A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis

Alker, A. T.; Aspiras, A. E.; Dunbar, T. L.; Farrell, M. V.; Fedoriouk, A.; Jones, J. E.; Mikhail, S. R.; Salcedo, G. Y.; Moore, B. S.; Shikuma, N. J.

doi:10.1101/2023.01.31.526474

bioRxiv · 10.1101/2023.01.31.526474

A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis

Alker, A. T.·Aspiras, A. E.·Dunbar, T. L.·Farrell, M. V.·Fedoriouk, A.·Jones, J. E.·Mikhail, S. R.·Salcedo, G. Y.·Moore, B. S.·Shikuma, N. J.

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Abstract

A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.

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Alker, A. T., Aspiras, A. E., Dunbar, T. L., Farrell, M. V., Fedoriouk, A., Jones, J. E., Mikhail, S. R., Salcedo, G. Y., Moore, B. S., Shikuma, N. J.. 2023-01-31. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. https://doi.org/10.1101/2023.01.31.526474

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