Molecular Zoo: The TALE’s Tale

This post represents the first in what I hope will be an ongoing series on the molecules that make biology, well, interesting! (It also happens to be my 50th post ever on this blog). Being alive requires taking chemistry to the extreme. At the heart of every cell is the massive information storage molecule, DNA. DNA itself contains the chemical code to produce all the proteins and RNAs of the cell. The human genome alone contains the instructions for building tens of thousands of proteins, which carry out a wide range of jobs that include breaking down food, maintaining cell shape, switching genes on and off, and more.

When it comes to promoting the beauty of biological molecules, nobody does it better than David Goodsell, whose Molecule of the Month page at the PDB is without compare. Having read his book The Machinery of Life several years ago, I will forever be awe-inspired by the molecules that make life possible. In this series I hope that, in addition to talking about old favorites, I will be able to present unique molecules that often go unnoticed. The first comes from a bacterium whose survival depends on invading and hijacking the cells of unsuspecting plants.

Members of the parasitic bacterial genus Xanthomonas have a peculiar survival strategy. When infecting a plant, they release proteins called TALEs (short for transcription activator-like effectors) into the host cell. There they interact with the host genome to switch on certain genes that make the plant cell a more favorable host to the invaders. In other words, these bacteria are producing eukaryotic transcription factors to manipulate the host cell. The TALE genotype lies in a bacterial genome, but the phenotype is realized by a plant cell!

As if that weren’t enough, TALEs have a stunningly unique structure and mode of action. Far from being a blob of a protein, TALEs have an elegant repeating structure, with a one-to-one correspondence between a repeating protein element and a base of DNA. The image at the top of the page shows a TALE binding to its DNA target. The TALE is colored to highlight its repeating units, which each binds to a single base in the DNA. The entire TALE is encoded in a single gene. The picture below that shows a cutaway view looking down the double helix, showing you the tightness of contact the TALE makes with DNA.

Given its structure, biologists were quick to hypothesize that TALEs operate by a code. Since there is a one-to-one correspondence between protein unit and DNA base, perhaps there is also a chemical code where particular sets of recognition amino acids in the TALE correspond to each of the four bases of DNA. It’s since been discovered that in each repeating unit two amino acids act to recognize a base of DNA. Since these two amino acids are repeated in the same position of each of the TALE’s units, though their identities vary, they are called repeat-variable diresidues (RVDs). There do appear to be general rules, but there are a lot of factors to consider. A recent report (Streubel et al., 2010), for instance, recommends incorporating RVDs that bind strongly to their recognition bases with hydrogen bonds. Some amino acids do not form hydrogen bonds, so even though they might confer high specificity of binding, the TALE falls off the DNA too easily. The same study showed that TALE units are not completely modular. Asparagine + isoleucine usually binds to adenine, but not if it is used in a repeat. Likewise with asparagine + glycine, which usually binds thymine. However, repeats of histidine + aspartic acid bound repeats of cytosine; and repeats of asparagine + asparagines bound repeats of guanine (but not adenine, which they were thought to do). The original (“naïve”) TALE code is shown in the table.

Though challenges remain, TALEs are interesting proteins to engineer. They have the rare advantage of a general set of rules and a clear starting point.