All Outputs (86)

Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay (2020)
Journal Article

We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity arises for two reasons. First, one of the products of the auxiliary enzyme is a substrat... Read More about Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay.

A Sustainable Chemicals Manufacturing Paradigm Using CO2 and Renewable H2 (2020)
Journal Article

© 2020 The Author(s) The chemical industry must decarbonize to align with UN Sustainable Development Goals. A shift toward circular economies makes CO2 an attractive feedstock for producing chemicals, provided renewable H2 is available through techno... Read More about A Sustainable Chemicals Manufacturing Paradigm Using CO2 and Renewable H2.

A gold standard, CRISPR/Cas9-based complementation strategy reliant on 24 nucleotide bookmark sequences (2020)
Journal Article

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Phenotypic complementation of gene knockouts is an essential step in establishing function. Here, we describe a simple strategy for ‘gold standard’ complementation in which the mutant allele i... Read More about A gold standard, CRISPR/Cas9-based complementation strategy reliant on 24 nucleotide bookmark sequences.

A genome-wide approach for identification and characterisation of metabolite-inducible systems (2020)
Journal Article

© 2020, The Author(s). Inducible gene expression systems are vital tools for the advancement of synthetic biology. Their application as genetically encoded biosensors has the potential to contribute to diagnostics and to revolutionise the field of mi... Read More about A genome-wide approach for identification and characterisation of metabolite-inducible systems.

A complete genome sequence of Cupriavidus necator H16 (DSM 428) (2019)
Journal Article

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw (2019)
Journal Article

Background: A consolidated bioprocessing (CBP), where lignocellulose is converted into the desired product(s) in a single fermentative step without the addition of expensive degradative enzymes, represents the ideal solution of renewable routes to ch... Read More about Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw.

The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases (2019)
Journal Article

Carbonic anhydrase catalyses the interconversion of carbon dioxide and water to bicarbonate and protons. It was unknown if the industrial relevant acetogen Clostridium autoethanogenum possesses these enzymes. We identified two putative carbonic anhyd... Read More about The carbonic anhydrase of Clostridium autoethanogenum represents a new subclass of β-carbonic anhydrases.

Phosphorylation and functionality of CdtR in Clostridium difficile (2019)
Journal Article

The production of TcdA, TcdB and CDT in Clostridium difficile PCR ribotype 027, is regulated by the two-component system response regulator CdtR. Despite this, little is known about the signal transduction pathway leading to the activation of CdtR. I... Read More about Phosphorylation and functionality of CdtR in Clostridium difficile.

A novel conjugal donor strain for improved DNA transfer into Clostridium spp. (2019)
Journal Article

© 2019 The Authors Importance: The ability to transfer genetic material into a target organism is crucial for the development of a wide range of targeted genetic manipulation techniques. Overcoming the organisms’ native restriction systems which targ... Read More about A novel conjugal donor strain for improved DNA transfer into Clostridium spp..

The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16 (2019)
Journal Article

Background 3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacter... Read More about The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16.

RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium (2019)
Journal Article

Members of the genus Clostridium represent a diverse assemblage of species exhibiting both medical and industrial importance. Deriving both a greater understanding of their biology, while at the same time enhancing their exploitable properties, requi... Read More about RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium.

Generation of a fully erythromycin-sensitive strain of Clostridioides difficile using a novel CRISPR-Cas9 genome editing system (2019)
Journal Article

© 2019, The Author(s). Understanding the molecular pathogenesis of Clostridioides difficile has relied on the use of ermB-based mutagens in erythromycin-sensitive strains. However, the repeated subcultures required to isolate sensitive variants can l... Read More about Generation of a fully erythromycin-sensitive strain of Clostridioides difficile using a novel CRISPR-Cas9 genome editing system.

Genome-scale model of C. autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide (2019)
Journal Article

Clostridium autoethanogenum is an industrial microbe used for the commercial-scale production of ethanol from carbon monoxide. While significant progress has been made in the attempted diversification of this bioprocess, further improvements are desi... Read More about Genome-scale model of C. autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide.

Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum (2019)
Journal Article

Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reporte... Read More about Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum.

Homologous overexpression of hydrogenase and glycerol dehydrogenase in Clostridium pasteurianum to enhance hydrogen production from crude glycerol (2019)
Journal Article

This study reports engineering of a hypertransformable variant of C. pasteurianum for bioconversion of glycerol into hydrogen (H2). A functional glycerol-triggered hydrogen pathway was engineered based on two approaches: (1) increasing product yield... Read More about Homologous overexpression of hydrogenase and glycerol dehydrogenase in Clostridium pasteurianum to enhance hydrogen production from crude glycerol.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development (2019)
Journal Article

© 2019 The Author(s) 2019. Published by Oxford University Press. Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-stat... Read More about Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii (2019)
Journal Article

Clostridium beijerinckii is a potentially important industrial microorganism as it can synthesize valuable chemicals and fuels from various carbon sources. The establishment of convenient to use, effective gene tools with which the organism can be ra... Read More about CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii.

The Rnf complex is an energy-coupled transhydrogenase essential to reversibly link cellular NADH and ferredoxin pools in the acetogen acetobacterium woodii (2018)
Journal Article

© 2018 American Society for Microbiology. The Rnf complex is a respiratory enzyme that catalyzes the oxidation of reduced ferredoxin to the reduction of NAD + , and the negative free energy change of this reaction is used to generate a transmembrane... Read More about The Rnf complex is an energy-coupled transhydrogenase essential to reversibly link cellular NADH and ferredoxin pools in the acetogen acetobacterium woodii.

Functional genetic elements for controlling gene expression in Cupriavidus necator H16 (2018)
Journal Article

A robust and predictable control of gene expression plays an important role in synthetic biology and biotechnology applications. Development and quantitative evaluation of functional genetic elements such as constitutive and inducible promoters, as w... Read More about Functional genetic elements for controlling gene expression in Cupriavidus necator H16.

Effect of antibiotic treatment on the formation of non-spore Clostridium difficile persister-like cells (2018)
Journal Article

Background: The spore is the virulence factor identified to be involved in the recurrence of the disease caused by Clostridium difficile. Objectives: To demonstrate that lethal antibiotic concentrations induce the appearance of C. difficile persister... Read More about Effect of antibiotic treatment on the formation of non-spore Clostridium difficile persister-like cells.