The ubiquitous yeast Saccharomyces cerevisiae was a part of human civilization before history was recorded and is essential for making bread, beer and wine, among other agriculturally important products.

The genome of the yeast Scheffersomyces stipitis was sequenced and annotated by DOE Joint Genome Institute researchers. Credit: Courtesy of Tom Jeffries.

S. cerevisiae is not, however, typical of the more than 1,500 yeast species found around the world. Yeasts are physically hard to distinguish, and it is easy to think they are all the same. Metabolically, genetically and biochemically, however, yeasts are highly diverse, according to an announcement from the Lawrence Berkeley National Laboratory. Characteristics such as their thick cell walls and tolerance of pressure changes that could rupture other cells mean yeasts are easily scaled up for industrial processes.

In addition, yeasts are easy to grow and modify and are not associated with many human illnesses. While these capabilities can be used for a wide range of biotechnological applications, including biofuel production, industry so far has only harnessed a fraction of the diversity available among yeast species.

To help boost the use of a wider range of yeasts and to explore the use of genes and pathways encoded in their genomes, a team led by researchers at the U.S. Department of Energy Joint Genome Institute (JGI), a DOE Office of Science User Facility at the Lawrence Berkeley National Laboratory, conducted a comparative genomic analysis of 29 yeasts, including 16 whose genomes were newly sequenced and annotated.

In the study, published Aug. 15 in Proceedings of the National Academy of Sciences (PNAS), the team mapped various metabolic pathways to yeast growth profiles.

“Obtaining a complete genome of a microbe that is industrially important greatly stimulates research in the area,” senior author Tom Jeffries, professor emeritus at University of Wisconsin-Madison, said of the work. “This is particularly true when the genomic sequence is accompanied by a high-quality annotation of the genes, and the JGI annotation pipeline is one of the best in the field. We can expect an explosive interest in yeast biology in the coming years.”

Yeast genetic diversity

Yeasts (which are classified as fungi) can use a wide range of carbon and energy sources, ranging from cellulosic (six carbon) and hemicellulosic (five carbon) sugars to methanol, glycerol and acetic acid. Products include ethanol and other alcohols, esters, organic acids, carotenoids, lipids and vitamins. In fact, vitamin complexes and some nutritional supplements are derived from yeasts.

“We sequenced these diverse genomes to expand the catalog of genes, enzymes and pathways encoded in these genomes for producing biofuels and bio-based products we use in daily life,” said Igor Grigoriev, JGI fungal program head and co-senior author of the manuscript.

Sequencing these less-known yeasts and characterizing their metabolic pathways helps fill in knowledge gaps regarding the fungal enzymes that can help convert a wide range of sugars into biofuel, added study first author Robert Riley of JGI. The well-known yeast S. cerevisiae, for example, ferments glucose, but not the other sugars found in plant biopolymers.

One of the newly sequenced yeasts is Pachysolus tannophilus, which can ferment xylose — otherwise known as wood sugar, as it is derived from hemicellulose — and, along with cellulose, is one of the main constituents of woody biomass. It is only distantly related to well-studied xylose fermenters such as Scheffersomyces stipitis — another yeast sequenced by JGI.

These distances are huge. “We might think of yeasts as simple unicellular, creatures similar to each other, but, in fact, their genetic diversity is like the difference between human and invertebrate sea squirt,” Riley said. “We sequenced these diverse genomes to discover and facilitate the next generation of biotechnological workhorse yeasts for producing the fuels and products we use in daily life. We also discovered a genetic code change that, if not understood, will impede the yeasts’ biotechnological use.”

Genetic code reassignment

In P. tannophilus, the team found a change in one of the three-letter codons that represent one of the 20 regularly used amino acids. That change from CUG-Ser to CUG-Ala is only the second observed case of a nonstop codon reassignment (a change from one amino acid to another rather than from one amino acid to a stop codon) in nuclear genomes.

“While we don’t know why and how this happened, genes with CUG codons may not produce functional proteins when expressed in an organism with different genetic code (and) will code for a different amino acid,” Grigoriev said.

“The CUG-Ala reassignment is important to biotechnology because, in order to express novel biotechnologically useful genes from diverse yeasts into workhorses like Saccharomyces, we need to know if the yeasts' genetic codes are the same,” Riley added. “If they aren't, expressing the novel genes won't work, because the proteins will be incorrectly translated.”

“With the advent of new genetic tools that can rapidly manipulate an organism’s DNA, publication of these new genomic yeast sequences will open up many new platforms for bio-engineering cellulose-degrading, lipid-producing, acid-tolerant yeasts that use a wide range of substrates and produce many different primary and secondary metabolites,” Jeffries said.