Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans.

MINIREVIEW Cell Wall-Related Bionumbers and Bioestimates of Saccharomyces cerevisiae and Candida albicans Frans M. Klis, Chris G. de Koster, Stanley Brul ‹Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands Bionumbers and bioestimates are valuable tools in biological research. Here we focus on cell wall-related bionumbers and bioestimates of the budding yeast Saccharomyces cerevisiae and the polymorphic, pathogenic fungus Candida albicans. We discuss the linear relationship between cell size and cell ploidy, the correlation between cell size and specific growth rate, the effect of turgor pressure on cell size, and the reason why using fixed cells for measuring cellular dimensions can result in serious underestimation of in vivo values. We further consider the evidence that individual buds and hyphae grow linearly and that exponential growth of the population results from regular formation of new daughter cells and regular hyphal branching. Our calculations show that hyphal growth allows C. albicans to cover much larger distances per unit of time than the yeast mode of growth and that this is accompanied by strongly increased surface expansion rates. We therefore predict that the transcript levels of genes involved in wall formation increase during hyphal growth. Interestingly, wall proteins and polysaccharides seem barely, if at all, subject to turnover and replacement. A general lesson is how strongly most bionumbers and bioestimates depend on environmental conditions and genetic background, thus reemphasizing the importance of well-defined and carefully chosen culture conditions and experimental approaches. Finally, we propose that the numbers and estimates described here offer a solid starting point for similar studies of other cell compartments and other yeast species. I n their paper “A feeling for the numbers in biology,” Phillips and Milo (1) present a convincing case for a more quantitative approach in biological research. An important advantage of moving from a qualitative to a more quantitative understanding of a biological process is that one learns to view one’s observations from a different perspective. A feeling for the numbers involved assists in prioritizing hypotheses and selecting better experimental approaches and leads to surprising insights. For industrial purposes, genetic engineering, and synthetic biology, a quantitative approach becomes even more important, whereas for modeling of biological processes, accurate bionumbers and bioestimates are crucial. Numerous interesting bionumbers can be found at the website http://bionumbers.hms.harvard.edu/ (2). The cell wall of yeasts accounts for up to 30% of the cellular biomass on a dry weight basis and thus represents a substantial metabolic investment of the cell. Here we focus on cell wall-related bionumbers and bioestimates of two important fungi: the workhorse Saccharomyces cerevisiae and the human pathogen Candida albicans. CELLULAR DIMENSIONS OF SACCHAROMYCES CEREVISIAE The shape of the parent cell and the growing bud of the yeast S. cerevisiae (and of C. albicans when growing in the yeast form) approximates a prolate ellipsoid. This allows accurate estimation of the volume and surface area of parent cell and bud by measuring their length (major axis) and width (minor axis). For example, the volume V ⫽ ␲ab2/6 (where a is the major and b is the minor axis) and is usually expressed in ␮m3 or fl (1 ␮m3 ⫽ 1 fl ⫽ 10⫺15 liter). The online calculator “Ellipsoid” at http://planetcalc.com/ 149/ allows rapid calculation of both volume and surface area of ellipsoids. The cellular dimensions of parent cells of S. cerevisiae, which is usually grown at 30°C, have been extensively investigated. They vary widely and depend on cell ploidy, growth rate, and nutrient status and also on turgor pressure and the number of buds formed by the parent cell. Table 1 shows that in exponential-phase cul- 2 ec.asm.org Eukaryotic Cell p. 2–9 tures growing in rich medium, the average volume of parent cells is proportional to ploidy, increasing from ⬃44 ␮m3 for haploid cells to ⬃244 ␮m3 for hexaploid cells (3). This agrees with the median values of 42 ␮m3 and 82 ␮m3 obtained with haploid and diploid cells, respectively (4); see also reference 5, in which average volumes of 56 and 95 ␮m3 are presented for haploid and diploid cells, respectively. Table 1 further shows that the ratio of surface area and volume is inversely correlated with cell ploidy, decreasing by ⬃40% (from 1.38 ␮m⫺1 for haploid cells to 0.79 ␮m⫺1 for hexaploid cells). This is consistent with the observation that in diploid cells the transcript levels of genes that are involved in cell wall formation are generally lower than in haploid cells (6). The mean volume of parent cells of S. cerevisiae not only increases with increasing ploidy but, as has been shown for diploid cells, also positively correlates with the specific growth rate (Table 2), increasing from 29 ␮m3 at a specific growth rate of 0.045 h⫺1 (doubling time of ⬃15 h) to 95 ␮m3 at 0.46 h⫺1 (doubling time of ⬃1.5 h) (5, 7); a similar trend has been observed for haploid cells (8, 9). Interestingly, reduced growth resulting from either nutrient limitation or gene mutation is accompanied not only by a decrease in cellular volume but also by increased tolerance toward various stress conditions such as heat and oxidative stress (10). Similarly, post-exponential-phase yeast cells become rapidly more resistant to the wall-degrading enzyme preparation Zymolyase (11). This raises the question of whether nutrient sensing pathways, such as the Ras-cyclic AMP-protein kinase A signaling pathway and the Snf1 and TORC1 pathways (12), control specific cell wall properties, depending on nutrient availability. Finally, the inverse rela- Published ahead of print 15 November 2013 Address correspondence to Frans M. Klis, . Copyright © 2014, American Society for Microbiology. All Rights Reserved. doi:10.1128/EC.00250-13 January 2014 Volume 13 Number 1 Minireview TABLE 1 Effect of cell ploidy on dimensions, volume, biomass, surface area, and the ratio of surface area over volume of S. cerevisiae parent cellsa Ploidy Length (␮m) Width (␮m) Vol (␮m3) Biomass (dry wt, pg) Surface area (␮m2) Surface/vol (␮m⫺1) 1 2 3 4 5 6 4.76 6.16 7.66 7.97 9.42 10.1 4.18 5.06 5.97 6.20 6.64 6.80 44 83 143 161 218 245 16.5 31.2 53.9 60.5 82.1 92.3 60 92 134 144 179 194 1.38 1.12 0.93 0.90 0.82 0.79 a This table is based on data from plate-grown cells (3). The biomass (dry weight) was calculated by multiplying the volume with the density (1.11) (88) to obtain the biomass (wet weight) of the cell and multiplying the obtained value with the dry weight fraction (0.34) of the wet weight (89). tionship between surface area and cell volume probably favors the use of small (haploid) cells in cell surface engineering when the primary goal is to maximize the number of surface-located (...truncated)