Field of Science

How to look like an idiot...

A fairly embarrassing thing happened yesterday afternoon. My supervisor's PI (the one who owns the lab and is in charge of all the research) came by to see how we were doing and he asked me about my bioinformatics project. My bioinformatics project involves looking at bits DNA from our bacteriophage and trying to work out what it does, using all sorts of clever internet search programs (mostly BLAST actually).

The conversation went something like this:

PI: So, hows the work going?

Lab Rat: Fine. I'm pretty sure about the first sequence, it's got a fairly obvious NrdG domain, and it's really conserved with other NrdG domains. I reckon it's a NrdG.

PI: Great. So what does an NrdG domain do? Why have we got one in the phage?

Lab Rat: *frantically scans notes*. Uh, an NrdG domain, uh, ribonucleotide reductase, uh, class III anaerobic ribonucleotide reductase. Um. assembles deoxyribonucleotides.

PI: ...

Lab Rat: I'll look it up.

So my first task this morning was heading over to PubMed. For those not in the know, PubMed is the worlds most wonderful search engine, which scans all the science reviews and papers and can usually find the one you want. For those who are interested, here is a brief overview of what NrdG domains are:

NrdG is a domain in a protein, which basically means that it is an area of the protein with a recognisable structure. Search engines such as InterProScan are designed to look for these domains in proteins and show you where they are. You can then (if you do your research properly) go to PubMed and find out what the domain does.

One of the most important tasks in a cell is the replication of cellular DNA. DNA is built up from small subunits, or monomers, known as deoxyribonucleotides. In order to replicate the DNA the cell must have enough of these monomers to make a new strand of DNA. However most cells do not replicate all the time, at different times in their life cycles they will need different concentrations of deoxyribonucleotides inside the cell.

Enter ribonucleotide reductase: This controls the concentration of DNA monomers within the cell. It works by using oxygen to generate a tyrosyl radical (basically just a very reactive molecule, radicals are very reactive and have been shown to play an important role in catalysis). The tyrosyl radical then catalysis the reaction, producing new DNA monomers. Control of ribonucleotide reductase therefore, controls the amount of DNA monomers.

The problem with this is that some bacteria don't use oxygen. These are known as anaerobic bacteria. Without oxygen, they cannot generate the tyrosyl radical, which is vital for the reaction to occur. So how do they manage it? This (finally) is where my NrdG domain comes in. The NrdG domain contains a class III reductase, which is an anaerobic reductase. Instead of using oxygen to create a tyrosyl radical, it uses a different system to produce a glycyl radical. Still a radical (so it still has high reactive power) but made from a different molecule (glycerol rather than tyrosine).

The golden question is of course, what is this doing in my phage? Bacteriophages don't make DNA, they invade bacteria and use that bacteria to make DNA for them. Also, my bacteria is a lytic phage which means that it's only in the bacteria for a short amount of time before killing it. (unlike lysogenic phages, which hang around in the bacteria for long lengths of time. Lysogenic phages often carry bits of DNA which their bacterial hosts will find useful).

For a phage to carry a ribonucleotide reductase is not, however, such a bad idea. The host for my phage is a bacteria which can survive in both aerobic (with oxygen) and anaerobic (without oxygen) conditions. It is plausible, therefore, that the phage carries with it a gene that helps the bacteria to make DNA, especially in anaerobic conditions, when most cellular processes tend to be slower anyway. That way the phage can get its DNA made up and packaged as quickly as possible and then break out of the bacteria.

Feel free to ask any questions in the comments :)

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