ReviewStationary phase in yeast
Introduction
When starved of an essential nutrient, cells of Saccharomyces cerevisiae cease mitotic division and arrest within the G1 phase of the mitotic cell cycle. The arrested cells subsequently acquire a variety of characteristics that collectively define the stationary phase of growth 1., 2.. These changes include a dramatic reduction in the overall rate of growth, an accumulation of the storage carbohydrate, glycogen, an increased resistance to a variety of environmental stresses, including heat shock, a thickening of the cell wall, and an increased ability to survive extended periods of starvation. A similar set of changes occurs when cells are starved of either a nitrogen, phosphate or carbon source 1., 3.. However, it is not yet clear if the final resting state is identical in each of these instances. In particular, it has been suggested that a true stationary phase might only be reached following carbon-source deprivation 2., 4. (Fig. 1). In any case, the above differences between G1 and stationary phase suggest that this resting state might be a distinct, out-of-cycle phase of growth.
Although stationary phase is a critical aspect of yeast cell biology, research in this area has lagged far behind that on the mitotic cell cycle. There have been few systematic genetic studies of stationary phase and we still do not have many useful molecular markers for this growth phase. As a result, some of the most basic questions regarding this resting state remain unanswered. This review will examine some of the reasons for this rather ‘stationary’ pace of progress and will suggest experiments aimed at stimulating new interest in this research area. In particular, the potential utility of genomic strategies for stationary phase research will be discussed.
Section snippets
Signaling pathways regulating stationary phase biology
The entry into stationary phase is regulated by the Ras and Tor signal transduction pathways, both of which are critical modulators of cell growth 5., 6•.. The S. cerevisiae Ras proteins, Ras1p and Ras2p, are small GTP-binding proteins that activate the cAMP-dependent protein kinase PKA [5]. The Tor proteins, Tor1p and Tor2p, are themselves serine/threonine-specific protein kinases 6•., 7.. Both of these signaling pathways positively regulate a variety of processes, such as protein translation,
Ras/PKA pathway targets
Recent studies have identified the Rim15p protein kinase as a PKA substrate required for stationary phase entry [9]. Mutants lacking Rim15p are viable but fail to assume the characteristics of stationary phase upon nutrient deprivation. These effects on stationary phase appear to be mediated, at least in part, by the Gis1p transcription factor [10•]. It is not yet known if Gis1p is a substrate of Rim15p or if the control by this protein kinase is more indirect. Interestingly, gis1 mutants are
Tor pathway targets
The protein kinase C homologue Pkc1p is part of a signaling pathway that regulates yeast cell integrity by controlling cell wall biosynthesis and the actin cytoskeleton [16]. Interestingly, this Pkc1p pathway was recently found to be both required for stationary phase survival and inhibited by the activity of the Tor pathway 17., 18.. In addition, inactivation of the Tor pathway was shown to result in cell wall alterations that were dependent upon Pkc1p activity [17]. Since the yeast cell wall
Coordinating stationary phase entry
A key question that remains concerns the manner in which the yeast cell coordinates the control by the Ras and Tor signaling pathways. The inactivation of either of these pathways results in a constitutive stationary phase-like arrest 5., 6•.. This happens even in rich growth media, where the other pathway might be expected to remain active and to continue signaling for growth. One explanation for these results is that these two pathways might be coordinately controlled in some manner that has
Mutants defective for stationary phase survival
A recent study has shown that proteins in the Srb complex of the RNA polymerase II holoenzyme are required for the entry into a normal stationary phase [24••]. Mutations that inactivate this complex disrupt the normal patterns of gene expression that occur upon nutrient deprivation 24••., 25.. These observations led to the suggestion that these Srb proteins might be targets of signaling pathways responsible for coordinating yeast cell growth with nutrient availability [24••]. This prediction
Stationary phase as a model for the study of aging?
S. cerevisiae cells can undergo two different types of aging. The first is ‘replicative aging’, and is measured by the finite number of divisions that a particular cell has undergone 34., 35.. The second, ‘chronological aging’, refers to the total lifespan of a given cell and is the sum of the replicative lifespan and the time spent in a quiescent state [36]. Recent studies have shown that stationary phase figures prominently in both of these aging processes 36., 37••., 38., 39.. In particular,
Is stationary phase a distinct, out-of-cycle growth phase?
A central question that remains unresolved concerns the very nature of the S. cerevisiae stationary phase. Is this resting state truly an unique phase of growth, distinct from all major phases of the mitotic cycle? An alternative hypothesis is that stationary phase represents an extended G1 phase, where the cells are exhibiting an especially slow rate of growth. This alternative was raised in response to observations indicating that several stationary phase characteristics were also exhibited
Genomic approaches to the study of stationary phase
The recent advent of functional genomics has provided tools that should facilitate future research on stationary phase biology. For example, two recent studies have used these technologies to directly examine the possibility that stationary phase is a distinct phase of growth. In the first study, a whole-genome expression analysis with microarrays identified 45 genes with a stationary phase-specific expression pattern (M Werner-Washburne, personal communication). Importantly, 14 of these genes
Conclusions
Although I have focused on the budding yeast S. cerevisiae in this review, the issues discussed are relevant to resting states in many, if not all, organisms. In most cases, it is still not clear whether a given resting state is a distinct phase of growth, and on the whole we do not have many useful markers for a quiescent state. However, this situation is likely to change significantly in the near future. The development of new technologies has poised the field for rapid progress in addressing
Acknowledgements
I thank Margaret Werner-Washburne and Gerald Johnston for sharing their thoughts on stationary phase, Margaret Werner-Washburne for sharing data before its publication, and Jeffrey Stack and the members of the Herman laboratory for their comments on the manuscript. Research in my laboratory is supported by grants from the National Institutes of Health and the National Science Foundation.
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
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