Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy.

A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g.

Core and auxiliary functions of one-carbon metabolism in exposed by a systems-level analysis of transcriptional and physiological responses.

The soil bacterium is a robust biomanufacturing host that assimilates a broad range of substrates while efficiently coping with adverse environmental conditions. is equipped with functions related to one-carbon (C1) compounds (e.g.

An automated workflow for multi-omics screening of microbial model organisms.

Multi-omics datasets are becoming of key importance to drive discovery in fundamental research as much as generating knowledge for applied biotechnology. However, the construction of such large datasets is usually time-consuming and expensive. Automation might enable to overcome these issues by streamlining workflows from sample generation to data analysis.

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes.

Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach.

Synthetic biology in Europe: current community landscape and future perspectives.

Synthetic biology has captivated scientists' imagination. It promises answers to some of the grand challenges society is facing: worsening climate crisis, insufficient food supplies for ever growing populations, and many persisting infectious and genetic diseases. While many challenges remain unaddressed, after almost two decades since its inception a number of products created by engineered biology are starting to reach the public.

Identification of ultra-thin molecular layers atop monolayer terraces in sub-monolayer organic films with scanning probe microscopy.

The morphology of sub-monolayer sexithiophene films has been investigated in situ and ex situ as a function of the substrate temperature of deposition. In this thickness range, monolayer terraces formed of edge-on molecules, i.e.

Homeostasis of the biosynthetic metabolome.

Metabolite concentrations vary across conditions and such metabolome changes are relevant for metabolic and gene regulation. Here, we used LC-MS/MS to explore metabolite concentration changes in . We measured 101 primary metabolites in 19 experimental conditions that include various nutrients and stresses.

Engineering Yeast for Methanol Assimilation.

Conferring methylotrophy on industrial microorganisms would enable the production of diverse products from one-carbon feedstocks and contribute to establishing a low-carbon society. Rebuilding methylotrophs, however, requires a thorough metabolic refactoring and is highly challenging. Only recently was synthetic methylotrophy achieved in model microorganisms─ and baker's yeast .

Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli.

Synthetic metabolic pathways are a burden for engineered bacteria, but the underlying mechanisms often remain elusive. Here we show that the misregulated activity of the transcription factor Cra is responsible for the growth burden of glycerol overproducing E. coli.

Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism.

Enzymes maintain metabolism, and their concentration affects cellular fitness: high enzyme levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR interference (CRISPRi) to study the consequences of decreasing E. coli enzymes below wild-type levels.

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions.

Background: Pseudomonas putida is a metabolically versatile, genetically accessible, and stress-robust species with outstanding potential to be used as a workhorse for industrial applications. While industry recognises the importance of robustness under micro-oxic conditions for a stable production process, the obligate aerobic nature of P. putida, attributed to its inability to produce sufficient ATP and maintain its redox balance without molecular oxygen, severely limits its use for biotechnology applications.

Crosstalk between transcription and metabolism: how much enzyme is enough for a cell?

Cells employ various mechanisms for dynamic control of enzyme expression. An important mechanism is mutual feedback-or crosstalk-between transcription and metabolism. As recently suggested, enzyme levels are often much higher than absolutely needed to maintain metabolic flux.

Twist of generalized skyrmions and spin vortices in a polariton superfluid.

We study the spin vortices and skyrmions coherently imprinted into an exciton-polariton condensate on a planar semiconductor microcavity. We demonstrate that the presence of a polarization anisotropy can induce a complex dynamics of these structured topologies, leading to the twist of their circuitation on the Poincaré sphere of polarizations. The theoretical description of the results carries the concept of generalized quantum vortices in two-component superfluids, which are conformal with polarization loops around an arbitrary axis in the pseudospin space.

Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay.

Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary studies. Saccharomyces cerevisiae was used as an in vivo test tube and p53 proteins derived from human and five commonly used animal models were chosen as proof of concept.