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The Batman among Bacteria genes

Imagine a set of genes that lie quiet and then come into their own when needed. Something like Batman rising when Gotham needs him, if you want a popular parallel. Cool, eh ? In Prof Mahadevan’s lab at IISc, the “Batman” among bacterial genes has been under the radar.

Bacteria are a highly versatile and adaptive group of organisms that share the world with us. Since the mid 20th century, the bacterium Escherichia coli has been one of the most intensively studied organisms in the world, heralding the emergence of “molecular genetics”. Despite the vast amount of knowledge we have about these bacteria, our understanding of many things about their genome is still vague.

Many bacterial genomes carry stretches of potentially functional DNA code that remain silent and cannot be induced to produce the proteins they encode. Aptly called “cryptic” genes, they are found in many microbes, including soil bacteria, yeasts and the ubiquitous E.coli. Although cryptic genes are not expressed, curiously, they are not rendered useless by accumulated mutations like pseudogenes or non-coding “junk” DNA. Why do bacteria maintain the excess baggage of these non-operational DNA stretches?

It turns out that cryptic genes are not as silent as they were thought to be. Mutations in the regions of DNA that control the genes’ expression can turn on these genes. The work in Prof. Mahadevan’s lab at the Indian Institute of Science has mainly focussed on the bgl operon – a cluster of cryptic genes responsible for using the naturally occurring compounds beta-glucosides as alternative energy sources in the absence of glucose. Beta-glucosides like arbutin and salicin are part of the arsenal plants have, against being eaten. They are bitter, distasteful compounds, made of a sugar attached to an aromatic molecule. By growing bacteria in a medium (a “broth”) containing beta-glucosides, mutated strains which have the usually silent bgl genes turned on can be isolated.

Using these mutated strains (called Bgl+), Prof. Mahadevan’s lab has shown that bacteria expressing the bgl genes have an advantage over bgl non-expressing strains when food is scarce. When easy-to-use conventional nutrients like sugar are used up by the growing bacteria, most of them die. In these situations, Bgl+ bacteria can not only use beta-glucosides as unconventional energy sources, they can also take up and use small proteins released by dead or dying cells - the bgl genes make it possible for them to do this. Under such nutrient-limited conditions, Bgl+ bacteria therefore not only survive, they also reproduce, just the way Darwin had predicted.

The proteins encoded by the bgl genes help bacteria take in beta-glucosides and detach the aromatic molecule from the glucose moiety. The aromatic compounds are often toxic, since plants produce beta-glucosides to protect themselves from herbivores. This, then gave rise to another intriguing possibility; could the Bgl+ bacteria use these compounds not only as energy sources, but also to protect themselves? “Yes, they can”, says Prof. Mahadevan, “Robert Sonowal, one of my bright students, found that the toxic aromatic compounds released by Bgl+ bacteria can deter and in some cases even kill predators like amoebae and nematodes that feed on these bacteria. In fact, the predator-prey roles are reversed in this case as the bacteria now feed on the dead predators!”

Once activated, the bgl genes are also capable of evolving new functions. When Bgl+ bacteria capable of using arbutin were exposed to a novel beta-glucoside called esculin, mutant strains capable of utilising esculin were obtained. “It’s a beautiful case of Darwinian evolution and selection in nutrient use”, explains Prof. Mahadevan. If the bgl genes are so useful, why are they cryptic? Why are Bgl+ bacteria so uncommon among the gut isolates? Why don’t bacteria expressing these genes outcompete other bacteria? “The current focus of the lab is to investigate whether Bgl+ bacteria are disadvantaged when compared to Bgl- strains when conventional nutrients like glucose and peptides are freely available”, states Prof. Mahadevan. If this is so, the Bgl+ and Bgl- states could oscillate depending on the environment. Aspart from their work on the bgl operon, Prof. Mahadevan’s lab also works on identifying and discovering the evolving functions of other beta-glucosidase metabolising cryptic genes belonging to the chb and asc groups in E. coli.