Hudson Lab

Axel, Anna, and Emil attended the 14th EWMBC in Seville. Axel and Emil presented posters on growth arrest cyanobacteria and Anna gave a presentation on ppGpp interactome in plants and cyanobacteria.

We are happy to be a part of S2B: Solar 2 Butanol. An EU project coordinated by Yagut Allahverdiyeva at the University of Turku. We will create photosynthetic films containing highly engineered butanol-producing cyanobacteria. Bruno, Maria, and Ulysse will work on the project from KTH.

Bruno was an invited speaker at the 18th International Congress on Photobiology (IUBP-MEPSA) in Perth, Australia. He presented our work on enzyme clustering in cyanobacteria

Paul was an invited speaker at the PortoSynH2 symposium in Porto, the 2nd European Conference on Photosynthesis in Padova, and the European Biotechnology Congress in Rotterdam. He presented the group's work on interaction proteomics and enzyme screening and met our collaborators from Sweden, Hungary, Italy, and Spain.

Venice on the way to ePS2 conference

Paul and Axel traveled to TU Graz to attend a UNITE! workshop. Axel presented on growth-arrested cyanobacteria.

Rui and Michael's paper on CRSIPRi screens in Synechocystis was published in The Plant Cell. We report on essentiality of many genes in this model strain across 11 growth conditions. We also find genes that are expressed "wastefully," in some growth conditions. Thank you to Gilles Peltier and Yonghua Li-Bensson at CEA Cadarache, where Rui spent 3 months on a FEMS fellowship. Michael provides all data in an interactive web application "ShinyLib."

There is also an Editorial summary, "What do photosynthetic organisms need to thrive in all circumstances?"

CRISPR interference screens reveal growth–robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions

Paul was an invited speaker at the Gordon Conference on Photosynthesis, at Sunday River Resort, Maine. His talk was in the session, "Manipulation of Photosynthesis for Energy and Products." The talk was

"Chemoproteomics to Identify Metabolite Regulation of Photosynthesis and Carbon Fixation”

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 application of chemoproteomics methods to identify metabolite-protein interactions in the proteomes of cyanobacteria and chloroplasts. In a first study, 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. Finally, I will describe efforts in mutagenizing enzymes to reduce sensitivity to metabolite regulation, by high-throughput screening of the effect of enzyme mutation on both cell growth and product synthesis rates.

Above: A graphical abstract for the presentation. The protein landscape subfigure is from Wittman et al 2019

We were collaborators on a recent paper from the Pia Lindberg group in Uppsala, published in Metabolic Engineering. Nick and Elias contributed with genome re-sequencing of several cyanobacteria strains that had been evolved to tolerate phenylalanine. The more-tolerant strains also produced more phenylalanine. It will be interesting to investigate the molecular mechanisms behind this increased secretion. Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production

Paul, Ute, Anna, and Axel attended the 16th Nordic Photosynthesis Congress in Umeå. Paul, Ute, and Anna presented talks and Axel was inspired to do start new projects.

Rui, Elias, and Emil went to the Marina Bay Sands in Singapore for the Metabolic Engineering 15. Emil and Elias had posters and Rui gave a flash talk on CRISPRi libraries in cyanobacteria.

*Rui winning fans in Singapore (blurry) *

Paul published an invited review on the bacterial Calvin cycle. in Seminars on Cell and Developmental Biology. The article covers new discoveries on how the Calvin cycle is regulated at different levels (transcriptional, translational, and post-translationally) in both lithoautotrophic and photoautotrophic bacteria.

The article is part of a themed issue on the Calvin cycle edited by Christine Raines and Amanda Cavanaugh, and there are many interesting articles also on plant carbon fixation.

PH helped organize a Swedish Symposium on Enzyme Engineering, along Christian Schnepel and Per-Olof Syrén at KTH. The all-day symposium was held at Alba Nova Unversity Center. We had over 90 participants from all over Sweden (and a few international). From our group, Ute presented her and Anna S work on in vivo enzyme engineering.

Emil and Paul presented at the annual KTH Department of Proteomics "Protein Corner," day, at SciLifeLab.

We hosted a semi-annual consortium meeting for the SSF-funded project Redesinging Photosynthesis for Future Food Security (ARC19-0051), at SciLifeLab. Coordinator Åsa Strand and project partners Alizee Malnöe and Magnus Hertzberg came from Umeå with some from their groups. From our group, Ute and Anna presented on progress on Calvin cycle engineering and interaction proteomics.

Update August 2023: The positions have been filled

Are you our new team member? Come work with our outstanding team of experimental and computational biologists. We are hiring postdocs and a Ph.D. student in the field of syntethic and systems biology of CO2-fixing bacteria. The projects involve creation of genetic libraries of cyanobacteria and novel high-throughput screening platforms. Applicants with experience in microbial physiology, metabolic engineering, or photosynthesis are encouraged to apply! See more and apply at links below

Post-Doc in regulation of carbon fixation and photosynthesis

Graduate student in synthetic biology

Paul and Axel attended KTH Transformation Day. This years theme was transformation of the food industry. There were talks from food industry representatives and KTH researchers about their efforts to make the food industry more sustainable. Paul presented the concept of our new SSF FFF project to prouce food ingredients from CO2, and about the potential for microbes to be a edible protein source.

A summary of the day is here

Markus and Nick's paper was published in Metabolic Engineering. Markus used computational modeling to predict gene modifications to increase production of the bioplastic from formate. Nick created the recombinant strains and found production of PHB from formate could be increased 100% with an added phosphoketolase. Formate is an interesting substrate since it can be produced by electroreduction of CO2.

"Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator,"

Paul and Ute traveled to Liverpool to attend the 17th ISPP. Paul gave a talk on interaction proteomics and regulation of enzyme activity in Synechocystis, and Ute presented a poster on the role of RNAses in cyanobacteria.

Ivana's paper on CRISPR/Cas gene editing in Synechocystis is published in ACS Synthetic Biology. The Cas9 enzyme is quite toxic to Synechocystis, so careful control using a riboswitch was necessary to successfuly edit the genome. Collaboration with Nigel Minton group who had previously developed RiboCas in Clostridia. Plasmids will be available for community via Addgene.

Paul presented at the 18th ICPR in New Zealand (over Zoom). The conference theme was Photosynthesis Research - Fundamental and Applied Science for Energy and Food Security and our presentation was in the session Synthetic Biology.

Paul presented our work on interaction proteomics in Synechocystis at the Nordic Algae Symposium in Turku: Elevating Nordic Algal Biotechnology.

Our will coordinate a new project funded by the Swedish Foundation for Strategic Research, as part of their Food, Feed, and Forest program.

Our project will convert CO2 into food ingredients such as palm oil, using cyanobacteria and yeast. These microbes will be optimized using state-of-the-art technologies at SciLifeLab. The project will run 2022-2025 and other partners are Prof. Verena Siewers (Chalmers), Per-Olof Syren (KTH), and Håkan Jönsson (KTH).

Press release from SciLifeLab here

graphic from SSF

Nick and Paul travelled to Nottingham for the Synthetic Biology UK conference. Nick presented on our barcoded transposon library in Cupriavidus. Paul presented on our various approaches to enhancing CO2 fixation in cyanobacteria.

Nick winning fans in Nottingham

Michael's paper, Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator was accepted in eLife. The paper explores enzyme expression and essentiality in Cupriavidus necator, grown in different conditions. This strain is of industrial interest since it can produce the bioplastic PHB from a range of substrates, including H2+CO2 and formate, a C1 chemical that can be produced from electricity and CO2. A main finding of the paper is that many enzymes are underutilized, as they are in abundance or excess even when not needed. For example, the Calvin cycle is expressed even during growth on sugar. This may be a way for this soil bacterium to quickly adapt to changing nutrient conditions. The list of essential genes in multiple growth conditions will also be useful for others working on this promising strain.

Kiyan's paper, Cycling between growth and production phases increases cyanobacteria bioproduction of lactate was published in Metabolic Engineering. The paper presents a strategy for increasing productivity of cyanobacteria by controlling when and how much of fixed CO2 is diverted to product biosynthesis instead of cell growth. Up to 90% of fixed CO2 could be converted to lactate using a CRISPR interference metabolic switch. Oscillating this switch allowed cells to cycle between growth and product synthesis, resulting in a 3-fold higher overall product titer comparaed to when no switch was present.

Paul presented at the CeBiTec Research Conference in Bielefeld. The theme of this yaers conference was "Prospects and challenges for the development of algal biotechnology." This was the first in-person conference in 1.5 years!

Check out and register to attend the 15th Nordic Photosynthesis Congress in Gothenburg! The theme is, "Capturing light to power the planet." This will be a great conference about various aspects of photosynthesis, including metabolic engineering of plants and cyanobacteria! Paul is helping to organize along with Cornelia Spetea-Wiklund (Gothenburg University) and Alexey Amunts (Stockholm University). We have a fantastic invited speaker lineup from all over Europe, and we will select about 20 abstracts to give talks. The meeting is NOT restricted to just the Nordics! See the attached flyer. Registration deadline is 15 August. The event will be in person!

Cyanobacteria Biotechnology, edited by Paul Hudson, is now published by Wiley VCH. This book contains 17 chapters on cyanobacteria metabolism and applications, written by leading experts from around the world. The book is part of Wiley's Advanced Biotechnology series. There will soon be a PDF format. Thank you to all the contributing authors, and to my group who helped review chapters and gave advice.

Front cover

Jan's paper Slow Protein Turnover Explains Limited Protein-Level Response to Diurnal Transcriptional Oscillations in Cyanobacteria was published in Frontiers in Microbiology. Jan combined three systems biology techniques, transcriptomics, proteomics, and ribosome-profling, with a simple mathematical model to show that protein abundances in cyanobacteria do not significantly change over the day/night cycle, while their mRNA and translation levels do. This puzzle can be explained by a slow protein turnover.

Paul presented at the seminar on Carbon capture and utilization, organized by Royal Swedish Academy of Engineering (IVA). The webinar is available online (Swedish).

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes is published in PLoS Computational Biology.

In this computational work, Johannes found one thousand non-cyanobacterial genomes containing the Calvin cycle, and compared them to close relatives that lacked the Calvin cycle. We wondered how bacteria integrate a newly-acquired Calvin cycle into their metabolism. Using multiple analyses, including a machine learning algorithm, he found some key differences in the abundance of genes and protein family domains between these two groups. The software he developed for this analysis is RedMAGPIE, for "Reductive pentose phosphate pathway Machine-Assisted Genomic Pattern Identification and Evaluation." Perhaps most interesting are genes and protein domains of unknown function that were revealed to be of high importance. Some of these likely play a role in regulating the Calvin cycle, and could be targets for metabolic engineering. RedMAGPIE ranks genetic adaptations to the Calvin cycle to construct a recipe for an autotrophic microbe.

Behold! We have for a while wanted our own website. It was important for us to be able to share our software, data, and publications in a coherent way, so as to make a faithful impression on visitors. We are so pleased with the layout and imagery! This website was designed and built by Balthazar Berling Kelpe. We use Cirrus Cumulus by Clara Sambot for our logo.

Paul gave a 2 minute pitch at the AlgaeEurope 2020 (virtual). The conference was focused on cultivation and engineering of microalgae for economical production of chemicals. You can see the pitch here.

Paul presented at the 4th International Conference on Plant Synthetic Biotechnology, Bioengineering, and Biotechnology. Originally planned for Copenhagen, it was also held virtually. No worry! The conference covered plants, microalgae, and cyanobacteria. I suppose one benefit of virtual conferences is that it is possible to attend so many!

Kiyan successfully defended his Ph.D. thesis, Improving cyanobacteria productivity: From theory to assay. The defense was held over Zoom. The opponent was Danny Ducat from Michigan State. Thanks for getting up so early! The committee was Karin Stensjö from Uppsala, Carl Johan Franzén from Chalmers, and Veronique Chotteau from KTH. Congratulations to Kiyan!

We attended the 11th European Workshop on Molecular Biology of Cyanobacteria, which is held every two years. This time it was organized by Paula Tamagnini of Porto, but was virtual. While we were bummed not to be able to visit Porto, the conference went off well with three days of new research in the cyanobacteria world. Paul and Michael gave talks (see Resources page). Markus and Jan gave posters.

Our group will be part of a new Center for Plant Biotechnology, funded by SSF (Swedish Foundation for Strategic Research) as one of four Agenda 2030 Research Centers. Our center is led by Prof. Åsa Strand of Umeå University and will focus on enhancing the rate photosynthesis in plant by engineering both the Calvin cycle and light protection. Other center partners are Alizee Malnoe of Umeå University and Alexey Amunts of Stockholm University/SciLifeLab. The center will begin in Fall 2020. See Press Release from SciLifeLab.

Paul was granted an Ascending Investigator in Biotechnology-Based Synthesis and Production Research award by Novo Nordisk Fonden, as part of their Research Leadership Program. This is an honor! We will work on high-throughput screening of Calvin cycle variants. Read more about ours and the other awards in the area of Biotechnology-based synthesis and production here.

Ivana presented at this year's Nordic Algae Symposium in Uppsala. The topic was CRISPR technologies in cyanobacteria. The NAS is arranged yearly by the NordAqua Nordforsk Center of Excellence.

Paul presented at the Moving Across, Art is Science event at Stallet, Kungsträgården. It was a short presentation about our work on cyanobacteria, and there was an improv group who interepreted our ideas with skits. Thanks to Sandra Petrus-Reurer and the organizing committee from Karolinska Institutet for this invitation!

Lun and Kiyan's paper on pooled CRISPRi libraries in cyanobacteria was published in Nature Communications. Thank you to Johannes for RNA-Seq analysis, and to Sara Björk and Håkan Jönsson for the collaboration with droplet microfluidics technology. Michael led data analysis and also was the figures guru. Michael's visualization of Synechocystis gene fitness is available on our Resources page. Johannes's RNA-Seq data workup software RiboPipe is available on our Software page.

Ivana Cengic defended her Ph.D. thesis, Synthetic Biology Approaches for Improving Production of Fatty-Acid Derived Compounds in Cyanobacteria. The opponent was Prof. Annegret Wilde of Freiburg University, Germany. Other committee members were Prof. Peter Lindblad from Uppsala, Prof. Cornelia Spetea from Gothenburg, and Docent Francesco Gentilli from Umeå. Congratulations to Ivana!