Protists and their plastids

A quick skim through this blog reveals fairly quickly that I have a slight fixation on bacteria. I like to research them, read about them, and then blog about them, most specifically about their cell walls. However life contains more than just bacteria, and occasionally, strange though it might seem, people write papers about such non-bacterial things, and they end up on my desk with a small post-it attached reminding me that I have a presentation for my supervision group coming up.

So for the sake of my supervision, and to prevent myself becoming too scientifically blinkered, I took a quick foray this weekend into the murky world of protists, the strange and wonderful organisms that occupy the taxonomic equivalent of the 'misc.' draw in a filing cabinet. The creatures that are neither plant, nor animal, nor demonstrably bacteria. Many of them are single celled, some of them photosynthesise, and they all seem to occupy little evolved niches of their own, producing proteins with no noticeable homologues in any other branch of life.

The paper has the rather terrifying title of : "Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium". And I am not ashamed to admit that I had to go double-check the meaning of several of those words.

Dinoflagellates are little organisms that live in water, and mostly look a little like the picture on the right. Many of them are marine organisms, making up a large amount of the photosynthesising biomass in the ocean, and occasionally blooming to form 'red tides', leading to whole sweeps of water turning bright red (possibly occasionally on biblical command). The photosynthetic ones contain chloroplasts, which are wrapped up in three membranes, rather than the usual two. These, like all chloroplasts, contain their own genetic material (known as plastid genes), although unlike plant plastids, they don't seem to contain very many, and those that they do posess are found on little minicircles.

What the paper is interested in is whether there are any other genes in the chloroplast which aren't in minicircle form. There are, afterall, only 12 genes encoded on the minicircles, which is a small amount for a plastid. In order to explore this, it uses a characteristic property of the dinflagellate species it's working with. All organisms, when making proteins, make them from an mRNA copy of the genetic code. This mRNA copy tends to have a long string of adenosine residues added to the end, in order to prevent the mRNA getting degraded. This happens in our dinoflagellate species as well, but it doesn't happen to the plastid genes.

However instead of getting multiple adenosine repeats the plastid genes get multiple uracil repeats. It's just a different base, but it allows the mRNA made in the nucleus, and the mRNA made by the chloroplast to be separated. You can probe for adenosine enriched and adenosine depleted mRNA as shown on the gel below (A and B show different species). The psbA mRNA is clearly strongly present A+ (adenosine enriched) and therefore codes for a nuclear encoded protein. Conversely, the 23S RNA is A- (adenosine depleted) and is coded for in the chloroplast, from a plastid gene.

(Image taken from reference below)

The paper selected 300 random poly-uridine mRNAs (A-) and sequenced them to see if they corresponded to genes found in minicircles, or whether they might be plastid genes held in some different architecture. All the A- mRNA corresponded to the 12 genes discovered in the minicircle. They carried out rarefaction analysis to see if their sample size was large enough, apparently it was, in fact 300 clones was way in excess of the amount needed to find a further, non-minicircled-gene.

This suggests that minicircles are the only architecture for plastid genes and, importantly, that there really are only 12 genes contained in the chloroplast of the dinoflagellate Lingulodinium. This is a very small number of genes, all the rest have somehow migrated to the nucleus, leaving these 12 behind. And it's still very much an open question about why these have been left behind. The paper, in its discussion section puts forward the possibility of size. The genes that have been left behind all code for some of the longer proteins usually found in chloroplasts, although the paper does have the good grace to admit that that's not the most convincing of arguments.

It's worlds away from my little bacteria. But still just as fascinating.
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Wang, Y. (2006). Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium Nucleic Acids Research, 34 (2), 613-619 DOI: 10.1093/nar/gkj438