Saccharomyces cerevisiae

• 1. Introduction

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  In May 2013, the Oregon legislature named an official state microbe, and the winner was Saccharomyces cerevisiae. Lawmakers cited craft beer, which had shaped both the state's economy and its sense of identity. The honoree was a single-celled fungus, the same organism that makes bread dough rise in kitchens around the world.

  Yet this humble cell is also counted among the most intensively studied eukaryotes in molecular and cell biology. Researchers treat it as the yeast counterpart of the bacterium Escherichia coli. It has had its genome read from end to end, been rebuilt in the laboratory, and been packed into a capsule meant for an interplanetary round trip.

  How did a microbe from the brewery and the bakery become a favorite of the laboratory? What does a cell that divides by budding reveal about sex, aging and DNA repair? And why does a species sold as a medicine occasionally turn dangerous? The answers begin with where the yeast actually lives.

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• 2. Sugar Fungus

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  The name Saccharomyces comes from Latinized Greek. Saccharon means sugar and myces means fungus, so the genus is literally the sugar-fungus. The species name cerevisiae is Latin for of beer.

  Aliases abound. Brewer's yeast and baker's yeast are the best known, though the source notes that other species also brew and bake. Ale yeast and top-fermenting yeast describe its habits in the brewery, and budding yeast describes how it divides. In Asia it also goes by ragi yeast, a name tied to the making of tapai.

  In the wild, the story begins on fruit. Grapes before they ripen are almost free of yeast, but ripe ones carry it, and the species is believed to have first been isolated from grape skin. It also lives in oak bark all year round.

  The cells cannot travel through the air, so they need a ride. Queens of social wasps, including Vespa crabro and Polistes species, spend the winter as adults and can keep yeast cells from autumn through spring. They then pass the yeast to their offspring.

  In 2016, Stefanini and colleagues examined the gut of the social wasp Polistes dominula. It holds S. cerevisiae strains, and it also holds hybrids of S. cerevisiae with a relative, S. paradoxus. The gut turned out to offer conditions that push cells to form spores and germinate them again, which favors mating among strains and with S. paradoxus cells.

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• 3. From Sour Loaves to Cake Yeast

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  Around the 15th century, beer makers learned by trial and error that boiling a hopped wort produced a drink that was not sour. Nobody knew why. In earlier times, brewing and leavening relied on mixed cultures of wild bacteria, especially Lactobacillus, together with yeasts, and the results were acidic. Boiling killed unwanted bacteria, and hops carry natural chemicals that hold back the acid-makers while yeast thrives.

  By the 19th century, bread bakers were getting their yeast from brewers. That supply helped create sweet-fermented breads such as the Imperial Kaisersemmel roll, which lacked the sourness of older loaves. Meanwhile, many brewers drifted from top-fermenting S. cerevisiae toward bottom-fermenting S. pastorianus.

  The Vienna Process of 1846 is often remembered for putting steam in baking ovens. The source stresses something else. It brought high milling, in which grain is cracked in stages instead of crushed in a single pass, along with better ways to grow and harvest top-fermenting yeast, called press-yeast.

  Louis Pasteur's work refined microbiology and made pure strains possible. In 1879, Great Britain introduced specialized vats for growing S. cerevisiae. Around the turn of the 20th century, American producers began using centrifuges to concentrate it. Yeast became a major industry, cheaper and easier to distribute, and fresh cake yeast became the standard leaven in much of the Western world.

  During World War II, Fleischmann's developed granulated active dry yeast for the United States armed forces. It needed no refrigeration, kept longer and tolerated heat better, and it remains the standard yeast in American military recipes. The company also produced a yeast that rose twice as fast. In the 1970s, Lesaffre introduced instant yeast, which has taken market share from both fresh and dry forms.

  In the brewery, the species is called top-fermenting because its water-repelling surface makes clumps cling to carbon dioxide bubbles and float to the top of the vessel. It ferments warmer than lager yeast. Near 21 degrees Celsius, or with fluctuating temperatures, it can form fruity esters. Lager yeast works at about 5 degrees Celsius, where S. cerevisiae goes dormant.

  Bakers once took the yeast-filled foam from brewers' ale, known as barm, and sold it as barm cake. Today brewing and baking strains are somewhat different. One variant, S. cerevisiae var. diastaticus, is a notorious spoiler that triggers secondary fermentation in packaged beer.

  The cells have other jobs as well. Grown into nutritional yeast, they supply amino acids and B-complex vitamins and appear in vegan cheese substitutes. Grown in selenium-rich media, they yield organic selenium compounds that animals absorb more easily. Aquarium keepers use yeast in plastic bottles as a cheap source of carbon dioxide for plants, with one bubble every 3-7 seconds.

  The yeast is also a suitable host for producing therapeutic recombinant proteins, a use that depends on how well scientists understand its inner workings.

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• 4. Budding and Mating

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  A mature S. cerevisiae cell is round to ovoid, only 5-10 micrometers across, and it reproduces by budding. In a well-fed culture, every cell wears a bud, because building the bud fills the whole cell cycle. The bud grows until it matches the size of an adult cell by the time it separates.

  The split is lopsided. The daughter emerges at two-thirds the size of the mother, while the mother barely changes. That asymmetry makes yeast a useful stand-in for stem cells, which also divide unevenly to renew themselves and to differentiate.

  The timing breaks a rule found in many cells. Budding starts in late G1 and finishes only about halfway through the next cycle. The spindle can assemble before DNA copying is complete, and there is no clearly defined G2 phase. The source describes this as less extensive regulation than in higher eukaryotes.

  Two linked events carry out the cut. A ring of actin and myosin II tightens while a chitinous wall called the primary septum grows. Disturbing either one disrupts the other. Septins form a ring at the future bud site in late G1 and become an hourglass once the bud emerges. Microtubules matter far less.

  Yeast cells come in two forms. Haploid cells carry one set of chromosomes and divide simply by mitosis, though they generally die under severe stress. Diploid cells, the preferred form, can respond to stress by undergoing meiosis and producing four haploid spores.

  There are two mating types, called a and alpha, which show primitive sex differences. Cells of opposite type fuse into a diploid, shuffling chromosomes in the process. The signaling machinery that drives mating, built around a G protein-coupled receptor and a three-tier MAPK cascade, is homologous to equipment in human cells.

  In 2006, Ruderfer and colleagues studied the ancestry of natural strains. They concluded that outcrossing happens only about once every 50,000 cell divisions. Mating mostly occurs between close relatives, partly because opposite-type cells share the same sac, the ascus, after one meiosis, and partly because a haploid cell often produces cells of the opposite type when it divides.

  If outcrossing is that rare, then making new genetic variation cannot be the main reason the species keeps meiosis. The authors favored another idea, that meiosis persists because it repairs DNA through recombination, a benefit collected every time meiosis happens. Mutants lacking the gene rad52 support that view. They show reduced meiotic recombination and are more sensitive to X-rays and to DNA-damaging chemicals.

  A related process the source calls genome renewal purges harmful recessive mutations that pile up during long stretches of asexual diploid growth. That cleanup brings us to the question of what happens to cells as they grow old.

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• 5. The Model Cell

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  Researchers shopping for a laboratory organism look for small size, a short generation time, easy handling and well-understood genetics. S. cerevisiae scores well on all of these. Its doubling time is 1.25-2 hours at 30 degrees Celsius, so many lines can be grown cheaply and quickly.

  It also divides by meiosis, which opens the door to sexual genetics. Scientists can add genes or delete them by homologous recombination, and growing it as a haploid makes knockout strains easy to build. As a eukaryote, it shares the complex internal structure of plants and animals, without the large share of non-coding DNA that muddies research in higher organisms.

  On the 24th of April 1996, the yeast genome sequence was released into the public domain, the first complete genome of any eukaryote. It runs to about 12,156,677 base pairs and 6,275 genes, compactly arranged on 16 chromosomes. Only about 5,800 of those genes are believed to be functional.

  At least 31% of yeast genes have counterparts in the human genome. Many proteins important in human biology were first found by studying their yeast homologs, including cell cycle proteins, signaling proteins and protein-processing enzymes. Even the vitamin biotin owes a debt to the species, since a yeast growth assay underpinned its isolation, crystallization and structural determination.

  Gene names follow a code. Take YGL118W. The Y marks a yeast gene, G means chromosome 7, the seventh letter of the alphabet, and L means the left arm. The number 118 gives the position counted from the centromere, and W says the coding sequence sits on the Watson strand.

  A collection of deletion mutants now covers 90% of the genome. A 2010 map of genetic interactions covers about 75% of genes. It drew on 5.4 million two-gene comparisons, in which each pair was knocked out together and the cell's fitness was compared with what the single knockouts predicted. The map identified 170,000 interactions.

  The approach checks itself. The genes Par32, Ecm30 and Ubp15 had profiles resembling genes in the Gap1-sorting module, and knocking them out disrupted that process, confirming they belong to it. Genes with similar profiles tend to share a pathway, so the network can guess the jobs of uncharacterized genes.

  The toolkit keeps growing. It includes the yeast two-hybrid method for protein interactions, tetrad analysis, a library of about 4,700 viable haploid deletion strains, a GFP fusion library for tracking where proteins sit, and a TAP tag library for purifying proteins. Stanford University's deletion project knocked out every gene to learn its function.

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• 6. Aging and Rejuvenation

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  For more than five decades, S. cerevisiae has served as a model for aging, and it has pointed to more mammalian aging genes than any other model organism. Scientists measure aging in two ways. Replicative life span counts how many times a cell divides, while chronological life span measures how long a cell survives without dividing. A typical mother cell manages about 26 divisions on average.

  Limiting glucose or amino acids in the growth medium extends both measures, in yeast and in other organisms. Researchers first assumed the sir2 enzyme was responsible, but the effect turned out to be independent of it. Boosting sir2 and fob1 does lengthen replicative life by preventing buildup of extrachromosomal rDNA circles, a suspected cause of yeast senescence.

  Dietary restriction may work through lower signaling in the TOR pathway, which governs how cells respond to nutrients. Mutations that dampen TOR lengthen both life spans, and the same has been seen in other animals. A mutant lacking Ras2 along with another gene gained a tenfold increase in chronological life span under calorie restriction, the largest increase achieved in any organism.

  Mother cells bud off young daughters but age through successive generations and eventually die. Meiosis changes that. Spores made by an aged cell have the same replicative potential as spores made by a young cell, so meiosis seems to wipe away age-related damage. What that damage is remains unknown.

  In starving cells that are not dividing, reactive oxygen species rise, and DNA damage accumulates, including apurinic or apyrimidinic sites and double-strand breaks. As these cells age chronologically, they also lose ability to repair breaks in their own DNA.

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• 7. Rebuilt Chromosomes and Lost Capsule

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  The international Synthetic Yeast Genome Project, known as Sc2.0, aims to build a designer version of the S. cerevisiae genome from scratch, one more stable than the natural one. The redesign strips out all transposons, repetitive elements and many introns. Every UAG stop codon becomes UAA, and the transfer RNA genes move to a new neochromosome.

  As of March 2017, 6 of the 16 chromosomes had been synthesized and tested. No significant fitness defects appeared.

  A second experiment went the opposite direction. By repeatedly joining chromosome ends and deleting centromeres, researchers fused all 16 chromosomes into one. Its transcriptome and traits are nearly identical to the wild type. The giant chromosome supports life, but the strain grows more slowly across environments and competes, reproduces and survives less well.

  Yeast has also tried spaceflight. A living sample was included in the Living Interplanetary Flight Experiment, a small capsule designed for a three-year interplanetary round trip on the Russian Fobos-Grunt spacecraft, launched in late 2011. The test targeted transpermia, the idea that life could survive travel between planets inside rocks blasted off one world by an impact.

  The mission failed. Fobos-Grunt never escaped low Earth orbit, and on the 15th of January 2012 it fell into the Pacific Ocean in an uncontrolled re-entry, instruments and all. The next planned deep-space exposure mission for S. cerevisiae is called BioSentinel.

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• 8. Helper and Hazard

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  The strain S. cerevisiae var. boulardii is manufactured industrially and used as a probiotic medication in humans and animals. Moderate-quality evidence shows it reduces the risk of antibiotic-associated diarrhea in adults and children, and cuts adverse effects from Helicobacter pylori eradication therapy. There is some evidence that it prevents, but does not treat, traveler's diarrhoea. It may help as an adjunct in acute diarrhoea in adults and children, and in persistent diarrhoea in children. It may also ease allergic rhinitis.

  In clinical trials, patients tolerated it well, with side effects similar to control groups, and no fungemia was reported. Clinical practice tells a different story. Fungemia cases have been reported, mainly in patients with weakened immunity or central vascular catheters. Some researchers say to avoid the treatment in them, while others only urge caution.

  The species is a proven opportunistic pathogen, though of low virulence, and infections are very rare given how widely it is used. It has been found on the skin, in the mouth and throat, and in the digestive tract and vagina of healthy people. One review found it in 6% of human intestine samples. Experts disagree on whether it is a true member of the normal microbiota, since it originates in food. After oral doses, healthy people clear it from the intestine within 5 days.

  It accounts for 0.45-1.06% of yeast-induced vaginitis. Some affected women were partners of bakers and carried the same strain their partners used in baking. As of 1999, no case had been reported in women working in bakeries themselves.

  Invasive infection is the serious side. When yeast reaches the bloodstream or deep tissue such as the lungs, liver or spleen, more than 30% of cases end in death even with treatment. It causes 1% to 3.6% of nosocomial fungemia cases, and is much rarer than Candida albicans, even in patients weakened by cancer. Every patient in a comprehensive review had at least one predisposing condition.

  The yeast can enter through the mucosa of the mouth or gut, or through contaminated intravascular catheters. Catheters, antibiotic therapy and weakened immunity are the main risk factors. The source adds that S. boulardii accounts for about 40% of invasive Saccharomyces infections and is more likely than other strains to infect people with normal immunity. Medical staff handling probiotic preparations can transfer it to catheters on their hands. One case involved a baker whose surgically removed lung nodule contained S. cerevisiae, probably from inhaling dry baking yeast powder.

  Strains differ in danger. Most environmental strains cannot grow above 35 degrees Celsius, whereas virulent strains grow above 37 and often up to 39, and rarely up to 42. As of 2017, the European Food Safety Authority requires that any viable strain that grows above 37 degrees and enters food or feed must show no resistance to antimycotic drugs.

  Heat tolerance is not the only factor. Other traits linked to virulence include producing enzymes such as proteinase and phospholipase, invasive growth, sticking to mammalian cells, and surviving hydrogen peroxide, the chemical macrophages use against invaders. Forming branching chains called pseudohyphae is sometimes linked as well, though it may be common in harmless strains too.

  The yeast also leaves a trace in human immunity. Antibodies against S. cerevisiae appear in 60-70% of patients with Crohn's disease and 10-15% of those with ulcerative colitis, so they may help doctors tell the two inflammatory bowel diseases apart.

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