Article
Biotechnology & Applied Microbiology
Ugochi Jennifer Nwaokorie, Kristina Reinmets, Lorena Azevedo de Lima, Pratik Rajendra Pawar, Kurshedaktar Majibullah Shaikh, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: Gas fermentation is a sustainable approach to produce fuels and chemicals using gas-fermenting microbes. Acetogens that use the Wood-Ljungdahl pathway are the most advanced biocatalysts for gas fermentation, but our understanding of the genes involved in the C-1-fixing gene cluster is incomplete. This study investigates the role of two genes, hp and nbp, in gas-fermenting acetogen Clostridium autoethanogenum.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Nicholas Fackler, James Heffernan, Alex Juminaga, Damien Doser, Shilpa Nagaraju, R. Axayacatl Gonzalez-Garcia, Sean D. Simpson, Esteban Marcellin, Michael Kopke
Summary: Gas fermentation by Clostridium autoethanogenum is a commercial process for sustainable biomanufacturing of fuels and chemicals using low-cost C1 feedstocks, but progress in pathway engineering and gene function elucidation is hindered by a lack of genetic tools.Efforts towards pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods.
Article
Biotechnology & Applied Microbiology
Robert Nogle, Shilpa Nagaraju, Sagar M. Utturkar, Richard J. Giannone, Vinicio Reynoso, Ching Leang, Robert L. Hettich, Wayne P. Mitchell, Sean D. Simpson, Michael C. Jewett, Michael Kopke, Steven D. Brown
Summary: Clostridium autoethanogenum is a model acetogen used for ethanol production and is also being developed for carbon-negative production of acetone and isopropanol through gas fermentation. A plasmid called pCA was assembled for strain DSM10061 (JA1-1) and is predicted to encode seven open-reading frames. The availability of the pCA sequence will aid in understanding its physiological role and optimizing genetic tools.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Craig Woods, Christopher M. Humphreys, Claudio Tomi-Andrino, Anne M. Henstra, Michael Kopke, Sean D. Simpson, Klaus Winzer, Nigel P. Minton
Summary: Most bacterial genes remain poorly characterized, and transposon insertion sequencing is a high-throughput technique that can help rectify this deficiency, although it is limited to species with efficient DNA transfer procedures. Researchers have developed approaches to overcome this barrier in autotrophic species, enabling the determination of essential genes required for utilizing carbon monoxide as the sole carbon and energy source.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Lorena Azevedo de Lima, Henri Ingelman, Kush Brahmbhatt, Kristina Reinmets, Craig Barry, Audrey Harris, Esteban Marcellin, Michael Kopke, Kaspar Valgepea
Summary: The study investigates the performance of Clostridium autoethanogenum in gas fermentation at different growth rates and evaluates the metabolic responses using various methods. The findings reveal that faster growth supports higher yields and productivities, and transcriptional regulation plays a significant role in facilitating faster growth. Additionally, the cells maintain sufficient baseline gene expression to respond rapidly to the availability of CO and H-2.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Kaspar Valgepea, Gert Talbo, Nobuaki Takemori, Ayako Takemori, Christina Ludwig, Vishnuvardhan Mahamkali, Alexander P. Mueller, Ryan Tappel, Michael Kopke, Sean Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Summary: Microbes that can recycle C-1 greenhouse gases into fuels and chemicals are crucial for the sustainability of future industries. In this study, the absolute proteomics technique was used to quantify protein concentrations in the acetogen Clostridium autoethanogenum, revealing the importance of proteome allocation for C-1 fixation.
Article
Microbiology
Parsa Ghadermazi, Angela Re, Luca Ricci, Siu Hung Joshua Chan
Summary: Gas fermentation is a promising method to convert low-cost waste gases into valuable chemicals. This study used modeling and kinetic ensemble modeling to analyze metabolic engineering interventions for increased 2,3-butanediol production and reduced carbon loss. The results suggested that interventions targeting by-products branching from acetyl-CoA and pyruvate are effective strategies.
Article
Biochemistry & Molecular Biology
Soo Jae Kwon, Joungmin Lee, Hyun Sook Lee
Summary: Acetate supplementation has been shown to alleviate CO inhibition in Clostridium sp. AWRP, leading to increased production of ethanol and 2,3-butanediol in bioreactor experiments. This approach can potentially shorten cultivation time for fermentative experiments using CO-containing gases.
PROCESS BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Luca Ricci, Valeria Agostino, Debora Fino, Angela Re
Summary: Gas fermentation by acetogens of the genus Clostridium is a promising technology for producing biochemicals and biofuels from industrial waste gases. Among acetogenic organisms, C. ljungdahlii shows higher efficiency in producing 2,3-butanediol compared to C. autoethanogenum. The presence of mineral elements Zinc and Iron has a significant positive influence on the titer and productivity of 2,3-butanediol.
FERMENTATION-BASEL
(2021)
Article
Biotechnology & Applied Microbiology
Martijn Diender, James C. Dykstra, Ivette Parera Olm, Serve W. M. Kengen, Alfons J. M. Stams, Diana Z. Sousa
Summary: This study shows that ethanol acts as an important intermediate and co-substrate during carboxydotrophic growth of Clostridium autoethanogenum. The mutant strain lacking the Ald subunit of the main bifunctional aldehyde/alcohol dehydrogenase has poor ethanol oxidation capabilities. The direction of ethanol metabolism is dynamic during carboxydotrophic acetogenesis.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jimmy Martinez-Ruano, Andres Suazo, Fabian Veliz, Fabian Otalora, Raul Conejeros, Ernesto Gonzalez, German Aroca
Summary: This study investigates the effect of pH control and addition of a redox mediator on the growth and metabolites distribution of Clostridium autoethanogenum during electro-fermentation. The results show that pH control and the use of a redox mediator significantly improve biomass generation and the production of lactate and acetate during electro-fermentation.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2023)
Article
Biotechnology & Applied Microbiology
Margaux Poulalier-Delavelle, Jonathan P. Baker, James Millard, Klaus Winzer, Nigel P. Minton
Summary: Acetogenic bacteria have the ability to convert CO2 into useful chemicals and fuels, making them important for achieving Net Zero. However, introducing cas9-containing vectors into Acetobacterium woodii was not successful due to toxicity and a recognition site for an endogenous restriction-modification system. This study developed a Python script to identify PAM candidates of the A. woodii CRISPR/Cas system and successfully created deletions and insertions using synthetic CRISPR arrays.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Anton Rueckel, Anne Oppelt, Philipp Leuter, Philipp Johne, Sebastian Fendt, Dirk Weuster-Botz
Summary: Synthesis gas fermentation is a promising microbial process for producing fuels and platform chemicals from renewable sources. This study investigated batch processes and continuous gassing with biogenic syngas, and found that both Clostridium carboxidivorans and Clostridium autoethanogenum showed good fermentation performance with biogenic syngas. However, achieving full carbon conversion to ethanol is still challenging.
FERMENTATION-BASEL
(2022)
Article
Biotechnology & Applied Microbiology
Hongrae Im, Taegwang An, Rokgyu Kwon, Soeun Park, Young-Kee Kim
Summary: The study found that adding 0.5 g/L tryptone and peptone showed the best volumetric ethanol productivities, which were increased by 45.9% and 44.3% compared to the control experiment. Ethanol production did not increase at a supplement concentration higher than 0.5 g/L.
BIOTECHNOLOGY AND BIOPROCESS ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Taegwang An, Young -Kee Kim
Summary: The effect of tungsten and selenium on cell growth and metabolite production was investigated in this study. Selenium had a greater impact on cell growth and total metabolite production compared to tungsten. Increasing tungsten concentration resulted in a significant increase in the ethanol/acetic acid production ratio.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Pawel Piatek, Christopher Humphreys, Mahendra P. Raut, Phillip C. Wright, Sean Simpson, Michael Kopke, Nigel P. Minton, Klaus Winzer
Summary: Acetogenic bacteria use quorum sensing to communicate and coordinate carbon resource management and electron sink utilization in the Wood-Ljungdahl pathway.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Craig Woods, Christopher M. Humphreys, Claudio Tomi-Andrino, Anne M. Henstra, Michael Kopke, Sean D. Simpson, Klaus Winzer, Nigel P. Minton
Summary: Most bacterial genes remain poorly characterized, and transposon insertion sequencing is a high-throughput technique that can help rectify this deficiency, although it is limited to species with efficient DNA transfer procedures. Researchers have developed approaches to overcome this barrier in autotrophic species, enabling the determination of essential genes required for utilizing carbon monoxide as the sole carbon and energy source.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Nicole Pearcy, Marco Garavaglia, Thomas Millat, James P. Gilbert, Yoseb A. Song, Hassan Hartman, Craig R. Woods, Claudio Tomi-Andrino, Rajesh Reddy Bommareddy, Byung-Kwan P. Cho, David A. A. Fell, Mark D. Poolman, John R. A. King, Klaus D. Winzer, Jamie A. Twycross, Nigel P. D. Minton
Summary: This study presents the development of a genome-scale metabolic model (GSM) for C. necator H16 linked with the BioCyc database. The integration of experimental observations and omics data improves the accuracy of the model and provides insights for designing metabolic engineering strategies for C. necator H16.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Ivana Cengic, Ines C. Canadas, Nigel P. Minton, Elton P. Hudson
Summary: In this study, a theophylline-responsive riboswitch-induced CRISPR/Cas9 system was developed for precise and markerless genome editing in cyanobacterium. This single-vector system enables multiplexed editing and allows for the generation of markerless mutants.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Guillaume Pregnon, Nigel P. Minton, Philippe Soucaille
Summary: E. limosum B2, an acetogen capable of producing butyrate and acetate from methanol, was subjected to adaptive laboratory evolution on methanol mineral medium. The evolved populations showed a significant increase in growth rate and exhibited changes in protein and methylome profiles, indicating the involvement of epigenetic regulation in metabolic improvements.
Article
Biochemical Research Methods
Bashir L. Rumah, Benedict H. Claxton Stevens, Jake E. Yeboah, Christopher E. Stead, Emily L. Harding, Nigel P. Minton, Ying Zhang
Summary: In this study, a CRISPR/Cas9 genome editing system was constructed and successfully utilized to delete and insert genes in two types of methanotrophic bacteria, Methylococcus capsulatus Bath and Methylocystis parvus OBBP. The combination of homology-directed repair achieved high frequencies of gene deletions and insertions. Various parameters were also investigated to optimize the CRISPR/Cas9 system in Methylocystis parvus OBBP. This work demonstrated the first efficient CRISPR/Cas9 system generating scarless clean gene deletions and insertions in methanotroph genomes.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Environmental Sciences
Fadi G. Mirza, Muna A. Tahlak, Rachelle Bou Rjeili, Komal Hazari, Farah Ennab, Charlie Hodgman, Amar Hassan Khamis, William Atiomo
Summary: Polycystic ovary syndrome (PCOS) not only affects conception, but also increases the risk of adverse pregnancy outcomes such as hypertension, miscarriage, and gestational diabetes. This narrative review summarizes the current knowledge regarding these complications in women with PCOS and highlights the need for further research on the potential confounding impact of obesity.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Microbiology
Jonathan R. R. Humphreys, Bisrat J. J. Debebe, Stephen P. P. Diggle, Klaus Winzer
Summary: Solventogenic clostridia are anaerobic, spore-forming bacteria that produce acetone, butanol, and ethanol through biphasic metabolism. However, these bacteria have a tendency to degenerate, losing their ability to produce solvents and spores, which is a problem for industrial applications. Through comparative genomics and ultra-deep sequencing, researchers identified the spo0A gene as key to the degeneration process in Clostridium beijerinckii NCIMB 8052. Mutations in this gene and genes regulating its expression and activity were found in hotspot regions of degenerate variants. This study provides new insights into clostridial strain degeneration and spore regulation network.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Immunology
Alexander M. Rawson, Andrew W. Dempster, Christopher M. Humphreys, Nigel P. Minton
Summary: Clostridium botulinum is a bacteria that is classified based on its ability to produce botulinum neurotoxin (BoNT). BoNT is the main virulence factor and the cause of botulism, a potentially fatal disease characterized by paralysis. The BoNT is used for medical treatments and in the cosmetic industry due to its potency and specificity.
Article
Microbiology
Jonathan R. Humphreys, Zak Bean, Jamie Twycross, Klaus Winzer
Summary: Lanthipeptide synthetases, present in all domains of life, catalyze an important step in lanthipeptide biosynthesis. LanM-like proteins, found in Clostridium species, are associated with agr quorum sensing operons. The physiological role and mode of action of these proteins are unclear. In this study, the LanM-like protein CA_C0082 was shown to act as an effector of Agr quorum sensing, controlling granulose formation and spore and solvent production in Clostridium acetobutylicum.
Article
Microbiology
James Millard, Alexander Agius, Ying Zhang, Philippe Soucaille, Nigel Peter Minton
Summary: Targeted mutations in Eubacterium limosum were achieved using an inducible counter-selective system combined with a non-replicative integrating mutagenesis vector. This system allowed for precise gene deletions, including genes involved in histidine biosynthesis, methanol metabolism, and L-carnitine demethylation. The desired mutants could be obtained with only one induction step after the initial selection of transformant colonies. This approach enables quick and efficient gene editing of E. limosum.
Article
Plant Sciences
Alison Tidy, Norliza Abu Bakar, David Carrier, Ian D. Kerr, Charlie Hodgman, Malcolm J. Bennett, Ranjan Swarup
Summary: AXR4 is an endoplasmic reticulum accessory protein that regulates the trafficking of auxin influx carriers AUXIN1 and LIKE-AUX2.
Article
Chemistry, Analytical
Malak A. Jaber, Bruna de Falco, Salah Abdelrazig, Catharine A. Ortori, David A. Barrett, Dong-Hyun Kim
Summary: In comprehensive lipidomics studies, accurate quantification is hindered by unwanted variations such as lipid degradation, matrix effects, and non-linear responses of instruments. This study employed an in vivo labelling strategy to generate C-13-labelled internal standards (C-13-ISs) from different species for more accurate and quantitative lipidomics analysis. The use of C-13-labelled P. pastoris extract as internal standards resulted in significant reduction in lipid variations compared to other normalization methods. This study highlights the benefit of in vivo labelling strategy in reducing technical and analytical variations in lipidomics studies.
ANALYTICAL METHODS
(2023)
Article
Biotechnology & Applied Microbiology
Barbara Bourgade, James Millard, Christopher M. Humphreys, Nigel P. Minton, M. Ahsanul Islam
Summary: This study demonstrates the significance of a replicating shuttle vector for genetic and metabolic engineering in industrially important M. thermoacetica. The vector was successfully applied for non-native ethanologenesis, allowing ethanol production in this organism.
FERMENTATION-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Charlie Hodgman, Gulafshana Hafeez Khan, William Atiomo
Summary: Pre-eclampsia, a common complication in pregnancy, is characterized by high blood pressure and organ damage. The research identifies the shortage of Coenzyme A and conflicting cellular regulatory mechanisms as the cause. This study provides insights into the molecular basis of pre-eclampsia, explains the risk factor of polycystic ovary syndrome, and suggests potential treatments and risk reduction strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)