Just like you and me, bacteria have ‘favorite’ foods – though in the case of bacteria, 'favorite' translates to those which are energetically favorable or most accessible. Different bacteria have different preferences, based on their environments and the neighboring microbes that compete for or complement energy sources. Given a niche where many different carbohydrate resources are available, how do bacteria regulate their preferential food source? New research published in the Journal of Bacteriology shows a system of small RNAs help regulate polysaccharide usage in the human gut-residing Bacteroides genus.
Living in the intestine provides the Gram-negative Bacteroides a wide variety of carbohydrate sources based on their host’s diet and location within the host. These bacteria are not only able to utilize glucose and other simple sugars, but can also exploit more complex polysaccharide chains due to genomic regions called Polysaccharide Utilization Loci (PULs) that confer the ability to break down polysaccharides and glycans. The PULs are highly regulated, in part because each loci is highly specific for a particular substrate. Now a new layer of control adds to the already-complex regulatory circuit that determines preferential PUL activation.
One PUL, Don (for deglycosylation of N-glycans) is highly expressed in an extraintestinal infection model and can deglycosylate N-glycans from serious fluid components. First author Yanlu Cao, working with senior author C. Jeffrey Smith, initiated a transcriptional analysis of B. fragilis, which revealed a small antisense RNA (sRNA) signal upstream of the donC gene, which encodes an outer membrane protein that binds and recognizes the N-glycan substrate.
To show the activity of donS in this system, the authors measured transcription of donC in medium containing human transferrin as its sole carbon source (inducing conditions), or in medium containing glucose (non-inducing conditions). Inducing conditions resulted in nearly 1000-fold induction of donC expression. In a strain lacking donS, donC was induced 5-fold higher than this, showing the ability of this sRNA to fine-tune expression levels. A strain that overexpressed donS repressed the Don PUL so strongly that the strain was unable to grow with transferrin.
What happens when B. fragilis is grown with multiple carbon sources (mirroring the gut)? Preferred substrates cause catabolite-mediated repression to determine the maximally expressed PUL, so is there a role for sRNAs in this environment? A wild-type B. fragilis strain grown in inducing conditions has high levels of donC, but addition of glucose leads to much lower donC expression, as the bacterium shifts to a glucose-based (and more energy-conserving) metabolism. Without donS, the null mutant was 20-60 times less able to repress donC with glucose addition (see figure, right), suggesting that sRNA expression may help the bacterium respond to multiple nutrient sources.
In addition to the detailed work on the DonC PUL, the authors identified fourteen additional PULs with sRNA sequences, which were controlled by a common Bacteroidetes promoter sequence. The research team also identified candidate sRNAs in several Bacteroides species, suggesting broad conservation of sRNA regulation of metabolism. In such a metabolically flexible genus, it makes sense to have several regulatory mechanisms to quickly modify gene expression for maximal energy gain (and minimal unnecessary expenditure).
Bacteroides dedicates nearly one-fifth of its genome to carbohydrate metabolism, some of which we are only beginning to understand. As we better define the substrates this important microbiome member can use, understanding the regulation of the genetic circuits to utilize these substrates may help us promote the growth of desired species while inhibiting unwanted growth.
-- Julie Wolf