Despite their importance, the vast majority of ECF σs remain uncharacterized, and no computational method exists for determining the set of genes regulated by an ECF σ (its regulon).ĮCF σs are small (∼200 amino acids) and contain two well-conserved globular domains, σ 4 and σ 2, that interact respectively with the -35 and -10 regions of the core promoter ( 1). ECF σs regulate genes involved in differentiation, metal homeostasis, outer membrane integrity, oxygen response, and other processes ( 5– 8). Group 4 σs, also called extracytoplasmic function (ECF) σs, are the most abundant and diverse group, often representing 5 to 10% of the regulatory repertoire ( 3, 4). The Group 2 to 4 alternative σs are active under specific growth or environmental conditions and effect specialized transcriptional programs by directing RNAP to a smaller set of distinct promoters. The Group 1 housekeeping σs are highly conserved, universally essential, and responsible for recognizing thousands of promoters in each bacterial genome. A vast majority of σs belong to the σ 70 family, which consists of four phylogenetically and structurally related groups ( 2). In bacteria, a major point of transcriptional regulation is the use of sigma factors (σs) to direct RNA polymerase (RNAP) to specific promoters ( 1). This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid–nucleotide interactions that determine promoter specificity. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. De novo determination of regulatory interactions requires accurate prediction of regulators’ DNA binding and precise determination of biologically significant binding sites. I have no trouble with blueberries, in fact she'd live off berries if she had a choice so it was a fair compromise to put blueberries in this muffin recipe.īlueberries are super rich in vitamins and minerals anyhow, so we all win! (In the photo above, she's a bit of a mess.Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. These days, with Vienna being a little more picky, I'm always looking for creative ways to get her to eat superfoods like oats, flax or almonds. I made these muffins 'mini' because they are good for little hands and then you can eat two or three. My dear friend Candice made a variation of these for our little ones to snack on when I visited her last weekend and I just had to make them! The original recipe came from the Ambitious Kitchen blog but I made some joyous changes. In comparison, it has about 50% more fiber than oatmeal. This means it fills it keeps you fuller longer. Oat bran isn't an ingredient I use that often, but I should! It has a lot of soluble fiber and once it reaches the digestive system absorbs nearly 25 times its weight in liquid.

These muffins are packed with fiber from the ground almonds, flax and oat bran.

They are the perfect snack for the mid-aft munchies! You actually feel like you're eating something substantial. I just love the texture that oat bran gives these muffins. These muffins remind me of raisin bran muffins my mom used to bake for my brother and I when we were little.

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