scholarly journals Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

2020 ◽  
Vol 21 (20) ◽  
pp. 7497
Author(s):  
Xin Wang ◽  
Setsuko Komatsu
Keyword(s):  
Cellular Responses ◽  
Molecular Networks ◽  
Genetic Enhancement ◽  
Flooding Tolerance ◽  
Climatic Zones ◽  
Post Translational Modifications ◽  
Flooding Stress ◽  
Recent Developments ◽  
Flood Response ◽  
Proteomic Techniques

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

scholarly journals Plant Morphological, Physiological and Anatomical Adaption to Flooding Stress and the Underlying Molecular Mechanisms

2021 ◽  
Vol 22 (3) ◽  
pp. 1088
Author(s):  
Weitao Jia ◽  
Maohua Ma ◽  
Jilong Chen ◽  
Shengjun Wu
Keyword(s):  
Molecular Mechanisms ◽  
Sequence Similarity ◽  
Survival Strategies ◽  
Ethylene Response Factor ◽  
Flooding Tolerance ◽  
Plant Tolerance ◽  
Flooding Stress ◽  
Crop Varieties ◽  
The Future ◽  
Plant Acclimation

Globally, flooding is a major threat causing substantial yield decline of cereal crops, and is expected to be even more serious in many parts of the world due to climatic anomaly in the future. Understanding the mechanisms of plants coping with unanticipated flooding will be crucial for developing new flooding-tolerance crop varieties. Here we describe survival strategies of plants adaptation to flooding stress at the morphological, physiological and anatomical scale systemically, such as the formation of adventitious roots (ARs), aerenchyma and radial O2 loss (ROL) barriers. Then molecular mechanisms underlying the adaptive strategies are summarized, and more than thirty identified functional genes or proteins associated with flooding-tolerance are searched out and expounded. Moreover, we elaborated the regulatory roles of phytohormones in plant against flooding stress, especially ethylene and its relevant transcription factors from the group VII Ethylene Response Factor (ERF-VII) family. ERF-VIIs of main crops and several reported ERF-VIIs involving plant tolerance to flooding stress were collected and analyzed according to sequence similarity, which can provide references for screening flooding-tolerant genes more precisely. Finally, the potential research directions in the future were summarized and discussed. Through this review, we aim to provide references for the studies of plant acclimation to flooding stress and breeding new flooding-resistant crops in the future.

scholarly journals Interplay between ADP-ribosyltransferases and essential cell signaling pathways controls cellular responses

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Flurina Boehi ◽  
Patrick Manetsch ◽  
Michael O. Hottiger
Keyword(s):  
Cell Signaling ◽  
Signaling Pathways ◽  
Intracellular Signaling ◽  
Cellular Responses ◽  
Dynamic Regulation ◽  
Post Translational Modifications ◽  
Adp Ribosylation ◽  
Cellular Processes ◽  
Adp Ribosyltransferase ◽  
Cell Signaling Pathways

AbstractSignaling cascades provide integrative and interactive frameworks that allow the cell to respond to signals from its environment and/or from within the cell itself. The dynamic regulation of mammalian cell signaling pathways is often modulated by cascades of protein post-translational modifications (PTMs). ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases and manifests as mono- (MARylation) or poly- (PARylation) ADP-ribosylation depending on the addition of one or multiple ADP-ribose units to protein substrates. ADP-ribosylation has recently emerged as an important cell regulator that impacts a plethora of cellular processes, including many intracellular signaling events. Here, we provide an overview of the interplay between the intracellular diphtheria toxin-like ADP-ribosyltransferase (ARTD) family members and five selected signaling pathways (including NF-κB, JAK/STAT, Wnt-β-catenin, MAPK, PI3K/AKT), which are frequently described to control or to be controlled by ADP-ribosyltransferases and how these interactions impact the cellular responses.

scholarly journals SwissPalm: Protein Palmitoylation database

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 261 ◽  
Author(s):  
Mathieu Blanc ◽  
Fabrice David ◽  
Laurence Abrami ◽  
Daniel Migliozzi ◽  
Florence Armand ◽  
...  
Keyword(s):  
Protein S ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Chemical Methods ◽  
Post Translational Modifications ◽  
P Protein ◽  
Multiple Alignments ◽  
Protein Palmitoylation ◽  
Recent Developments ◽  
Pathway Analyses

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm (http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

Lysine methylation and the regulation of p53

2012 ◽  
Vol 52 ◽  
pp. 79-92 ◽  
Author(s):  
Simon M. Carr ◽  
Shonagh Munro ◽  
Nicholas B. La Thangue
Keyword(s):  
Cell Cycle ◽  
Transcriptional Activation ◽  
Genotoxic Stress ◽  
Cellular Responses ◽  
Future Research ◽  
Lysine Methylation ◽  
Post Translational Modifications ◽  
Cycle Arrest ◽  
Tumour Suppressor Protein ◽  
Protein Functions

The p53 tumour suppressor protein functions as a guardian against genotoxic stress. This function is mediated in part by the transcriptional activation of genes involved in cell-cycle arrest, apoptosis, DNA repair and autophagy. The activity of p53 is regulated by a complex array of post-translational modifications, which function as a code to determine cellular responses to a given stress. In this chapter we highlight recent advances in our understanding of this code, with particular reference to lysine methylation, and discuss implications for future research.

scholarly journals Metabolomic systems biology of trypanosomes

Parasitology ◽  
2010 ◽  
Vol 137 (9) ◽  
pp. 1285-1290 ◽  
Author(s):  
MICHAEL P. BARRETT ◽  
BARBARA M. BAKKER ◽  
RAINER BREITLING
Keyword(s):  
Systems Biology ◽  
Biological Systems ◽  
Cellular Responses ◽  
Future Research ◽  
Metabolomic Analysis ◽  
Environmental Perturbation ◽  
Recent Developments ◽  
Systematic Identification ◽  
Metabolomics Analysis ◽  
Identification And Quantification

SUMMARYMetabolomics analysis, which aims at the systematic identification and quantification of all metabolites in biological systems, is emerging as a powerful new tool to identify biomarkers of disease, report on cellular responses to environmental perturbation, and to identify the targets of drugs. Here we discuss recent developments in metabolomic analysis, from the perspective of trypanosome research, highlighting remaining challenges and the most promising areas for future research.

scholarly journals With or without You: Co-Chaperones Mediate Health and Disease by Modifying Chaperone Function and Protein Triage

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3121
Author(s):  
Selin Altinok ◽  
Rebekah Sanchez-Hodge ◽  
Mariah Stewart ◽  
Kaitlan Smith ◽  
Jonathan C. Schisler
Keyword(s):  
Protein Quality ◽  
Cellular Stress Response ◽  
Therapeutic Approaches ◽  
Post Translational Modifications ◽  
Chaperone Function ◽  
Recent Developments ◽  
The Face ◽  
Health And Disease ◽  
Shock Proteins ◽  
Triage Decisions

Heat shock proteins (HSPs) are a family of molecular chaperones that regulate essential protein refolding and triage decisions to maintain protein homeostasis. Numerous co-chaperone proteins directly interact and modify the function of HSPs, and these interactions impact the outcome of protein triage, impacting everything from structural proteins to cell signaling mediators. The chaperone/co-chaperone machinery protects against various stressors to ensure cellular function in the face of stress. However, coding mutations, expression changes, and post-translational modifications of the chaperone/co-chaperone machinery can alter the cellular stress response. Importantly, these dysfunctions appear to contribute to numerous human diseases. Therapeutic targeting of chaperones is an attractive but challenging approach due to the vast functions of HSPs, likely contributing to the off-target effects of these therapies. Current efforts focus on targeting co-chaperones to develop precise treatments for numerous diseases caused by defects in protein quality control. This review focuses on the recent developments regarding selected HSP70/HSP90 co-chaperones, with a concentration on cardioprotection, neuroprotection, cancer, and autoimmune diseases. We also discuss therapeutic approaches that highlight both the utility and challenges of targeting co-chaperones.

scholarly journals Characterization of the XTH Gene Family: New Insight to the Roles in Soybean Flooding Tolerance

2018 ◽  
Vol 19 (9) ◽  
pp. 2705 ◽  
Author(s):  
Li Song ◽  
Babu Valliyodan ◽  
Silvas Prince ◽  
Jinrong Wan ◽  
Henry Nguyen
Keyword(s):  
Expression Pattern ◽  
Stress Responses ◽  
Germination Rate ◽  
Gene Expression Pattern ◽  
Growth Stages ◽  
Flooding Tolerance ◽  
Specific Expression ◽  
Flooding Stress ◽  
Specific Expression Pattern

Xyloglucan endotransglycosylases/hydrolases (XTHs) are a class of enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks and play an important role in regulating cell wall extensibility. However, little is known about this class of enzymes in soybean. Here, 61 soybean XTH genes (GmXTHs) were identified and classified into three subgroups through comparative phylogenetic analysis. Genome duplication greatly contributed to the expansion of GmXTH genes in soybean. A conserved amino acid motif responsible for the catalytic activity was identified in all GmXTHs. Further expression analysis revealed that most GmXTHs exhibited a distinct organ-specific expression pattern, and the expression level of many GmXTH genes was significantly associated with ethylene and flooding stress. To illustrate a possible role of XTH genes in regulating stress responses, the Arabidopsis AtXTH31 gene was overexpressed in soybean. The generated transgenic plants exhibited improved tolerance to flooding stress, with a higher germination rate and longer roots/hypocotyls during the seedling stage and vegetative growth stages. In summary, our combined bioinformatics and gene expression pattern analyses suggest that GmXTH genes play a role in regulating soybean stress responses. The enhanced soybean flooding tolerance resulting from the expression of an Arabidopsis XTH also supports the role of XTH genes in regulating plant flooding stress responses.

scholarly journals Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING

2020 ◽  
Author(s):  
Natalia Zamorano Cuervo ◽  
Audray Fortin ◽  
Elise Caron ◽  
Stéfany Chartier ◽  
Nathalie Grandvaux
Keyword(s):  
Redox Regulation ◽  
Type I Interferon ◽  
Cellular Responses ◽  
Innate Immune ◽  
Type I ◽  
Post Translational Modifications ◽  
Inhibitory Function ◽  
Host Interaction ◽  
Interferon Pathway

AbstractProtein function is regulated by post-translational modifications, among which reversible oxidation of Cys (Cys ox-PTM) emerged as a key regulatory mechanism of cellular responses. The redox regulation of virus-host interactions is well documented, but in most cases, proteins subjected to Cys ox-PTM remain unknown. The identification of Cys ox-PTM sites in vivo is essential to underpin our understanding of the mechanisms of the redox regulation. In this study, we present a proteome-wide identification of reversible Cys ox-PTM sites in vivo during stimulation by oxidants using a maleimide-based bioswitch method coupled to mass spectrometry. We identified 2720 unique Cys ox-PTM sites encompassing 1473 proteins with distinct abundance, location and functions. Label-free quantification (LFQ)-based analysis revealed the enrichment of ox-PTM in numerous pathways, many relevant to virus-host interaction. Here, we focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway induced upon detection of cytosolic DNA. We provide the first in vivo demonstration of reversible oxidation of Cys148 and Cys206 of STING. Molecular analyses led us to establish a new model in which Cys148 oxidation is constitutive, while Cys206 oxidation is inducible by oxidative stress or by the natural ligand 2’3’-cGAMP. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation through the constraint of a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This provides new ground for the design of therapies targeting STING relevant to autoinflammatory disorders, immunotherapies and vaccines.Brief summary of the main resultsThe function of proteins is regulated by post-translational modifications, among which reversible oxidation of Cys recently emerged as a key component. Comprehension of redox regulation of cellular responses requires identification of specific oxidation sites in vivo. Using a bioswitch method to specifically label Cys subjected to reversible oxidation coupled to mass spectrometry, we identified thousands of novel oxidation sites. Many are relevant to virus-host interaction pathways. Here, we focused on the oxidation of STING, an adaptor critical for activating the innate immune type I interferon pathway engaged upon cytosolic DNA sensing. Molecular studies led us to establish a new model in which STING Cys148 is oxidized at basal levels, while Cys206 oxidation is induced by oxidative stress and ligand binding. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation. This study provides ground for novel research avenues aimed at designing therapeutics that target this pathway.

scholarly journals Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

2020 ◽  
Vol 24 (1) ◽  
pp. 83-91
Author(s):  
Sanjeev K. Dhungana ◽  
Hong-Sik Kim ◽  
Beom-Kyu Kang ◽  
Jeong-Hyun Seo ◽  
Hyun-Tae Kim ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Flooding Tolerance ◽  
Stressed Condition ◽  
Susceptible Cultivar ◽  
Effective Measure ◽  
Flooding Stress ◽  
Soybean Leaf ◽  
Molecular Information

AbstractFlooding stress causes severe yield reduction in soybean worldwide. The development of stress-tolerant cultivars could be an effective measure to reduce the negative effects of flooding stress. Molecular information on the gene expression pattern of tolerant and susceptible genotypes under flooding stress could be valuable to improve the flooding tolerance in soybean. The objective of this study was to analyze the differentially expressed genes (DEGs) revealed by RNA sequencing in the soybean leaf tissues of tolerant (‘Paldalkong’ and ‘Danbaekkong’) and susceptible (‘NTS1116’) cultivars under flooding stress. Seedlings were grown in a well-watered condition up to the V1–V2 stage and flood-stressed by inundating ~ 10-cm water for 14 days. A total of 22,468 genes were differentially expressed in flood-stressed condition compared to the well-watered control condition, out of which 13,729, 13,405, and 13,160 were differentially expressed in ‘Paldalkong’, ‘Danbaekkong’, and ‘NTS1116’, respectively. A higher number of some of the flooding tolerance-related genes such as lipoxygenase, expansin, glutathione S-transferase, and sugar efflux transporter were up-regulated in the tolerant cultivars than in the susceptible cultivar. The number of some abscisic acid-related transcription factors of basic leucine zipper domain and myeloblastosis families was also higher in the tolerant cultivars than in the susceptible cultivar. The molecular information about the DEGs of tolerant and susceptible cultivars obtained in the present study could be valuable to improve the flooding tolerance in soybeans.

scholarly journals Post-Translational Modifications of Proteins Have Versatile Roles in Regulating Plant Immune Responses

2019 ◽  
Vol 20 (11) ◽  
pp. 2807 ◽  
Author(s):  
Junjie Yin ◽  
Hong Yi ◽  
Xuewei Chen ◽  
Jing Wang
Keyword(s):  
Immune Response ◽  
Cellular Responses ◽  
Innate Immune ◽  
Fine Tuning ◽  
Host Cells ◽  
Callose Deposition ◽  
Post Translational Modifications ◽  
Transcriptional Reprogramming ◽  
Regulatory Changes ◽  
Signal Activation

To protect themselves from pathogens, plants have developed an effective innate immune system. Plants recognize pathogens and then rapidly alter signaling pathways within individual cells in order to achieve an appropriate immune response, including the generation of reactive oxygen species, callose deposition, and transcriptional reprogramming. Post-translational modifications (PTMs) are versatile regulatory changes critical for plant immune response processes. Significantly, PTMs are involved in the crosstalk that serves as a fine-tuning mechanism to adjust cellular responses to pathogen infection. Here, we provide an overview of PTMs that mediate defense signaling perception, signal transduction in host cells, and downstream signal activation.

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