Using the Methods of Systems Biology for Predicting Perspective Target Genes to Select C3 and C4 Cereals for Oxidative Stress Resistance

Дорошков, А. В.; Bobrovskikh, Aleksandr

doi:10.18699/vj18.339

Cited by 4 publications

(9 citation statements)

References 30 publications

(37 reference statements)

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“…The stress response gene networks also change in the process of evolution; therefore, analysis of the systems of interacting genes, taking into account evolutionary patterns and expression data, allows the identification of features of the organization of response systems to stress factors and their most significant components promising for gene prioritization [16][17][18][19]. One promising approach in this regard is phylostratigraphic analysis.…”

Section: Introductionmentioning

confidence: 99%

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Мустафин

Zamyatin

Konstantinov

et al. 2019

Genes

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Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants.

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Section: Introductionmentioning

confidence: 99%

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Мустафин

Zamyatin

Konstantinov

et al. 2019

Genes

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“…The catalytic efficiency (Kcat/Km) of the plant GPX is similar to other peroxidases (10 3 –10 6 M − 1 s − 1 ), but lower than that of APXs, CATs and human GPX (10 7 –10 8 M − 1 s − 1 ) ( Bela et al, 2015 ). Even though the role of GPX in the utilization of peroxide for plants is ambiguous in comparison with animals (due to presence of advanced ascorbate system in the cell), nevertheless, it has a similar number of paralogs as APX in plants, and many copies are highly conservative protein structure Doroshkov & Bobrovskikh (2018) . The term “glutathione peroxidase” itself is inaccurate for this enzyme since it has been shown that the enzyme is the 5th group of thioredoxin-dependent thiol peroxidases ( Navrot et al, 2006 ) and uses thioredoxins as a substrate, and not glutathione.…”

Section: Survey Methodologymentioning

confidence: 99%

“…In the AOS, there are individual enzyme-coding genes that have high importance for the functioning system in general, especially in stress conditions. Doroshkov & Bobrovskikh (2018) found the relationship between the evolutionary features of antioxidant enzymes and their expression levels for predicting prospective targets for selection across cereals. The authors identified groups of highly conserved genes with a high level of mRNA expression and a group of less conservative with a low-level expression.…”

Section: Survey Methodologymentioning

confidence: 99%

Subcellular compartmentalization of the plant antioxidant system: an integrated overview

Bobrovskikh

Зубаирова

Kolodkin

et al. 2020

PeerJ

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The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.

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“…The catalytic efficiency (Kcat/Km) of the plant GPX is similar to other peroxidases (103-106 M −1 s −1 ), but lower than that of APXs, CATs and human GPX (107-108 M −1 s −1 ) (Bela et al, 2015). Even though the role of GPX in the utilization of peroxide for plants is ambiguous in comparison with animals (due to presence of advanced ascorbate system in the cell), nevertheless, it has a similar number of paralogs as APX in plants, and many copies are highly conservative protein structure Doroshkov and Bobrovskikh (2018). The term "glutathione peroxidase" itself is inaccurate for this enzyme since it has been shown that the enzyme is the 5th group of thioredoxin-dependent thiol peroxidases (Navrot et al, 2006) and uses thioredoxins as a substrate, and not glutathione.…”

Section: Main Features Of the Antioxidant System Componentsmentioning

confidence: 96%

“…In the AOS, there are individual enzyme-coding genes that have high importance for the functioning system in general, especially in stress conditions. Doroshkov and Bobrovskikh (2018) found the…”

Section: Stress-response Of the Antioxidant System Componentsmentioning

confidence: 99%

Peer Review #2 of "Subcellular compartmentalization of the plant antioxidant system: an integrated overview (v0.1)"

2020

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Antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of 7 main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts further reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system reveals to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.

show abstract

Using the Methods of Systems Biology for Predicting Perspective Target Genes to Select C3 and C4 Cereals for Oxidative Stress Resistance

Cited by 4 publications

References 30 publications

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Subcellular compartmentalization of the plant antioxidant system: an integrated overview

Peer Review #2 of "Subcellular compartmentalization of the plant antioxidant system: an integrated overview (v0.1)"

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