Michael Jahn

We recently noticed problems to map next generation sequencing reads to certain regions of the Streptococcus genome, our pet organism for the study of pathogenic bacteria at the MPUSP. An extensive re-sequencing effort using short and long read methods revealed that the original assembly contained various errors, particularly for repetitive rRNA/tRNA operons (published now in MRA). Our new assembly fixes these errors and adds two new tRNAs, becoming the current reference assembly for Streptococcus pyogenes. It’s available on NCBI datasets.

We published our second paper about C.necator in AEM which uses a barcoded transposon library to study its energy metabolism. This is not only a continuation of our previous work but also a systematic survey in the spirit of the landmark paper by R. Cramm, 2008 – in this extensive review, the author meticulously collected all known information about the energy metabolism of this interesting organism. Our work investigated the relative importance of all formate dehydrogenases, hydrogenases, and electron transport chain complexes experimentally, with several remarkable findings. This study was a fruitful collaboration between three groups that I am sincerely grateful for, Paul Hudsons lab, Oliver Lenz’ lab, and Emmanuelle Charpentier’s lab.

Very happy that our newest CRISPRi library paper was finally published in The Plant Cell from Oxford University Press. The paper takes a deep dive into the subtle tradeoffs between growth rate and growth robustness in photosynthetic bacteria. All fitness data are available online in my R Shiny App ShinyLib.

Together with my colleagues at Science for Life Lab, Stockholm, we have submitted a new manuscript with the second iteration of our CRISPR interference library in cyanobacteria. The paper is currently in revision but can already be accessed on BioRxiv.org. It’s filled to brim with new insights about fitness tradeoffs in photosynthetic bacteria, such as fitness cost for the highly expressed photosystem and light harvesting protein machines. Special thanks to Rui Miao who is the shared first author with me.

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.

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.