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 Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

2017 ◽  
Vol 114 (31) ◽  
pp. E6457-E6465 ◽  
Author(s):  
Alexandra-M. Reimers ◽  
Henning Knoop ◽  
Alexander Bockmayr ◽  
Ralf Steuer
Keyword(s):  
Resource Allocation ◽  
Optimal Allocation ◽  
Allocation Problem ◽  
Time Dependent ◽  
Metabolic Reconstruction ◽  
Resource Allocation Problem ◽  
Trade Offs ◽  
A Genome ◽  
Phototrophic Growth ◽  
Insight Into

Cyanobacteria are an integral part of Earth’s biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2. Growth and metabolism of cyanobacteria are inherently tied to the diurnal rhythm of light availability. As yet, however, insight into the stoichiometric and energetic constraints of cyanobacterial diurnal growth is limited. Here, we develop a computational framework to investigate the optimal allocation of cellular resources during diurnal phototrophic growth using a genome-scale metabolic reconstruction of the cyanobacterium Synechococcus elongatus PCC 7942. We formulate phototrophic growth as an autocatalytic process and solve the resulting time-dependent resource allocation problem using constraint-based analysis. Based on a narrow and well-defined set of parameters, our approach results in an ab initio prediction of growth properties over a full diurnal cycle. The computational model allows us to study the optimality of metabolite partitioning during diurnal growth. The cyclic pattern of glycogen accumulation, an emergent property of the model, has timing characteristics that are in qualitative agreement with experimental findings. The approach presented here provides insight into the time-dependent resource allocation problem of phototrophic diurnal growth and may serve as a general framework to assess the optimality of metabolic strategies that evolved in phototrophic organisms under diurnal conditions.

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 Optimal proteome allocation strategies for phototrophic growth in a light-limited chemostat

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Marjan Faizi ◽  
Ralf Steuer
Keyword(s):  
Computational Models ◽  
Coarse Grained ◽  
Small Scale ◽  
Cell Physiology ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Light Gradient ◽  
Trade Offs ◽  
Phototrophic Growth ◽  
Allocation Strategies

Abstract Background Cyanobacteria and other phototrophic microorganisms allow to couple the light-driven assimilation of atmospheric $$\text {CO}_{2}$$ CO 2 directly to the synthesis of carbon-based products, and are therefore attractive platforms for microbial cell factories. While most current engineering efforts are performed using small-scale laboratory cultivation, the economic viability of phototrophic cultivation also crucially depends on photobioreactor design and culture parameters, such as the maximal areal and volumetric productivities. Based on recent insights into the cyanobacterial cell physiology and the resulting computational models of cyanobacterial growth, the aim of this study is to investigate the limits of cyanobacterial productivity in continuous culture with light as the limiting nutrient. Results We integrate a coarse-grained model of cyanobacterial growth into a light-limited chemostat and its heterogeneous light gradient induced by self-shading of cells. We show that phototrophic growth in the light-limited chemostat can be described using the concept of an average light intensity. Different from previous models based on phenomenological growth equations, our model provides a mechanistic link between intracellular protein allocation, population growth and the resulting reactor productivity. Our computational framework thereby provides a novel approach to investigate and predict the maximal productivity of phototrophic cultivation, and identifies optimal proteome allocation strategies for developing maximally productive strains. Conclusions Our results have implications for efficient phototrophic cultivation and the design of maximally productive phototrophic cell factories. The model predicts that the use of dense cultures in well-mixed photobioreactors with short light-paths acts as an effective light dilution mechanism and alleviates the detrimental effects of photoinhibition even under very high light intensities. We recover the well-known trade-offs between a reduced light-harvesting apparatus and increased population density. Our results are discussed in the context of recent experimental efforts to increase the yield of phototrophic cultivation.

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.

You Only Traverse Twice: A YOTT Placement, Routing, and Timing Approach for CGRAs

2021 ◽  
Vol 20 (5s) ◽  
pp. 1-25
Author(s):  
Michael Canesche ◽  
Westerley Carvalho ◽  
Lucas Reis ◽  
Matheus Oliveira ◽  
Salles Magalhães ◽  
...  
Keyword(s):  
Execution Time ◽  
High Performance ◽  
Coarse Grained ◽  
Optimal Placement ◽  
Greedy Heuristics ◽  
High Quality ◽  
Solution Quality ◽  
Graph Traversal ◽  
Trade Offs ◽  
Graph Properties

Coarse-grained reconfigurable architecture (CGRA) mapping involves three main steps: placement, routing, and timing. The mapping is an NP-complete problem, and a common strategy is to decouple this process into its independent steps. This work focuses on the placement step, and its aim is to propose a technique that is both reasonably fast and leads to high-performance solutions. Furthermore, a near-optimal placement simplifies the following routing and timing steps. Exact solutions cannot find placements in a reasonable execution time as input designs increase in size. Heuristic solutions include meta-heuristics, such as Simulated Annealing (SA) and fast and straightforward greedy heuristics based on graph traversal. However, as these approaches are probabilistic and have a large design space, it is not easy to provide both run-time efficiency and good solution quality. We propose a graph traversal heuristic that provides the best of both: high-quality placements similar to SA and the execution time of graph traversal approaches. Our placement introduces novel ideas based on “you only traverse twice” (YOTT) approach that performs a two-step graph traversal. The first traversal generates annotated data to guide the second step, which greedily performs the placement, node per node, aided by the annotated data and target architecture constraints. We introduce three new concepts to implement this technique: I/O and reconvergence annotation, degree matching, and look-ahead placement. Our analysis of this approach explores the placement execution time/quality trade-offs. We point out insights on how to analyze graph properties during dataflow mapping. Our results show that YOTT is 60.6 , 9.7 , and 2.3 faster than a high-quality SA, bounding box SA VPR, and multi-single traversal placements, respectively. Furthermore, YOTT reduces the average wire length and the maximal FIFO size (additional timing requirement on CGRAs) to avoid delay mismatches in fully pipelined architectures.

scholarly journals Coarse-grained tight-binding models

2021 ◽  
Author(s):  
Tianxiang Liu ◽  
Li Mao ◽  
Mats-Erik Pistol ◽  
Craig Pryor
Keyword(s):  
Quantum Well ◽  
Computing Time ◽  
Numerical Test ◽  
Tight Binding ◽  
Computation Time ◽  
Coarse Grained ◽  
Weakly Bound ◽  
Trade Offs ◽  
Full Calculation ◽  
Binding Models

Abstract Calculating the electronic structure of systems involving very different length scales presents a challenge. Empirical atomistic descriptions such as pseudopotentials or tight-binding models allow one to calculate the effects of atomic placements, but the computational burden increases rapidly with the size of the system, limiting the ability to treat weakly bound extended electronic states. Here we propose a new method to connect atomistic and quasi-continuous models, thus speeding up tight-binding calculations for large systems. We divide a structure into blocks consisting of several unit cells which we diagonalize individually. We then construct a tight-binding Hamiltonian for the full structure using a truncated basis for the blocks, ignoring states having large energy eigenvalues and retaining states with an energy close to the band edge energies. A numerical test using a GaAs/AlAs quantum well shows the computation time can be decreased to less than 5% of the full calculation with errors of less than 1%. We give data for the trade-offs between computing time and loss of accuracy. We also tested calculations of the density of states for a GaAs/AlAs quantum well and find a ten times speedup without much loss in accuracy.

scholarly journals Massive Phenotypic Measurements Reveal Complex Physiological Consequences of Differential Translation Efficacies

2017 ◽  
Author(s):  
Adam Paul Arkin ◽  
Guillaume Cambray
Keyword(s):  
Growth Rate ◽  
Translation Initiation ◽  
Protein Production ◽  
Protein Biosynthesis ◽  
Cellular Growth ◽  
Sequence Variants ◽  
Release Rates ◽  
Trade Offs ◽  
Fluctuating Environments ◽  
Protein Overproduction

ABSTRACTControl of protein biosynthesis is at the heart of resource allocation and cell adaptation to fluctuating environments. One gene’s translation often occurs at the expense of another’s, resulting in global energetic and fitness trade-offs during differential expression of various functions. Patterns of ribosome utilization—as controlled by initiation, elongation and release rates—are central to this balance. To disentangle their respective determinants and physiological impacts, we complemented measurements of protein production with highly parallelized quantifications of transcripts’ abundance and decay, ribosome loading and cellular growth rate for 244,000 precisely designed sequence variants of an otherwise standard reporter. We find highly constrained, non-monotonic relationships between measured phenotypes. We show that fitness defects derive either from protein overproduction, with efficient translation initiation and heavy ribosome flows; or from unproductive ribosome sequestration by highly structured, slowly initiated and overly stabilized transcripts. These observations demonstrate physiological impacts of key sequence features in natural and designed transcripts.

scholarly journals Thermodynamic Limits and Optimality of Microbial Growth

Entropy ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. 277
Author(s):  
Nima Saadat ◽  
Tim Nies ◽  
Yvan Rousset ◽  
Oliver Ebenhöh
Keyword(s):  
Microbial Growth ◽  
Black Box ◽  
Cellular Growth ◽  
Modeling Approaches ◽  
Theoretical Approaches ◽  
Growing Cell ◽  
Limiting Nutrient ◽  
Growth Laws ◽  
Thermodynamic Limits ◽  
Optimality Principles

Understanding microbial growth with the use of mathematical models has a long history that dates back to the pioneering work of Jacques Monod in the 1940s. Monod’s famous growth law expressed microbial growth rate as a simple function of the limiting nutrient concentration. However, to explain growth laws from underlying principles is extremely challenging. In the second half of the 20th century, numerous experimental approaches aimed at precisely measuring heat production during microbial growth to determine the entropy balance in a growing cell and to quantify the exported entropy. This has led to the development of thermodynamic theories of microbial growth, which have generated fundamental understanding and identified the principal limitations of the growth process. Although these approaches ignored metabolic details and instead considered microbial metabolism as a black box, modern theories heavily rely on genomic resources to describe and model metabolism in great detail to explain microbial growth. Interestingly, however, thermodynamic constraints are often included in modern modeling approaches only in a rather superficial fashion, and it appears that recent modeling approaches and classical theories are rather disconnected fields. To stimulate a closer interaction between these fields, we here review various theoretical approaches that aim at describing microbial growth based on thermodynamics and outline the resulting thermodynamic limits and optimality principles. We start with classical black box models of cellular growth, and continue with recent metabolic modeling approaches that include thermodynamics, before we place these models in the context of fundamental considerations based on non-equilibrium statistical mechanics. We conclude by identifying conceptual overlaps between the fields and suggest how the various types of theories and models can be integrated. We outline how concepts from one approach may help to inform or constrain another, and we demonstrate how genome-scale models can be used to infer key black box parameters, such as the energy of formation or the degree of reduction of biomass. Such integration will allow understanding to what extent microbes can be viewed as thermodynamic machines, and how close they operate to theoretical optima.

scholarly journals The evolutionary convergence of avian lifestyles and their constrained coevolution with species' ecological niche

2015 ◽  
Vol 282 (1821) ◽  
pp. 20151808 ◽  
Author(s):  
Paola Laiolo ◽  
Javier Seoane ◽  
Juan Carlos Illera ◽  
Giulia Bastianelli ◽  
Luis María Carrascal ◽  
...  
Keyword(s):  
Life Histories ◽  
Ecological Niche ◽  
Optimal Allocation ◽  
Reproductive Investment ◽  
Cost Of Reproduction ◽  
Phenotypic Evolution ◽  
Realized Niche ◽  
Trade Offs ◽  
The Cost ◽  
Species Variability

The fit between life histories and ecological niche is a paradigm of phenotypic evolution, also widely used to explain patterns of species co-occurrence. By analysing the lifestyles of a sympatric avian assemblage, we show that species' solutions to environmental problems are not unbound. We identify a life-history continuum structured on the cost of reproduction along a temperature gradient, as well as habitat-driven parental behaviour. However, environmental fit and trait convergence are limited by niche filling and by within-species variability of niche traits, which is greater than variability of life histories. Phylogeny, allometry and trade-offs are other important constraints: lifetime reproductive investment is tightly bound to body size, and the optimal allocation to reproduction for a given size is not established by niche characteristics but by trade-offs with survival. Life histories thus keep pace with habitat and climate, but under the limitations imposed by metabolism, trade-offs among traits and species' realized niche.

Value of Water in a Drying Climate

2012 ◽  
Keyword(s):  
Climate Change ◽  
Public Policy ◽  
East Coast ◽  
Optimal Allocation ◽  
Policy Issues ◽  
Merino Wool ◽  
Trade Offs ◽  
Rural Settings ◽  
The World ◽  
Expert Team

Are we making the best use of water? How do we judge this? Are there trade-offs between upstream and downstream water use? What are these and how are they resolved? Disputes over water allocations are, second to climate change, the dominant environmental and public policy issues of the present era. We are called upon to resolve such controversies using the principles of sustainable development, which integrates ecology, economics and ethics. This timely book establishes a template for all types of resource allocation disputes, whether in Australia or overseas. An expert team of ecologists, economists and sustainability experts spent three years interviewing people in the Little Swanport catchment, seeking answers to the optimal allocation of water on the Tasmanian East Coast. The hinterland of this area produces some of the most valuable merino wool in the world, the estuary grows mouth-watering oysters, and much of the land is in near-pristine condition, providing very valuable biodiversity resources. The book is written in an easy-to-read style and gradually evolves to become the story of everyday life of one small Australian catchment. It is about people living in rural settings in the upper catchment with soils and rainfall suitable for farming; people residing in coastal settlements in the lower catchment; people working and relaxing in the estuary where fishing and aquaculture occur; and people and their business in adjacent towns.

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