expression system in Rhodococcus opacus PD630

(2019) Drew DeLorenzo et al.   ACS Synthetic Biology

Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds

(2019) Winston E. Anthony et al.   Biotechnology for Biofuels

Rhodococcus as A Versatile Biocatalyst in Organic Synthesis

(2019) Busch et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis

(2019) Jieying Deng et al.   METABOLIC ENGINEERING

Dynamic gene expression engineering as a tool in pathway engineering

(2019) Xiaolin Shen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Optimization of the Expression of Nitrilase from Alcaligenes denitrificans in Rhodococcus rhodochrous to Improve the Efficiency of Biocatalytic Synthesis of Ammonium Acrylate

(2019) K. V. Lavrov et al.   APPLIED BIOCHEMISTRY AND MICROBIOLOGY

A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH

(2019) Youxiang Liang et al.   METABOLIC ENGINEERING

Bioconversion of renewable feedstocks by Rhodococcus opacus

(2019) Anamika Chatterjee et al.   CURRENT OPINION IN BIOTECHNOLOGY

Isolation of two plasmids, pRET1100 and pRET1200, from Rhodococcus erythropolis IAM1400 and construction of a Rhodococcus – Escherichia coli shuttle vector

(2018) Ei-Tora Yamamura   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Application of methylation in improving plasmid transformation into Helicobacter pylori

(2018) Huilin Zhao et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Escherichia coli as a host for metabolic engineering

(2018) Sammy Pontrelli et al.   METABOLIC ENGINEERING

Core element characterization of Rhodococcus promoters and development of a promoter-RBS mini-pool with different activity levels for efficient gene expression

(2018) Song Jiao et al.   New Biotechnology

Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis

(2018) Mohammad Tajparast et al.   PLoS One

New cblA gene participates in regulation of cobalt-dependent transcription of nitrile hydratase genes in Rhodococcus rhodochrous

(2018) Konstantin V. Lavrov et al.   RESEARCH IN MICROBIOLOGY

Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630

(2018) Drew M. DeLorenzo et al.   ACS Synthetic Biology

Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus

(2018) William R. Henson et al.   METABOLIC ENGINEERING

Conjugational delivery of chromosomal integrative constructs for gene expression in the carbendazim-degrading Rhodococcus erythropolis D-1

(2018) Yang Tao et al.   ANNALS OF MICROBIOLOGY

Overexpression of epoxide hydrolase in Rhodococcus ruber with high robustness for the synthesis of chiral epichlorohydrin

(2018) Youxiang Liang et al.   PROCESS BIOCHEMISTRY

Rewiring neutral lipids production for the de novo synthesis of wax esters in Rhodococcus opacus PD630

(2017) Mariana P. Lanfranconi et al.   JOURNAL OF BIOTECHNOLOGY

CRISPR/Cas9-coupled recombineering for metabolic engineering of Corynebacterium glutamicum

(2017) Jae Sung Cho et al.   METABOLIC ENGINEERING

Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1

(2017) Antonio Juarez et al.   Microbial Cell Factories

Functional differentiation of 3-ketosteroid Δ1-dehydrogenase isozymes in Rhodococcus ruber strain Chol-4

(2017) Govinda Guevara et al.   Microbial Cell Factories

Construction of a BioBrick™ compatible vector system for Rhodococcus

(2017) James Ellinger et al.   PLASMID

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

(2017) Drew M. DeLorenzo et al.   ACS Synthetic Biology

CRISPR/Cas9 in Genome Editing and Beyond

(2016) Haifeng Wang et al.   Annual Review of Biochemistry

CRISPR technologies for bacterial systems: Current achievements and future directions

(2016) Kyeong Rok Choi et al.   BIOTECHNOLOGY ADVANCES

Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances

(2016) James M. Wagner et al.   FUNGAL GENETICS AND BIOLOGY

Ammonium acrylate biomanufacturing by an engineered Rhodococcus ruber with nitrilase overexpression and double-knockout of nitrile hydratase and amidase

(2016) Jizhe Sun et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Development of a genetically engineered Escherichia coli strain for plasmid transformation in Corynebacterium glutamicum

(2016) Hedan Li et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Localization of Low Copy Number Plasmid pRC4 in Replicating Rod and Non-Replicating Cocci Cells of Rhodococcus erythropolis PR4

(2016) Divya Singhi et al.   PLoS One

The glyoxylate shunt is essential for CO2-requiring oligotrophic growth of Rhodococcus erythropolis N9T-4

(2015) Takanori Yano et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

(2015) Mohammad Tajparast et al.   BMC Systems Biology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons

(2015) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Induction and carbon catabolite repression of phenol degradation genes in Rhodococcus erythropolis and Rhodococcus jostii

(2014) Juraj Szőköl et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

VirS, an OmpR/PhoB subfamily response regulator, is required for activation of vapA gene expression in Rhodococcus equi

(2014) Tsutomu Kakuda et al.   BMC MICROBIOLOGY

Enhanced Translocation and Growth of Rhodococcus erythropolis PR4 in the Alkane Phase of Aqueous-Alkane Two Phase Cultures Were Mediated by GroEL2 Overexpression

(2014) Hayato Takihara et al.   MICROBES AND ENVIRONMENTS

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

(2014) Esteban Martínez-García et al.   Microbial Cell Factories

Expression of acylamidase gene in Rhodococcus erythropolis strains

(2014) K. V. Lavrov et al.   RUSSIAN JOURNAL OF GENETICS

Saccharification of Cellulose by Recombinant Rhodococcus opacus PD630 Strains

(2013) Stephan Hetzler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization and engineering of an o-xylene dioxygenase for biocatalytic applications

(2013) Dockyu Kim et al.   BIORESOURCE TECHNOLOGY

Engineering xylose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production

(2013) Kazuhiko Kurosawa et al.   Biotechnology for Biofuels

Survival of GFP-tagged Rhodococcus sp. D310-1 in chlorimuron-ethyl-contaminated soil and its effects on the indigenous microbial community

(2013) Minghua Xiong et al.   JOURNAL OF HAZARDOUS MATERIALS

Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes

(2013) Theresa Siegl et al.   METABOLIC ENGINEERING

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

(2013) Matthew H Larson et al.   Nature Protocols

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

(2013) Stephan Binder et al.   NUCLEIC ACIDS RESEARCH

Engineering of a Xylose Metabolic Pathway in Rhodococcus Strains

(2012) Xiaochao Xiong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

LplR, a Repressor Belonging to the TetR Family, Regulates Expression of the l-Pantoyl Lactone Dehydrogenase Gene in Rhodococcus erythropolis

(2012) Dayong Si et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of Cj1051c as a Major Determinant for the Restriction Barrier of Campylobacter jejuni Strain NCTC11168

(2012) Jeffrey P. Holt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Promoter engineering: Recent advances in controlling transcription at the most fundamental level

(2012) John Blazeck et al.   Biotechnology Journal

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries

(2012) Kuk-Ki Hong et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Identification of a methanol-inducible promoter from Rhodococcus erythropolis PR4 and its use as an expression vector

(2012) Yusuke Kagawa et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition

(2012) Yuchao Ma et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Molecular characterization of three 3-ketosteroid-Δ1-dehydrogenase isoenzymes of Rhodococcus ruber strain Chol-4

(2012) Laura Fernández de las Heras et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Construction of a novel sacB-based system for marker-free gene deletion in Corynebacterium glutamicum

(2011) Yanzhen Tan et al.   PLASMID

Analyses of both thealkBGene Transcriptional Start Site andalkBPromoter-Inducing Properties ofRhodococcussp. Strain BCP1 Grown onn-Alkanes

(2010) M. Cappelletti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New Vector System for Random, Single-Step Integration of Multiple Copies of DNA into the Rhodococcus Genome

(2010) K. I. Sallam et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production

(2010) Kazuhiko Kurosawa et al.   JOURNAL OF BIOTECHNOLOGY

Identification of nitrile hydratase-producing Rhodococcus ruber TH and characterization of an amiE-negative mutant

(2009) Yuchao Ma et al.   BIORESOURCE TECHNOLOGY

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

Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY

Biodegradation potential of the genus Rhodococcus

(2008) L MARTINKOVA et al.   ENVIRONMENT INTERNATIONAL

Expression of Rhodococcus opacus alkB genes in anhydrous organic solvents

(2008) Yuka Sameshima et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Improvement of bacterial transformation efficiency using plasmid artificial modification

(2008) Kazumasa Yasui et al.   NUCLEIC ACIDS RESEARCH

A novel method to generate unmarked gene deletions in the intracellular pathogen Rhodococcus equi using 5-fluorocytosine conditional lethality

(2008) R. van der Geize et al.   NUCLEIC ACIDS RESEARCH