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Environmental conditions shape the nature of a minimal bacterial genome

Antczak, Magdalena, Michaelis, Martin, Wass, Mark N. (2019) Environmental conditions shape the nature of a minimal bacterial genome. Nature Communications, 10 (1). ISSN 2041-1723. (doi:10.1038/s41467-019-10837-2)

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.

Item Type: Article
DOI/Identification number: 10.1038/s41467-019-10837-2
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Mark Wass
Date Deposited: 19 Jul 2019 09:23 UTC
Last Modified: 19 Jul 2019 09:35 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/75457 (The current URI for this page, for reference purposes)
Antczak, Magdalena: https://orcid.org/0000-0003-1503-1849
Michaelis, Martin: https://orcid.org/0000-0002-5710-5888
Wass, Mark N.: https://orcid.org/0000-0001-5428-6479
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