scholarly journals Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating pericarp cracking in Akebia trifoliata fruit

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pectate Lyases ◽  
Fruit Cracking ◽  
Tandem Mass Tag ◽  
High Yields

Abstract Background: Akebia trifoliata (Thunb.) Koidz, a perennial wild woody liana, can be used as biofuel to generate bioenergy, as well as a traditional Chinese medicine plant,and new potential edible fruit crop, due to its high yields in fields, wide adaptability, high economic, medicinal and nutritive values, and tolerance tocultivation conditions. However, the pericarp of A. trifoliata cracks longitudinallyalong the ventral suture during fruit ripening, which is a serious problem that limits its usefulness and causes significant losses in yield and commercial value. Furthermore, there have been no known investigations on fruit cracking and its molecular mechanisms in A. trifoliata . Results: In this study, the dynamic structural changes in fruit pericarps were observed, revealing that the cell wall of fruit pericarp became thinner, and had reduced integrity, and that the cell walls began to degrade in the cracking fruits compared to those observed in non-cracking fruits. Moreover, analyses of the complementary RNA- sequencing-based transcriptomes and tandem mass tag-based proteomes at different development stages during fruit ripening were performed, and the expression of various genes and proteins was found to be changed after cracking, The mRNA levels of 20 differentially expressed genes and 17 differentially abundant proteins (DAPs) involved in cell wall metabolism were further analyzed; 20 DAPs were also validated through parallel reaction monitoring analysis. Among these, pectate lyases and pectinesterase involved in pentose and glucuronate interconversions, β-galactosidases 2 involved in galactose metabolism, were significantly up-regulated in cracking fruits compared to levels in non-cracking fruits, suggesting that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits and important clues for further studies on the genetic improvement of A. trifoliata and the breeding of non-cracking varieties.

scholarly journals Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating peel cracking in Akebia trifoliata fruit

2019 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Fruit Ripening ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Sugar Metabolism ◽  
Potential Candidate ◽  
Proteomics Data ◽  
Galactose Metabolism ◽  
Fruit Cracking

Abstract Background Akebia trifoliata (Thunb.) Koidz, can be used as a new potential candidate biofuel and bioenergy crop due to its high productivity, adaptability and tolerance to cultivation conditions. However, the pericarp of A. trifoliata cracks open longitudinally and disperses its seeds along the ventral suture during fruit ripening, which is a serious problem that limits the usefulness of its biofuel feedstocks and causes significant losses of yield and commercial value. However, there have been no known previous investigations of the fruit cracking and its molecular mechanisms in A. trifoliata.Results The dynamic structural changes of the fruit peels were observed. In the non-cracking stage of growth, the exocarp was dense, had an orderly arrangement, and the cuticle was complete and distributed continuously. However, the cells became thinner, had reduced integrity, lost cell wall structures, and there was cell wall break down, in the fruit cracking stage. Moreover, analysis of the complementary RNA sequencing based transcriptomes and tandem mass tag based proteomes at different development stages of the fruit ripening, were performed to detect the genes and proteins related to the fruit cracking in A. trifoliata. A total of 20 differentially expressed genes and 17 differentially abundant proteins were identified from the transcriptomics and proteomics data that contribute to the fruit cracking, by participating in the biosynthesis of the phenylpropanoid pathway, galactose metabolism, pentose, and glucuronate interconversions, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Several candidate genes and proteins related to pentose and glucuronate interconversions (pectate lyases and pectinesterase) and galactose metabolism (β-galactosidases 1 and β-galactosidases 2) may play key roles in A. trifoliata fruit cracking.Conclusions Complementary transcriptome and proteome level analyses indicated that a complex molecular network was controlling the fruit cracking process. This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits. The candidate genes/proteins identified in this study may be useful for the genetic improvement of A. trifoliata and other crops.

scholarly journals Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pests And Diseases ◽  
Fruit Cracking ◽  
Resistant Varieties ◽  
Fruit Decay

Abstract Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

scholarly journals Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2281
Author(s):  
Qian Ma ◽  
Chunxue Su ◽  
Chun-Hai Dong
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Structural Protein ◽  
Ros Scavenging ◽  
Glutathione S Transferase ◽  
Tandem Mass Tag ◽  
Genes Encoding ◽  
Plant Hormone Signaling

Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of ‘NL-6′ treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.

scholarly journals Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1335
Author(s):  
Hsueh-Yuan Chang ◽  
Cindy B. S. Tong
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Phenotypic Differences ◽  
Genes Encoding ◽  
A Cell ◽  
Phenotypic Groups

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

Structural Studies of Fibrinolysis by Electron and Light Microscopy

1999 ◽  
Vol 82 (08) ◽  
pp. 277-282 ◽  
Author(s):  
Yuri Veklich ◽  
Jean-Philippe Collet ◽  
Charles Francis ◽  
John W. Weisel
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Plasminogen Activator ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Degradation Products ◽  
Molecular Model ◽  
Three Dimensional ◽  
Tissue Type ◽  
Type Plasminogen Activator

IntroductionMuch is known about the fibrinolytic system that converts fibrin-bound plasminogen to the active protease, plasmin, using plasminogen activators, such as tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator. Plasmin then cleaves fibrin at specific sites and generates soluble fragments, many of which have been characterized, providing the basis for a molecular model of the polypeptide chain degradation.1-3 Soluble degradation products of fibrin have also been characterized by transmission electron microscopy, yielding a model for their structure.4 Moreover, high resolution, three-dimensional structures of certain fibrinogen fragments has provided a wealth of information that may be useful in understanding how various proteins bind to fibrin and the overall process of fibrinolysis (Doolittle, this volume).5,6 Both the rate of fibrinolysis and the structures of soluble derivatives are determined in part by the fibrin network structure itself. Furthermore, the activation of plasminogen by t-PA is accelerated by the conversion of fibrinogen to fibrin, and this reaction is also affected by the structure of the fibrin. For example, clots made of thin fibers have a decreased rate of conversion of plasminogen to plasmin by t-PA, and they generally are lysed more slowly than clots composed of thick fibers.7-9 Under other conditions, however, clots made of thin fibers may be lysed more rapidly.10 In addition, fibrin clots composed of abnormally thin fibers formed from certain dysfibrinogens display decreased plasminogen binding and a lower rate of fibrinolysis.11-13 Therefore, our increasing knowledge of various dysfibrinogenemias will aid our understanding of mechanisms of fibrinolysis (Matsuda, this volume).14,15 To account for these diverse observations and more fully understand the molecular basis of fibrinolysis, more knowledge of the physical changes in the fibrin matrix that precede solubilization is required. In this report, we summarize recent experiments utilizing transmission and scanning electron microscopy and confocal light microscopy to provide information about the structural changes occurring in polymerized fibrin during fibrinolysis. Many of the results of these experiments were unexpected and suggest some aspects of potential molecular mechanisms of fibrinolysis, which will also be described here.

scholarly journals Valorization of sugarcane bagasse by chemical pretreatment and enzyme mediated deconstruction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vihang S. Thite ◽  
Anuradha S. Nerurkar
Keyword(s):  
Cell Wall ◽  
Sugarcane Bagasse ◽  
Structural Changes ◽  
Enzymatic Saccharification ◽  
Dry Weight ◽  
Gravimetric Analysis ◽  
Chemical Pretreatment ◽  
Cell Wall Degrading Enzymes ◽  
First Time ◽  
Soluble Components

Abstract After chemical pretreatment, improved amenability of agrowaste biomass for enzymatic saccharification needs an understanding of the effect exerted by pretreatments on biomass for enzymatic deconstruction. In present studies, NaOH, NH4OH and H2SO4 pretreatments effectively changed visible morphology imparting distinct fibrous appearance to sugarcane bagasse (SCB). Filtrate analysis after NaOH, NH4OH and H2SO4 pretreatments yielded release of soluble reducing sugars (SRS) in range of ~0.17–0.44%, ~0.38–0.75% and ~2.9–8.4% respectively. Gravimetric analysis of pretreated SCB (PSCB) biomass also revealed dry weight loss in range of ~25.8–44.8%, ~11.1–16.0% and ~28.3–38.0% by the three pretreatments in the same order. Release of soluble components other than SRS, majorly reported to be soluble lignins, were observed highest for NaOH followed by H2SO4 and NH4OH pretreatments. Decrease or absence of peaks attributed to lignin and loosened fibrous appearance of biomass during FTIR and SEM studies respectively further corroborated with our observations of lignin removal. Application of commercial cellulase increased raw SCB saccharification from 1.93% to 38.84%, 25.56% and 9.61% after NaOH, H2SO4 and NH4OH pretreatments. Structural changes brought by cell wall degrading enzymes were first time shown visually confirming the cell wall disintegration under brightfield, darkfield and fluorescence microscopy. The microscopic evidence and saccharification results proved that the chemical treatment valorized the SCB by making it amenable for enzymatic saccharification.

scholarly journals Protective Effect of Psoralea corylifolia L. Seed Extract against Palmitate-Induced Neuronal Apoptosis in PC12 Cells

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Yunkyoung Lee ◽  
Hee-Sook Jun ◽  
Yoon Sin Oh
Keyword(s):  
Pc12 Cells ◽  
Molecular Mechanisms ◽  
Neuronal Cell ◽  
Marker Genes ◽  
Heme Oxygenase 1 ◽  
Mrna Levels ◽  
Protective Effects ◽  
Psoralea Corylifolia ◽  
Antioxidant Genes ◽  
Bax Protein

The extract of Psoralea corylifolia seeds (PCE) has been widely used as a herbal medicine because of its beneficial effect on human health. In this study, we investigated the protective effects and molecular mechanisms of PCE on palmitate- (PA-) induced toxicity in PC12 cells, a neuron-like cell line. PCE significantly increased cell viability in PA-treated PC12 cells and showed antiapoptotic effects, as evidenced by decreased expression of cleaved caspase-3, cleaved poly(ADP-ribose) polymerase, and bax protein as well as increased expression of bcl-2 protein. In addition, PCE treatment reduced PA-induced reactive oxygen species production and upregulated mRNA levels of antioxidant genes such as nuclear factor (erythroid-derived 2)-like 2 and heme oxygenase 1. Moreover, PCE treatment recovered the expression of autophagy marker genes such as beclin-1 and p62, which was decreased by PA treatment. Treatment with isopsoralen, one of the major components of PCE extract, also recovered the expression of autophagy marker genes and reduced PA-induced apoptosis. In conclusion, PCE exerts protective effects against lipotoxicity via its antioxidant function, and this effect is mediated by activation of autophagy. PCE might be a potential pharmacological agent to protect against neuronal cell injury caused by oxidative stress or lipotoxicity.

scholarly journals Molecular Mechanisms of ZC3H12C/Reg-3 Biological Activity and Its Involvement in Psoriasis Pathology

2021 ◽  
Vol 22 (14) ◽  
pp. 7311
Author(s):  
Mateusz Wawro ◽  
Jakub Kochan ◽  
Weronika Sowinska ◽  
Aleksandra Solecka ◽  
Karolina Wawro ◽  
...  
Keyword(s):  
Family Member ◽  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Inflammatory Diseases ◽  
Association Studies ◽  
Psoriasis Patient ◽  
Genome Wide Association Studies ◽  
Mrna Levels ◽  
Transcript Levels

The members of the ZC3H12/MCPIP/Regnase family of RNases have emerged as important regulators of inflammation. In contrast to Regnase-1, -2 and -4, a thorough characterization of Regnase-3 (Reg-3) has not yet been explored. Here we demonstrate that Reg-3 differs from other family members in terms of NYN/PIN domain features, cellular localization pattern and substrate specificity. Together with Reg-1, the most comprehensively characterized family member, Reg-3 shared IL-6, IER-3 and Reg-1 mRNAs, but not IL-1β mRNA, as substrates. In addition, Reg-3 was found to be the only family member which regulates transcript levels of TNF, a cytokine implicated in chronic inflammatory diseases including psoriasis. Previous meta-analysis of genome-wide association studies revealed Reg-3 to be among new psoriasis susceptibility loci. Here we demonstrate that Reg-3 transcript levels are increased in psoriasis patient skin tissue and in an experimental model of psoriasis, supporting the immunomodulatory role of Reg-3 in psoriasis, possibly through degradation of mRNA for TNF and other factors such as Reg-1. On the other hand, Reg-1 was found to destabilize Reg-3 transcripts, suggesting reciprocal regulation between Reg-3 and Reg-1 in the skin. We found that either Reg-1 or Reg-3 were expressed in human keratinocytes in vitro. However, in contrast to robustly upregulated Reg-1 mRNA levels, Reg-3 expression was not affected in the epidermis of psoriasis patients. Taken together, these data suggest that epidermal levels of Reg-3 are negatively regulated by Reg-1 in psoriasis, and that Reg-1 and Reg-3 are both involved in psoriasis pathophysiology through controlling, at least in part different transcripts.

Cell Wall Permeability of Pinto Bean Cotyledon Cells Regulates In Vitro Fecal Fermentation and Gut Microbiota

2021 ◽  
Author(s):  
Yanrong Huang ◽  
Sushil Dhital ◽  
Feitong Liu ◽  
Xiong Fu ◽  
Qiang Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Structural Changes ◽  
Microbiota Composition ◽  
Colonic Fermentation ◽  
Pinto Bean ◽  
Wall Permeability ◽  
Cell Wall Permeability ◽  
Cotyledon Cells ◽  
Whole Foods

Processing induced structural changes of whole foods on regulation of colonic fermentation rate and microbiota composition are least understood and often overlooked. In the present study, intact cotyledon cells from...

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