Kaspar Valgepea

Kaspar Valgepea
University of Tartu · Institute of Technology

PhD

About

44
Publications
26,451
Reads
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1,312
Citations
Citations since 2017
28 Research Items
991 Citations
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Introduction
I am a young group leader fascinated by the ingenious and complex yet highly efficient and optimized metabolism of microbial cells. In general, I am interested in quantitative understanding of the governing principles of metabolism in bacteria at a whole-cell level. The recently established ERA Chair in Gas Fermentation Technologies aims to address global challenges of biosustainability through integration of gas fermentation technologies with systems and synthetic biology with a focus on both fundamental understanding of acetogen metabolism and on metabolic engineering of superior cell factories.
Additional affiliations
March 2019 - January 2021
University of Tartu
Position
  • Group Leader
Description
  • Group Leader of ERA Chair in Gas Fermentation Technologies
September 2018 - February 2019
University of Tartu
Position
  • Research Associate
Description
  • Research Fellow within the ERA Chair in Synthetic Biology
March 2015 - June 2018
The University of Queensland
Position
  • PostDoc Position
Description
  • I apply molecular systems biology approaches to acetogenic gas fermentation processes.
Education
September 2010 - June 2014
Tallinn University of Technology
Field of study
  • Chemistry and Gene Technology
September 2008 - June 2010
Tallinn University of Technology
Field of study
  • Applied Chemistry and Biotechnology
September 2003 - June 2006
Tallinn University of Technology
Field of study
  • Applied Chemistry and Biotechnology

Publications

Publications (44)
Article
Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics da...
Article
Full-text available
Living biological systems display a fascinating ability to self-organize their metabolism. This ability ultimately determines the metabolic robustness that is fundamental to controlling cellular behavior. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic...
Article
High levels of anthropogenic CO2 emissions are driving the warming of global climate. If this pattern of increasing emissions does not change, it will cause further climate change with severe consequences for the human population. On top of this, the increasing accumulation of solid waste within the linear economy model is threatening global biosus...
Article
Full-text available
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use abs...
Article
Full-text available
Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Ac...
Preprint
Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon ( C1 ) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO 2 ) into valuable products are the most advanced biocata...
Preprint
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are of growing importance in transitioning to the biosustainable production of renewable chemicals and fuels. Acetogens are particularly interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has already been commercialised. Most non-commercial acetogen str...
Article
Full-text available
RNA-seq is a powerful technique for transcriptome profiling while involving elaborate sample processing before library sequencing. We show that RNA-seq library preparation kits can strongly affect the outcome of an RNA-seq experiment.
Article
Microbial electrosynthesis enables the production of value-added chemicals from CO2 and electrons provided by an electrode. Clostridium ljungdahlii is an electroactive acetogen that potentially could be used in microbial electrosynthesis systems. However, the optimal operational parameters for microbial electrosynthesis using C. ljungdahlii are not...
Article
Full-text available
Acetogens harness the Wood-Ljungdahl Pathway, a unique metabolic pathway for C1 capture close to the thermodynamic limit. Gas fermentation using acetogens is already used for CO-to-ethanol conversion at industrial-scale and has the potential to valorise a range of C1 and waste substrates to short-chain and medium-chain carboxylic acids and alcohols...
Preprint
Transcriptome analysis via RNA sequencing (RNA-seq) has become a standard technique employed across various biological fields of study. This rapid adoption of the RNA-seq approach has been mediated, in part, by the development of different commercial RNA-seq library preparation kits compatible with standard next-generation sequencing (NGS) platform...
Preprint
Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Ac...
Chapter
Biomass has evolved as a promising renewable resource and an alternative to fossil resources. However, bio-based products have not yet fully reached into the society. The reason could be the lower cost competitiveness of bio-based products compared with fossil-based products. At the same time, there is also a stress on bio-based industries to impro...
Preprint
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use abs...
Article
Full-text available
Utilising one-carbon substrates such as carbon dioxide, methane, and methanol is vital to address the current climate crisis. Methylotrophic metabolism enables growth and energy generation from methanol, providing an alternative to sugar fermentation. Saccharomyces cerevisiae is an important industrial microorganism for which growth on one-carbon s...
Article
Full-text available
Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO2 and H2 revealed that captured carbon (460 ± 80 mmol/gDCW/day)...
Preprint
Full-text available
Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO 2 and H 2 revealed that captured carbon (460 ± 80 mmol/gDCW/da...
Article
Full-text available
Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood-Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterization of acetogen metabolism has recently improved, ke...
Article
Full-text available
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...
Preprint
Full-text available
Microbial fermentation for chemical production is becoming more broadly adopted as an alternative to petrochemical refining. Fermentation typically relies on sugar as a feed-stock. However, one-carbon compounds like methanol are a more sustainable alternative as they do not compete with arable land. This study focused on engineering the capacity fo...
Preprint
Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood-Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterisation of acetogen metabolism has recently improved, ke...
Article
Gas fermentation is emerging as an economically attractive option for the sustainable production of fuels and chemicals from gaseous waste feedstocks. Clostridium autoethanogenum can use CO and/or CO2 + H2 as its sole carbon and energy sources. Fermentation of C. autoethanogenum is currently being deployed on a commercial scale for ethanol producti...
Patent
Full-text available
The invention provides microorganisms and methods for the production of polyhydroxybutyrate (PHB) from gaseous substrates. In particular , the invention provides a non-natu rally occurring Wood-Ljungdahl microorganism comprising (a) an enzyme that converts acetyl-CoA to acetoacetyl-CoA , (b) an enzyme that converts acetoacetyl-CoA to 3-hydroxy buty...
Article
Full-text available
IntroductionQuantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen. Objective To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors. Methods Anaerobic cultures were mixed with anaerobic acetonitrile...
Article
Full-text available
Background The global demand for affordable carbon has never been stronger, and there is an imperative in many industrial processes to use waste streams to make products. Gas-fermenting acetogens offer a potential solution and several commercial gas fermentation plants are currently under construction. As energy limits acetogen metabolism, supply o...
Article
Acetogens are attractive organisms for the production of chemicals and fuels from inexpensive and non-food feedstocks such as syngas (CO, CO2 and H2). Expanding their product spectrum beyond native compounds is dictated by energetics, particularly ATP availability. Acetogens have evolved sophisticated strategies to conserve energy from reduction po...
Article
Increasing the throughput of systems biology-based experimental characterization of in silico-designed strains has great potential for accelerating the development of cell factories. For this, analysis of metabolism in steady state is essential as only this enables the unequivocal definition of the physiological state of cells, which is needed for...
Article
Cells usually respond to changing growth conditions with a change of specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is important for understanding metabolic regulation in response to changing μ. Thus, we analysed the proteome res...
Article
Elimination of acetate overflow in aerobic cultivation of Escherichia coli would improve many bioprocesses as acetate accumulation in the growth environment leads to numerous negative effects, e.g. loss of carbon, inhibition of growth, target product synthesis, etc. Despite many years of studies, the mechanism and regulation of acetate overflow are...
Article
Full-text available
The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. We present here an in-silico framework to infer relevant metabolic p...
Article
Three different label-free proteome quantification methods – APEX, emPAI and iBAQ – were evaluated to measure proteome-wide protein concentrations in the cell. All the methods were applied to a sample from Escherichia coli chemostat culture. A Pearson squared correlation of approximately 0.6 among the three quantification methods was demonstrated....
Article
Regulation levels of the gene expression cascade controlling protein levels and metabolic fluxes for cells to achieve faster growth have not been elaborated in acceptable detail. Furthermore, there is need for specific growth rate (μ) dependent absolute quantitative transcriptome and proteome data to understand the molecular relationships for enabl...
Article
Three different label-free proteome quantification methods--APEX, emPAI and iBAQ--were evaluated to measure proteome-wide protein concentrations in the cell. All the methods were applied to a sample from Escherichia coli chemostat culture. A Pearson squared correlation of approximately 0.6 among the three quantification methods was demonstrated. Im...
Article
Full-text available
Growth substrates, aerobic/anaerobic conditions, specific growth rate (μ) etc. strongly influence Escherichia coli cell physiology in terms of cell size, biomass composition, gene and protein expression. To understand the regulation behind these different phenotype properties, it is useful to know carbon flux patterns in the metabolic network which...
Article
Full-text available
Nutrient-limited continuous cultures in chemostats have been used to study microbial cell physiology for over 60 years. Genome instability and genetic heterogeneity are possible uncontrolled factors in continuous cultivation experiments. We investigated these issues by using high-throughput (HT) DNA sequencing to characterize samples from different...
Article
Full-text available
The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for tar...
Article
Specific growth rate dependent gene expression changes of Escherichia coli K12 MG1655 were studied by microarray and real-time PCR analyses. The bacteria were cultivated on glucose limited minimal medium using the accelerostat method (A-stat) where starting from steady state conditions (chemostat culture) dilution rate is constantly increased. At s...
Article
Growth space of Lactococcus lactis subsp. lactis IL1403 was studied at constant growth rate using D-stat cultivation technique. Starting from steady state conditions in a chemostat culture (mu = 0.2 h(-1)), the pH and/or temperature were continuously changed in the range of 5.4-6.4 and 26-34 degrees C, respectively, followed by the return to the in...
Article
Quasi steady state growth of Lactococcus lactis IL 1403 was studied in glucose-limited A-stat cultivation experiments with acceleration rates (a) from 0.003 to 0.06 h(-2) after initial stabilization of the cultures in chemostat at D = 0.2-0.3 h(-1). It was shown that the high limit of quasi steady state growth rate depended on the acceleration rate...

Questions

Questions (5)
Question
I have to ship a batch of purified proteins at ambient temperature to a collaborator. The functional state, activity, and folding of the proteins after shipping are not important as they will be used for proteomics analysis. The proteins have been His-tag purified and precipitated with the methanol-chloroform-water method. I am wondering whether it would be better to ship the proteins as precipitates or freeze-dry the precipitate before shipment. Maybe the protein will be less stable as a precipitate compared to as freeze-dried during shipment, thus causing degradation and loss of material. On the other hand, re-solubilisation of freeze-dried proteins could be challenging, which might also lead to loss of material from incomplete re-solubilisation.
I know that each protein could behave differently but I would very much appreciate any comments on whether in general shipment as precipitate or as freeze-dried at ambient temperature could be better, i.e. lower degradation and loss of material?
Thanks a lot in advance!
Question
I am looking for literature comparing growth and/or by-product patterns between arginine-supplemented and non-supplemented bacterial cultures.
Thanks in advance!

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Projects

Projects (2)
Project
Gas fermentation is a microbial process that contributes to the fullfilement of the sustainable development goals (SDGs) of the United Nations. The process converts waste and greenhouse gases into commodity chemicals and fuels. Thus, world’s climate is positively affected. This project aims to collect the essays by stakeholders from science, business and society and to make them available to the community. If you want to collobarate on this project don't hesitate to contacted us and we add you to the list of collobarators.
Project
The main aim of my research in this project is to intergrate steady-state gas fermentation experiments with systems biology tools (e.g. proteomics, metabolomics, genome-scale metabolic modeling) to study Clostdridium autotethanogenum for understanding and eventually overcoming the energetic limitations in acetogens’ metabolism. More information here: http://www.aibn.uq.edu.au/an-integrated-systems-and-synthetic-biology-platform-to-expand-the-product-spectrum-of-acetogens