Abstract

Abstract

Abstract

Short CV

Karim Fahmy received his PhD at the University of Freiburg in membrane protein research. During his postdoc studies as a Howard Hughes Medical Institute Fellow with Prof. Tom Sakmar at Rockefeller University, New York, he performed seminal work in combining site-directed mutagenesis with infrared spectroscopy to elucidate functional mechanisms of G protein-coupled receptors. After his habilitation at the University of Freiburg he joined the Helmholtz-Zentrum Dresden-Rossendorf heading the Department of Biophysics. His lab investigates and develops synthetic membrane mimetics to reveal the influence of the lipidic phase on membrane protein function. In addition to various spectroscopies, the lab uses calorimetric methods to investigate both biomolecular interactions as well as the systems biology of lipids in metabolic processes of synthetic minimal cells. Novel evaluation methods for microcalorimetric data are developed based on these simplest organisms. Karim Fahmy is affiliated Professor at the University of Dresden. He has headed the Molecular Biophysics Section of the German Biophysical Society and is recipient of the Hans-Griesebach-Price of the University of Freiburg.

Abstract

Short CV

Lee received his BS and MS degrees in Environmental Engineering from Lehigh University. After completing his PhD in Civil Engineering at the University of Texas at Austin, he started as an Assistant Professor of Chemical, Biochemical, and Environmental Engineering at the University of Maryland Baltimore County, where he is now Professor. Lee also serves as President-Elect of the Association of Environmental Engineering and Science Professors (AEESP) and Executive Editor at the Journal of Hazardous Materials. He is the recipient of the ES&T James J. Morgan Early Career Award, the National Science Foundation Career Award, and the AEESP Award for Outstanding Teaching in Environmental Engineering and Science.

Abstract

Short CV

Prof. Pablo I. Nikel earned a Ph.D. in Biotechnology and Molecular Biology (2009) in Argentina. After working in the US (Rice University, supported by the ASM), Pablo moved to Europe as a post-doctoral fellow, funded by the European Molecular Biology Organization (EMBO) and the MSCA of the European Commission, working in the laboratory of Prof. Víctor de Lorenzo (Madrid). Since 2017, he has been leading the Systems Environmental Microbiology Group at DTU Biosustain. Pablo’s team aims at rewriting Pseudomonas putida’s core biochemistry through synthetic metabolism for biosynthesis of novel compounds with a focus on new-to-nature fine chemicals (www.sem-cfb.com). The ambition of this research programme is to expand the limits of microbial biochemistry by engineering P. putida to access compounds that, as of today, are exclusively produced via traditional chemistry nowadays. Pablo is Full Professor of the Technical University of Denmark (since 2023) and, among other obligations, he is Editor-in-Chief of Current Opinion in Biotechnology and a cofounder of BioHalo, a spin-out company from his laboratory pursuing biological production of fluorochemicals.

Abstract

Short CV

Annemiek ter Heijne is professor in (Bio)Recovery Technology for Circular Economy at the Environmental Technology group of Wageningen University & Research (The Netherlands). She obtained her PhD degree on Microbial Fuel Cells and has continued her career in Wageningen working on different applications that involve the interaction between microorganisms and electrodes. She has been board member and president of ISMET, the International Society of Microbial Electrochemistry & Technology, and her teaching focuses on Renewable Energy Technologies and Microbial Electrochemistry. In her free time, she loves to spend time with her family, she likes spending time outdoor (hiking and running), and cooking (vegan) food.

Abstract

Figure 1. Enzymatic cascade towards metaraminol starting from renewables. The cascade comprises of a carboxylic acid reduction (1), a carboligation (2) and a transamination (3) step. The aliphatic precursors pyruvate and L -alanine can be produced microbially from second generation feedstocks (D-glucose, D-xylose) in suitable amounts. In situ product removal (ISPR) is used to shift the reaction equilibrium of the transamination step.

Short CV

Dörte Rother holds a diploma degree in biology from RWTH Aachen University. She conducted her PhD at the Heinrich-Heine University Düsseldorf (with research stays at Karolinska Institute Stockholm, University of Freiburg and University of Stuttgart). In 2008 she received a DFG-postdoc scholarship to work at Aachen University and became in 2009 postdoctoral student at the IBG-1: Biotechnology at Research Center Jülich. In 2012 she started her own Helmholtz-young investigators group in Jülich, additionally funded by a ERC-starting grant in 2017. In 2018 Dörte Rother was appointed as full professor for `synthetic enzyme cascades’ at Aachen University and leads the group `biocatalysis’ at Research Center Jülich. She has three children. She received the DECHEMA-Prize 2018 and the Biotrans Junior Award 2019 for her outstanding research activities in multi-step biocatalysis and sustainable process development.

Abstract

Abstract

The evolution of oxygenic photosynthesis in the ancestors of modern-day cyanobacteria gave rise to perhaps the most important biological process within our biosphere: the assimilation of atmospheric CO2 into organic biomass and the release of molecular oxygen as a byproduct. While properties of cyanobacterial growth in axenic cultures are increasingly understood, there are still many open questions regarding the limits of cyanobacterial growth. In particular, the economic viability of cyanobacterial biotechnology is still constrained by low growth rates and low areal productivities.

In the talk, I will discuss computational models of cyanobacterial metabolism and growth, from genome-scale reconstructions to coarse-grained kinetic models of growth. A particular focus will be optimality and resource allocation. That is, how do microbial and, in particular, cyanobacterial cells allocate their finite cellular resources, such as a finite proteome or a finite cytosolic space, to ensure maximal evolutionary success in a given environment. A second theme will concern the implications of resource allocation for cyanobacterial productivity. It is shown that high maximal growth rates are not a sufficient or necessary property for high phototrophic productivity. Finally, I will discuss how the perspective from (optimal) resource allocation can help us to understand the evolution of interactions between phototrophic and heterotrophic microbes as part of microbial ecosystems.

Short CV

Ralf Steuer studied Physics in Munich and Berlin. Previous works include time-series analysis, information theory, analysis of metabolomic data, and computational model of cellular metabolism. Within the past 10 years a particular focus has been on computational descriptions of cyanobacterial metabolism and growth. The research group published genome-scale metabolic reconstructions of several cyanobacterial strains and pioneered the use of large-scale models of time-dependent resource-allocation in phototrophic microorganisms.

Metabolic engineering of microbes to produce compounds of interest often involves dramatic alteration of metabolite pools. An often-overlooked consequence is that accumulating metabolites may negatively affect enzyme activity through competitive or allosteric inhibition. Additionally, post-translational regulation of enzyme activity can complicate metabolic engineering, as pathway flux becomes less sensitive to artificial enzyme overexpression. Here I will describe our adaptation of two chemoproteomics methods to identify metabolite-protein interactions in the proteomes of cyanobacteria and chloroplasts. These techniques rely on changes in thermal stability or of proteolytic digestion susceptibility in the presence of an effector metabolite, and together allow us to map metabolite-protein binding surfaces. In an initial effort, we found widespread interaction of tested metabolites with enzymes in central carbon metabolism, but that only a fraction of these interactions affect catalysis. For example, the Calvin cycle intermediate glyceraldehyde phosphate (GAP) stimulated activity of the Calvin cycle enzyme F/SBPase in reducing conditions, representing a feed-forward activation of the cycle. In oxidizing conditions however, GAP inhibited the enzyme by promoting aggregation. I will also describe efforts in mutagenizing enzymes to reduce sensitivity to metabolite regulation, by high-throughput screening of the effects of enzyme mutation on both cell growth and product synthesis rates.

Paul Hudson is associate professor in the School of Biotechnology at KTH Royal Institute of Technology in Stockholm, Sweden. He studied chemical engineering at NC State and UC Berkeley, and did post-doctoral training at KTH on bacterial surface display (2012-2014). His research as a group leader is on metabolic engineering of CO2-fixing bacteria, with focus on Calvin cycle bacteria such as cyanobacteria. The research uses systems biology methods such as proteomics to study CO2 fixation metabolism, and to guide engineering strategies for enhancing CO2 uptake and conversion. His group also develops synthetic biology tools in these strains.

Floodplains within mountainous catchments are dynamic reservoirs of carbon and nutrients, and experience seasonal flooding due to snowmelt and drainage. Climate change is rapidly altering snowpack and melt dynamics, resulting in greater variability in flooding and droughts. The variable hydrology drives spatial and temporal redox gradients within floodplain soils, with largely unknown consequences for carbon storage in and export from such ecosystems. In this presentation, I will report on a high-resolution monitoring campaign across extremely low and high river discharge years, foreshadowing climate change predictions, in a headwater catchment in the Rocky Mountains (Colorado, US). Combining in-field biogeochemical measurements with molecular and geochemical measurements, I will show that such extreme hydrological extremes undermine mineral and metabolic constraints on soil carbon cycling, altering pathways and rates of carbon loss from mountainous floodplains. Global implications of our findings for predicting climate change impacts on carbon cycling within dynamic floodplains globally will be discussed.

Prof. Dr. Marco Keiluweit is interested in how biogeochemical mechanisms controlling carbon and nutrient cycles in soil and sediments respond to climate and land use change. He completed his PhD at Oregon State University, and worked as a postdoc at Stanford University and as Assistant Professor at the University of Massachusetts-Amherst. He is now Professor of Soil & Microbial Biogeochemistry in the Institute of Earth Surface Dynamics at the University of Lausanne, Switzerland. His research combines laboratory, greenhouse, and field experiments with advanced analytical tools such as synchrotron spectroscopy, chemical imaging, and molecular microbiology. His group’s work links fine-scale biogeochemical mechanisms to landscape-scale processes within natural and managed ecosystems. Prof. Keiluweit has acquired numerous grants and has received several prestigious awards, including US DOE Lawrence Scholar and NSF Early Career awards.

Among different synthetic protocols, electrochemical exfoliation [1] of layered materials is a very promising approach that offers high yield, great efficiency, low cost, simple instrumentation, and excellent up‐scalability. Remarkably, playing with electrochemical parameters enables functionali-zation and tunable material properties and increases the material diversities from graphene to a broad spectrum of 2D semiconductors [2].

High solution processability of 2D materials via electrochemistry also offers hybridization/ functionalization of 2D materials and improve their processabilities into functionalized inks/paste/formulations. Wet chemistry also enables us to develop transition metal carbides/nitrides (Mxene) via safe and sustainable flouride-free approaches.

Figure 1. Schematic illustration of electrochemical exfoliation methodology and different 2D
materials which could be produced via this method

References:
[1] Adv. Mater. 2020, 32, 1907857.
[2] Adv. Mater. 2020, 32, 1907244; Small 2019, 15, 1901265; Angew. Chem. Int. Ed. 2018, 57, 4677-4681; Angew. Chem. Int. Ed. 2018, 57, 15491-15495.

Cyanobacteria, prokaryotic microorganisms with basically the same oxygenic photosynthesis as higher plants, are excellent green cell microfactories for sustainable generation of renewable chemicals and fuels from solar energy and CO2. In the presentation I will visualize the concept green cell factories by discussing two examples: (i) Generation of functional semisynthetic [FeFe]-hydrogenases linking to the native metabolism in living cells of cyanobacteria cells, and (ii) Engineering cyanobacteria to produce the bulk chemical and blend-in molecule butanol from sunlight and CO2.
[FeFe] hydrogenases are the most efficient molecular catalysts known to date with regards to H2 production. Cyanobacteria harbor native [NiFe] hydrogenase(s) but no [FeFe] hydrogenase. A heterologously expressed [FeFe] hydrogenase was synthetically activated in a hydrogenase deficient strain of the cyanobacterium Synechocystis PCC 6803 (1). H2-evolution assays showed that the non-native, semi-synthetic enzyme links to the native metabolism in living cells. The artificial activation technology was expanded to a newly discovered [FeFe]-hydrogenase which when expressed in Synechocystis showed stable expression and significant H2 production under different environmental conditions (2). This semisynthetic [FeFe]-hydrogenase remained functional in vivo in cells of Synechocystis for several days. The developed technology opens up unique possibilities to investigate not only [FeFe]-hydrogenases but also other metalloenzymes in a photosynthetic microbial cell environment, completely bypassing the many challenges of e.g. biological maturation and regulations.

Cyanobacteria lack the butanol biosynthetic pathways and corresponding relevant gene(s). Introduction of a single gene encoding KivD results in isobutanol producing strains. Further engineering and long-term experiments demonstrated a maximal cumulative isobutanol titer of 1.2 gram per liter (3, unpublished). Similarly, introducing a complete 1-butanol pathway, together with additional enzymes to increase the pool of acetyl-CoA, resulted in cells with a cumulative titer of 4.8 g per L, and a maximal rate of 600 mg 1-butanol per L and day and carbon partitioning of 60% (4-6). Present progress towards a practical system will be presented and discussed.

(1) Wegelius et al 2018. Generation of a functional, semisynthetic [FeFe]-hydrogenase in a photosynthetic microorganism. Energy & Environmental Science 11: 3163-3167

(2) Wegelius et al 2021. Semisynthetic [FeFe]-hydrogenase with stable expression and H2 production capacity in a photosynthetic microbe. Cell Reports Physical Science 2: 100376

(3) Xie & Lindblad. 2022. Effects of expressing 2-keto acid pathway enzymes on photosynthetic isobutanol production. Microbial Cell Factories 21: 17

(4) Wichmann et al 2021. Engineering Biocatalytic Solar Fuel Production: The PHOTOFUEL Consortium. Trends in Biotechnology 39: 323-327

(5) Liu et al 2021. Engineering cyanobacteria for photosynthetic butanol production. In: Photosynthesis. Biotechnological Applications with Microalgae (Ed: Rögner) 2: 33-56. Walter de Gruyter GmbH, Berlin/Boston (6) Liu et al 2022. Current advances in engineering cyanobacteria and their applications for photosynthetic butanol production. Current Opinion in Biotechnology 73: 143-150

The prevailing view of biological evolution is not unlike bricolage/pastiche/tinkering—in sharp contrast with rational engineering. Yet, different paths often lead to solutions that coincide or converge whether they emerge from naturally-occurring evolution or rationally designed. Such a conjunction—often presented as a mere anecdote— in fact reveals the ability of biological systems to physically explore solution spaces and gravitate towards information-rich attractors, which can be found through different routes. This scenario evokes one of heterotic computing, a non-conventional type of data processing in which the solution to a problem is not delivered through numerical calculations but through its embodiment in a material object. Once left to undergo a physical process the object manages a large number of parameters for reaching a multi objective optimum. The course of information is thus a physical flow and the outcome is a physical currency. The consequences of this notion for bioengineering are remarkable, as it enables solutions to multi-objective optimization challenges not yet amenable to all-rational approaches. The ensuing technical question is how to bring about hyper-diversification not only of genomic sequences but also environmental and context-dependent parameters for securing the desired performance of a given synthetic device. This issue will be illustrated with a number of practical cases where naturally-occurring or artificially enhanced variability was key to find ideal outcomes to otherwise intractable design hitches of interest for industrial and environmental biotechnology. (1) Al-ramahi et al. (2021) ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces. Comms Biology 4: 1169. (2) Tas et al. (2020) Contextual dependencies expand the re-usability of genetic inverters. Nature Comms 12: 355.