scholarly journals Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

Antioxidants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 257
Author(s):  
Qiang Li ◽  
Hélène San Clemente ◽  
Yongrui He ◽  
Yongyao Fu ◽  
Christophe Dunand
Keyword(s):  
Reactive Oxygen Species ◽  
Comparative Analysis ◽  
Gene Network ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Evolutionary Process ◽  
Gene Families ◽  
Eucalyptus Species ◽  
Gene Gain ◽  
Oxygen Species

Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensis, E. globulus, E. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process.

scholarly journals Parallel Molecular Evolution of Catalases and Superoxide Dismutases—Focus on Thermophilic Fungal Genomes

Antioxidants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1047
Author(s):  
Katarína Chovanová ◽  
Miroslav Böhmer ◽  
Andrej Poljovka ◽  
Jaroslav Budiš ◽  
Jana Harichová ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Molecular Evolution ◽  
Elevated Temperatures ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Gene Families ◽  
Superoxide Dismutases ◽  
Thermophilic Fungi ◽  
Enzymatic Antioxidants ◽  
Oxygen Species

Catalases (CAT) and superoxide dismutases (SOD) represent two main groups of enzymatic antioxidants that are present in almost all aerobic organisms and even in certain anaerobes. They are closely interconnected in the catabolism of reactive oxygen species because one product of SOD reaction (hydrogen peroxide) is the main substrate of CAT reaction finally leading to harmless products (i.e., molecular oxygen and water). It is therefore interesting to compare the molecular evolution of corresponding gene families. We have used a phylogenomic approach to elucidate the evolutionary relationships among these two main enzymatic antioxidants with a focus on the genomes of thermophilic fungi. Distinct gene families coding for CuZnSODs, FeMnSODs, and heme catalases are very abundant in thermophilic Ascomycota. Here, the presented results demonstrate that whereas superoxide dismutase genes remained rather constant during long-term evolution, the total count of heme catalase genes was reduced in thermophilic fungi in comparison with their mesophilic counterparts. We demonstrate here, for the newly discovered ascomycetous genes coding for thermophilic superoxide dismutases and catalases (originating from our sequencing project), the expression patterns of corresponding mRNA transcripts and further analyze translated protein sequences. Our results provide important implications for the physiology of reactive oxygen species metabolism in eukaryotic cells at elevated temperatures.

scholarly journals Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase

2009 ◽  
Vol 149 (4) ◽  
pp. 1848-1859 ◽  
Author(s):  
Vaibhav Srivastava ◽  
Manoj Kumar Srivastava ◽  
Kamel Chibani ◽  
Robert Nilsson ◽  
Nicolas Rouhier ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Superoxide Dismutase ◽  
Alternative Splicing ◽  
Isoelectric Point ◽  
Gene Network ◽  
Reactive Oxygen ◽  
Oxygen Species

scholarly journals Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight

2014 ◽  
Vol 14 (1) ◽  
pp. 4 ◽  
Author(s):  
Manabu Sugimoto ◽  
Youko Oono ◽  
Oleg Gusev ◽  
Takashi Matsumoto ◽  
Takayuki Yazawa ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Expression Analysis ◽  
Gene Network ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Characterization and significance of extracellular polymeric substances, reactive oxygen species, and extracellular electron transfer in methanogenic biocathode

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Basem S. Zakaria ◽  
Bipro Ranjan Dhar
Keyword(s):  
Reactive Oxygen Species ◽  
Stainless Steel ◽  
Electron Transfer ◽  
Anaerobic Digestion ◽  
Carbon Fibers ◽  
Extracellular Polymeric Substances ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Extracellular Electron Transfer ◽  
Oxygen Species

AbstractThe microbial electrolysis cell assisted anaerobic digestion holds great promises over conventional anaerobic digestion. This article reports an experimental investigation of extracellular polymeric substances (EPS), reactive oxygen species (ROS), and the expression of genes associated with extracellular electron transfer (EET) in methanogenic biocathodes. The MEC-AD systems were examined using two cathode materials: carbon fibers and stainless-steel mesh. A higher abundance of hydrogenotrophic Methanobacterium sp. and homoacetogenic Acetobacterium sp. appeared to play a major role in superior methanogenesis from stainless steel biocathode than carbon fibers. Moreover, the higher secretion of EPS accompanied by the lower ROS level in stainless steel biocathode indicated that higher EPS perhaps protected cells from harsh metabolic conditions (possibly unfavorable local pH) induced by faster catalysis of hydrogen evolution reaction. In contrast, EET-associated gene expression patterns were comparable in both biocathodes. Thus, these results indicated hydrogenotrophic methanogenesis is the key mechanism, while cathodic EET has a trivial role in distinguishing performances between two cathode electrodes. These results provide new insights into the efficient methanogenic biocathode development.

scholarly journals Exploration of the Potential Mechanisms of Wumei Pill for the Treatment of Ulcerative Colitis by Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Jinke Huang ◽  
Yijun Zheng ◽  
Jinxin Ma ◽  
Jing Ma ◽  
Mengxiong Lu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Reactive Oxygen Species ◽  
Gene Network ◽  
Target Gene ◽  
Target Genes ◽  
Reactive Oxygen ◽  
Network Pharmacology ◽  
Oxygen Species ◽  
Active Ingredients ◽  
Drug Ingredient

Background. Wumei pill (WMP) has a long history of colitis treatment in China, but the protective mechanisms have not been elucidated. To uncover the potential mechanisms of WMP against ulcerative colitis (UC), the network pharmacology approach was utilized in this study. Methods. Public databases were utilized to identify the potential targets of WMP and genes related to UC. Based on the identified overlapping common targets, drug-ingredient-target gene network, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) analysis were conducted. Molecular docking was carried out to verify the selected key active ingredients and core targets. Results. 129 active ingredients and 622 target genes were obtained. The drug-ingredient-target gene network revealed 52 active ingredients of WMP acting on 73 targets related to UC. GO analysis revealed that biological processes were mainly associated with oxidative stress, such as, reactive oxygen species metabolic processes, response to oxidative stress, cellular response to oxidative stress, response to reactive oxygen species, and regulation of reactive oxygen species metabolic processes. KEGG analysis revealed that the immune- and inflammation-related pathways, tumor-related signaling pathways, and microbial infection-related signaling pathways were the most significant. PPI network identified 13 core target genes. The molecular docking results indicated the formation of stable bonds between the active ingredients and core target genes. Conclusions. The approach of network pharmacology reveals the key ingredients, potential core targets, and biological process of WMP in the treatment of UC. The mechanisms of action of WMP involve anti-inflammation, antioxidation, and modulation of immunity, which provides evidence for the therapeutic role of WMP in UC.

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