Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium

Phage serine integrase-mediated genome engineering for efficient expression of chemical biosynthetic pathway in gas-fermenting Clostridium ljungdahlii

(2019) He Huang et al.   METABOLIC ENGINEERING

A xylose-inducible expression system and a CRISPRi-plasmid for targeted knock-down of gene expression in Clostridioides difficile

(2019) Ute Müh et al.   JOURNAL OF BACTERIOLOGY

Recent Advances in the Metabolic Engineering of Klebsiella pneumoniae: A Potential Platform Microorganism for Biorefineries

(2019) Mi Na Rhie et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Autotrophic Biodiesel Production from the Thermotolerant Microalga Chlorella sorokiniana by Enhancing the Carbon Availability with Temperature Adjustment

(2019) Yoon Young Choi et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii

(2019) Qi Li et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR genome editing systems in the genus Clostridium: a timely advancement

(2019) Kathleen N. McAllister et al.   JOURNAL OF BACTERIOLOGY

Programmed gRNA Removal System for CRISPR-Cas9-Mediated Multi-Round Genome Editing in Bacillus subtilis

(2019) Hayeon Lim et al.   Frontiers in Microbiology

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Clostridial Genetics: Genetic Manipulation of the Pathogenic Clostridia

(2019) S. A. Kuehne et al.   Microbiology Spectrum

Microbial CRISPRi and CRISPRa Systems for Metabolic Engineering

(2019) Yi Zheng et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

CRISPR-Cas12a-Mediated Gene Deletion and Regulation in Clostridium ljungdahlii and Its Application in Carbon Flux Redirection in Synthesis Gas Fermentation

(2019) Ran Zhao et al.   ACS Synthetic Biology

Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization

(2019) Zhiqiang Wen et al.   Microbial Biotechnology

Metabolic Engineering of Bacteria for Renewable Bioethanol Production from Cellulosic Biomass

(2019) Sanchita Banerjee et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Evaluating the Pathway for Co-fermentation of Glucose and Xylose for Enhanced Bioethanol Production Using Flux Balance Analysis

(2019) Richa Arora et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Biosugar Production from Gracilaria verrucosa with Sulfamic Acid Pretreatment and Subsequent Enzymatic Hydrolysis

(2018) Mi-Ra Park et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

(2018) Karel Sedlar et al.   BMC GENOMICS

Genome engineering of Clostridium difficile using the CRISPR-Cas9 system

(2018) S. Wang et al.   CLINICAL MICROBIOLOGY AND INFECTION

Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

(2018) Jie Zhang et al.   METABOLIC ENGINEERING

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

(2018) Benjamin M. Woolston et al.   METABOLIC ENGINEERING

Multiplexed CRISPR-Cpf1-Mediated Genome Editing in Clostridium difficile toward the Understanding of Pathogenesis of C. difficile Infection

(2018) Wei Hong et al.   ACS Synthetic Biology

Recent Developments of the Synthetic Biology Toolkit for Clostridium

(2018) Rochelle C. Joseph et al.   Frontiers in Microbiology

Effects of nutritional enrichment on acid production from degenerated (non-solventogenic) Clostridium acetobutylicum strain M5

(2018) Ji Eun Woo et al.   Applied Biological Chemistry

RNAseq-based Transcriptome Assembly of Clostridium acetobutylicum for Functional Genome Annotation and Discovery

(2018) Matthew T. Ralston et al.   AICHE JOURNAL

Metabolic engineering of Clostridium acetobutylicum for the production of butyl butyrate

(2018) Hyeon Ji Noh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Exploitation of novel wild type solventogenic strains for butanol production

(2018) Fengxue Xin et al.   Biotechnology for Biofuels

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

(2018) Jie Zhang et al.   JOURNAL OF BIOTECHNOLOGY

AU-Rich Long 3′ Untranslated Region Regulates Gene Expression in Bacteria

(2018) Ju-Ping Zhao et al.   Frontiers in Microbiology

Genome shuffling improved the nucleosides production in Cordyceps kyushuensis

(2017) Yanming Wang et al.   JOURNAL OF BIOTECHNOLOGY

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

(2017) François Wasels et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum

(2017) Katrin M. Schwarz et al.   METABOLIC ENGINEERING

Enhanced solvent production by metabolic engineering of a twin-clostridial consortium

(2017) Zhiqiang Wen et al.   METABOLIC ENGINEERING

Cas9 Nickase-Assisted RNA Repression Enables Stable and Efficient Manipulation of Essential Metabolic Genes in Clostridium cellulolyticum

(2017) Tao Xu et al.   Frontiers in Microbiology

Using CRISPR-Cas9-mediated genome editing to generate C. difficile mutants defective in selenoproteins synthesis

(2017) Kathleen N. McAllister et al.   Scientific Reports

Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938

(2016) Paul A. Lawson et al.   ANAEROBE

A roadmap for gene system development in Clostridium

(2016) Nigel P. Minton et al.   ANAEROBE

Extending CRISPR-Cas9 Technology from Genome Editing to Transcriptional Engineering in the Genus Clostridium

(2016) Mark R. Bruder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced butanol production by increasing NADH and ATP levels in Clostridium beijerinckii NCIMB 8052 by insertional inactivation of Cbei_4110

(2016) Jun Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Efficient gene knockdown in Clostridium acetobutylicum by synthetic small regulatory RNAs

(2016) Changhee Cho et al.   BIOTECHNOLOGY AND BIOENGINEERING

Gene transcription repression inClostridium beijerinckiiusing CRISPR-dCas9

(2016) Yi Wang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824

(2016) Benjamin J. Willson et al.   Biotechnology for Biofuels

Construction of a restriction-less, marker-less mutant useful for functional genomic and metabolic engineering of the biofuel producer Clostridium acetobutylicum

(2016) Christian Croux et al.   Biotechnology for Biofuels

Genome editing of Clostridium autoethanogenum using CRISPR/Cas9

(2016) Shilpa Nagaraju et al.   Biotechnology for Biofuels

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

(2016) Takashi Yamano et al.   CELL

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

(2016) Jason M. Peters et al.   CELL

The role of small acid-soluble proteins (SASPs) in protection of spores of Clostridium botulinum against nitrous acid

(2016) Carolyn A. Meaney et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species

(2016) Paul A. Lawson et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Stable and enhanced gene expression in Clostridium acetobutylicum using synthetic untranslated regions with a stem-loop

(2016) Joungmin Lee et al.   JOURNAL OF BIOTECHNOLOGY

Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

(2016) Bernd Zetsche et al.   NATURE BIOTECHNOLOGY

Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable “Clean” Mutant Selection in Clostridium beijerinckii as an Example

(2016) Yi Wang et al.   ACS Synthetic Biology

CRISPR/Cas9-Based Efficient Genome Editing in Clostridium ljungdahlii, an Autotrophic Gas-Fermenting Bacterium

(2016) He Huang et al.   ACS Synthetic Biology

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium

(2016) Michael E. Pyne et al.   Scientific Reports

Optimal spore germination in Clostridium botulinum ATCC 3502 requires the presence of functional copies of SleB and YpeB, but not CwlJ

(2015) Carolyn A. Meaney et al.   ANAEROBE

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

(2015) Tao Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A novel arabinose-inducible genetic operation system developed for Clostridium cellulolyticum

(2015) Jie Zhang et al.   Biotechnology for Biofuels

Current progress of targetron technology: Development, improvement and application in metabolic engineering

(2015) Ya-Jun Liu et al.   Biotechnology Journal

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

(2015) Bernd Zetsche et al.   CELL

I-SceI-mediated scarless gene modification via allelic exchange in Clostridium

(2015) Ning Zhang et al.   JOURNAL OF MICROBIOLOGICAL METHODS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Genetic engineering of Clostridium acetobutylicum to enhance isopropanol-butanol-ethanol production with an integrated DNA-technology approach

(2015) Sandip B. Bankar et al.   RENEWABLE ENERGY

Neuroprotective Effects ofClostridium butyricumagainst Vascular Dementia in Mice via Metabolic Butyrate

(2015) Jiaming Liu et al.   Biomed Research International

Current progress of targetron technology: Development, improvement and application in metabolic engineering

(2015) Ya-Jun Liu et al.   Biotechnology Journal

Chemostat cultivation and transcriptional analyses of Clostridium acetobutylicum mutants with defects in the acid and acetone biosynthetic pathways

(2014) Daniel Hönicke et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Technical guide for genetic advancement of underdeveloped and intractable Clostridium

(2014) Michael E. Pyne et al.   BIOTECHNOLOGY ADVANCES

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

Metabolic engineering of Clostridium acetobutylicum for butyric acid production with high butyric acid selectivity

(2014) Yu-Sin Jang et al.   METABOLIC ENGINEERING

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

(2014) Michelle L. Luo et al.   NUCLEIC ACIDS RESEARCH

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Improvement of ClosTron for successive gene disruption in Clostridium cellulolyticum using a pyrF-based screening system

(2013) Gu-Zhen Cui et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824

(2013) Katalin Kovács et al.   Biotechnology for Biofuels

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

(2013) Charlotte M Wilson et al.   Biotechnology for Biofuels

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

(2013) Lei S. Qi et al.   CELL

Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices

(2013) Nicholas De Lay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

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

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli

(2013) Seung Min Yoo et al.   Nature Protocols

Expanding the Repertoire of Gene Tools for Precise Manipulation of the Clostridium difficile Genome: Allelic Exchange Using pyrE Alleles

(2013) Yen Kuan Ng et al.   PLoS One

The Role of Flagella in Clostridium difficile Pathogenesis: Comparison between a Non-Epidemic and an Epidemic Strain

(2013) Soza T. Baban et al.   PLoS One

A Targetron System for Gene Targeting in Thermophiles and Its Application in Clostridium thermocellum

(2013) Georg Mohr et al.   PLoS One

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

(2013) Olga A. Soutourina et al.   PLoS Genetics

Targeted gene engineering in Clostridium cellulolyticum H10 without methylation

(2012) Gu-zhen Cui et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2012) John T. Heap et al.   NUCLEIC ACIDS RESEARCH

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

(2012) M. Jinek et al.   SCIENCE

Enhanced Butanol Production Obtained by Reinforcing the Direct Butanol-Forming Route in Clostridium acetobutylicum

(2012) Y.-S. Jang et al.   mBio

Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum

(2011) Alok Malaviya et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Mutagenic Analysis of the Clostridium difficile Flagellar Proteins, FliC and FliD, and Their Contribution to Virulence in Hamsters

(2011) Tanis C. Dingle et al.   INFECTION AND IMMUNITY

Small RNAs in the Genus Clostridium

(2011) Y. Chen et al.   mBio

Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium thermocellum and Creation of a pta Mutant

(2010) S. A. Tripathi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Transcription termination by nuclear RNA polymerases

(2009) P. Richard et al.   GENES & DEVELOPMENT

The ClosTron: Mutagenesis in Clostridium refined and streamlined

(2009) John T. Heap et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM