The Forsburg Lab pombe Pages:
Introduction

Welcome to the Forsburg Lab, a research group in the Molecular & Computational Biology Section in the Dept of Biological Sciences at the University of Southern California (USC) in Los Angeles, CA. This page will introduce you to us and to the fission yeast Schizosaccharomyces pombe (the model organism we employ for our research). Inside pages will describe information about DNA replication and our work in the cell cycle and in meiosis.

Our research is conducted in a beautiful, state of the art building at the University of Southern California (USC) in Los Angeles. We are part of the Molecular & Computational Biology Section in the Dept of Biological Sciences in the College of Letters, Arts and Sciences (the "College"). From USC, we can just see the famous HOLLYWOOD sign.

Founded in 1880, USC is the oldest independent teaching and research university in the Western US--and the largest private employer in Los Angeles! (Check out the factbook for more information). It is a private university, not to be confused with the State-run University of California system. The 30,000 students at USC are about equally divided between graduate and undergraduate scholars. The College is located at the University Park Campus just south of downtown Los Angeles and right next to historic Exposition Park. Want to check out the weather in LA today? Visit Tommy Cam: the camera with the view of the statue nicknamed "Tommy Trojan" in the center of campus.

The University has a vibrant intellectual and cultural life with stellar reputations not only in medicine and research, but in diverse other areas including, but not limited to architecture, public policy, and fine arts. In addition to the College, there are also numerous professional schools at USC including the Keck School of Medicine. Sports fans know that the USC Trojans are a powerhouse in college athletics, especially in football. USC alumni are an accomplished lot known for their fierce loyalty.

There are lots of cultural events on campus: visit the USC events calendar . Los Angeles is the second largest city in the country, with a lively and diverse population. There are a wealth of activities, so check out this citywide calendar . You can get started at the Experience LA page which includes transit information, and also visit the CultureLA site. Get to know the city by taking a walking tour.

Our lab started out at The Salk Institute in La Jolla, CA , about 150 miles south of Los Angeles in the lovely city of San Diego. We were there from 1993 to 2004.

Studying fission yeast

What's fission yeast? Yeast is a very general term, and covers a broad range of unicellular fungi. You can find out more about various yeasts by visiting the web pages listed in the yeast virtual library. Most people are familiar with brewer's or baker's yeast, Saccharomyces cerevisiae. For a cooking-oriented description of this well-domesticated eukaryote, visit this discussion from Red Star Yeast Company, which includes some simple experiments to introduce yeast biology tothe consumer.

However, the species that we study is the fission yeast Schizosaccharomyces pombe. The word pombe means beer in Swahili, and this yeast was originally isolated in millet beer from eastern Africa. It can be used to brew, although not really recommended. S. pombe and closely related species have been isolated from grape juice, kambucha tea, and arak. S. pombe particularly useful in the laboratory, where we use it as a model system for cell division. For an introduction to the use of model systems in biology, see this supplement from The Scientist. We have information about original characterization of S. pombe, and more detailed description of the derivation of the standard wild type isolate.

Why is yeast relevant to biomedical research? Normal cell division is central to normal growth and development not only of yeast cells, but of humans as well. But humans are very complicated, so it is easier to establish basic principles in simple model organisms. Importantly, the human versions of a number of yeast cell cycle and DNA repair genes have been found to be directly involved in human cell division. Malfunctions can lead tocancer or birth defects. The normal activity of these genes is most easily studied in the yeast cells, which are readily manipulated in the laboratory. This provides important insights into their mechanisms in humans, which helps direct experiments in more complicated cell types. Studying the control of cell division in yeast is thus very relevant to human health and understanding many clinical disorders. That's why two researchers studying cell division in yeast received the 2001 Nobel Prize in Physiology or Medicine, along with a third investigator studying sea urchins! For a description of their landmark research, visit this illustrated presentation from the Nobel site in Sweden.

Yeast research Both S. pombe and Sacch. cerevisiae are harmless, rapidly growing eukaryotes that are popular as model systems to understand basic biological processes. They have many differences, and the comparison between them is uniquely informative, making the yeasts a powerful pair of experimental systems. For example, many of the genes that regulate normal cell division in complex organisms such as humans also exist and function the same way in yeasts, but each species provides distinct insights. Fission yeast cells grow quickly (the generation time of S. pombe is between 2 and 4 hours) and are easy to manipulate in the laboratory, so we can learn about the function of these conserved regulators very rapidly in yeast, and such knowledge can be used to understand what happens in complex systems in which experiments are more difficult.

Fission yeast cells are rod shaped and divide by medial fission. S. pombe is a popular system for studies of cell growth and division, partly because of its regular size. The cells shown in panel A of the figure are wild type cells, viewed under the microscope and treated with a fluorescent dye that stains the DNA in the nucleus. The nuclei are the bright blobs in the center of the cells. At the bottom of the panel, you can see a cell that has divided, with two nuclei and a medial septum. The bar indicates scale and is 10 microns long.

If the cells have a mutation that prevents the normal progression of the cell cycle, they become very elongated. This occurs because the cells can continue to grow but are unable to divide (panel B). These mutants are called cdc mutants, for cell division cycle.

Many people ask us how different are S. pombe and Sacch. cerevisiae? The answer is, VERY different. According to some methods of comparison, S. pombe diverged from the ascomycete lineage before Sacch. cerevisiae separated from the filamentous fungi Aspergillus or Penicillium. Based on recent studies, S. pombe is formally classified as an archaeascomycete. The NCBI Taxonomy Browser gives the following lineage: Eukaryota/ Fungi/ Ascomycota/ Archiascomycetes/ Schizosaccharomycetales/ Schizosaccharomycetaceae/ Schizosaccharomyces. The phylogeny of S. pombe is a point of ongoing discussion, but a recent exciting paper on fungal evolution indicates that the divergence between ascomycetes and archaeascomycetes is on the order of 1144 million years ago! That's over 4 fold longer than previous suspected. This review article describes the lineages of all common model organisms.

Not surprisingly, S. pombe biology is quite distinct from that of Sacch. cerevisiae. For a discussion of their differences, you might check out this review. For a sense of biological history, you can read the original description of S. pombe which dates from 1893.

For other useful pages specific to fission yeast biology, and pombe lab homepages, check out our list of pombe on the web. If you are interested in working with S. pombe, you can start with our list of Frequently Asked Questions. Our pombe methods pages contain lots of information including links and protocols for molecular genetics. We also have an index of useful fission yeast plasmids. Want to know the equivalent S. cerevisiae genes for S. pombe cell cycle genes? Visit our gene conversion table.

S. japonicus Recently, a cousin of S. pombe had its genome sequenced at the Broad Institute. Schizosaccharomyces japonicus is also a fission yeast. However, it is able to grow hyphally, making invasive filaments in the agar. It also has 8-spored asci (octads). It will be interesting to see how this species develops as a companion model to S. pombe.

The fission yeast life cycle

A cartoon of the fission yeast life cycle is shown below (with a link to a larger version). The cells' nuclei, containing the DNA, are drawn in blue. As well as the normal vegetative or mitotic cycle (the series of events that allow one yeast cell to divide into two), the cartoon diagrams the specialized meiotic cycle that results after two cells conjugate. You can also see this diagrammed with actual cell photos, along with a more detailed description of the events of the cell cycle.

The real strength of the yeast system is its facile genetics. We can isolate mutants, characterize the genes required for a given process, and move from a relatively abstract genetic description to a very precise, concrete biochemical description of what the gene products actually do. Often, these genes are the same as those found in complex systems, including humans. Our lab is primarily interested in DNA replication and what happens between the START of the cell cycle and the initiation of S phase, with a secondary interest in DNA replication during meiosis.

Our work has focused on a family of proteins called MCM proteins, and their regulators. (Panel B of the photograph above actually shows you an mcm2 mutant). These proteins are found in all eukaryotes and even in archaea, making them a very ancient, and very important, component of cell division control. MCM proteins are essential for normal DNA replicaiton and cell division.

We are also investigating DNA replication during meiosis. In humans, this specialized division results in production of gametes: eggs and sperm, each with half the genetic complement of a normal diploid cell. Click here for a more detailed description of the difference between the cell cycle and meiotic division. In yeast, the gametes are called spores. The process of mating to form a diploid, and meiosis to form spores (diagrammed above) provides a sort of lifeboat for this normally haploid organism. Spores are highly resistant to environmental stress, and protect the yeast in a dormant state until the surroundings improve. The micrograph at right shows you the four spores packaged in the shell of the parent cell, called an ascus. We are studying how meiotic S phase differs from events in the haploid cell cycle.

The next pages discuss DNA replication and our research and publications in more detail.

Pombe Beer

If you use fission yeast to brew with malt and hops (European style), the results are disappointing as described in this article. My lab has also tried brewing with pombe with results very similar to what it reports. The sulfurous nose was very noticeable and increased with time. I've been told that pombe generates the largest number of foul-tasting compounds for any fermentation. But of course, this is not a traditional method, so maybe it tastes better with millet. Or perhaps it's just an acquired taste.

We have also made bread with it; that was more successful and was actually tasty, although it is not as robust at rising as standard baker's yeast.

© S. L. Forsburg .