From Rags to Riches: Exploiting the Calvin‐Benson‐Bassham Cycle for Biomanufacturing

F Federici, E Orsi, PI Nikel - ChemCatChem, 2023 - Wiley Online Library
Industrial chemical production largely relies on fossil fuels, resulting in the unavoidable
release of carbon dioxide (CO2) into the atmosphere. The concept of a circular carbon …

Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion

AG Dodge, CJ Thoma, MR O'Connor, LP Wackett - Mbio, 2024 - Am Soc Microbiol
Microbial response to toxic fluoride anion has traditionally been studied by adding inorganic
fluoride salts to growth media. Fluoride is known to spontaneously transit the membrane as …

The pAblo· pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria

E Kozaeva, ZS Nielsen… - Nucleic acids …, 2024 - academic.oup.com
A synthetic biology toolkit, exploiting clustered regularly interspaced short palindromic
repeats (CRISPR) and modified CRISPR-associated protein (Cas) base-editors, was …

Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440

NT Wirth, K Rohr, A Danchin, PI Nikel - Mbio, 2023 - Am Soc Microbiol
Thymidylate kinases (TMPKs) play an essential role in DNA biosynthesis across all domains
of life by catalyzing dTMP phosphorylation to dTDP. In Pseudomonas putida KT2440, a …

[HTML][HTML] Saccharomyces boulardii promoters for control of gene expression in vivo

C Sands, KA Hedin, R Vazquez-Uribe… - Microbial Cell …, 2024 - Springer
Background Interest in the use of engineered microbes to deliver therapeutic activities has
increased in recent years. The probiotic yeast Saccharomyces boulardii has been …

Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production

M Meliawati, DC Volke, PI Nikel… - Microbial …, 2024 - Wiley Online Library
Paenibacillus polymyxa is a non‐pathogenic, Gram‐positive bacterium endowed with a rich
and versatile metabolism. However interesting, this bacterium has been seldom used for …

[HTML][HTML] Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering

J Shin, DC Zielinski, BO Palsson - Metabolic Engineering, 2024 - Elsevier
Understanding diverse bacterial nutritional requirements and responses is foundational in
microbial research and biotechnology. In this study, we employed knowledge-enriched …

[HTML][HTML] Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida

DC Volke, N Gurdo, R Milanesi, PI Nikel - Metabolic Engineering, 2023 - Elsevier
Pseudomonas putida, a microbial host widely adopted for metabolic engineering, processes
glucose through convergent peripheral pathways that ultimately yield 6-phosphogluconate …

[HTML][HTML] BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data

J Dénéréaz, JW Veening - Access Microbiology, 2024 - microbiologyresearch.org
To streamline the analysis and visualization of bacterial growth and gene expression data
obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use …

[HTML][HTML] Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves

MA Reiter, JA Vorholt - BMC bioinformatics, 2024 - Springer
Background Recording and analyzing microbial growth is a routine task in the life sciences.
Microplate readers that record dozens to hundreds of growth curves simultaneously are …