This shorter episode is about a tiny, single-celled alga – Chlamydomonas reinhardtii – that’s managed to have a big impact. UC Berkeley plant biologist Sabeeha Merchant explains why she works on this alga, how researchers managed to sequence its genome, and what it has to teach us about other organisms – like plants. [Editor’s Note: Merchant is also a faculty scientist in the Environmental Genomics & Systems Biology Division of the Berkeley Lab Biosciences Area.]
Allison: And now, a JGIota – a snippet about JGI-related research, tools, people, discoveries and more. I’m Allison Joy, your host for this Iota.
For 25 years, the JGI has been supporting genomics research. In honor of this year’s 25th anniversary, we’re taking a look back at all kinds of species JGI researchers have studied. There are plants, there are fungi, there are bacteria – and today, we’re focusing on a single-celled alga, called Chlamydomonas reinhardtii.
Sabeeha Merchant: Chlamydomonas has been sort of the little, the baby who is now an adult <laugh> in the lab for a long time.
Allison: Sabeeha Merchant is a professor of plant and microbial biology at UC Berkeley. And although Chlamydomonas is relatively new to the lab scene, it’s very old in real terms.
Sabeeha Merchant: So there’s this common ancestor between plants and Chlamydomonas, which means that when we study Chlamydomonas, we learn something about the plants. But, it’s easier to work with Chlamydomonas, because it’s a microbe. You can grow it in a glass flask or in a beaker, so you don’t need to have fields or greenhouses to do the work. So you can do a lot of experiments quickly,
Allison: And when you have a lot of questions about plants — like, say, how to maximize their potential as alternatives to fossil fuels — that’s a huge plus. Even though Chlamydomonas isn’t itself a potential source for biofuel, it can teach us a lot about other organisms that are. For example, Chlamy is a model for studying lipid production in other algae. Added bonus: It’s very well-studied.
Sabeeha Merchant: It’s a single cell organism. So it means that when you have a million cells there, they’re all identical. So when you study something, you get a good response that you can measure. So that’s why we study Chlamydomonas.
Allison: Sabeeha has been working with Chlamydomonas for almost her entire career, and mainly, looking at the Chlamydomonas genome. And, like many genomes, it takes a bit of decoding work to figure out what each Chlamydomonas gene actually does – what protein it eventually makes.
Sabeeha Merchant: So Chlamydomonas is eukaryotic, just like our cells are eukaryotic, meaning that most of the genes have introns. So when you look at the DNA sequence of the gene, you don’t actually know what the protein looks like because the bits that are the exons that code for the protein have to be stitched together by removing the introns.
Allison: To tackle that intron problem early on, Sabeeha and other researchers looked beyond the DNA sequence. They used other genetic materials as a way in – sequences that were downstream from the DNA, and involved in the process of going from a DNA sequence to messenger RNA, to a protein.
Sabeeha Merchant: People would try to sequence what were called cDNAs or complementary DNAs that are copies of the messenger RNA. And the whole community was really interested, because of course the cDNAs tell you something about the sequence of a protein you may be interested in.
Allison: And naturally, the JGI was involved in work like this for the Chlamydomonas genome. When that genome was being sequenced, the JGI got about thirty scientists together for a big event.
Sabeeha Merchant: Which they used to call, uh, Jamboree where they invited people from the community to come to JGI.
Allison: Their mission was to take a look at the genome. And then, based on what each gene in that genome looked like, and using previous research, they set out to figure out what different Chlamydomonas genes could do. They were annotating those genes.
Sabeeha Merchant: We spent a week at JGI annotating genes. It was so exciting because by then, of course, I think we already had, you know, the yeast genome was already sequenced. There was a cyanobacterial genome sequence. And so everybody was like hungry to get the Chlamydomonas genome,
Allison: And it paid off! That work completed the original reference genome. It was published in 2007 and it’s fueled lots of other research since.
Sabeeha Merchant: Much of what we know about sort of chloroplast based photosynthesis. Those proteins were all discovered originally in Chlamydomonas.
Allison: And this work still continues – Sabeeha’s lab, on its own or working collaboratively with other researchers, has used Chlamy as a reference in sequencing four other green algae genomes. One recent publication out of Sabeeha’s lab shows that Chlamydomonas actually carry a special kind of gene called a polycistronic gene. Polycistronic genes are special, because while most RNA that comes from eukaryotes produces one protein, RNA from polycistronic genes can produce two, three, or even four proteins.
So it may be single-celled, but Chlamydomonas is pretty special, and we can learn a lot about all kinds of different organisms and biological processes by studying it.
Sabeeha Merchant: In terms of meeting our energy needs. Chlamydomonas is probably not an organism that we can grow like in bulk. Right. It’s more like a lab rat, right? So we use Chlamydomonas for discovery.
Allison: And that’s what makes this little algae so vital to the JGI’s Fungal & Algal Program. That’s a wrap on this JGIota. But you can find out more about Chlamydomonas – and other discoveries the JGI has made in its 25-year tenure – on our website. There’s a link in the show notes!
This episode was written and produced by Menaka Wilhelm, and hosted by me, Allison Joy! We had production help from Massie Ballon and Ashleigh Papp.
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Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science located at Lawrence Berkeley National Lab in Berkeley, California.
Thanks for tuning in – until next time!
- JGI@25: The Little Alga That Could
- Chlamydomonas reinhardtii on Phytozome and PhycoCosm
- JGI Blog Post: Green Algae Reveal One mRNA Encodes Many Proteins
- JGI News Release: Green Alga Genome Project Catalogs Carbon Capture Machinery and Reveals Identity as Ancient Cousin of Land Plants and Animals
- The original sequence: Science
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