A new Nature Comm paper: How a bacterium adapts its membrane fluidity to temperature without a thermometer

A new collaborative paper with Greg Bokinsky has just came out in Nature Communications! You find it here: paper link.

When temperature changes, the kinetics of enzymes change (think of the Arrhenius law) as well as their diffusive properties (the diffusion coefficient depends linearly on temperature, at constant viscosity). The change in the diffusion coefficient of cytosolic and membrane proteins is different since membrane proteins are dependent on the change in membrane fluidity (via, the membrane viscosity change). Some of those changes are large, whereas others are small. Their magnitudes depend on the precise biochemistry of the associated molecules, which is outside of the realm of control by the microbe, and all molecular changes to temperature propagate in a nonlinear way to the phenotype. The only measure a microbe has — to somehow control this — is by adjusting protein expression and hereby change its molecular composition, including the lipid composition of its membrane. To achieve this, the microbe needs mechanisms akin to thermometers and homeostatic controls — similarly to the thermostats in your house!

Dr Greg Bokinsky, from the nanoscience department of the TU Delft, developed a mass spectrometry based method for the measurement of the most important intermediates and enzymes of fatty acid and lipid metabolism in Escherichia coli. He used this method to monitor the temperature response of this metabolic system as function of time. Since this bacterium does not measure membrane fluidity, like other organisms do, he was interested in figuring out how fluxes in lipid metabolism are repartitioned in response to temperature to adjust the membrane lipid composition such that membrane fluidity remains (almost) independent of temperature.

We got involved in this because Greg found that several adaptive mechanisms act concertedly and on different time scales. Metabolic regulation on a time scale of second to minutes, and gene expression adaptation on a time scale of tens of minutes. Also, it remained unclear which enzymes were likely temperature sensitive — this is hard to determine in vitro because of the complexity of the substrates and the cell-free extract assays. We helped Greg to figure these things out, together with his students. The model we eventually ended up with was remarkably simple and powerful in describing the data, giving us confidence in our understanding of this complex adaptive mechanism.

What I enjoyed most of this study, in addition to solving this puzzle with Greg, is the experiment that addresses the consequences of temperature maladaptation. It turns that the diffusion of one of the components of the respiratory chain can become rate-limiting when the temperature drops, the membrane fluidity is increased which effectively removes this rate limitation and restores fast growth. This is shown in Figure 5 of the paper, when E. coli grows on succinate.

We hope you enjoy this work!

New review: The pectin metabolizing capacity of the human gut microbiota

Ecem Yuksel, Remco Kort, and colleagues wrote a new review about the different bacteria in our intestines that can degrade a certain kind of dietary fiber called pectin, and how this can benefit our gut health. Check out the review here! (Picture from here)

The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome’s response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.

Bas speaks at VU’s Opening Academic Year

The new academic year kicked off on 2 September 2024 with the Opening Academic Year. This year’s theme was ‘Reasons for Hope’. Bas was interviewed as part of the panel and spoke as the Director of AIMMS about how we are committed to making a positive impact on life and the environment by accelerating breakthroughs in molecular science. He also highlighted our initiatives to unite a new generation of thinkers to address complex societal challenges, including organizing hackathons.

Reaching out the general public: our research was mentioned in C2W:Mens & Molecule

C2W:Mens & Molecule is a Dutch publication platform (including a magazine) for independent science journalism for chemistry and life sciences. Our current research on usage of alternative cofactors (e.g. replacing the NADH/NAD couple) in novel metabolic engineering strategies for microbial biotechnology has recently feature in this magazine. We carry out this research in collaboration with labs from the universities in Wageningen and Delft, all working on different aspects. At the VU, four of us are working on the project Lies, Maaike, Bas and myself.

You find the article here: https://www.sciencelink.net/verdieping/meer-grip-op-het-metabolisme-van-microben/22138.article.

Summer school “Economic Principles in Cell Biology”

Maaike and Pranas participated in the third summer school on Economic Principles in Cell Biology that took place on the 8-11th July, 2024, in Paris and online. Lab PhD students Francesco and Luis also attended the lectures online. Maaike was one of some 30 participants selected for in-person attendance, and Pranas gave one of the introductory lectures, “An inventory of cell components” (together with Diana Széliová, University of Vienna). A small size of this course came to our advantage for the social part: we enjoyed both the science and the beers at the Seine (and watching EURO2024!) with colleagues coming from different parts of the continent and beyond.

The scientific part of the summer school was accompanied by two more soft-skills oriented activities: first, the workshop on the creative process in science, Night Science by Martin Lercher. You might have heard of the editorials- and podcast series of Martin and Itai Yanai under the same name – give it a listen if you haven’t! The last day was dedicated for the Atelier SEnS, a workshop on exploring the relationship between one’s personal values and the research they conduct.

The summer school is an activity that emerged from the community initiative of the same name that aimed to bring the colleagues working under similar philosophy together. It all started as a monthly seminar via Zoom in early 2020, organized by a handful of professors (including our own Frank!), and the community expanded over time. Eventually, an idea to write an open-source textbook started gaining momentum. The book project is led by Wolfram Liebermeister at INRAE (France), and Pranas is one of the coordinators of the initiative since recently. The summer school is one of the ways to promote the textbook project, and to test its didactical value in practice.

Overall, it was a very nice experience, and quite a relaxed one (in both best and worst ways of it). The 2025 summer school, if all things turn as planned, will be held in Vienna, with a lot of improvements/changes planned, so we are quite excited to join it if it materializes!

How genetic circuits can optimally tune metabolic protein concentrations

Since cells have finite biosynthetic resources for protein synthesis, a rise in one protein concentration is generally at the expense of that of others. A logical consequence is then that phenotypic traits trade-off: cells cannot excel at everything. They cannot grow fast and be very stress tolerant and adaptive to new conditions at the same time. Another consequence is that protein under- and over-expression without a long-term fitness benefit is likely selected against. 

How do cells then decide on the expression level of proteins? Can they even tune protein concentrations optimally — to prevent wasteful over-expression and suboptimal under-expression? What do cells try to achieve by changing protein concentrations? How can they decide that tuning is finished and that protein concentrations are optimal?

In this new paper (https://doi.org/10.1042/EBC20230045), we can gave an overview of how cell can achieve growth-rate-maximising tuning of metabolic protein concentrations, via optimal gene expression of metabolic genes. We pioneered this method in Berkhout et al.(https://doi.org/10.1038/srep01417) and generalised it in Planqué et al. (https://doi.org/10.1371/journal.pcbi.1006412), and applied its way of thinking to understand the regulation of ribosomal gene expression in E. coli in Bosdriesz et al. (https://doi.org/10.1111/febs.13258). Here we give an elementary overview of this theoretical method. We apply it to understand the gene-regulatory feedback regulation of amino-acid metabolism. 

Some more background information on this way of thinking can also be found in some teaching material I wrote for a course on enzyme kinetics (https://teusinkbruggemanlab.nl/course-information-from-enzyme-kinetics-to-models-of-metabolism/).

We hope that we have inspired you to think also about how cellular objectives can be achieved by gene-regulatory circuits.

Our take on the practical aspects of genome-scale modeling

Some time ago, we started an initiative in the lab to collect all the best (and worst) practices on how to reconstruct, curate, and simulate genome-scale metabolic models (GEMs). A total of 7 colleagues, including a visiting PhD student Gioele Lazzari from the University of Verona, and a MSc rotation student Steven Wijnen, have put their forces together with Pranas to reflect on their experience, share tips, tricks, and caveats on the art of genome-scale modeling. After months of discussions, writing, and polishing, we would like to share the first public version of the handbook as an early Valentine’s present to the community :).

We cover topics from the very basics on data collection to make GEMs to rather advanced material, such as creating context-specific or community metabolic models. The handbook is accompanied by two Jupyter notebooks that can be used for training colleagues new to GEMs, or in your teaching. All materials are licensed under CC-BY-NC, which permits unrestricted non-commercial use of the materials as long as attribution is given.

It has been a great experience, and the initiative has been received very well by the lab members outside of this writing group. We invite fellow colleagues to contribute with ideas, thinking, and writing, if they see value in a community effort to share their best practices. You are always welcome to drop a line to Pranas on these matters.

Happy modeling!

Our research featured in Quanta Magazine

Microbiologists are searching for a universal theory of how bacteria form communities based not on their species but on the roles they play.

A new article in the popular science magazine Quanta has highlighted our work on metabolic preferences and their genomic markers. How can we identify rules of microbial communities? What are the traits that determine success in a community? What level of abstraction is useful when thinking about the many species of bacteria living in a given community? How can we design microbial consortia? These are some of the questions that the research (including our own) described in this article is trying to unravel. Exciting times for microbial ecology!

Read the article here: https://www.quantamagazine.org/the-quest-for-simple-rules-to-build-a-microbial-community-20240117/

Herwig to lead €5M NWO Perspective Grant Consortium for plant-based fermentations

The Netherlands Organisation for Scientific Research (NWO) granted the FERMI Perspective proposal led by Herwig Bachmann from the Systems Biology Lab. The project aims to accelerate the protein transition by improving the taste of plant-based products through fermentation by microbes. With colleagues from the Wageningen University and TU Delft and 10 industrial partners, the project will combine experimental and computational methods to unravel the biochemistry of the underlying conversions: which chemistry, enzymes and pathways turn beany and grassy flavours into meaty or neutral ones? This knowledge should accelerate a shift towards a more plant-based diet and will contribute to a more sustainable food production chain.

For more info, see the infographic below (click to enlarge).

Overview over the FERMI project

We wrote a paper for a special issue celebrating the 50th anniversary of Metabolic Control Analysis

Which metabolic enzymes should a cell change in concentration to give rise to a large change in steady-state metabolic flux? Which enzymes should an experimentalist inhibit to reduce the flux the most?
Why are some kinase-phosphatase couples in cellular signal transduction ultra-sensitive to changes in signals, while others are not? What is the function of negative feedback in metabolic pathways? How can you design metabolic pathways that are insensitive to particular environmental changes and highly sensitive to others?

Answering such questions requires consideration of enzymes active in networks, as their activity and network influence depend on their reactant concentrations, which are co-determined by all enzymes in the network. Answering such questions therefore needs a systems perspective. One that is quantitative also; as all enzymes influence the network’s functions but to different degrees. The concept of a single rate-limiting step is therefore generally overly simplistic.

Now about 50 years ago, two papers were published, one by Burns & Kacser and another by Heinrich & Rapoport, which dealt with a sensitivity analysis of metabolic pathways to change in enzyme activities and concentrations. They also managed to derive theorems relating sensitivity coefficients. Those coefficients come in two forms: elasticity coefficients and control coefficients, and their products are called response coefficients. We invite you to check out those papers, they have not aged. The entire framework is called Metabolic Control Analysis (MCA).

Bas (Teusink) and myself grew up as young scientists in the scientific community of MCA due to our PhD supervisor, Prof Dr Hans Westerhoff, who was one of the pioneers and advocates of MCA. MCA was therefore part of our training and thinking, and we have published papers about this theory.

What always attracted me (Frank) as how Christine Reder‘s formulation of MCA makes the relation between reaction stoichiometry and enzyme kinetics so clear, and in completely general terms. By using concepts from linear algebra and enzyme kinetics, the control of enzymes on steady-state properties of enzyme networks could be written down in completely general terms. This gave me confidence that a general theory about cellular metabolism and growth can be derived, applicable across all domains of life. Aiming for this has been a research theme throughout my career.

One aspect of Reder’s theory is that the null space of the stoichiometric matrix is used to derive the summation theorems of MCA. But the null space is not unique, which always bothered me when I was a PhD student. This was changed when David Fell, Stefan Schuster and Thomas Dandekar generalised the definition of metabolic pathways in a unique manner, using a concept that is related to the null space of the stoichiometric matrix. They showed that any steady-state flux solution of a stoichiometric matrix is convex combination of a set of unique flux vectors, called elementary flux modes (EFMs). This solved the problem of the entire set of summation theorems (although I do not know whether any one ever published this). EFMs are (beautiful) mathematical objects with extremely appealing mathematical properties for biotechnology and evolutionary biology.

We worked for quite some time on EFMs in the context of the optimisation of stoichiometric models and of dynamic models (containing stoichiometry and enzyme kinetics). It turns that EFMs are the solution of optimisations of enzyme networks, given enzyme kinetics, where one aims to maximise a steady-state flux by optimising enzyme concentrations that sum to a fixed total. They are also the elementary solutions of flux balance analysis computations, considering only reaction stoichiometry and not enzyme kinetics.

If evolution maximises the growth rate of cells then what would be the flux control coefficients of all the optimally expressed enzymes? MCA suggests that you cannot answer this question, because you do not know the enzyme kinetics, and therefore you do not know the elasticity coefficients. But it turns out that you can! This was realised by Klipp & Heinrich, and even earlier by Burn & Kacser in a more simplified setting (in Burn’s thesis). The context of Klipp & Heinrich is regrettably also too simplified to consider the entire metabolic network of a cell that is growing at its maximal rate by having expressed all its enzymes optimally.

The solution to this problem we offer in our paper to the special issue of Biosystems celebrating the 50th anniversary of MCA. You can find the paper here. It is quite a read, we know, but it contains all the main ideas from start to end. We hope that it inspires you to become familiar with MCA, enzyme kinetics, and stoichiometric modelling concepts.