Systems Biotechnology Group


Research Focus:

The research group Systems Biotechnology works in the core areas quantitative physiology and manipulation of redox balances with the overall aim of the sustainable production of chemicals and energy carriers. Currently this includes production of chemicals in phototrophs, such as Synechocystis sp. PCC6803 and Rhodobacter sphaeroides on the one hand and heterotrophs (e.g. E. coli, P. putida and Yeast) on the other hand. The goals are to directly produce value added chemicals from CO2 and sunlight and also to use low molecular weight products from phototrophic carbon fixation (also from heterogenic catalysis) as a feedstock in the heterotrophs. The manipulation of redox balances also lays the basis for hydrogen production using photolysis of water in combination with bioelectrochemical systems and / or biofilm reactors.
The group rests on three main pillars: (i) Modelling of metabolism (including metabolic flux analysis and genome scale modelling), (ii) quantitative analytics (metabolite concentrations and isotope enrichments) and (iii) in-depth physiology using advanced culture techniques and systems biology characterization. The research platform 'Biophotovoltaics' is currently associated with the group exploring the feasibbility to use microbial electrochemical technologies (MET) to generate electricity from photolysis of water and to separate oxygen and evolution.


2019 (3)

  • Lai, B., Nguyen, A.V., Krömer, J.O., (2019):
    Characterizing the anoxic phenotype of Pseudomonas putida using a bioelectrochemical system
    Methods Protoc. 2 (2), art. 26
    full text (url)
  • Tschörtner, J., Lai, B., Krömer, J.O., (2019):
    Biophotovoltaics: green power generation from sunlight and water
    Front. Microbiol. 10 , art. 866
    full text (url)
  • Vassilev, I., Kracke, F., Freguia, S., Keller, J., Krömer, J.O., Ledezma, P., Virdis, B., (2019):
    Microbial electrosynthesis system with dual biocathode arrangement for simultaneous acetogenesis, solventogenesis and carbon chain elongation
    Chem. Commun. 55 (30), 4351 - 4354
    full text (url)

2018 (8)

  • Averesch, N.J.H., Krömer, J.O., (2018):
    Metabolic engineering of the shikimate pathway for production of aromatics and derived compounds – present and future strain construction strategies
    Front. Bioeng. Biotechnol. 6 , art. 32
    full text (url)
  • Averesch, N.J.H., Martínez, V.S., Nielsen, L.K., Krömer, J.O., (2018):
    Toward synthetic biology strategies for adipic acid production: An in silico tool for combined thermodynamics and stoichiometric analysis of metabolic networks
    ACS Synth. Biol. 7 (2), 490 - 509
    full text (url)
  • Kracke, F., Lai, B., Yu, S., Krömer, J.O., (2018):
    Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation – A chance for metabolic engineering
    Metab. Eng. 45 , 109 - 120
    full text (url)
  • Krieg, T., Phan, L.M.P., Wood, J.A., Sydow, A., Vassilev, I., Krömer, J.O., Mangold, K.-M., Holtmann, D., (2018):
    Characterization of a membrane-separated and a membrane-less electrobioreactor for bioelectrochemical syntheses
    Biotechnol. Bioeng. 115 (7), 1705 - 1716
    final draft (pdf)
  • Varela, C., Schmidt, S.A., Borneman, A.R., Pang, C.N.I., Krömer, J.O., Khan, A., Song, X., Hodson, M.P., Solomon, M., Mayr, C.M., Hines, W., Pretorius, I.S., Baker, M.S., Roessner, U., Mercurio, M., Henschke, P.A., Wilkins, M.R., Chambers, P.J., (2018):
    Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains
    Metab. Eng. 49 , 178 - 191
    full text (url)
  • Vassilev, I., Gießelmann, G., Schwechheimer, S.K., Wittmann, C., Virdis, B., Krömer, J.O., (2018):
    Anodic electro-fermentation: Anaerobic production of L-Lysine by recombinant Corynebacterium glutamicum
    Biotechnol. Bioeng. 115 (6), 1499 - 1508
    final draft (pdf)
  • Vassilev, I., Hernandez, P.A., Batlle-Vilanova, P., Freguia, S., Krömer, J.O., Keller, J., Ledezma, P., Virdis, B., (2018):
    Microbial electrosynthesis of isobutyric, butyric, caproic acids, and corresponding alcohols from carbon dioxide
    ACS Sustain. Chem. Eng. 6 (7), 8485 - 8493
    full text (url)
  • Yu, S., Lai, B., Plan, M.R., Hodson, M.P., Lestari, E.A., Song, H., Krömer, J.O., (2018):
    Improved performance of Pseudomonas putida in a bioelectrochemical system through overexpression of periplasmic glucose dehydrogenase
    Biotechnol. Bioeng. 115 (1), 145 - 155
    full text (url)

2017 (4)

  • Averesch, N.J.H., Prima, A., Krömer, J.O., (2017):
    Enhanced production of para-hydroxybenzoic acid by genetically engineered Saccharomyces cerevisiae
    Bioprocess. Biosyst. Eng. 40 (8), 1283 - 1289
    full text (url)
  • Gold, D.A., O'Reilly, S.S., Watson, J., Degnan, B.M., Degnan, S.M., Krömer, J.O., Summons, R.E., (2017):
    Lipidomics of the sea sponge Amphimedon queenslandica and implication for biomarker geochemistry
    Geobiology 15 (6), 836 - 843
    full text (url)
  • Koch, C., Kuchenbuch, A., Kracke, F., Bernhardt, P.V., Krömer, J.O., Harnisch, F., (2017):
    Predicting and experimental evaluating bio-electrochemical synthesis — A case study with Clostridium kluyveri
    Bioelectrochemistry 118 , 114 - 122
    full text (url)
  • Watson, J.R., Krömer, J.O., Degnan, B.M., Degnan, S.M., (2017):
    Seasonal changes in environmental nutrient availability and biomass composition in a coral reef sponge
    Mar. Biol. 164 (6), art. 135
    full text (url)

2017 (1)

  • Theodosiou, E., Breisch, M., Julsing, M.K., Falcioni, F., Bühler, B., Schmid, A., (2017):
    An artificial TCA cycle selects for efficient α-ketoglutarate dependent hydroxylase catalysis in engineered Escherichia coli
    Biotechnol. Bioeng. 114 (7), 1511 - 1520
    final draft (pdf)

2015 (1)

  • Theodosiou, E., Frick, O., Bühler, B., Schmid, A., (2015):
    Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation
    Microb. Cell. Fact. 14 , art. 108
    full text (url)

New concepts for an integrative bio economy: Sustainable Valorization of CO2 and sunlight
This project aims to generate a sustainable resource platform on the basis of CO2 driven by light energy from sunlight. Several target compounds and reactor platforms are considered and a comparison of state of the art biotechnological- and heterogeneous catalysis is performed. Target molecules include 4-Hydroxyprolin, methane, methanol, oxalic and tartaric acid.


Funded by Freistaat Sachsen

Diese Maßnahme wird mitfinanziert mit Steuermitteln auf Grundlage des von den Abgeordneten des Sächsischen Landtags beschlossenen Haushalts.

(This project is co-financed by means of taxation based on the budget adopted by the representatives of the Landtag of Saxony.)


How do sponges and bacteria together maintain productivity on coral reefs?
Integrating invertebrate biology, microbiology, genomics and metabolomics, this project aims to listen in on conversations between a Great Barrier Reef sponge and its bacterial symbionts. Coral reefs thrive in nutrient-poor tropical seas by relying on efficient retention and recycling of essential elements, and marine sponges are proving critically important in this role. They achieve this by cooperating with metabolically diverse bacterial symbionts via mechanisms that are largely unknown. Using the first and most advanced genome-enabled sponge in the world, this project seeks to reveal genomic and metabolic details of the partnership, with potential to inform environmental restoration, pharmaceuticals and biotechnology.

ARC

The project is a collaboration with the Degnan labs at the University of Queensland (Brisbane, Australia) and  funded through the Australian Research Council (DP170102353).

Fluxomics – Quantifying the metabolic phenotype (Higrade 2018)
With the rise of Systems Biology tools in many areas of the life sciences, data on gene expression, protein abundance and metabolite concentrations become readily available, yet the quantification of intracellular reaction rates (fluxes) is still a non-trivial task for many researchers. This course introduces different concepts of metabolic flux analysis in a hands-on format and enable researchers to develop a quantitative description of their organism or consortium of study.


Masterstudiengang Biochemie, Universität Leipzig (Sommersemester)
Modul: "Quantitative Biologie für eine nachhaltige Umwelt- und industrielle Biotechnologie"

Erwerb von Fertigkeiten in der quantitativen Beschreibung biologischer Prozesse. Nachweis der Lernkompetenz durch Berechnung von maximal möglichen Ausbeuten sowohl in Produktionssystemen als auch bei Abbauprozessen und durch Verfolgung von Stoffflüssen. Dies legt die Grundlage zur Beschreibung der Nachhaltigkeit biologischer Systeme.

Hierbei kommen biologische Datensätze und Modellierungsansätze der Systembiologie zum Einsatz. Die Absolventen erlernen sowohl das Erstellen von Modellen einerseits und die Prozessierung der Daten andererseits. Es werden sowohl stöchiometrische als auch thermodynamische Ansätze verfolgt, um unterschiedliche Prozesse in den Bereichen weiße Biotechnologie und Umweltbiotechnologie zu beschreiben.


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Quantitative physiology of Synechocystis sp PCC6803 in response to light availability
Synechocystis is an important model organism for Cyanobacteria, which are considered as phototrophic platform organisms in biotechnology. This thesis aims at quantifying intracellular metabolite concentrations in response to light. These metabolites are the building blocks for biotechnological processes based on CO2. It will involve cultivation of microbes, sampling and mass spectrometry. Knowledge in microbial metabolism and a strong interest in quantitative work are desired.


Fluxomics of Cyanobacteria using 13C tracers
This project aims to determine uptake kinetics of isotopic tracers into the metabolism of Synechocystis sp. PCC6803. It will involve cultivation of microbes, sampling and mass spectrometry. A fundamental interest in microbiology and analytics is desired.


Photolysis of water in a bioelectrochemical system as a path to hydrogenporoduction
Hydrogen is considered a key energy carrier of the future. Splitting water into oxygen and hydrogen is a great way to generate H2. In this project we explore the capability of Cyanobacteria to catalyse this process and use an electrochemical system to separate H2. Being a fundamental research project, creativity and interest in electrochemical technology as well as microbiology are paramount.