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bioRxiv · 10.1101/2025.01.20.633913

Investigation of the Cyanothece nitrogenase cluster in Synechocystis: a blueprint for engineering nitrogen fixing photoautotrophs

Liu, D.·Bandyopadhyay, A.·Liberton, M.·Pakrasi, H. B.·Bhattacharyya-Pakrasi, M.
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Abstract

The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria such as Cyanothece is frequently selected by nature for nitrogen fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain under explored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of a Synechocystis 6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and to define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, the nif genes from Cyanothece 51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genes nifHDK, nifBSUENPVZTXW as well as hesAB are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar powered conversion of atmospheric nitrogen into nitrogen rich compounds, a stride towards a greener world. IMPORTANCEIntegrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen rich products in a green and energy efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen fixing ability.

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Liu, D., Bandyopadhyay, A., Liberton, M., Pakrasi, H. B., Bhattacharyya-Pakrasi, M.. 2025-01-21. Investigation of the Cyanothece nitrogenase cluster in Synechocystis: a blueprint for engineering nitrogen fixing photoautotrophs. https://doi.org/10.1101/2025.01.20.633913

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