Bacterial Amino Acid Auxotrophies Enable Energetically Costlier Proteomes

Kasalo, Niko; Domazet-Lošo, Tomislav; Domazet-Lošo, Mirjana (2025) Bacterial Amino Acid Auxotrophies Enable Energetically Costlier Proteomes. International Journal of Molecular Sciences, 26 (5). ISSN 1422-0067

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Abstract

The outsourcing of amino acid (AA) production to the environment is relatively common across the tree of life. We recently showed that the massive loss of AA synthesis capabilities in animals is governed by selective pressure linked to the energy costs of AA production. Paradoxically, these AA auxotrophies facilitated the evolution of costlier proteomes in animals by enabling the increased use of energetically expensive AAs. Experiments in bacteria have shown that AA auxotrophies can provide a fitness advantage in competition with prototrophic strains. However, it remains unclear whether energy-related selection also drives the evolution of bacterial AA auxotrophies and whether this affects the usage of expensive AAs in bacterial proteomes. To investigate these questions, we computationally determined AA auxotrophy odds across 980 bacterial genomes representing diverse taxa and calculated the energy costs of all their proteins. Here, we show that auxotrophic AAs are generally more expensive to synthesize than prototrophic AAs in bacteria. Moreover, we found that the cost of auxotrophic AAs significantly correlates with the cost of their respective proteomes. Interestingly, out of all considered taxa, Mollicutes and Borreliaceae—chronic pathogens highly successful in immune evasion—have the most AA auxotrophies and code for the most expensive proteomes. These findings indicate that AA auxotrophies in bacteria, similar to those in animals, are shaped by selective pressures related to energy management. Our study reveals that bacterial AA auxotrophies act as costly outsourced functions, enabling bacteria to explore protein sequence space more freely. It remains to be investigated whether this relaxed use of expensive AAs also enabled auxotrophic bacteria to evolve proteins with improved or novel functionality.

Item Type:	Article
Uncontrolled Keywords:	bacteria; amino acids; auxotrophy; energy costs; selection; evolution; functional outsourcing
Subjects:	NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology
Divisions:	Division of Molecular Biology
Projects:	Project title Project leader Project code Project type Napredne metode i tehnologije u znanosti o podatcima i kooperativnim sustavima-DATACROSS Sven Lončarić; Ivan Petrović; Tomislav Šmuc; Andrej Jokić KK.01.1.1.01.009 EK
Depositing User:	Lorena Palameta
Date Deposited:	27 Mar 2025 11:31
URI:	http://fulir.irb.hr/id/eprint/9677
DOI:	10.3390/ijms26052285

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