Why Sequence Chlamydomonas by New Methods?

Chlamydomonas is a well studied model organism for which microarray gene expression data and the nuclear genome sequence are available. Still, our knowledge of gene expression is limited, since microarray technology is not ideal for detecting low-abundance mRNAs and small changes in gene expression. Sequencing an organism that has such a set of genomic resources via new methods, specifically 454 and Solexa sequencing, will allow researchers to compare the available approaches for analyzing gene expression. They will then be able to use the most appropriate one to more efficiently evaluate the conditions that favor a particular metabolism in Chlamydomonas, with specific emphasis on those that generate energy-rich products. As a model organism for photosynthetic eukaryotes, it is expected that lessons learned from Chlamydomonas will be applicable to the development of similar pathways in other, more industrially useful algae.

The performance of the 454 and Solexa platforms will be compared to that of high-density microarrays for the study of global gene expression in nutrient- and oxygen-deprived Chlamydomonas. Besides confirming the expression characteristics obtained by means of traditional microarrays, this project should also provide more quantitative information regarding high- and moderate-abundance messages and identify novel lower-abundance transcripts that are differentially expressed. It should also identify short gene sequences that have not been detected by other methods.

These alternative methods of transcript profiling should be applicable to any organism for which a genome sequence is available. Indeed, microarray platforms are not available for many ecologically important organisms, including many abundant phytoplankton species in the nutrient-poor oceans. The proposed development of this methodology opens the door to similar analyses for these organisms and to comparative protein expression analyses among the different algae. Such comparisons might be particularly interesting for organisms that have adapted to different environments and have developed different strategies for coping with both prevalent and fluctuating environmental conditions.

Principal Investigators: Maria L. Ghirardi and Michael Seibert (Natl. Renewable Energy Lab.), Arthur R. Grossman (Carnegie Inst. of Washington), Sabeeha Merchant and and Matteo Pellegrini (Univ. of California, Los Angeles), and Matthew C. Posewitz (Colorado School of Mines, Natl. Renewable Energy Lab.).

Program: CSP 2009