T.T.H. Maire | TU Delft Repository

Slowest possible replicative life at frigid temperatures for yeast

Journal article (2022) - Diederik S. Laman Trip, Théo Maire, Hyun Youk

Determining whether life can progress arbitrarily slowly may reveal fundamental barriers to staying out of thermal equilibrium for living systems. By monitoring budding yeast’s slowed-down life at frigid temperatures and with modeling, we establish that Reactive Oxygen Species (ROS) and a global gene-expression speed quantitatively determine yeast’s pace of life and impose temperature-dependent speed limits - shortest and longest possible cell-doubling times. Increasing cells’ ROS concentration increases their doubling time by elongating the cell-growth (G1-phase) duration that precedes the cell-replication (S-G2-M) phase. Gene-expression speed constrains cells’ ROS-reducing rate and sets the shortest possible doubling-time. To replicate, cells require below-threshold concentrations of ROS. Thus, cells with sufficiently abundant ROS remain in G1, become unsustainably large and, consequently, burst. Therefore, at a given temperature, yeast’s replicative life cannot progress arbitrarily slowly and cells with the lowest ROS-levels replicate most rapidly. Fundamental barriers may constrain the thermal slowing of other organisms’ lives. ...

Keeping still life away from death

Functions and dynamics of gene expression during dormacy of Saccharomyces cerevisiae spores

Doctoral thesis (2022) - T.T.H. Maire

While life is present everywhere on earth, each individual species can only grow and proliferate in a specific set of conditions. Moreover due to inherent fluctuation of the environment, individual organisms are often periodically confronted to stressful conditions that prohibit growth, reproduction and increase mortality. One of the most common strategy to cope with these harmful conditions is to shield and quietly wait for the storm to finish. Indeed upon change of the environment, many organisms enter "dormancy", whereby they differentiate into a distinct resting form with additional protection, storage and with greatly reduced internal activity (dormant state). Although relying on widely different molecular basis, specialized dormant stage are found in virtually every group of living organisms, including endospores of bacteria, spores of fungi, seeds of plants, cysts of protists and diapaused eggs of animals. Even after sometimes years of apparent inactivity, dormant organisms can resume growth and reproduction upon sudden improvement of environmental conditions. How such organisms manage to keep the potential to resume growth while having a nearly ceased activity? Over the last 20 years, scientists have uncovered various physiological and molecular mechanisms that control entry and exit of dormancy. However a basic understanding of what exactly happens during dormancy, i.e how to survive while stopping nearly all internal activity, is still missing. Two reasons are likely responsible for that knowledge gap. A first conceptual obstacle is a general view that since by definition nothingmuch happens during dormancy, nothing important happens. A second technical obstacle is the lack of sensitive enough instruments to quantify the "nearly ceased" activity during dormancy. As a result, very few studies have established the concrete link between a vanishing internal activity and the ability to survive during dormancy in a single experimental system. In this thesiswe propose to focus on dormant Saccharomyces cerevisiae yeast spores to specifically investigate the links between gene expression and the ability to survive during week-long dormancy. ...

While life is present everywhere on earth, each individual species can only grow and proliferate in a specific set of conditions. Moreover due to inherent fluctuation of the environment, individual organisms are often periodically confronted to stressful conditions that prohibit growth, reproduction and increase mortality. One of the most common strategy to cope with these harmful conditions is to shield and quietly wait for the storm to finish. Indeed upon change of the environment, many organisms enter "dormancy", whereby they differentiate into a distinct resting form with additional protection, storage and with greatly reduced internal activity (dormant state). Although relying on widely different molecular basis, specialized dormant stage are found in virtually every group of living organisms, including endospores of bacteria, spores of fungi, seeds of plants, cysts of protists and diapaused eggs of animals. Even after sometimes years of apparent inactivity, dormant organisms can resume growth and reproduction upon sudden improvement of environmental conditions. How such organisms manage to keep the potential to resume growth while having a nearly ceased activity? Over the last 20 years, scientists have uncovered various physiological and molecular mechanisms that control entry and exit of dormancy. However a basic understanding of what exactly happens during dormancy, i.e how to survive while stopping nearly all internal activity, is still missing. Two reasons are likely responsible for that knowledge gap. A first conceptual obstacle is a general view that since by definition nothingmuch happens during dormancy, nothing important happens. A second technical obstacle is the lack of sensitive enough instruments to quantify the "nearly ceased" activity during dormancy. As a result, very few studies have established the concrete link between a vanishing internal activity and the ability to survive during dormancy in a single experimental system. In this thesiswe propose to focus on dormant Saccharomyces cerevisiae yeast spores to specifically investigate the links between gene expression and the ability to survive during week-long dormancy.

Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability

Journal article (2020) - Théo Maire, Tim Allertz, Max A. Betjes, Hyun Youk

Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur-and by how much-within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to-without nutrients-express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression-including RNA polymerases-decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared with their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition. ...

Evaluation of Schink et al.

Having the Gem Shine through a Fog

Journal article (2019) - Diederik S. Laman Trip, Théo Maire, Hyun Youk

One snapshot of the peer review process for “Death Rate of E. coli during Starvation Is Set by Maintenance Cost and Biomass Recycling” (Schink et al., 2019). ...