scholarly journals Metabolomic Alterations in the Digestive System of the Mantis Shrimp Oratosquilla oratoria Following Short-Term Exposure to Cadmium

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingjiang Xu ◽  
Huan Liu ◽  
Dianfeng Han ◽  
Lihua Ren ◽  
Xianghong Gong ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Energy Metabolism ◽  
Differential Expression ◽  
Digestive System ◽  
Fatty Acid Esters ◽  
Transmembrane Transport ◽  
Cd Stress ◽  
Mantis Shrimp ◽  
Oratosquilla Oratoria

Mantis shrimp Oratosquilla oratoria is an economically critical aquatic species along the coast of China but strongly accumulates marine pollutant cadmium (Cd) in its digestive system. It is necessary to characterize the toxicity of Cd in the digestive system of mantis shrimp. The metabolic process is an essential target of Cd toxicity response. In this work, we used ultra-performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC-TOF-MS) for untargeted metabolomics to characterize the metabolic changes in the digestive system of O. oratoria, exposed to 0.05 mg/L for 96 h. The aim of this study was to further investigate the effect of O. oratoria on Cd response to toxicity and develop biomarkers. Metabolomics analysis showed the alteration of metabolism in the digestive system of mantis shrimp under Cd stress. A total of 91 metabolites were differentially expressed and their main functions were classified into amino acids, phospholipids, and fatty acid esters. The enrichment results of differential metabolite functional pathways showed that biological processes such as amino acid metabolism, transmembrane transport, energy metabolism, and signal transduction are significantly affected. Based on the above results, the Cd-induced oxidative stress and energy metabolism disorders were characterized by the differential expression of amino acids and ADP in mantis shrimp, while the interference of transmembrane transport and signal transduction was due to the differential expression of phospholipids. Overall, this work initially discussed the toxicological response of Cd stress to O. oratoria from the metabolic level and provided new insights into the mechanism.

scholarly journals Identification of glycolysis related pathways in pancreatic adenocarcinoma and liver hepatocellular carcinoma based on TCGA and GEO datasets

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ji Li ◽  
Chen Zhu ◽  
Peipei Yue ◽  
Tianyu Zheng ◽  
Yan Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Energy Metabolism ◽  
Pancreatic Adenocarcinoma ◽  
Digestive System ◽  
Prognostic Significance ◽  
R Package ◽  
The Cancer Genome Atlas ◽  
System Structure ◽  
Liver Hepatocellular Carcinoma

Abstract Background Abnormal energy metabolism is one of the characteristics of tumor cells, and it is also a research hotspot in recent years. Due to the complexity of digestive system structure, the frequency of tumor is relatively high. We aim to clarify the prognostic significance of energy metabolism in digestive system tumors and the underlying mechanisms. Methods Gene set variance analysis (GSVA) R package was used to establish the metabolic score, and the score was used to represent the metabolic level. The relationship between the metabolism and prognosis of digestive system tumors was explored using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Volcano plots and gene ontology (GO) analyze were used to show different genes and different functions enriched between different glycolysis levels, and GSEA was used to analyze the pathway enrichment. Nomogram was constructed by R package based on gene characteristics and clinical parameters. qPCR and Western Blot were applied to analyze gene expression. All statistical analyses were conducted using SPSS, GraphPad Prism 7, and R software. All validated experiments were performed three times independently. Results High glycolysis metabolism score was significantly associated with poor prognosis in pancreatic adenocarcinoma (PAAD) and liver hepatocellular carcinoma (LIHC). The STAT3 (signal transducer and activator of transcription 3) and YAP1 (Yes1-associated transcriptional regulator) pathways were the most critical signaling pathways in glycolysis modulation in PAAD and LIHC, respectively. Interestingly, elevated glycolysis levels could also enhance STAT3 and YAP1 activity in PAAD and LIHC cells, respectively, forming a positive feedback loop. Conclusions Our results may provide new insights into the indispensable role of glycolysis metabolism in digestive system tumors and guide the direction of future metabolism–signaling target combined therapy.

scholarly journals Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Guichun Wu ◽  
Yuqiang Zhang ◽  
Bo Wang ◽  
Kaihuai Li ◽  
Yuanlai Lou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Amino Acids ◽  
Secondary Metabolites ◽  
Carbohydrate Metabolism ◽  
Virulence Factors ◽  
Global Gene Expression ◽  
Xanthomonas Oryzae ◽  
Oxidation Reduction ◽  
Phenylpropanoid Biosynthesis

Abstract Background Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. Results Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. Conclusion Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.

scholarly journals Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

BMC Genomics ◽  
2016 ◽  
Vol 17 (S14) ◽  
Author(s):  
Anastasiya Vladimirovna Snezhkina ◽  
George Sergeevich Krasnov ◽  
Andrew Rostislavovich Zaretsky ◽  
Alex Zhavoronkov ◽  
Kirill Mikhailovich Nyushko ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Energy Metabolism ◽  
Differential Expression ◽  
Alternatively Spliced

scholarly journals F-actin-dependent Translocation of the Rap1 GDP/GTP Exchange Factor RasGRP2

2004 ◽  
Vol 279 (19) ◽  
pp. 20435-20446 ◽  
Author(s):  
Mariía J. Caloca ◽  
José L. Zugaza ◽  
Miguel Vicente-Manzanares ◽  
Francisco Sánchez-Madrid ◽  
Xosé R. Bustelo
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Subcellular Distribution ◽  
Actin Polymerization ◽  
Biological Effects ◽  
Actin Dynamics ◽  
Exchange Factor ◽  
Common Structure ◽  
Direct Association ◽  
P21 Activated Kinase

RasGRPs constitute a new group of diacylglycerol-dependent GDP/GTP exchange factors that activate Ras subfamily GTPases. Despite a common structure, Ras-GRPs diverge in their GTPase specificity, subcellular distribution, and downstream biological effects. The more divergent family member is RasGRP2, a Rap1-specific exchange factor with low affinity toward diacylglycerol. The regulation of RasGRP2 during signal transduction has remained elusive up to now. In this report, we show that the subcellular localization of Ras-GRP2 is highly dependent on actin dynamics. Thus, the induction of F-actin by cytoskeletal regulators such as Vav, Vav2, Dbl, and Rac1 leads to the shift of RasGRP2 from the cytosol to membrane ruffles and its co-localization with F-actin. Treatment of cells with cytoskeletal disrupting drugs abolishes this effect, leading to an abnormal localization of RasGRP2 in cytoplasmic clusters of actin. The use of Rac1 effector mutants indicates that the RasGRP2 translocation is linked exclusively to actin polymerization and is independent of other pathways such as p21-activated kinase JNK, or superoxide production. Biochemical experiments demonstrate that the translocation of RasGRP2 to membrane ruffles is mediated by the direct association of this protein with F-actin, a property contained within its 150 first amino acids. Finally, we show that the RasGRP2/F-actin interaction promotes the regionalized activation of Rap1 in juxtamembrane areas of the cell. These results reveal a novel function of the actin cytoskeleton in mediating the spatial activation of Ras subfamily GTPases through the selective recruitment of GDP/GTP exchange factors.

scholarly journals ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases

2021 ◽  
Vol 8 ◽  
Author(s):  
Yutao Huang ◽  
Zijian Jiang ◽  
Xiangyu Gao ◽  
Peng Luo ◽  
Xiaofan Jiang
Keyword(s):  
Signal Transduction ◽  
Amino Acids ◽  
Cell Adhesion ◽  
Tandem Repeats ◽  
Critical Role ◽  
The Other ◽  
Biological Functions ◽  
Armadillo Repeat ◽  
The One ◽  
Similar Domain

Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.

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