Oscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models

Oscillatory ROP GTPase Activation Leads the Oscillatory Polarized Growth of Pollen Tubes

“…Oscillating phenomenon is common in biological systems for propagating signals and spatially and temporally coordinating biological processes and is under tight regulation by "the oscillator" at cellular and molecular levels (Bessho and Kageyama, 2003;Patnaik, 2003;Merrow and Roenneberg, 2004). The circadian clock is the most studied oscillation.…”

“…The mechanism of circadian clock involves a gene expression circuit with both feed-forward and negative feedback controls, resulting rhythmic expressions of key transcriptional regulators (Badiu, 2003;Bessho and Kageyama, 2003;Millar, 2004). In biological systems, there exist many types of noncircadian cellular oscillations with much shorter periods, e.g., seconds or minutes, such as Ca 2ϩ waves in plant and animal cells (Allen et al, 1999;Lee et al, 2002), oscillations of metabolites in continuous culture of the budding yeast (Patnaik, 2003), periodic lamellipodial contractions in spreading and migrating animal cells (Giannone et al, 2004), cAMP-mediated waves of cell aggregation in Dictyostelium (Maeda et al, 2004), and oscillatory tip growth of pollen tubes . Unlike the circadian clock, many of these rapid oscillations with a period of minutes or even seconds, are unlikely to involve periodic changes in gene expression.…”

Calcium participates in feedback regulation of the oscillating ROP1 Rho GTPase in pollen tubes

“…An interesting question is whether there exists a common design principle for highly diverse biological oscillation phenomena, ranging from circadian rhythms in various organisms to rapid cyclic changes in signaling events, such as cellular calcium. It has been shown that oscillations with relatively long periods, such as circadian clocks, involve feedbackmediated oscillatory changes in the transcription of key transcription factors (3)(4)(5); however, some oscillatory changes are independent of gene expression, such as biochemical metabolism (6), cellular signaling (7), calcium fluxes (8), and cytoskeletal dynamics-mediated cell movement (9,10).…”

Lyapunov comparison of noise‐filtering methods for oscillating yeast cultures

“…These oscillations have been reported in small, laboratory-scale reactors (Bellgardt, 1994;Beuse et al, 1998;Murray et al, 2001;Satroutdinov et al, 1992), which are largely unaffected by environmental disturbances. The nature of the oscillations, including the absence of oscillatory behavior itself, depends on the operating conditions, notably the dilution rate and the mass transfer rate of oxygen to the fermentation broth (Beuse et al, 1998;Jones and Kompala, 1999).Both metabolic processes and transport between the cells and the extracellular fluid contribute to the occurrence and control of oscillations, and their interactions are complex and not yet fully understood (Patnaik, 2003). This limitation makes it difficult to propose quantitative descriptions of oscillatory fermentations that are adequate without being too complicated.…”

“…Most modeling efforts have thus focused either in detail on the cellular metabolism with little attention to extracellular transport or primarily on the macroscopic variables of interest through mass balances coupled to heavily lumped kinetics. Both kinds of models have been reviewed recently (Duboc et al, 1996;Patnaik, 2003) and are therefore not discussed here.These models were based on observations with small, laboratory-scale reactors, where nonideal features such as process noise and spatial gradients can usually be ignored. However, these effects become significant in the realistic conditions of production-scale bioreactors, thus making it difficult to translate laboratory-scale models directly to larger bioreactors (Gillard and Tragardh, 1999;Rohner and Meyer, 1995).…”