A Geographically Diverse Collection of<i>Schizosaccharomyces pombe</i>Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

Brown, William R. A.; Liti, Gianni; Rosa, Carlos A.; James, Stephen A.; Roberts, Ian N.; Robert, Vincent; Jolly, N.P.; Tang, Wenhao; Baumann, Peter; Green, Carter; Schlegel, Kristina; Young, Jonathan H.; Hirchaud, Fabienne; Leek, Spencer; Thomas, Geraint; Blomberg, Anders

doi:10.1534/g3.111.001123

Cited by 77 publications

(113 citation statements)

References 36 publications

(47 reference statements)

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“…Despite being haploid, S. pombe undergoes an extended G 2 phase of the cell cycle, presenting an opportunity for unequal crossover between sister chromatids, a likely mechanism for such large duplications. We note that large duplications are commonly observed segregating in the S. pombe population (Brown et al 2011;Fawcett et al 2014).…”

Section: Insertion Bias Among Insertion-deletion Mutations (Indels)mentioning

confidence: 65%

“…In the wild, S. pombe occurs in small, incompletely isolated populations with only weak population structure resulting from recent global dispersal (Brown et al 2011;Jeffares et al 2015). Beyond this, little is known of its natural ecology.…”

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confidence: 99%

“…In a collection of 81 natural isolates, all but one were haploid, with the sole diploid most likely resulting from biparental inbreeding (Brown et al 2011). Under laboratory conditions, transient diploids do occur after mating but are generally unstable.…”

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confidence: 99%

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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

et al. 2015

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The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an 1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 3 10 210 mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.KEYWORDS mutation accumulation; effective population size; biased gene conversion; fission yeast M UTATION is the ultimate source of all genetic differences within and among species. Mutation may alter the sequence of the genome via single-base substitutions; change the length of the genome by means of insertions, deletions, and duplications; or alter genome architecture via changes in chromosomal ploidy. The rate at which each of these events occurs in nature is largely obscured in a comparison of individuals or species owing to the action of natural selection and drift. An unbiased estimate of the rate and spectrum of spontaneous mutations can be obtained by passing replicate individuals through thousands of generations of mutation accumulation (MA). Under this protocol, which imposes a very small effective population size during passage, selection will have little influence on the fate of new mutations.The fission yeast Schizosaccharomyces pombe is a member of the largest and most diverse fungal phylum, Ascomycota, and is a key model system in cell biology. In the wild, S. pombe occurs in small, incompletely isolated populations with only weak population structure resulting from recent global dispersal (Brown et al. 2011;Jeffares et al. 2015). Beyond this, little is known of its natural ecology. It is, however, often recovered from natural fermentations and was isolated originally from East African millet beer.Notwithstanding the uncertainty regarding its ecology, the life cycle of S. pombe in the wild is likely to be predominantly haploid. In a collection of 81 natural isolates, all but one were haploid, with the sole diploid most likely resulting from biparental inbreeding (Brown et al. 2011). ...

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Section: Insertion Bias Among Insertion-deletion Mutations (Indels)mentioning

confidence: 65%

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confidence: 99%

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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

et al. 2015

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“…A study of 88 independent natural isolates of S. pombe showed that this fission yeast is karyotypically variable, and that one Japanese strain, CBS 2777, contains four chromosomes (8). In the present study, we determined the genome sequence and organization of CBS 2777 and found that it is related to the karyotype of the laboratory strains by a complex rearrangement.…”

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confidence: 56%

“…S6), suggesting that all four strains are mosaics that recently descended from a small pool of relatively diverse natural founder strains, as has been observed for Saccharomyces cerevisiae industrial isolates (13). The two other Japanese strains, CBS 2775 and 2776 (8), were isolated at the same time and in the same location as CBS 2777 and have the same genotype, but contain three chromosomes. The close relationships among these three strains also suggest that the chromosome rearrangement in CBS 2777 is of recent origin.…”

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confidence: 64%

Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe

Brown

Thomas

Lee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochore assembly is unclear. Schizosaccharomyces pombe is an important experimental system for investigating centromere function, but all of the previous work with this species has exploited a single strain or its derivatives. The laboratory strain and most other S. pombe strains contain three chromosomes, but one recently discovered strain, CBS 2777, contains four. We show that the genome of CBS 2777 is related to that of the laboratory strain by a complex chromosome rearrangement. As a result, two of the kinetochores in CBS 2777 contain the central core sequences present in the laboratory strain centromeres, but lack adjacent heterochromatin. The closest block of heterochromatin to these rearranged kinetochores is ∼100 kb away at new telomeres. Despite lacking large amounts of adjacent heterochromatin, the rearranged kinetochores bind CENP-A Cnp1 and CENP-C Cnp3 in similar quantities and with similar specificities as those of the laboratory strain. The simplest interpretation of this result is that constitutive kinetochore assembly and heterochromatin formation occur autonomously.yeast | microbial diversity | epigenesis T he fission yeast Schizosaccharomyces pombe is a key system for the experimental study of centromere function. To date, all of this work has involved the strain 968h 90 and its derivatives 972h − and 975h + , each of which contains three chromosomes. Each of these chromosomes contains a kinetochore embedded in heterochromatin (1) and resembles the centromeres of many metazoan organisms; consequently they have been intensively studied. These studies have demonstrated that heterochromatin is necessary for the formation of new kinetochores (2-4), but that once formed, kintetochores (5) can be maintained on a circular plasmid in the absence of heterochromatin. In evolution, novel centromeres form on regions of chromosomes lacking heterochromatin but subsequently acquire it (6, 7), an order of events at odds with the conclusions of published studies of S. pombe. Thus, the relationship between heterochromatin and kinetochore assembly in S. pombe requires investigation using new approaches.A study of 88 independent natural isolates of S. pombe showed that this fission yeast is karyotypically variable, and that one Japanese strain, CBS 2777, contains four chromosomes (8). In the present study, we determined the genome sequence and organization of CBS 2777 and found that it is related to the karyotype of the laboratory strains by a complex rearrangement. We show that two of the centromeres in CBS 2777 lack flanking heterochromatic repeated sequences. This DNA is not detectably associated with siRNA and does not show any detectable enrichment of Rad21 (cohesin) binding. Despite these differences in flanking DNA, the rearranged centromeres in CBS 2777 bind the cons...

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A system of miniaturized stirred bioreactors for parallel continuous cultivation of yeast with online measurement of dissolved oxygen and off‐gas

Klein

Schneider

Heinzle

2012

Biotech & Bioengineering

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Chemostat cultivation is a powerful tool for physiological studies of microorganisms. We report the construction and application of a set of eight parallel small-scale bioreactors with a working volume of 10 mL for continuous cultivation. Hungate tubes were used as culture vessels connected to multichannel-peristaltic pumps for feeding fresh media and removal of culture broth and off-gas. Water saturated air is sucked into the bioreactors by applying negative pressure, and small stirrer bars inside the culture vessels allow sufficient mixing and oxygen transfer. Optical sensors are used for non-invasive online measurement of dissolved oxygen, which proved to be a powerful indicator of the physiological state of the cultures, particularly of steady-state conditions. Analysis of culture exhaust-gas by means of mass spectrometry enables balancing of carbon. The capacity of the developed small-scale bioreactor system was validated using the fission yeast Schizosaccharomyces pombe, focusing on the metabolic shift from respiratory to respiro-fermentative metabolism, as well as studies on consumption of different substrates such as glucose, fructose, and gluconate. In all cases, an almost completely closed carbon balance was obtained proving the reliability of the experimental setup.

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A Geographically Diverse Collection ofSchizosaccharomyces pombeIsolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

Cited by 77 publications

References 36 publications

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe

A system of miniaturized stirred bioreactors for parallel continuous cultivation of yeast with online measurement of dissolved oxygen and off‐gas

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