Saturday, April 30, 2011

Diatom shapes and biomineralization: a chromatin connection?

Diatoms are fascinating eukaryotes. The belong to a distinct lineage, the stramenopiles. Peek into any pond water sample through a microscope and you will be sure to find them, with a great diversity of beautiful shapes and a peculiar cell wall. Apparently, diatoms were test objects for microscopic lenses in the 19th century. The cell wall is mostly composed of silica and is called a frustule. The frustule is composed of two "valves" (imagine a petridish with its cover), the upper valve is called the epitheca and is slightly larger (the petridish cover) than the lower one, the hypotheca (the petridish base). These are joined together by girdle bands. During cell division, one daughter cell inherits the hypotheca and the other the epitheca, and they both become the epitheca of the new cell. Thus one daughter is always smaller than the parent, but we wont get into how this is resolved. Immediately after cell division, a new valve is formed and biomineralized. Silica is precipitated in a specialized vesicle and this involves a remarkable group of proteins called the silaffins. So remarkable that it is worth examining a sequence of one of them.


Beyond the signal peptide sequence, the sequence is of low compositional complexity with lysine and serine residues dominating the sequence landscape. The lysine residues are heavily modified by oligo N-methyl propylamine units, hydroxylation and methylation, while the serines are mostly phosphorylated. An interesting point of note is that these modifications appear to follow a certain code based on the sequence of neighboring residues and might show species-specific differences (click to read). All this makes the silaffin a very cationic polypeptide. At acidic pH, the above conditions in the silaffins is a perfect environment for precipitating silica particles. Take a solution of silicic acid and add silaffins, and lo and behold, silica precipitates. You can read about this remarkable study by Kroger, Deutzmann and Sumper here. Further addition of free long-chain polyamines (another major component of the cell wall) and phosphates to a solution of silicic acid results in the precipitation of silica in honeycomb-like hexagonal nanopatterns resembling those seen in the diatom cell wall (click to read). So what does all this have to do with chromatin?

Above figure taken from Sumper et al. Angew Chem Int Ed Engl. 2007;46(44):8405-8.

Recently, while surveying the distribution of chromatin domains involved in protein methylation and demethylation in eukaryotes, we encountered a distinct lineage-specific expansion of SET domain proteins in the diatoms (Click here to access these proteins). Some of these, inPhaeodactylum and Fragilariopsis are fused to a spermidine synthase-like Rossmann fold domain (e.g. the Phaeodactylum protein PHATRDRAFT_42788), and one protein inFragilariopsis is further fused to a methylated lysine-binding chromo domain (Note: in the model Thalassiosira pseudonana, the orthologous spermidine synthase domain, THAPSDRAFT_21371, appears to be a solo domain). Normally, one might speculate that these proteins are involved in chromatin function. The only problem is that these diatom proteins are all secreted!

The SET domains are protein methyltransferases, and transfer methyl groups to the epsilon-amino group of lysines on proteins. The most well characterized SET domains are those that modify lysine residues in histone tails. Thus far, SET domain containing protein were not known to be secreted. The classical spermidine synthases transfer propylamine groups to putrescine. Putting the pieces together for these diatoms proteins, it is rather obvious that these secreted SET domain proteins are the ones most likely to catalyze lysine methylation in silaffins. The spermidine synthase domains would then catalyze transfer of propylamine units to lysines, and perhaps also contribute to the formation of free polyamines. There are at least 3 families of secreted hydroxylases in diatoms that we reported in our study on various hydroxylases (for example,the Syn9-gp54 family of 2OGFeDO dependent hydroxylases; click here). We predict that among these are the enzymes that hydroxylate lysine residues. In a sense, the silaffin modifying code is like the histone code, with species-specific differences in the diatoms. Further, silaffin sequences are very different between the completely sequence diatoms. These in turn could be the basis of the various shapes of diatoms. Think about all this when you look at a diatom under a microscope the next time. You can read about this discovery on the silaffin modifying proteins and other protein methyltransferases and demethylases here.