Abstract
Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.
Highlights
Vitamin B12 variants SiderophoresFluctuation and the timescales of acquisition and Conditional versus continuous expression of re-Challenges for uptake receptor array design GlycansDeep learning and control theory
A bacterial cell may take up different B12 forms by expressing multiple receptors
How does natural selection set the number of receptor variants? How does selection tune the binding affinities of different receptor variants in an array? How does the design of receptor arrays shape the competitive and cooperative processes that define bacterial communities?
Summary
Bacterial cells express multiple receptors to take up polymorphic iron-scavenging siderophores and energy containing glycans. How does selection tune the binding affinities of different receptor variants in an array? I synthesize aspects of receptor arrays for vitamin B12 analogs, for siderophores, and for glycans. By considering these different cases together, deeper principles of receptor variety and specificity emerge. Competition over corrinoid variants shapes the receptor arrays of individual species and the dynamics of bacterial communities. Bacteria often express an array of siderophore uptake receptors for types produced by other species[7]. The ubiquitous battle for free iron sets the design of siderophore uptake receptor arrays. How are different receptors tuned to compete for taking up the diversity of B12 variants?
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