Identifying pathways in algae that produce oil without
killing them
(August 5, 2015) While
most people might know some algae as “pond scum,” to the U.S. Department of
Energy (DOE), they are tiny organisms that could provide a source of
sustainable fuels. Like plants, they can convert light into energy-rich
chemical compounds; unlike plants, they require less space and don’t need
arable soil to grow.
Some algae like Chlamydomonas reinhardtii (or “Chlamy,” as
it’s known to its large research community) produce energy-dense oils or lipids
when stressed, and these lipids can then be converted into fuels. However,
researchers walk a fine line in not killing the goose that lays the golden
eggs, in this case, stressing the algae just enough to produce lipids, but not
enough to kill them. Published ahead online July 27, 2015 in the journal Nature
Plants, a team led by scientists from the U.S. Department of Energy Joint
Genome Institute (DOE JGI), a DOE Office of Science User Facility, analyzed the
genes that are being activated during algal lipid production, and in particular
the molecular machinery that orchestrates these gene activities inside the cell
when it produces lipids.
“We know how to stress the algae,” said the study’s first
author Chew Yee Ngan of the DOE JGI. “What we don’t know is how to keep the
algae alive at the same time, until now.”
Stressful searches
As part of the DOE Office of Science’s efforts to study
algae for energy and environmental applications, the DOE JGI has published over
75 percent of all publicly available algal genomes. One of these is the Chlamy
reference genome, which was released back in 2007. Until now, very little is
known about the protein factor that can regulate lipid production. To find more
of them, the team cultured Chlamy cells and starved them of nitrogen or sulfur,
both of which are stress conditions to which Chlamy responds by producing
lipids. They then analyzed the complex of DNA and proteins known as chromatin
that define what genes are being activated, as well as the expression profiles
or transcriptome, and compared these to non-stressed Chlamy cells.
“We’re looking for changes in starved cells vs. cells that
are happily growing,” Ngan explained. Through careful analysis of genome-wide
data sets, they narrowed down their search to identify two transcription
factors that appeared to play a pivotal role in lipid accumulation, and then
studied one of them, PSR1, in detail. “In studying the chromatin modifications,
we can read out changes in the proteins bound to DNA on a genome-wide scale and
then specifically target those genes whose regulation profiles are changed
under lipid-producing conditions.”