In Part 4, we looked at the relatively recent discovery of the bacterial second messenger molecule cyclic-di-GMP. The decisions bacteria make weigh heavily on the amount of this molecule found within the cell. However, how a bacterial cell knows how much c-di-GMP there is ultimately remains a mystery. The focus of early research involved finding what regulated the synthesis and degradation of c-di-GMP. Thus, the majority of publications in print focus on the enzymes that perform these functions, GGDEFs and EALs. Also, by deleting certain GGDEFs or EALs from a bacterium, scientists were able to determine what effect this change would have on the cell’s decision making and lifestyle. Most research was performed in medically relevant species like Vibrio and Pseudomonas. This short-sighted focus has led to a distinct role of c-di-GMP in the cell that may not be absolute. I digress…

A cell produces c-di-GMP in response to some environmental signal. Now what?

Great question; one that is still not answered. Various proteins have been shown to interact with or bind c-di-GMP including the PilZ domain. The list of c-di-GMP effectors has grown slightly over the past few years to include examples of transcriptional regulators in both Vibrio and Pseudomonas (VpsT and FleQ, respectively). Transcriptional regulators are proteins that help carry out the decisions made by a cell by regulating gene transcription. However, these are only two examples from two bacteria. What about the vast number of other bacteria out there? How do they “see” c-di-GMP? Cyclic-di-GMP is a vital component to bacterial decision making even though our knowledge of how it is seen by a cell is a huge unknown.

My hypotheses and speculations (with some evidence)

In the last chapter of my dissertation (under embargo), I investigated what other protein domains could potentially bind c-di-GMP bioinformatically. Using my methods, I could predict proteins in the nonredundant database that could potentially bind c-di-GMP. One group of proteins I found were those already shown to bind other nucleotides like ATP. I was able to test my method against a publication that biochemistry and proteomics to identify c-di-GMP binding proteins from Pseudomonas. This crude “chemical proteomic” approach identified around 200 potential binding proteins of which the method I created also found several of the same proteins without the exhaustive time and effort of “wet bench” experiments.

This is not a post about how good I am at science. This is a post about using new and different methods to answer questions within science not unlike the investigation that identified the PilZ domain as the c-di-GMP binding protein in the first place. Unfortunately, my time in the lab was over before I could test my hypotheses, but my curiosity and passion live on. I will say that I predict receiver domains are very common c-di-GMP binding effectors that will be the next major discovery in this elusive mystery of how cells use c-di-GMP to make decisions.

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