Environmental conditions shape the nature of a minimal bacterial genome

Magdalena Antczak, Martin Michaelis () and Mark N. Wass ()
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Magdalena Antczak: University of Kent
Martin Michaelis: University of Kent
Mark N. Wass: University of Kent

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract Of the 473 genes in the genome of the bacterium with the smallest genome generated to date, 149 genes have unknown function, emphasising a universal problem; less than 1% of proteins have experimentally determined annotations. Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins. Proteins that are still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins. Twenty-four likely transporter proteins are identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell in a nutrient-rich environment after removal of metabolic enzymes. Hence, the environment shapes the nature of a minimal genome. Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and identify crucial gaps for further development.

Date: 2019
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DOI: 10.1038/s41467-019-10837-2

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