TY - JOUR
T1 - Subcellular compartmentalization of the plant antioxidant system
T2 - An integrated overview
AU - Bobrovskikh, Aleksandr
AU - Zubairova, Ulyana
AU - Kolodkin, Alexey
AU - Doroshkov, Alexey
N1 - Funding Information:
The following grant information was disclosed by the authors: Russian Science Foundation: 19-74-10037.
Funding Information:
The ideal way would be to build such a blueprint model as a live online system in the environment, similar to the one proposed by JWS Online (https://jjj.bio.vu.nl/). The models on JWS Online are aligned with FAIR (Findable, Accessible, Interoperable, Reusable) principles and can run online for either default parameters (curated and approved JWS team), or for parameters chosen by the user. The user can choose parameters based on his/her own experimental data or from curated databases, such as SABIO-RK (http://www.sabio.h-its.org/), or the data assembled at facilities of ELIXIR Research Infrastructure (https://elixir-europe.org/). Now user should do it manually. However, it is planned to do it automatically. For example, the user will go in the database, choose the appropriate organism and conditions, and run model simulations in the JWS Online environment. This is planned to implement within the framework of the recently started EOSC-Life project (European Open Science Cloud) supported by Horizon 2020.
Funding Information:
The study was carried out with a grant from the Russian Science Foundation (Project No. 19-74-10037). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
© Copyright 2020 Bobrovskikh et al.
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - Antioxidant system
KW - Antioxidants
KW - Compartments
KW - Mathematical modeling
KW - Plant cell
KW - Reactive oxygen species
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=85105185252&partnerID=8YFLogxK
U2 - 10.7717/PEERJ.9451
DO - 10.7717/PEERJ.9451
M3 - Review article
AN - SCOPUS:85105185252
VL - 8
JO - PeerJ
JF - PeerJ
SN - 2167-8359
M1 - e9451
ER -