scholarly journals Quantitative insights into the cyanobacterial cell economy

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Tomáš Zavřel ◽  
Marjan Faizi ◽  
Cristina Loureiro ◽  
Gereon Poschmann ◽  
Kai Stühler ◽  
...  
Keyword(s):  
Growth Rate ◽  
Coarse Grained ◽  
Translational Machinery ◽  
Coarse Grained Model ◽  
Green Biotechnology ◽  
Photosynthetic Productivity ◽  
Heterotrophic Microorganisms ◽  
Wide Range ◽  
Growth Laws ◽  
Phototrophic Growth

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

scholarly journals Quantitative insights into the cyanobacterial cell economy

2018 ◽  
Author(s):  
Tomáš Zavřel ◽  
Marjan Faizi ◽  
Cristina Loureiro ◽  
Gereon Poschmann ◽  
Kai Stühler ◽  
...  
Keyword(s):  
Growth Rate ◽  
Coarse Grained ◽  
Translational Machinery ◽  
Coarse Grained Model ◽  
Green Biotechnology ◽  
Photosynthetic Productivity ◽  
Heterotrophic Microorganisms ◽  
Wide Range ◽  
Growth Laws ◽  
Phototrophic Growth

AbstractPhototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacteriumSynechocystissp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.

scholarly journals A bacterial size law revealed by a coarse-grained model of cell physiology

2016 ◽  
Author(s):  
François Bertaux ◽  
Julius von Kügelgen ◽  
Samuel Marguerat ◽  
Vahid Shahrezaei
Keyword(s):  
Growth Rate ◽  
Cell Size ◽  
Mass Fraction ◽  
Structural Model ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Cell Physiology ◽  
Bacterial Physiology ◽  
Coarse Grained Model ◽  
Growth Laws

AbstractUniversal observations in Biology are sometimes described as “laws”. InE. coli, experimental studies performed over the past six decades have revealed major growth laws relating ribosomal mass fraction and cell size to the growth rate. Because they formalize complex emerging principles in biology, growth laws have been instrumental in shaping our understanding of bacterial physiology. Here, we discovered a novel size law that connects cell size to the inverse of the metabolic proteome mass fraction and the active fraction of ribosomes. We used a simple whole-cell coarse-grained model of cell physiology that combines the proteome allocation theory and the structural model of cell division. The model captures all available experimental data connecting the cell proteome composition, ribosome activity, division size and growth rate in response to nutrient quality, antibiotic treatment and increased protein burden. Finally, a stochastic extension of the model explains non-trivial correlations observed in single cell experiments including the adder principle. This work provides a simple and robust theoretical framework for studying the fundamental principles of cell size determination in unicellular organisms.

scholarly journals Optimal proteome allocation and the temperature dependence of microbial growth laws

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Francis Mairet ◽  
Jean-Luc Gouzé ◽  
Hidde de Jong
Keyword(s):  
Growth Rate ◽  
Stress Responses ◽  
Protein Unfolding ◽  
Microbial Growth ◽  
Coarse Grained ◽  
Effect Of Temperature ◽  
Temperature Sensitive ◽  
Coarse Grained Model ◽  
Proteomic Data ◽  
Growth Laws

AbstractAlthough the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.

Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

2017 ◽  
Vol 19 (27) ◽  
pp. 17698-17707 ◽  
Author(s):  
Jibao Lu ◽  
Chance Miller ◽  
Valeria Molinero
Keyword(s):  
Fuel Cell ◽  
Activity Coefficient ◽  
Water Uptake ◽  
Coarse Grained ◽  
Fuel Cell Membranes ◽  
Coarse Grained Model ◽  
Experimental Activity ◽  
Tetramethylammonium Chloride ◽  
Atomistic Models ◽  
Wide Range

The coarse-grained model FFpvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

scholarly journals A minimal model of protein allocation during phototrophic growth

2017 ◽  
Author(s):  
Marjan Faizi ◽  
Tomáš Zavřel ◽  
Cristina Loureiro ◽  
Jan Cerveny ◽  
Ralf Steuer
Keyword(s):  
Optimal Allocation ◽  
Protein Translation ◽  
Cellular Growth ◽  
Coarse Grained ◽  
Recent Experimental Data ◽  
Carbon Uptake ◽  
Minimal Growth ◽  
Trade Offs ◽  
Growth Laws ◽  
Phototrophic Growth

AbstractPhotoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.

scholarly journals Analyzing the electrogenicity of cytochrome c oxidase

2016 ◽  
Vol 113 (28) ◽  
pp. 7810-7815 ◽  
Author(s):  
Ilsoo Kim ◽  
Arieh Warshel
Keyword(s):  
Molecular Mechanisms ◽  
Molecular Level ◽  
Theoretical Models ◽  
Proton Pumping ◽  
Coarse Grained ◽  
Transfer Reactions ◽  
Coarse Grained Model ◽  
Fundamental Information ◽  
Wide Range ◽  
Charge Transfer Reactions

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically “invisible” steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

scholarly journals SNARE machinery is optimized for ultrafast fusion

2019 ◽  
Vol 116 (7) ◽  
pp. 2435-2442 ◽  
Author(s):  
Fabio Manca ◽  
Frederic Pincet ◽  
Lev Truskinovsky ◽  
James E. Rothman ◽  
Lionel Foret ◽  
...  
Keyword(s):  
Synaptic Vesicles ◽  
Snare Proteins ◽  
Coarse Grained ◽  
Optimum Number ◽  
Biological Processes ◽  
Cooperative Action ◽  
Fusion Barrier ◽  
Coarse Grained Model ◽  
Wide Range

SNARE proteins zipper to form complexes (SNAREpins) that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 s to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic vesicles much faster: in a 10th of a millisecond. We propose that, similar to the case of muscle myosins, the ultrafast fusion results from cooperative action of many SNAREpins. The coupling originates from mechanical interactions induced by confining scaffolds. Each SNAREpin is known to have enough energy to overcome the fusion barrier of 25–35 kBT; however, the fusion barrier only becomes relevant when the SNAREpins are nearly completely zippered, and from this state, each SNAREpin can deliver only a small fraction of this energy as mechanical work. Therefore, they have to act cooperatively, and we show that at least three of them are needed to ensure fusion in less than a millisecond. However, to reach the prefusion state collectively, starting from the experimentally observed half-zippered metastable state, the SNAREpins have to mechanically synchronize, which takes more time as the number of SNAREpins increases. Incorporating this somewhat counterintuitive idea in a simple coarse-grained model results in the prediction that there should be an optimum number of SNAREpins for submillisecond fusion: three to six over a wide range of parameters. Interestingly, in situ cryoelectron microscope tomography has very recently shown that exactly six SNAREpins participate in the fusion of each synaptic vesicle. This number is in the range predicted by our theory.

scholarly journals Modeling structure, stability and flexibility of double-stranded RNAs in salt solutions

2018 ◽  
Author(s):  
L. Jin ◽  
Y.Z. Shi ◽  
C.J. Feng ◽  
Y.L. Tan ◽  
Z.J. Tan
Keyword(s):  
Electrostatic Potential ◽  
Cell Metabolism ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Structure Stability ◽  
Salt Solutions ◽  
3D Structures ◽  
Coarse Grained Model ◽  
Wide Range

AbstractDouble-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions on 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions on thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that thermally unfolding pathway of a dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix and the calculated salt-dependent persistence lengths are in good accordance with experiments.

scholarly journals Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

2021 ◽  
Vol 8 ◽  
Author(s):  
Chenjie Feng ◽  
Ya-Lan Tan ◽  
Yu-Xuan Cheng ◽  
Ya-Zhou Shi ◽  
Zhi-Jie Tan
Keyword(s):  
Rna Structure ◽  
Coarse Grained ◽  
Spatial Confinement ◽  
Functional Roles ◽  
Coarse Grained Model ◽  
Mouse Mammary Tumor ◽  
Wide Range ◽  
Tumor Virus ◽  
Folded Structures ◽  
Rna Pseudoknot

Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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