scholarly journals Cell Growth Model with Stochastic Gene Expression Helps Understand the Growth Advantage of Metabolic Exchange and Auxotrophy

mSystems ◽  
2021 ◽  
Author(s):  
Dibyendu Dutta ◽  
Supreet Saini
Keyword(s):  
Gene Expression ◽  
Metabolic Flux ◽  
Growth Models ◽  
Stochastic Gene Expression ◽  
Cooperative Interactions ◽  
In The Wild ◽  
Cooperative Behaviors ◽  
State Growth ◽  
Cell Growth Model ◽  
Metabolic Exchange

Cooperative behaviors are highly prevalent in the wild, but their evolution is not understood. Metabolic flux models can demonstrate the viability of metabolic exchange as cooperative interactions, but steady-state growth models cannot explain why cooperators grow faster.

scholarly journals Cell growth model with stochastic gene expression helps understand the growth advantage of metabolic exchange and auxotrophy

2020 ◽  
Author(s):  
Dibyendu Dutta ◽  
Supreet Saini
Keyword(s):  
Gene Expression ◽  
Steady State ◽  
Cell Growth ◽  
Metabolic Flux ◽  
Growth Models ◽  
Evolution Of Cooperation ◽  
Growth Effect ◽  
Gene Expression Noise ◽  
In The Wild ◽  
Metabolic Exchange

AbstractDuring cooperative growth, microbes often experience higher fitness, due to sharing of resources by metabolic exchange and herd protection through biofilm structures. However, the trajectory of evolution of competitive species towards cooperation is not known. Moreover, existing models (based on optimisation of steady-state resources or fluxes) are often unable to explain the growth advantage for the cooperating species, even for simple reciprocally cross-feeding auxotrophic pairs. We present an abstracted model of cell growth that considers the stochastic burst-like gene expression of biosynthetic pathways of limiting biomass precursor metabolites, and directly connects their cellular levels to growth and division using a “metabolic sizer/adder” rule. Our model recapitulates Monod’s law and yields the experimentally observed right-skewed long-tailed distribution of cell doubling times. The model further predicts the growth effect of secretion and uptake of metabolites, by linking it to changes in the internal metabolite levels. The model also explains why auxotrophs may grow faster when provided the metabolite they cannot produce, and why a pair of reciprocally cross-feeding auxotrophs can grow faster than prototrophs. Overall, our framework allows us to predict the growth effect of metabolic interactions in microbial communities and also sets the stage to study the evolution of these interactions.ImportanceCooperative behaviours are highly prevalent in the wild, but we do not understand how it evolves. Metabolic flux models can demonstrate the viability of metabolic exchange as cooperative interactions, but steady-state growth models cannot explain why cooperators grow faster. We present a stochastic model that connects growth to the cell’s internal metabolite levels and quantifies the growth effect of metabolite exchange and auxotrophy. We show that a reduction in gene expression noise explains why cells that import metabolites or become auxotrophs can grow faster, and also why reciprocal cross-feeding of metabolites between complementary auxotrophs allow them to grow faster. Our framework can simulate the growth of interacting cells, which will enable us to understand the possible trajectories of the evolution of cooperation in silico.

scholarly journals Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts

BMC Biology ◽  
2013 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
José Viñuelas ◽  
Gaël Kaneko ◽  
Antoine Coulon ◽  
Elodie Vallin ◽  
Valérie Morin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stochastic Gene Expression ◽  
Chromatin Dynamics

Response of Interspecific Hybrid Species of Manchurian Ash to MJ and NO Signals and Preliminary Study on the Formation Mechanism of Drought Resistance Advantage

2021 ◽  
Author(s):  
Yang Cao ◽  
fei song ◽  
Xingtang Zhao ◽  
Liming He ◽  
Yaguang Zhan
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Drought Resistance ◽  
Interspecific Hybrid ◽  
Normal Growth ◽  
Control Group ◽  
Physiological Indicators ◽  
Manchurian Ash ◽  
In The Wild ◽  
Set Up

Abstract Background: In this study, sodium nitrate (SNP, a donor of nitric oxide) and methyl jasmonate (MJ) were used as exogenous hormones. The experiment was conducted with the offspring (interspecific hybrid) D110 of ash and ash, and their respective parents (non-interspecific hybrid) D113 and 4-3 as experimental materials. The experiment set up three experimental groups of drought stress, exogenous hormone SNP and MJ, and a control group under normal growth (non-drought stress), to study the physiological indicators and gene expression of manchurian ash. Result: The results showed that under drought stress and exogenous application of hormone SNP or MJ, there were significant differences between hybrids and parents in plant growth, photosynthesis, defense enzyme activity, hormone content and gene expression.Conclusions: This experiment provides a new theoretical support for the existing hormone breeding methods of manchurian ash, which can improve the drought resistance of manchurian ash and increase its survival rate in the wild. Increasing the growth rate and breeding efficiency of manchurian ash brings new ideas.

scholarly journals A single nuclei transcriptomic analysis of the Atlantic salmon gill through smoltification and seawater transfer

2020 ◽  
Author(s):  
Alexander C. West ◽  
Yasutaka Mizoro ◽  
Shona H. Wood ◽  
Louise M. Ince ◽  
Marianne Iversen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atlantic Salmon ◽  
Direct Evidence ◽  
Cell Types ◽  
Prior Work ◽  
In The Wild ◽  
Induced Changes ◽  
Freshwater Environments ◽  
Transcriptomic Studies

AbstractAnadromous salmonids begin life adapted to the freshwater environments of their natal streams before a developmental transition, known as smoltification, transforms them into marine-adapted fish. In the wild, the extending photoperiods of spring stimulates smoltification, typified by radical reprogramming of the gill from an ion-absorbing organ to ion-excreting organ. Prior work has highlighted the role of specialized “mitochondrion-rich” cells in delivering this phenotype. However, transcriptomic studies identify thousands of smoltification-driven differentially regulated genes, indicating that smoltification causes a multifaceted, multicellular change; but direct evidence of this is lacking.Here, we use single-nuclei RNAseq to characterize the Atlantic salmon gill during smoltification and seawater transfer. We identify 20 distinct clusters of nuclei, including known, but also novel gill cell types. These data allow us to isolate cluster-specific, smoltification-induced changes in gene expression. We also show how cellular make-up of the gill changes through smoltification. As expected, we noted an increase in the proportion of seawater mitochondrion-rich cells, however, we also identify a reduction of several immune-related cells. Overall, our results provide unrivaled detail of the cellular complexity in the gill and suggest that smoltification triggers unexpected immune reprogramming directly preceding seawater entry.

scholarly journals Molecular Basis for Anaerobic Growth of Saccharomyces cerevisiae on Xylose, Investigated by Global Gene Expression and Metabolic Flux Analysis

2004 ◽  
Vol 70 (4) ◽  
pp. 2307-2317 ◽  
Author(s):  
Marco Sonderegger ◽  
Marie Jeppsson ◽  
Bärbel Hahn-Hägerdal ◽  
Uwe Sauer
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Global Gene Expression ◽  
Anaerobic Growth ◽  
Flux Analysis ◽  
Atp Production ◽  
Redox Imbalance ◽  
Chemostat Cultures

ABSTRACT Yeast xylose metabolism is generally considered to be restricted to respirative conditions because the two-step oxidoreductase reactions from xylose to xylulose impose an anaerobic redox imbalance. We have recently developed, however, a Saccharomyces cerevisiae strain that is at present the only known yeast capable of anaerobic growth on xylose alone. Using transcriptome analysis of aerobic chemostat cultures grown on xylose-glucose mixtures and xylose alone, as well as a combination of global gene expression and metabolic flux analysis of anaerobic chemostat cultures grown on xylose-glucose mixtures, we identified the distinguishing characteristics of this unique phenotype. First, the transcript levels and metabolic fluxes throughout central carbon metabolism were significantly higher than those in the parent strain, and they were most pronounced in the xylose-specific, pentose phosphate, and glycerol pathways. Second, differential expression of many genes involved in redox metabolism indicates that increased cytosolic NADPH formation and NADH consumption enable a higher flux through the two-step oxidoreductase reaction of xylose to xylulose in the mutant. Redox balancing is apparently still a problem in this strain, since anaerobic growth on xylose could be improved further by providing acetoin as an external NADH sink. This improved growth was accompanied by an increased ATP production rate and was not accompanied by higher rates of xylose uptake or cytosolic NADPH production. We concluded that anaerobic growth of the yeast on xylose is ultimately limited by the rate of ATP production and not by the redox balance per se, although the redox imbalance, in turn, limits ATP production.

scholarly journals Role of Sigma Factors in Controlling Global Gene Expression in Light/Dark Transitions in the Cyanobacterium Synechocystis sp. Strain PCC 6803

2007 ◽  
Vol 189 (21) ◽  
pp. 7829-7840 ◽  
Author(s):  
Tina C. Summerfield ◽  
Louis A. Sherman
Keyword(s):  
Gene Expression ◽  
Global Gene Expression ◽  
Growth Conditions ◽  
Day Length ◽  
Regulation Of Transcription ◽  
Wild Type ◽  
Protein Levels ◽  
In The Wild ◽  
Altered Gene ◽  
Pcc 6803

ABSTRACT We report on differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 after light-dark transitions in wild-type, ΔsigB, and ΔsigD strains. We also studied the effect of day length in the presence of glucose on a ΔsigB ΔsigE mutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in the light, respectively. In the light, approximately 350 genes displayed transcript levels in the ΔsigD strain that were different from those of the wild type, with over 200 of these up-regulated in the mutant. In the dark, removal of SigB altered more than 150 genes, and the levels of 136 of these were increased in the mutant compared to those in the wild type. The removal of both SigB and SigE had a major impact on gene expression under mixotrophic growth conditions and resulted in the inability of cells to grow in the presence of glucose with 8-h light and 16-h dark cycles. Our results indicated the importance of group II σ factors in the global regulation of transcription in this organism and are best explained by using the σ cycle paradigm with the stochastic release model described previously (R. A. Mooney, S. A. Darst, and R. Landick, Mol. Cell 20:335-345, 2005). We combined our results with the total protein levels of the σ factors in the light and dark as calculated previously (S. Imamura, S. Yoshihara, S. Nakano, N. Shiozaki, A. Yamada, K. Tanaka, H. Takahashi, M. Asayama, and M. Shirai, J. Mol. Biol. 325:857-872, 2003; S. Imamura, M. Asayama, H. Takahashi, K. Tanaka, H. Takahashi, and M. Shirai, FEBS Lett. 554:357-362, 2003). Thus, we concluded that the control of global transcription is based on the amount of the various σ factors present and able to bind RNA polymerase.

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