scholarly journals Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

2018 ◽  
Author(s):  
François Vasseur ◽  
Moises Exposito-Alonso ◽  
Oscar Ayala-Garay ◽  
George Wang ◽  
Brian J. Enquist ◽  
...  
Keyword(s):  
Growth Rate ◽  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Seed Production ◽  
Allometric Scaling ◽  
Abiotic Stress Response ◽  
Scaling Exponents ◽  
Metabolic Scaling ◽  
Metabolic Scaling Theory ◽  
Growth Scaling

AbstractSeed plants vary tremendously in size and morphology. However, variation and covariation between plant traits may at least in part be governed by universal biophysical laws and biological constants. Metabolic Scaling Theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near constant allometric scaling exponents across species. However, observed variation in scaling exponents questions the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST correlated with relative growth rate, seed production and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings support a core MST prediction and suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology, and begin to link adaptive variation in allometric scaling to specific genes.Significance statementAre there biological constants unifying phenotypic diversity across scales? Metabolic Scaling Theory (MST) predicts mathematical regularity and constancy in the allometric scaling of growth rate with body size across species. Here, we show that adaptation to climate in Arabidopsis thaliana is associated with local strains that substantially deviate from the values predicted by MST. This deviation can be linked to increased stress tolerance at the expense of seed production, and it occurs through selection on genes that are involved in abiotic stress response and that are geographically correlated with climatic conditions. This highlights the evolutionary role of allometric diversification and helps establish the physiological bases of plant adaptation to contrasting environments.

scholarly journals Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

2018 ◽  
Vol 115 (13) ◽  
pp. 3416-3421 ◽  
Author(s):  
François Vasseur ◽  
Moises Exposito-Alonso ◽  
Oscar J. Ayala-Garay ◽  
George Wang ◽  
Brian J. Enquist ◽  
...  
Keyword(s):  
Growth Rate ◽  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Seed Production ◽  
Stress Resistance ◽  
Allometric Scaling ◽  
Hydrodynamic Resistance ◽  
Scaling Exponent ◽  
Scaling Exponents ◽  
Growth Scaling

Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes.

Genome-wide identification and analysis of GDSL-type esterases/lipases in watermelon (Citrullus lanatus)

2019 ◽  
Author(s):  
Runsheng Ren ◽  
Xingping Yang ◽  
Jinhua Xu ◽  
Man Zhang ◽  
Guang Liu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Driving Forces ◽  
Citrullus Lanatus ◽  
Morphological Development ◽  
Pathogen Defense ◽  
Abiotic Stress Response ◽  
Systematic Analysis ◽  
Duplication Events ◽  
Root Tissues

Abstract Background The GDSL esterase and lipase families play important roles in abiotic stress, pathogen defense, seed development and lipid metabolism. Identifying the lipase activity of a putative GDSL lipase is necessary to determine its function. Systematic analysis of the GDSL gene family is still lacking in Citrullus lanatus. Results In this study, we identified 65 watermelon GDSL-type esterase/lipase genes and divided these genes into 6 clades based on phylogeny. The phylogenetic relationship of watermelon GDSL genes compared with Arabidopsis thaliana GDSL esterases/lipases was also determined, and these genes were divided into four groups related to morphological development, abiotic stress response, pathogen defense, and secondary metabolism. The chromosomal location of these genes revealed that they are distributed unevenly across all 11 watermelon chromosomes. Analysis of duplication events suggested that segmental duplication and tandem duplication were the major driving forces of GDSL family evolution. Synteny analysis indicated that GDSLs in watermelon were highly homologous to those in Arabidopsis thaliana, melon and cucumber. Transcriptome analyses showed the tissue-specific and common expression of the GDSL genes in leaf and root tissues and identified nitrogen-related genes under low nitrogen (N) stress compared with optimal N conditions. Conclusions Our results provide a basis for selecting candidate watermelon GDSL genes for further studies to determine the biological functions of the GDSL genes in watermelon.

scholarly journals Arabidopsis thaliana calcium-dependent lipid-binding protein (AtCLB): a novel repressor of abiotic stress response

2011 ◽  
Vol 62 (8) ◽  
pp. 2679-2689 ◽  
Author(s):  
Kanishka de Silva ◽  
Bozena Laska ◽  
Christopher Brown ◽  
Heike Winter Sederoff ◽  
Mariya Khodakovskaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Stress Response ◽  
Binding Protein ◽  
Lipid Binding ◽  
Abiotic Stress Response ◽  
Lipid Binding Protein ◽  
Calcium Dependent

scholarly journals The Zinc-Finger Thylakoid-Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana

2018 ◽  
Vol 9 ◽  
Author(s):  
Karina L. Lopes ◽  
Ricardo A. O. Rodrigues ◽  
Marcos C. Silva ◽  
Wiliane G. S. Braga ◽  
Marcio C. Silva-Filho
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Stress Response ◽  
Membrane Protein ◽  
Zinc Finger ◽  
Thylakoid Membrane ◽  
Abiotic Stress Response

scholarly journals Cancer as a Model System for Testing Metabolic Scaling Theory

2021 ◽  
Vol 9 ◽  
Author(s):  
Alexander B. Brummer ◽  
Van M. Savage
Keyword(s):  
Lung Cancer ◽  
Tumor Volume ◽  
Metabolic Tumor Volume ◽  
Scaling Theory ◽  
Imaging Biomarkers ◽  
Scaling Exponents ◽  
Clinical Images ◽  
Cell Lung Carcinoma ◽  
Metabolic Scaling ◽  
Metabolic Scaling Theory

Biological allometries, such as the scaling of metabolism to mass, are hypothesized to result from natural selection to maximize how vascular networks fill space yet minimize internal transport distances and resistance to blood flow. Metabolic scaling theory argues two guiding principles—conservation of fluid flow and space-filling fractal distributions—describe a diversity of biological networks and predict how the geometry of these networks influences organismal metabolism. Yet, mostly absent from past efforts are studies that directly, and independently, measure metabolic rate from respiration and vascular architecture for the same organ, organism, or tissue. Lack of these measures may lead to inconsistent results and conclusions about metabolism, growth, and allometric scaling. We present simultaneous and consistent measurements of metabolic scaling exponents from clinical images of lung cancer, serving as a first-of-its-kind test of metabolic scaling theory, and identifying potential quantitative imaging biomarkers indicative of tumor growth. We analyze data for 535 clinical PET-CT scans of patients with non-small cell lung carcinoma to establish the presence of metabolic scaling between tumor metabolism and tumor volume. Furthermore, we use computer vision and mathematical modeling to examine predictions of metabolic scaling based on the branching geometry of the tumor-supplying blood vessel networks in a subset of 56 patients diagnosed with stage II-IV lung cancer. Examination of the scaling of maximum standard uptake value with metabolic tumor volume, and metabolic tumor volume with gross tumor volume, yield metabolic scaling exponents of 0.64 (0.20) and 0.70 (0.17), respectively. We compare these to the value of 0.85 (0.06) derived from the geometric scaling of the tumor-supplying vasculature. These results: (1) inform energetic models of growth and development for tumor forecasting; (2) identify imaging biomarkers in vascular geometry related to blood volume and flow; and (3) highlight unique opportunities to develop and test the metabolic scaling theory of ecology in tumors transitioning from avascular to vascular geometries.

scholarly journals Identification of Synchronized Role of Transcription Factors, Genes, and Enzymes in Arabidopsis thaliana under Four Abiotic Stress Responsive Pathways

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Samsad Razzaque ◽  
Rabab Mahdi ◽  
Aparna Islam
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Protein Interaction ◽  
Abiotic Stresses ◽  
Interaction Model ◽  
Literature Mining ◽  
Extensive Literature ◽  
Abiotic Stress Response ◽  
Protein Protein Interaction ◽  
Microarray Datasets

Microarray datasets are widely used resources to predict and characterize functional entities of the whole genomics. The study initiated here aims to identify overexpressed stress responsive genes using microarray datasets applying in silico approaches. The target also extended to build a protein-protein interaction model of regulatory genes with their upstream and downstream connection in Arabidopsis thaliana. Four microarray datasets generated treating abiotic stresses like salinity, cold, drought, and abscisic acid (ABA) were chosen. Retrieved datasets were firstly filtered based on their expression comparing to control. Filtered datasets were then used to create an expression hub. Extensive literature mining helped to identify the regulatory molecules from the expression hub. The study brought out 42 genes/TF/enzymes as the role player during abiotic stress response. Further bioinformatics study and also literature mining revealed that thirty genes from those forty-two were highly correlated in all four datasets and only eight from those thirty genes were determined as highly responsive to the above abiotic stresses. Later their protein-protein interaction (PPI), conserved sequences, protein domains, and GO biasness were studied. Some web based tools and software like String database, Gene Ontology, InterProScan, NCBI BLASTn suite, etc. helped to extend the study arena.

scholarly journals Testing allometric scaling relationships in plant roots

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Qiang Deng ◽  
Zhiyou Yuan ◽  
Xinrong Shi ◽  
T. Ryan Lock ◽  
Robert L. Kallenbach
Keyword(s):  
Plant Root ◽  
Woody Species ◽  
Plant Roots ◽  
Scaling Exponent ◽  
Terrestrial Plants ◽  
Natural Habitats ◽  
Scaling Exponents ◽  
Coarse Roots ◽  
Metabolic Scaling ◽  
Metabolic Scaling Theory

Abstract Background Metabolic scaling theory predicts that plant productivity and biomass are both size-dependent. However, this theory has not yet been tested in plant roots. Methods In this study, we tested how metabolic scaling occurs in plants using a comprehensive plant root dataset made up of 1016 observations from natural habitats. We generated metabolic scaling exponents by log-transformation of root productivity versus biomass. Results Results showed that the metabolic scaling exponents of fine root (< 2 mm in diameter) productivity versus biomass were close to 1.0 for all ecosystem types and functional groups. Scaling exponents decreased in coarse roots (> 2 mm in diameter). Conclusions We found isometric metabolic scaling in fine roots, a metabolically active organ similar to seedlings or saplings. Our findings also indicate a shift in metabolic scaling during plant development. Overall, our study supports the absence of any unified single constant scaling exponent for metabolism-biomass relationships in terrestrial plants, especially for forests with woody species.

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