Nico J Claassens

Nico J Claassens
Wageningen University & Research | WUR · Department of Food Sciences and Agrotechnology

PhD Microbiology

About

34
Publications
7,760
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,227
Citations
Introduction
Nico J Claassens currently works as an Assistant Professor at the Laboratory of Microbiology, Wageningen University, The Netherlands
Additional affiliations
January 2017 - June 2017
Wageningen University & Research
Position
  • PostDoc Position
September 2012 - present
Wageningen University & Research
Position
  • PhD Student

Publications

Publications (34)
Preprint
Codon usage refers to the occurrence of synonymous codons in protein-coding genes. It is known for decades that codon usage contributes to translation efficiency and hence to protein production levels. However, its role in protein synthesis is still only partly understood. This lack of understanding hampers the design of synthetic genes for efficie...
Chapter
In recent years the reductive glycine pathway (rGlyP) has emerged as a promising pathway for the assimilation of formate and other sustainable C1-feedstocks for future biotechnology. It was originally proposed as an attractive "synthetic pathway" to support formatotrophic growth due to its high ATP efficiency, linear structure, and limited overlap...
Article
Reducing the carbon intensity of the chemical industry has become a priority topic. The conversion of CO2 through combined electrochemical and microbial processes is an attractive perspective for scalable production with a reduced carbon footprint. CO2 can be electrochemically reduced to several one-carbon compounds such as carbon monoxide, formic...
Article
Full-text available
Synthetic biology, as a research field, brings together molecular life scientists, computational biologists, and social scientists to (re)engineer biological systems toward societally desired goals. Given the field’s broad multidisciplinarity and relatively young age, innovative educational methods are required to provide students with the needed b...
Article
Full-text available
Synthetic biology modifies biological systems with the aim of creating new biological parts, devices and even organisms. Systems biology deciphers the design principles of biological systems trying to derive the mathematical logic behind biological processes. Although different in their respective research approaches and questions, both disciplines...
Article
Full-text available
Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories’ biochemistry for rational bioproduction.
Preprint
Prokaryotic genes encoding functionally related proteins are often clustered in operons. The compact structure of operons allows for co-transcription of the genes, and for co-translation of the polycistronic messenger RNA to the corresponding proteins. This leads to reduced regulatory complexity and enhanced gene expression efficiency, and as such...
Article
Full-text available
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a s...
Article
Full-text available
The major bottleneck in commercializing biofuels and other commodities produced by microalgae is the high cost associated with phototrophic cultivation. Improving microalgal productivities could be a solution to this problem. Synthetic biology methods have recently been used to engineer the downstream production pathways in several microalgal strai...
Article
Hong et al. heterologously expressed the metabolic core of the reductive glycine pathway (rGlyP) as a sink for the anaerobic conversion of glycerol. This recent study concludes several reports in 2020 on the ATP-efficient, one-carbon-assimilating, rGlyP. Its engineering in diverse hosts could help the transformation toward renewable, one-carbon-bas...
Article
Full-text available
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D....
Article
Understanding the genetic design principles that determine protein production remains a major challenge. Although the key principles of gene expression were discovered 50 years ago, additional factors are still being uncovered. Both protein-coding and non-coding sequences harbor elements that collectively influence the efficiency of protein product...
Article
Full-text available
Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of phosphoglycolate was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, where it is referred to as photorespiration. While receiving little attention...
Article
Full-text available
Formate can be directly produced from CO2 and renewable electricity, making it a promising microbial feedstock for sustainable bioproduction. Cupriavidus necator is one of the few biotechnologically-relevant hosts that can grow on formate, but it uses the Calvin cycle, the high ATP cost of which limits biomass and product yields. Here, we redesign...
Preprint
Full-text available
Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of 2-phosphoglycolate, an essential process termed photorespiration, was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, but remains uncharacterized...
Preprint
Full-text available
Formate can be directly produced from CO2 and renewable electricity, making it a promising microbial feedstock for sustainable bioproduction. Cupriavidus necator is one of the few biotechnologically-relevant hosts that can grow on formate, but it uses the inefficient Calvin cycle. Here, we redesign C. necator metabolism for formate assimilation via...
Article
Full-text available
Conversion of biological feedstocks into value-added chemicals is mostly performed via microbial fermentation. An emerging alternative approach is the use of cell-free systems, consisting of purified enzymes and cofactors. Unfortunately, the in vivo and in vitro research communities rarely interact, which leads to oversimplifications and exaggerati...
Article
Full-text available
Methanol and formate are attractive microbial feedstocks as they can be sustainably produced from CO2 and renewable energy, are completely miscible, and are easy to store and transport. Here, we provide a biochemical perspective on microbial growth and bioproduction using these compounds. We show that anaerobic growth of acetogens on methanol and f...
Article
Full-text available
Escherichia coli has been widely used as a platform microorganism for both membrane protein production and cell factory engineering. The current methods to produce membrane proteins in this organism require the induction of target gene expression and often result in unstable, low yields. Here, we present a method combining a constitutive promoter w...
Article
Full-text available
One-carbon (C1) feedstocks can provide a vital link between cheap and sustainable abiotic resources and microbial bioproduction. Soluble C1 substrates, methanol and formate, could prove more suitable than gaseous feedstocks as they avoid mass transfer barriers. However, microorganisms that naturally assimilate methanol and formate are limited by a...
Article
Full-text available
The integration of electrochemical and microbial processes offers a unique opportunity to displace fossil carbon with CO2 and renewable energy as the primary feedstocks for carbon-based chemicals. Yet, it is unclear which strategy for CO2 activation and electron transfer to microbes has the capacity to transform the chemical industry. Here, we syst...
Article
The CRISPR-Cas9 nuclease has been re-purposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoters that regulate the expression...
Article
Full-text available
Different codon optimization algorithms are available that aim at improving protein production by optimizing translation elongation. In these algorithms, it is generally not considered how the altered protein coding sequence will affect the secondary structure of the corresponding RNA transcript, particularly not the effect on the 5′‐UTR structure...
Article
Full-text available
The replacement of fossil and agricultural feedstocks with sustainable alternatives for the production of chemicals and fuels is a societal and environmental necessity. This challenge can be tackled by using inorganic or one-carbon compounds as electron donors for microbial CO2fixation and bioproduction. Yet, considering the wide array of microbial...
Book
Full-text available
This lavishly illustrated book contains 67 chapters which aim to show that, rather than being just "germs" to be destroyed, microorganisms are essential for our health, environment, the Earth and its sustainable future. The chapters have been written by international experts in many aspects of microbiology, including recent breakthroughs presented...
Article
An extensive list of putative cellulosomal enzymes from C. thermocellum is now available in the public databanks, however, most of these remain unvalidated with regard to their activity and expression control mechanisms. This is particularly true of those enzymes putatively involved in hemicellulose deconstruction. Our research group has been worki...
Article
Full-text available
High-level, recombinant production of membrane-integrated proteins in Escherichia coli is extremely relevant for many purposes, but has also been proven challenging. Here we study a combination of transcriptional fine-tuning in E. coli LEMO21(DE3) with different codon usage algorithms for heterologous production of membrane proteins. The overexpres...
Article
Autotrophic microorganisms convert CO2 into biomass by deriving energy from light or inorganic electron donors. These CO2-fixing microorganisms have a large, but so far only partially realized, potential for the sustainable production of chemicals and biofuels. Productivities have been improved in autotrophic hosts through the introduction of produ...
Article
Akkermansia muciniphila colonizes the mucus layer of the gastrointestinal tract where the organism can be exposed to the oxygen that diffuses from epithelial cells. To understand how A. muciniphila is able to survive and grow at this oxic-anoxic interface, its oxygen tolerance, response and reduction capacities were studied. A. muciniphila was foun...
Article
Full-text available
The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms tha...
Article
The redundancy of the genetic code implies that most amino acids are encoded by multiple synonymous codons. In all domains of life, a biased frequency of synonymous codons is observed at the genome level, in functionally related genes (e.g., in operons), and within single genes. Other codon bias variants include biased codon pairs and codon co-occu...
Article
A wide range of proton-pumping rhodopsins (PPRs) have been discovered in recent years. Using a synthetic biology approach, PPR photosystems with different features can be easily introduced in nonphotosynthetic microbial hosts. PPRs can provide hosts with the ability to harvest light and drive the sustainable production of biochemicals or biofuels....

Projects

Project (1)