Evolution: how bacteria use essential amino acids (Introduction)

by David Turell , Thursday, November 23, 2023, 17:30 (156 days ago) @ David Turell

Make some, eat some:

https://ecoevocommunity.nature.com/posts/small-genomes-big-appetites-amino-acid-auxotro...

"In the microbial world, there is a divide between those that can produce all amino acids, and those that (like us) rely on their diet to obtain them. In certain environments, resources are so scarce or variable that microbes cannot rely on obtaining amino acids directly from their surroundings – they need to produce all amino acids on their own. Other environments are so rich that some microbes can afford not to produce amino acids (so-called amino acid auxotrophs), because these can be readily obtained from their surroundings. Synthesizing amino acids comes at a metabolic cost so if that cost can be avoided, we would expect microbes to lose the ability to synthesize certain amino acids over time. Why pay for something that you can get for free?

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"We wanted to know how common auxotrophy is across bacteria, which bacteria are auxotrophic, where auxotrophic bacteria are most likely to be found, and what other bacterial traits are associated with amino acid auxotrophy (see our paper - https://www.nature.com/articles/s41467-023-43435-4). Solving these mysteries would provide important insights into the most fundamental aspects of microbial adaptation that make them so successful across Earth’s ecosystems.

"The capacities for producing amino acids and other essential compounds are imprinted in the genome of any organism. If we know the genes involved in the production of amino acids, we can infer the capacity to produce these amino acids based on the presence of these genes in any given genome.

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"We found that most bacteria (78%) are likely able to produce all the amino acids they need to grow, although amino acid auxotrophy can be observed across members of most bacterial families. Consistent with evolutionary theory, we found that environments where we expect to see a higher availability of amino acids favor bacteria that cannot synthesize amino acids on their own. For example, fermented foods and the human gut are environments rich in amino acids, and these environments typically harbor many auxotrophic bacteria. The reason is simple – if a microbe has ready access to an ‘all-you-can-eat’ buffet that is open 24/7, where food is plentiful and never runs out, there is no advantage for a microbe to produce the amino acids it can easily get from its surroundings.

"Being unable to produce amino acids was not an exclusive feature of those microbes living in fermented food products or our guts. Mycoplasmas that parasitize our cells and cause important diseases are also often auxotrophic as they can obtain amino acids directly from the intracellular environment. We also observed that bacteria which are adapted to predate on other bacteria lacked many genes for amino acid production, including members of the Bdellovibrionaceae. Again, they can obtain these essential compounds from their victims, so they have evolved to avoid the energetic burden of synthesizing amino acids on their own.

"Being unable to produce amino acids was not an exclusive feature of those microbes living in fermented food products or our guts. Mycoplasmas that parasitize our cells and cause important diseases are also often auxotrophic as they can obtain amino acids directly from the intracellular environment. We also observed that bacteria which are adapted to predate on other bacteria lacked many genes for amino acid production, including members of the Bdellovibrionaceae. Again, they can obtain these essential compounds from their victims, so they have evolved to avoid the energetic burden of synthesizing amino acids on their own."

Comment: Bacteria play such an important role in our lives, it is critical to perform studies of this sort. Bacteria were at the start of life and are still here helping. We need to learn everything about them that we can.