Antarctic clam genes - What can they tell us about shell deposition??

Week one of my PhD and I’ve decided to start blogging... Seems like a good idea, right?

This week I’ve reviewed a key paper in my field (written by my supervisor) which is really the background to my project:

The genomic revolution is upon us. Scientists are beginning to unravel the mysteries of the genetic code and to understand what molecular tools can teach us about biology. One area using such tools is the study of molluscan biomineralisation; the process of secreting minerals onto an organic matrix to produce a hardened calcified structure – a shell.  A deeper, mechanistic understanding of the calcification pathway will facilitate accurate predictions on the affects of climate change, and specifically, ocean acidification. Material scientists and biotechnicians are also interested in biominerlisation due to the desirable properties of shell (high strength) and the prospect of engineering valuable pearls without the need for a live animal. One problem holding back the progress of the field is a lack mollusc data in molecular databases. Clark et al. (2010) therefore aimed to improve molecular resources for biomineralisation studies.

Clarke et al. (2010) sequenced the entire messenger RNA content (transcriptome) of the shell secreting organ (mantle) in a sentinel bivalve species, the Antarctic clam (Laternula elliptica).  The results were compared to a database containing known gene for biominerisation in molluscs and calcium homeostasis in vertebrates. The comparison annotates genes with “putative” functions, but currently no experimental work has been carried out to test them. Classical shell deposition genes such as tyrosinase and carbonic anhydrase were highly expressed (40%), along with previously unknown genes, such as protein coupled receptors. There was also a large amount of highly-expressed unknown genes where the database was unable to find any matches and therefore could not be annotated.

Photo of an Antarctic clam, Laternula elliptica.

The data produced by Clark et al. (2010) provides an important mollusc contribution to the molecular database which will allow for future comparative work, and also identifies new genes which may be involved in biomineralisation.  Whilst the described paper clearly provides a valuable contribution to the literature, an understanding of the finer details of the calcification pathway is a long way off. We still have no real clue on HOW molluscs build their shells. Future work should aim to characterise the function of the described biomineralisation genes using both hypothesis-driven experiments (knocking-out genes and measuring the effect) and fishing based methods (more sequencing). Also, methods such as in-situ and real-time gene expression analysis could be used to assess the spatial distribution of genes within the mantle. The genomic revolution may be here, but it represents very little without meaningful interpretation and future experimentation by “big picture”thinking biologists.

Reference:

Clark, M. S., Thorne, A. A. S., Viera, F. A., Power, D. M., Peck, L. S. (2010) Insights into the shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics. 11:362. http://www.biomedcentral.com/1471-2164/11/362