Gene essentiality in the solventogenic DSM 792.

Unlabelled: is a solventogenic, anaerobic, gram-positive bacterium that is commonly considered the model organism for studying acetone-butanol-ethanol fermentation. The need to produce these chemicals sustainably and with a minimal impact on the environment has revived the interest in research on this bacterium. The recent development of efficient genetic tools allows to better understand the physiology of this micro-organism, aiming at improving its fermentation capacities.

Alleviation of Carbon Catabolite Repression through and Inactivation in Clostridium acetobutylicum DSM 792.

Efficient bioconversion processes of lignocellulose-derived carbohydrates into chemicals have received increasing interest in the last decades since they represent a promising alternative to petro-based processes. Despite efforts to adapt microorganisms to the use of such substrates, one of their major limitations remains their inability to consume multiple sugars simultaneously. In particular, the solventogenic model organism Clostridium acetobutylicum struggles to efficiently use second generation (2G) substrates because of carbon catabolite repression mechanisms that prevent the assimilation of xylose and arabinose in the presence of glucose.

Genome-Wide TSS Distribution in Three Related Clostridia with Normalized Capp-Switch Sequencing.

Transcription initiation is a tightly regulated process that is crucial for many aspects of prokaryotic physiology. High-throughput transcription start site (TSS) mapping can shed light on global and local regulation of transcription initiation, which in turn may help us understand and predict microbial behavior. In this study, we used Capp-Switch sequencing to determine the TSS positions in the genomes of three model solventogenic clostridia: Clostridium acetobutylicum ATCC 824, C.

A CRISPR/Anti-CRISPR Genome Editing Approach Underlines the Synergy of Butanol Dehydrogenases in Clostridium acetobutylicum DSM 792.

Although is the model organism for the study of acetone-butanol-ethanol (ABE) fermentation, its characterization has long been impeded by the lack of efficient genome editing tools. In particular, the contribution of alcohol dehydrogenases to solventogenesis in this bacterium has mostly been studied with the generation of single-gene deletion strains. In this study, the three butanol dehydrogenase-encoding genes located on the chromosome of the DSM 792 reference strain were deleted iteratively by using a recently developed CRISPR-Cas9 tool improved by using an anti-CRISPR protein-encoding gene, Although the literature has previously shown that inactivation of either , , or had only moderate effects on the strain, this study shows that clean deletion of both and strongly impaired solvent production and that a triple mutant Δ Δ Δ was even more affected.

Adaptation and application of a two-plasmid inducible CRISPR-Cas9 system in Clostridium beijerinckii.

Recent developments in CRISPR technologies have opened new possibilities for improving genome editing tools dedicated to the Clostridium genus. In this study we adapted a two-plasmid tool based on this technology to enable scarless modification of the genome of two reference strains of Clostridium beijerinckii producing an Acetone/Butanol/Ethanol (ABE) or an Isopropanol/Butanol/Ethanol (IBE) mix of solvents. In the NCIMB 8052 ABE-producing strain, inactivation of the SpoIIE sporulation factor encoding gene resulted in sporulation-deficient mutants, and this phenotype was reverted by complementing the mutant strain with a functional spoIIE gene.

σ (σ) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii.

The solventogenic C. beijerinckii DSM 6423, a microorganism that naturally produces isopropanol and butanol, was previously modified by random mutagenesis. In this work, one of the resulting mutants was characterized.

Correction to: Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423.

Following the publication of this article [1], the authors noticed that Figs. 2, 3 and 4 were in the incorrect order and thus had incorrect captions.

Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423.

Background: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C.

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

CRISPR/Cas-based genetic engineering has revolutionised molecular biology in both eukaryotes and prokaryotes. Several tools dedicated to the genomic transformation of the Clostridium genus of Gram-positive bacteria have been described in the literature; however, the integration of large DNA fragments still remains relatively limited. In this study, a CRISPR/Cas9 genome editing tool using a two-plasmid strategy was developed for the solventogenic strain Clostridium acetobutylicum ATCC 824.

Transfer of Clostridium difficile Genetic Elements Conferring Resistance to Macrolide-Lincosamide-Streptogramin B (MLSB) Antibiotics.

Molecular analysis is an important tool to investigate Clostridium difficile resistance to macrolide-lincosamide-streptogramin B (MLSB). In particular, the protocols described in this chapter have been designed to investigate the genetic organization of erm(B)-containing elements and to evaluate the capability of these elements to transfer in C. difficile recipient strains using filter mating assay.

Draft Genome Sequence of Clostridium difficile Strain IT1118, an Epidemic Isolate Belonging to the Emerging PCR Ribotype 018.

Clostridium difficile PCR ribotype 018 has emerged in Italy, South Korea, and Japan, causing severe infections and outbreaks. In this study, we sequenced the genome of IT1118, an Italian clinical isolate, to clarify the molecular features contributing to the success of this epidemic type.

Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923).

Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776 (IFP923), an efficient producer of butyric acid. The genome consists of a single chromosome of 3.19 Mb and provides useful data concerning the metabolic capacities of the strain.

Integration of (B)-containing elements through large chromosome fragment exchange in .

In , (B) genes are located on mobile elements like Tn and Tn. In previous studies, some of these elements were transferred by conjugation-like mechanisms, mobilized by helper conjugative systems. In this study, we analyzed the genomes of several recipient strains that acquired either Tn or Tn-like elements.

Fluoroquinolone resistance does not impose a cost on the fitness of Clostridium difficile in vitro.

Point mutations conferring resistance to fluoroquinolones were introduced in the gyr genes of the reference strain Clostridium difficile 630. Only mutants with the substitution Thr-82→Ile in GyrA, which characterizes the hypervirulent epidemic clone III/027/NAP1, were resistant to all fluoroquinolones tested. The absence of a fitness cost in vitro for the most frequent mutations detected in resistant clinical isolates suggests that resistance will be maintained even in the absence of antibiotic pressure.

Inter- and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLSB.

Resistance to the macrolide-lincosamide-streptogramin B group of antibiotics in Clostridium difficile is generally due to erm(B) genes. Tn6194, a conjugative transposon initially detected in PCR-ribotype 027 isolates, is an erm(B)-containing element also detected in other relevant C. difficile PCR-ribotypes.

Clostridium difficile erm(B)-containing elements and the burden on the in vitro fitness.

In Clostridium difficile, resistance to the macrolide-lincosamide-streptogramin B group of antibiotics generally relies on erm(B) genes. In this study, we investigated elements with a genetic organization different from Tn5398, the mobilizable non-conjugative element identified in C. difficile strain 630.