4.7 Review

Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms

Related references

Note: Only part of the references are listed.
Review Genetics & Heredity

Cell-free gene expression: an expanded repertoire of applications

Adam D. Silverman et al.

NATURE REVIEWS GENETICS (2020)

Article Biotechnology & Applied Microbiology

Induced heterologous expression of the arginine deiminase pathway promotes growth advantages in the strict anaerobe Acetobacterium woodii

Matthias H. Beck et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2020)

Article Biotechnology & Applied Microbiology

Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways

Antje Krueger et al.

METABOLIC ENGINEERING (2020)

Article Biochemistry & Molecular Biology

In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design

Ashty S. Karim et al.

NATURE CHEMICAL BIOLOGY (2020)

Review Biochemical Research Methods

Pollution to products: recycling of 'above ground' carbon by gas fermentation

Michael Kopke et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination

Peng-Fei Xia et al.

ACS SYNTHETIC BIOLOGY (2020)

Review Biotechnology & Applied Microbiology

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

Charlotte Anne Vees et al.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Review Biotechnology & Applied Microbiology

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

Kyeong Rok Choi et al.

TRENDS IN BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum

Florence J. Annan et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii

Gabriele Philipps et al.

BIOTECHNOLOGY FOR BIOFUELS (2019)

Review Microbiology

CRISPR Genome Editing Systems in the Genus Clostridium: a Timely Advancement

Kathleen N. McAllister et al.

JOURNAL OF BACTERIOLOGY (2019)

Review Biotechnology & Applied Microbiology

Butanol production from lignocellulosic biomass: revisiting fermentation performance indicators with exploratory data analysis

Cansu Birgen et al.

BIOTECHNOLOGY FOR BIOFUELS (2019)

Review Biotechnology & Applied Microbiology

New Horizons in Acetogenic Conversion of One-Carbon Substrates and Biological Hydrogen Storage

Volker Mueler

TRENDS IN BIOTECHNOLOGY (2019)

Article Biochemical Research Methods

RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium

Ines C. Canadas et al.

ACS SYNTHETIC BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems

Sung Sun Yim et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

Article Biochemical Research Methods

Genome Engineering of Eubacterium limosum Using Expanded Genetic Tools and the CRISPR-Cas9 System

Jongoh Shin et al.

ACS SYNTHETIC BIOLOGY (2019)

Review Biotechnology & Applied Microbiology

Current status and applications of genome-scale metabolic models

Changdai Gu et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates

Quentin M. Dudley et al.

SYNTHETIC BIOLOGY (2019)

Review Cell Biology

Protein folding at extreme temperatures: Current issues

Georges Feller

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2018)

Review Biochemical Research Methods

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas

Christopher M. Humphreys et al.

CURRENT OPINION IN BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Codon harmonization - going beyond the speed limit for protein expression

Charlotte Mignon et al.

FEBS LETTERS (2018)

Article Biotechnology & Applied Microbiology

Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)

Benjamin M. Woolston et al.

METABOLIC ENGINEERING (2018)

Review Microbiology

Recent Developments of the Synthetic Biology Toolkit for Clostridium

Rochelle C. Joseph et al.

FRONTIERS IN MICROBIOLOGY (2018)

Article Microbiology

Deaminase-mediated multiplex genome editing in Escherichia coli

Satomi Banno et al.

NATURE MICROBIOLOGY (2018)

Review Agricultural Engineering

Lignin depolymerization and utilization by bacteria

Rong Xu et al.

BIORESOURCE TECHNOLOGY (2018)

Article Microbiology

Regulation of lactate metabolism in the acetogenic bacterium Acetobacterium woodii

Marie Charlotte Schoelmerich et al.

ENVIRONMENTAL MICROBIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Markerless genome editing in Clostridium beijerinckii using the CRISPR-Cpf1 system

Jie Zhang et al.

JOURNAL OF BIOTECHNOLOGY (2018)

Article Biochemical Research Methods

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Efficient gene knockdown in Clostridium acetobutylicum by synthetic small regulatory RNAs

Changhee Cho et al.

BIOTECHNOLOGY AND BIOENGINEERING (2017)

Review Biotechnology & Applied Microbiology

Synthetic gene designThe rationale for codon optimization and implications for molecular pharming in plants

Gina R. Webster et al.

BIOTECHNOLOGY AND BIOENGINEERING (2017)

Article Biochemical Research Methods

A two-plasmid inducible CRISPR/Cas9 genome editing tool for Clostridium acetobutylicum

Francois Wasels et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2017)

Article Food Science & Technology

Production of bioethanol by facultative anaerobic bacteria

Seyedeh Sara Soleimani et al.

JOURNAL OF THE INSTITUTE OF BREWING (2017)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Clostridium autoethanogenum for selective alcohol production

Fungmin Liew et al.

METABOLIC ENGINEERING (2017)

Article Biotechnology & Applied Microbiology

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

Kaspar Valgepea et al.

METABOLIC ENGINEERING (2017)

Article Biotechnology & Applied Microbiology

Enhanced ethanol formation by Clostridium thermocellum via pyruvate decarboxylase

Liang Tian et al.

MICROBIAL CELL FACTORIES (2017)

Article Multidisciplinary Sciences

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

Ioannis Mougiakos et al.

NATURE COMMUNICATIONS (2017)

Article Multidisciplinary Sciences

Effect of DNA sequence of Fab fragment on yield characteristics and cell growth of E-coli

Antti Kulmala et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens

Kaspar Valgepea et al.

CELL SYSTEMS (2017)

Review Biotechnology & Applied Microbiology

A review of computational tools for design and reconstruction of metabolic pathways

Lin Wang et al.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2017)

Review Biochemical Research Methods

Recent advances in systems metabolic engineering tools and strategies

Tong Un Chae et al.

CURRENT OPINION IN BIOTECHNOLOGY (2017)

Article Microbiology

A roadmap for gene system development in Clostridium

Nigel P. Minton et al.

ANAEROBE (2016)

Review Biotechnology & Applied Microbiology

Energetics and Application of Heterotrophy in Acetogenic Bacteria

Kai Schuchmann et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biotechnology & Applied Microbiology

A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii

Gina L. Lipscomb et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Genome editing of Clostridium autoethanogenum using CRISPR/Cas9

Shilpa Nagaraju et al.

BIOTECHNOLOGY FOR BIOFUELS (2016)

Article Biochemistry & Molecular Biology

Exploiting E-coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications

Yoan R. Monneau et al.

JOURNAL OF BIOMOLECULAR NMR (2016)

Article Biotechnology & Applied Microbiology

A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery

Ashty S. Karim et al.

METABOLIC ENGINEERING (2016)

Article Biotechnology & Applied Microbiology

In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation

Jin Chen et al.

METABOLIC ENGINEERING (2016)

Article Biotechnology & Applied Microbiology

Acetone production with metabolically engineered strains of Acetobacterium woodii

Sabrina Hoffmeister et al.

METABOLIC ENGINEERING (2016)

Article Genetics & Heredity

The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen

William J. Kelly et al.

STANDARDS IN GENOMIC SCIENCES (2016)

Article Microbiology

Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis

Frank R. Bengelsdorf et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii

Bastian Molitor et al.

SCIENTIFIC REPORTS (2016)

Article Biotechnology & Applied Microbiology

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

Tao Xu et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Review Biotechnology & Applied Microbiology

Bioenergetic constraints for conversion of syngas to biofuels in acetogenic bacteria

Johannes Bertsch et al.

BIOTECHNOLOGY FOR BIOFUELS (2015)

Article Biotechnology & Applied Microbiology

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Christopher M. Humphreys et al.

BMC GENOMICS (2015)

Review Biochemical Research Methods

Computational methods in metabolic engineering for strain design

Matthew R. Long et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

Review Microbiology

An updated evolutionary classification of CRISPR-Cas systems

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

REBASE-a database for DNA restriction and modification: enzymes, genes and genomes

Richard J. Roberts et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Codon Optimisation Is Key for Pernisine Expression in Escherichia coli

Marko Snajder et al.

PLOS ONE (2015)

Article Biotechnology & Applied Microbiology

Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii

Areen Banerjee et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)

Review Microbiology

CRISPR-Cas systems: beyond adaptive immunity

Edze R. Westra et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biotechnology & Applied Microbiology

A Genetic System for Clostridium ljungdahlii: a Chassis for Autotrophic Production of Biocommodities and a Model Homoacetogen

Ching Leang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica

Akihisa Kita et al.

JOURNAL OF BIOSCIENCE AND BIOENGINEERING (2013)

Article Biochemical Research Methods

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

Matthew H. Larson et al.

NATURE PROTOCOLS (2013)

Article Biotechnology & Applied Microbiology

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Harish Nagarajan et al.

MICROBIAL CELL FACTORIES (2013)

Review Microbiology

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Kommireddy Vasu et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2013)

Article Biochemistry & Molecular Biology

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

Svetlana A. Shabalina et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Multiplex Genome Engineering Using CRISPR/Cas Systems

Le Cong et al.

SCIENCE (2013)

Article Biochemical Research Methods

EuGene: maximizing synthetic gene design for heterologous expression

Paulo Gaspar et al.

BIOINFORMATICS (2012)

Review Microbiology

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

Nathan E. Lewis et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker

John T. Heap et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Biochemistry & Molecular Biology

Multistate approaches in computational protein design

James A. Davey et al.

PROTEIN SCIENCE (2012)

Article Multidisciplinary Sciences

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

Martin Jinek et al.

SCIENCE (2012)

Article Agricultural Engineering

Effect of temperature, pH and buffer presence on ethanol production from synthesis gas by Clostridium ragsdalei

Dimple K. Kundiyana et al.

BIORESOURCE TECHNOLOGY (2011)

Review Biochemical Research Methods

Advances in ethanol production

Claudia C. Geddes et al.

CURRENT OPINION IN BIOTECHNOLOGY (2011)

Review Biochemical Research Methods

Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production

Tina Luetke-Eversloh et al.

CURRENT OPINION IN BIOTECHNOLOGY (2011)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Clostridium tyrobutyricum for n-butanol production

Mingrui Yu et al.

METABOLIC ENGINEERING (2011)

Article Biotechnology & Applied Microbiology

Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli

Hugo G. Menzella

MICROBIAL CELL FACTORIES (2011)

Article Biotechnology & Applied Microbiology

Natural Competence in Thermoanaerobacter and Thermoanaerobacterium Species

A. Joe Shaw et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

Article Biochemical Research Methods

The ClosTron: Mutagenesis in Clostridium refined and streamlined

John T. Heap et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2010)

Article Biotechnology & Applied Microbiology

High-throughput generation, optimization and analysis of genome-scale metabolic models

Christopher S. Henry et al.

NATURE BIOTECHNOLOGY (2010)

Article Multidisciplinary Sciences

Clostridium ljungdahlii represents a microbial production platform based on syngas

Michael Koepke et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

A modular system for Clostridium shuttle plasmids

John T. Heap et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2009)

Article Biotechnology & Applied Microbiology

Automated design of synthetic ribosome binding sites to control protein expression

Howard M. Salis et al.

NATURE BIOTECHNOLOGY (2009)

Article Biochemistry & Molecular Biology

Improvement of bacterial transformation efficiency using plasmid artificial modification

Kazumasa Yasui et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

Mark Welch et al.

PLOS ONE (2009)

Article Microbiology

Old acetogens, new light

Harold L. Drake et al.

INCREDIBLE ANAEROBES: FROM PHYSIOLOGY TO GENOMICS TO FUELS (2008)

Article Microbiology

Enzymology of the Wood-Ljungdahl pathway of acetogenesis

Stephen W. Ragsdale

INCREDIBLE ANAEROBES: FROM PHYSIOLOGY TO GENOMICS TO FUELS (2008)

Review Biochemistry & Molecular Biology

Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation

Stephen W. Ragsdale et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2008)

Review Microbiology

The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)

Elizabeth Pierce et al.

ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biochemical Research Methods

The ClosTron:: A universal gene knock-out system for the genus Clostridium

John T. Heap et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2007)

Article Multidisciplinary Sciences

CRISPR provides acquired resistance against viruses in prokaryotes

Rodolphe Barrangou et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

Engineering a selectable marker for hyperthermophiles

SJJ Brouns et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Review Biochemistry & Molecular Biology

Type II restriction endonucleases: structure and mechanism

A Pingoud et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2005)

Review Biochemistry & Molecular Biology

Life with carbon monoxide

SW Ragsdale

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2004)

Article Biotechnology & Applied Microbiology

OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

AP Burgard et al.

BIOTECHNOLOGY AND BIOENGINEERING (2003)

Article Biochemistry & Molecular Biology

A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

RJ Roberts et al.

NUCLEIC ACIDS RESEARCH (2003)

Review Biotechnology & Applied Microbiology

Auxotrophic yeast strains in fundamental and applied research

JT Pronk

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2002)

Article Microbiology

Gene transfer to Clostridium cellulolyticum ATCC 35319

KCB Jennert et al.

MICROBIOLOGY-SGM (2000)