Michael Jahn

Purpose of the model In order to study the fundamental processes in photo-autotrophic bacteria, we developed a simplified cellular economy model for the simulation of these processes. The purpose of such models is not to reflect cellular behavior in its entire complexity, but rather to reduce complexity to an amount that still allows drawing significant conclusions while keeping the number of components and reactions as small as possible. The cellular economy model bundles fundamental processes in ‘super-enzymes’, single catalytic units that serve as proxies for similar pathways. Such coarse-grain models are useful to illustrate metabolic tradeoffs under different conditions without getting lost in details.

Our new paper, “Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator”, was finally published in eLife!. It was a long journey, taking almost two and a half years to submission and another six months of review and improvements to finally publish it. We combined several layers of genome-wide screens: MS proteomics, gene essentiality from a transposon mutant library, and resource balance analysis modeling. Combining these layers allowed us to show that C. necator is a bacterium in the making. It has several conflicting layers of regulation to tune gene expression of its highly versatile but complicated carbon and energy metabolism. Our results show for example that cells “waste” protein resources for autotrophic lifestyle even when no hydrogen is available. In the next sections, I will take a deep dive into the detailed findings of our paper.

Our new paper about protein utilization in the versatile lithoautotroph Cupriavidus necator (aka Ralstonia eutropha) was just deposited on BioRxiv.org. Integrating data from proteomics, resource allocation modeling, and a transposon mutant library, we found some really interesting things. For example, of the three chromosomes that C. necator owns, one encodes 80% of the protein mass (the housekeeping chromosome). The other chromosomes encode specialized functions like CO2 fixation genes and were probably acquired later in evolution. The expression of these genes conflicts with overlapping functions of the ancestral chromosome.

In a few days starts the 11th European workshop on the biology of cyanobacteria. It was planned to take place in beautiful Porto, Portugal. I was very much looking forward to this as I haven’t been on a conference for a whole year. But unfortunately COVID-19 forced the conference organizers to turn it into a digital meeting. This is not as exciting as visiting a real conference (and a new city!) and meeting people in person, but I’m nevertheless looking forward to it.

The corona virus crisis has overshadowed the life of many EU citizens for quite some time now, and will likely continue to do so for the coming months. The strict social distancing measures taken by many governments leave work places deserted, factories standing still and shops closed. However, one small country on the Northern edge of Europe is going it’s own way to tackle the CoV pandemic and it is highly interesting how this experiment will turn out. None the least as I am part of that experiment.

Finally, after 4 years of work with dozens of cultivations and millions of sequenced reads, our paper about a CRISPRi library in the model cyanobacterium Synechocystis was published in Nature Communications. What is this story about? Cyanobacteria are promising hosts for biotech production of (fine) chemicals. They are particularly interesting because they can grow solely on CO2 and sunlight. However, the productivities are low, the implemented pathways often instable, and the adaptation to varying amounts of light or CO2 not fully understood. Our group created a ’library’ (a mixed pool) of thousands of mutants, each one equipped qith a CRISPR based gene repression system repressing one gene at a time. By cultivating this pool of mutants under low light, high light, and a lactate production condition, better adapted mutants were enriched over time, and worse adapted mutants depleted. By these means we were able to find a handful of genes improving growth, acid tolerance, or lactate productivity.

The famous ggplot2 package for R has numerous packages extending its basic plot functions, including ggrepel that draws nice text labels for each point of a scatterplot. But I am using lattice for many years now, and came to like its look and customization options. However, one thing I was missing all the time is a simple one-line function to add small text labels to points in a scatter plot (a.k.a. dot plot, a.k.a. xyplot() in lattice).

My github activity is in free fall, my email response time is at least two days, and my stress level is lower than usual. What has happened, am I on vacation? Not quite, I’m in the middle of a five month parental leave with my almost one year old daughter Sophie. So far it’s been a joyful but also challenging time. Here are some thoughts about my own parental leave, about the conditions here in Sweden, and a comparison with other European countries.