scholarly journals The Redox Proteome of Thiol Proteins in the Rice Blast Fungus Magnaporthe oryzae

2021 ◽  
Vol 12 ◽  
Author(s):  
Xinrong Zhang ◽  
Zhenhua Zhang ◽  
Xiao-Lin Chen
Keyword(s):  
Magnaporthe Oryzae ◽  
Fungal Growth ◽  
Interaction Network ◽  
Pathogenic Fungi ◽  
Protein Domain ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Wide Range

Redox modification, a post-translational modification, has been demonstrated to be significant for many physiological pathways and biological processes in both eukaryotes and prokaryotes. However, little is known about the global profile of protein redox modification in fungi. To explore the roles of redox modification in the plant pathogenic fungi, a global thiol proteome survey was performed in the model fungal pathogen Magnaporthe oryzae. A total of 3713 redox modification sites from 1899 proteins were identified through a mix sample containing mycelia with or without oxidative stress, conidia, appressoria, and invasive hyphae of M. oryzae. The identified thiol-modified proteins were performed with protein domain, subcellular localization, functional classification, metabolic pathways, and protein–protein interaction network analyses, indicating that redox modification is associated with a wide range of biological and cellular functions. These results suggested that redox modification plays important roles in fungal growth, conidium formation, appressorium formation, as well as invasive growth. Interestingly, a large number of pathogenesis-related proteins were redox modification targets, suggesting the significant roles of redox modification in pathogenicity of M. oryzae. This work provides a global insight into the redox proteome of the pathogenic fungi, which built a groundwork and valuable resource for future studies of redox modification in fungi.

scholarly journals Structural, Evolutionary, and Functional Analysis of the Protein O-Mannosyltransferase Family in Pathogenic Fungi

2021 ◽  
Vol 7 (5) ◽  
pp. 328
Author(s):  
María Dolores Pejenaute-Ochoa ◽  
Carlos Santana-Molina ◽  
Damien P. Devos ◽  
José Ignacio Ibeas ◽  
Alfonso Fernández-Álvarez
Keyword(s):  
Functional Analysis ◽  
Secretory Pathway ◽  
Pathogenic Fungi ◽  
Fungal Pathogenesis ◽  
Post Translational Modification ◽  
Key Factors ◽  
Wide Range ◽  
Single Deletion ◽  
Asymmetrical Impact ◽  
Substrate Proteins

Protein O-mannosyltransferases (Pmts) comprise a group of proteins that add mannoses to substrate proteins at the endoplasmic reticulum. This post-translational modification is important for the faithful transfer of nascent glycoproteins throughout the secretory pathway. Most fungi genomes encode three O-mannosyltransferases, usually named Pmt1, Pmt2, and Pmt4. In pathogenic fungi, Pmts, especially Pmt4, are key factors for virulence. Although the importance of Pmts for fungal pathogenesis is well established in a wide range of pathogens, questions remain regarding certain features of Pmts. For example, why does the single deletion of each pmt gene have an asymmetrical impact on host colonization? Here, we analyse the origin of Pmts in fungi and review the most important phenotypes associated with Pmt mutants in pathogenic fungi. Hence, we highlight the enormous relevance of these glycotransferases for fungal pathogenic development.

scholarly journals Ubiquitination in the rice blast fungus Magnaporthe oryzae: from development and pathogenicity to stress responses

2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Yu Wang ◽  
Nan Yang ◽  
Yunna Zheng ◽  
Jiaolin Yue ◽  
Vijai Bhadauria ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Stress Responses ◽  
Rice Blast ◽  
Protein Localization ◽  
26S Proteasome ◽  
Blast Disease ◽  
Deubiquitinating Enzymes ◽  
Post Translational Modification ◽  
Protein Protein Interaction ◽  
Cellular Processes

AbstractUbiquitination is a vital protein post-translational modification (PTM) prevalent in eukaryotes. This modification regulates multiple cellular processes through protein degradation mediated by the 26S proteasome or affecting protein–protein interaction and protein localization. Magnaporthe oryzae causes rice blast disease, which is one of the most devastating crop diseases worldwide. In M. oryzae, ubiquitination plays important roles in growth, pathogenicity, stress response and effector-mediated plant-pathogen interaction. In this review, we summarize the roles of ubiquitination components in the above biological processes of M. oryzae, including single- or multi-subunit E3s, E2s, components of 26S proteasome and also deubiquitinating enzymes. The essential function of ubiquitination in plant-fungus interaction is also discussed. Moreover, this review presents several issues related to the ubiquitination system in M. oryzae, which need to be further explored in future researches.

scholarly journals Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Giuseppe Gianini Figueirêdo Leite ◽  
Bianca Lima Ferreira ◽  
Alexandre Keiji Tashima ◽  
Erika Sayuri Nishiduka ◽  
Edecio Cunha-Neto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mononuclear Cells ◽  
Interaction Network ◽  
Low Density ◽  
Mitochondrial Translation ◽  
Peripheral Blood Mononuclear ◽  
Protein Coding ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Host Defense System

Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.

scholarly journals Partners in crime: POPX2 phosphatase and its interacting proteins in cancer

2020 ◽  
Vol 11 (10) ◽  
Author(s):  
Pu Rum Kim ◽  
Songjing Zhang ◽  
Muhammad Bakhait Rahmat ◽  
Cheng-Gee Koh
Keyword(s):  
Cancer Progression ◽  
Interaction Network ◽  
Interacting Proteins ◽  
Cellular Functions ◽  
Cancer Cell Motility ◽  
Protein Protein Interaction ◽  
Binding Partners ◽  
Intracellular Signal ◽  
The Impact ◽  
Protein Protein Interaction Network

Abstract Protein phosphorylation and dephosphorylation govern intracellular signal transduction and cellular functions. Kinases and phosphatases are involved in the regulation and development of many diseases such as Alzheimer’s, diabetes, and cancer. While the functions and roles of many kinases, as well as their substrates, are well understood, phosphatases are comparatively less well studied. Recent studies have shown that rather than acting on fewer and more distinct substrates like the kinases, phosphatases can recognize specific phosphorylation sites on many different proteins, making the study of phosphatases and their substrates challenging. One approach to understand the biological functions of phosphatases is through understanding their protein–protein interaction network. POPX2 (Partner of PIX 2; also known as PPM1F or CaMKP) is a serine/threonine phosphatase that belongs to the PP2C family. It has been implicated in cancer cell motility and invasiveness. This review aims to summarize the different binding partners of POPX2 phosphatase and explore the various functions of POPX2 through its interactome in the cell. In particular, we focus on the impact of POPX2 on cancer progression. Acting via its different substrates and interacting proteins, POPX2’s involvement in metastasis is multifaceted and varied according to the stages of metastasis.

scholarly journals Protein-protein-interaction Network Organization of the Hypusine Modification System

2012 ◽  
Vol 11 (11) ◽  
pp. 1289-1305 ◽  
Author(s):  
Henning Sievert ◽  
Simone Venz ◽  
Oscar Platas-Barradas ◽  
Vishnu M. Dhople ◽  
Martin Schaletzky ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Large Scale ◽  
Affinity Purification ◽  
Interaction Network ◽  
Initiation Factor ◽  
Post Translational Modification ◽  
Comprehensive Overview ◽  
Data Set ◽  
Modification System ◽  
Protein Protein Interaction

Hypusine modification of eukaryotic initiation factor 5A (eIF-5A) represents a unique and highly specific post-translational modification with regulatory functions in cancer, diabetes, and infectious diseases. However, the specific cellular pathways that are influenced by the hypusine modification remain largely unknown. To globally characterize eIF-5A and hypusine-dependent pathways, we used an approach that combines large-scale bioreactor cell culture with tandem affinity purification and mass spectrometry: “bioreactor-TAP-MS/MS.” By applying this approach systematically to all four components of the hypusine modification system (eIF-5A1, eIF-5A2, DHS, and DOHH), we identified 248 interacting proteins as components of the cellular hypusine network, with diverse functions including regulation of translation, mRNA processing, DNA replication, and cell cycle regulation. Network analysis of this data set enabled us to provide a comprehensive overview of the protein-protein interaction landscape of the hypusine modification system. In addition, we validated the interaction of eIF-5A with some of the newly identified associated proteins in more detail. Our analysis has revealed numerous novel interactions, and thus provides a valuable resource for understanding how this crucial homeostatic signaling pathway affects different cellular functions.

scholarly journals Mechanism Analysis of Coix Seed in Gastric Cancer Treatment Based on Biological Network Modules

2020 ◽  
Vol 15 (5) ◽  
pp. 1934578X2092752
Author(s):  
Fengbin Zhang ◽  
Xiaoyan Liu ◽  
Bingjie Huo ◽  
Bing Li ◽  
Ruixing Zhang
Keyword(s):  
Gastric Cancer ◽  
Target Genes ◽  
Biological Network ◽  
Interaction Network ◽  
Mechanism Analysis ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Analysis Methods ◽  
Coix Seed ◽  
Modular Analysis

Coix seed, the mature seed of Coix lacryma-jobi L., is a traditional herb widely used in various cancer adjuvant treatments; however, its mechanism is unknown. The aim of this study was to reveal the multitarget mechanisms of Coix seed in the treatment of gastric cancer (GC) by biological network and modular analysis methods. Forty-one ingredients and 482 targets of Coix seed and 165 GC-related genes were obtained from databases. Twelve on-target genes ( AICDA, CASP3, EP300, ERBB2, FGFR2, IL12A, IL12B, IL1B, LOX, TJP1, TP53, and TRIB3) of Coix seed overlapped with GC-related genes. Using compound-target and protein–protein interaction network analyses, we discovered the core targets of Coix seed. Markov cluster algorithm-based modular analysis identified 5 potential module targets of Coix seed for GC. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated the vast actions of Coix seed, which involve pathways in cancer, the cell cycle, receptor signal transduction, deoxyribonucleic acid damage response, transcriptional regulation, apoptosis, and cell connections. This study elucidated the potential mechanisms of Coix seed on GC, which may lead to the development of an effective drug. Additionally, this study showed the feasibility of network and modular analysis methods to investigate traditional Chinese medicinal herbal mechanisms and may provide a new angle for further research in the field of anticancer mechanisms and multitarget drugs.

scholarly journals The efficiency of lactic acid bacteria against pathogenic fungi and mycotoxins

2018 ◽  
Vol 69 (1) ◽  
pp. 32-45 ◽  
Author(s):  
Adam Perczak ◽  
Piotr Goliński ◽  
Marcin Bryła ◽  
Agnieszka Waśkiewicz
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Animal Health ◽  
Fungal Growth ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Future Research ◽  
Mycotoxin Contamination ◽  
Mycotoxin Degradation ◽  
Wide Range

Abstract Mycotoxins are produced by some fungal species of the genera Aspergillus, Penicillium, and Fusarium and are common contaminants of a wide range of food commodities. Numerous strategies are used to minimise fungal growth and mycotoxin contamination throughout the food chain. This review addresses the use of lactic acid bacteria, which can inhibit fungal growth and participate in mycotoxin degradation and/or removal from contaminated food. Being beneficial for human and animal health, lactic acid bacteria have established themselves as an excellent solution to the problem of mycotoxin contamination, yet in practice their application in removing mycotoxins remains a challenge to be addressed by future research.

scholarly journals SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3260 ◽  
Author(s):  
Abdollah Dehzangi ◽  
Yosvany López ◽  
Ghazaleh Taherzadeh ◽  
Alok Sharma ◽  
Tatsuhiko Tsunoda
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
High Sensitivity ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Sumoylation Site ◽  
Translation Process ◽  
Wide Range

Post Translational Modification (PTM) is defined as the modification of amino acids along the protein sequences after the translation process. These modifications significantly impact on the functioning of proteins. Therefore, having a comprehensive understanding of the underlying mechanism of PTMs turns out to be critical in studying the biological roles of proteins. Among a wide range of PTMs, sumoylation is one of the most important modifications due to its known cellular functions which include transcriptional regulation, protein stability, and protein subcellular localization. Despite its importance, determining sumoylation sites via experimental methods is time-consuming and costly. This has led to a great demand for the development of fast computational methods able to accurately determine sumoylation sites in proteins. In this study, we present a new machine learning-based method for predicting sumoylation sites called SumSec. To do this, we employed the predicted secondary structure of amino acids to extract two types of structural features from neighboring amino acids along the protein sequence which has never been used for this task. As a result, our proposed method is able to enhance the sumoylation site prediction task, outperforming previously proposed methods in the literature. SumSec demonstrated high sensitivity (0.91), accuracy (0.94) and MCC (0.88). The prediction accuracy achieved in this study is 21% better than those reported in previous studies. The script and extracted features are publicly available at: https://github.com/YosvanyLopez/SumSec.

scholarly journals ANTIFUNGAL ACTIVITY OF ACTINOBACTERIA WITH A POTENTIAL TO INHIBIT RICE BLAST FUNGUS MAGNAPORTHE ORYZAE (ANAMORPH PYRICULARIA ORYZAE)

2021 ◽  
pp. 121-125
Author(s):  
THILAGAM R ◽  
BALAGURUNATHAN R ◽  
SANGEETHA M ◽  
HEMALATHA N
Keyword(s):  
Secondary Metabolites ◽  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Biochemical Characterization ◽  
Fungal Growth ◽  
Pathogenic Fungi ◽  
Antifungal Compound ◽  
Layer Chromatography ◽  
Selection Of

Objective: The aims of the present study were to screen the actinobacteria with high potential ability to produce secondary metabolites that have inhibitory activity against plant pathogenic fungi, Magnaporthe oryzae. Production of secondary metabolites was analysis by thin-layer chromatography and bioautography assay. Methods: Screening and selection of potential Streptomyces sp. morphological, cultural, physiological, and biochemical characterization of the screened isolate was carried out. Antifungal compound was confirmed by bioautography assay. Results: Bioautography method use in this study was found to be antifungal fraction from the crude extract. Antifungal secondary metabolites can be readily located on the plates by observing clear zones where active compounds inhibit fungal growth. Conclusion: The bioautography assay shows that this isolates can produce antifungal compound. Therefore, this isolate proves to be a promising microbe which can be further studied for its applications a biocontrol agent against rice blast fungi.

Sign in / Sign up

Export Citation Format

Share Document