scholarly journals Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fu Li ◽  
Zheng Zeng ◽  
Renyan Huang ◽  
Yanzhou Wang ◽  
Touming Liu
Keyword(s):  
Proteomic Analysis ◽  
Secondary Wall ◽  
Interaction Analysis ◽  
Molecular Model ◽  
Ramie Fiber ◽  
Bast Fiber ◽  
Textile Materials ◽  
Fiber Growth ◽  
Yield And Quality ◽  
Interacting Networks

Abstract Background Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie. Results Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, where fiber growth is at different stages. We identified 6971 non-redundant proteins from bast bark. Proteomic comparison revealed 983 proteins with differential expression between the two bark types. Of these 983 proteins, 46 were identified as the homolog of known secondary wall biosynthetic proteins of Arabidopsis, indicating that they were potentially associated with fiber growth. Then, we proposed a molecular model for the secondary wall biosynthesis of ramie fiber. Furthermore, interaction analysis of 46 candidate proteins revealed two interacting networks that consisted of eight cellulose biosynthetic enzymes and seven lignin biosynthetic proteins, respectively. Conclusion This study sheds light on the proteomic basis underlying bast fiber growth in ramie, and the identification of many candidates associated with fiber growth provides important basis for understanding the fiber growth in this crop.

scholarly journals Targeting AKT/mTOR and Bcl-2 for Autophagic and Apoptosis Cell Death in Lung Cancer: Novel Activity of a Polyphenol Compound

Antioxidants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 534
Author(s):  
Sucharat Tungsukruthai ◽  
Onrapak Reamtong ◽  
Sittiruk Roytrakul ◽  
Suchada Sukrong ◽  
Chanida Vinayanwattikun ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cell Death ◽  
Cancer Cells ◽  
Proteomic Analysis ◽  
Interaction Analysis ◽  
Time Dependent ◽  
The Novel ◽  
Protein Protein Interaction ◽  
Autophagy Induction ◽  
Acidic Vesicle

Autophagic cell death (ACD) is an alternative death mechanism in resistant malignant cancer cells. In this study, we demonstrated how polyphenol stilbene compound PE5 exhibits potent ACD-promoting activity in lung cancer cells that may offer an opportunity for novel cancer treatment. Cell death caused by PE5 was found to be concomitant with dramatic autophagy induction, as indicated by acidic vesicle staining, autophagosome, and the LC3 conversion. We further confirmed that the main death induction caused by PE5 was via ACD, since the co-treatment with an autophagy inhibitor could reverse PE5-mediated cell death. Furthermore, the defined mechanism of action and upstream regulatory signals were identified using proteomic analysis. Time-dependent proteomic analysis showed that PE5 affected 2142 and 1996 proteins after 12 and 24 h of treatment, respectively. The crosstalk network comprising 128 proteins that control apoptosis and 25 proteins involved in autophagy was identified. Protein–protein interaction analysis further indicated that the induction of ACD was via AKT/mTOR and Bcl-2 suppression. Western blot analysis confirmed that the active forms of AKT, mTOR, and Bcl-2 were decreased in PE5-treated cells. Taken together, we demonstrated the novel mechanism of PE5 in shifting autophagy toward cell death induction by targeting AKT/mTOR and Bcl-2 suppression.

Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie

Planta ◽  
2021 ◽  
Vol 254 (1) ◽  
Author(s):  
Qiaoyun He ◽  
Zheng Zeng ◽  
Fu Li ◽  
Renyan Huang ◽  
Yanzhou Wang ◽  
...  
Keyword(s):  
Bast Fiber ◽  
Fiber Growth

iTRAQ-based quantitative proteomic analysis of two transgenic soybean lines and the corresponding non-genetically modified isogenic variety

2019 ◽  
Vol 167 (1) ◽  
pp. 67-78
Author(s):  
Weixiao Liu ◽  
Zhe Zhang ◽  
Xuri Liu ◽  
Wujun Jin
Keyword(s):  
Proteomic Analysis ◽  
Interaction Analysis ◽  
Genetically Modified ◽  
Unintended Effects ◽  
Post Translational Modification ◽  
Absolute Quantitation ◽  
Protein Protein Interaction ◽  
Transduction Mechanisms ◽  
Isobaric Tags ◽  
Gm Soybean

Abstract To investigate the unintended effects of genetically modified (GM) crops, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed with seed cotyledons of two GM soybean lines, MON87705 and MON87701×MON89788, and the corresponding non-transgenic isogenic variety A3525. Thirty-five differentially abundant proteins (DAPs) were identified in MON87705/A3525, 27 of which were upregulated and 8 downregulated. Thirty-eight DAPs were identified from the MON87701×MON89788/A3525 sample, including 29 upregulated proteins and 9 downregulated proteins. Pathway analysis showed that most of these DAPs participate in protein processing in endoplasmic reticulum and in metabolic pathways. Protein–protein interaction analysis of these DAPs demonstrated that the main interacting proteins are associated with post-translational modification, protein turnover, chaperones and signal transduction mechanisms. Nevertheless, these DAPs were not identified as new unintended toxins or allergens and only showed changes in abundance. All these results suggest that the seed cotyledon proteomic profiles of the two GM soybean lines studied were not dramatically altered compared with that of their natural isogenic control.

Structures of cotton motes and mote fibers

1990 ◽  
Vol 48 (3) ◽  
pp. 678-679
Author(s):  
W. R. Goynes ◽  
B. F. Ingber ◽  
D. P. Thibodeaux
Keyword(s):  
Embryo Development ◽  
Exploratory Study ◽  
Cotton Seed ◽  
Secondary Wall ◽  
Main Body ◽  
Cotton Industry ◽  
Fiber Growth ◽  
Normal Seed ◽  
Thin Walled

A mote is a seedlike structure that is derived from an ovule, but that does not develop into a mature seed. In cotton, motes vary in size from tiny structures having no fibers, to those that appear to be full-sized seed with fibers approximately the length of fully-developed fibers. The size of the mote depends on the stage at which its development was arrested. In the cotton industry these undeveloped seed, as well as the quality of fibers produced by them, are of commercial importance. Results presented here are from an exploratory study to show differences between structures of normal seed and fibers, and motes and mote fibers.Cotton seed develop within a closed boll that is separated into compartments or locules. Embryo development is normally completed within the seed in approximately 35 days. Fiber growth initiates on the seedcoat surface as cells elongate to become thin-walled tubes until approximately 18-20 days postanthesis when the main body of the fiber, the secondary wall, begins to be laid down.

scholarly journals Key Stages of Fiber Development as Determinants of Bast Fiber Yield and Quality

Fibers ◽  
2018 ◽  
Vol 6 (2) ◽  
pp. 20 ◽  
Author(s):  
Natalia Mokshina ◽  
Tatyana Chernova ◽  
Dmitry Galinousky ◽  
Oleg Gorshkov ◽  
Tatyana Gorshkova
Keyword(s):  
Fiber Development ◽  
Bast Fiber ◽  
Yield And Quality ◽  
Fiber Yield

scholarly journals iTRAQ-Based Quantitative Glutelin Proteomic Analysis Reveals Differentially Expressed Proteins in Physiological Metabolism Process during Endosperm Development and their Impacts on Yield and Quality in Autotetraploid Rice

2020 ◽  
Author(s):  
Lin Xian ◽  
Yanxi Long ◽  
Meng Yang ◽  
Zhixiong Chen ◽  
Jinwen Wu ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Ribosomal Proteins ◽  
Storage Proteins ◽  
Enrichment Analysis ◽  
Endosperm Development ◽  
Lysine Biosynthesis ◽  
Yield And Quality ◽  
Autotetraploid Rice ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Abstract Background Autotetraploid rice, which is developed through chromosome set doubling using diploid rice, produces high-quality kernels that are rich in storage proteins. However, little information is available about the content of different proteins in autotetraploid rice and their proteomic analysis. Results The dynamic changes in four storage proteins, albumin, globulin, prolamin, and glutelin, were analyzed in the endosperm of autotetraploid rice (AJNT-4x) and in that of its diploid counterpart (AJNT-2x) for comparison. The contents of the four proteins were all higher during endosperm development in AJNT-4x than in AJNT-2x, but their change and composition were almost the same in the two materials. Then, iTRAQ was employed to analyze the glutelin profiles of AJNT-4x and AJNT-2x at 10 DAF, 15 DAF, and 20 DAF. A total of 1,326 proteins were identified in AJNT-4x and AJNT-2x using high-throughput LC-MS/MS. Among the 1,326 identified proteins, there were 362 DEPs in AJNT-4x compared with those in AJNT-2x and 372 DEPs between different development stages in AJNT-4x. Eight important upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and Q40689. Among them, B8AM24 and B8ARJ0 were related to the lysine biosynthesis process. GO enrichment analysis revealed that the critical functions of DEPs exhibited little overlap between the 10, 15, and 20 DAF groups. Endosperm glutelin accumulation was regulated mainly by different DEPs during the late stage, and 15 DAF was a critical regulating point for glutelin accumulation. KEGG pathway analysis showed that ribosomal proteins were significantly higher in AJNT-4x than in AJNT-2x at 10 DAF, and the protein processing, biosynthesis, and metabolism of amino acids were higher and more active in AJNT-4x at 15 DAF, while the peroxisome was richer in AJNT-4x at 20 DAF. The PPI network showed that ribosomal proteins gradually decreased with increasing endosperm development. Conclusions These results provide new insights into dynamic glutelin expression differences during endosperm development in autotetraploid rice, which will help in developing rice cultivars with increased yield and improved grain nutritional quality.

scholarly journals Phosphoproteome analysis reveals an extensive phosphorylation of proteins associated with bast fiber growth in ramie

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zheng Zeng ◽  
Fu Li ◽  
Renyan Huang ◽  
Yanzhou Wang ◽  
Touming Liu
Keyword(s):  
Protein Function ◽  
Functional Characterization ◽  
Stem Bark ◽  
Fiber Formation ◽  
Ramie Fiber ◽  
Post Translational Modifications ◽  
Fiber Growth ◽  
Phosphorylated Proteins ◽  
Ramie Fibers ◽  
Related Proteins

Abstract Background Phosphorylation modification, one of the most common post-translational modifications of proteins, widely participates in the regulation of plant growth and development. Fibers extracted from the stem bark of ramie are important natural textile fibers; however, the role of phosphorylation modification in the growth of ramie fibers is largely unknown. Results Here, we report a phosphoproteome analysis for the barks from the top and middle section of ramie stems, in which the fiber grows at different stages. A total of 10,320 phosphorylation sites from 9,170 unique phosphopeptides that were assigned to 3,506 proteins was identified, and 458 differentially phosphorylated sites from 323 proteins were detected in the fiber developmental barks. Twelve differentially phosphorylated proteins were the homologs of Arabidopsis fiber growth-related proteins. We further focused on the function of the differentially phosphorylated KNOX protein whole_GLEAN_10029667, and found that this protein dramatically repressed the fiber formation in Arabidopsis. Additionally, using a yeast two-hybridization assay, we identified a kinase and a phosphatase that interact with whole_GLEAN_10029667, indicating that they potentially target this KNOX protein to regulate its phosphorylation level. Conclusion The finding of this study provided insights into the involvement of phosphorylation modification in ramie fiber growth, and our functional characterization of whole_GLEAN_10029667 provide the first evidence to indicate the involvement of phosphorylation modification in the regulation of KNOX protein function in plants.

scholarly journals iTRAQ-Based Quantitative Glutelin Proteomic Analysis Reveals Differentially Expressed Proteins in the Physiological Metabolism Process during Endosperm Development and their Impacts on Yield and Quality in Autotetraploid Rice

2020 ◽  
Author(s):  
Lin Xian ◽  
Yanxi Long ◽  
Meng Yang ◽  
Zhixiong Chen ◽  
Jinwen Wu ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Ribosomal Proteins ◽  
Storage Proteins ◽  
Enrichment Analysis ◽  
Endosperm Development ◽  
Lysine Biosynthesis ◽  
Yield And Quality ◽  
Autotetraploid Rice ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Abstract Background: Autotetraploid rice, which is developed through chromosome set doubling using diploid rice, produces high-quality kernels that are rich in storage proteins. However, little information is available about the content of different proteins in autotetraploid rice and their proteomic analysis. Results: The dynamic changes in four storage proteins, albumin, globulin, prolamin, and glutelin, were analyzed in the endosperm of autotetraploid rice (AJNT-4x) and in that of its diploid counterpart (AJNT-2x) for comparison. The contents of the four proteins were all higher during endosperm development in AJNT-4x than in AJNT-2x, but their change and composition were almost the same in the two materials. Then, iTRAQ was employed to analyze the glutelin profiles of AJNT-4x and AJNT-2x at 10 DAF, 15 DAF, and 20 DAF. A total of 1,326 proteins were identified in AJNT-4x and AJNT-2 x using high-throughput LC-MS/MS. Among the 1,326 identified proteins, there were 362 DEPs in AJNT-4x compared with those in AJNT-2x and 372 DEPs between different development stages in AJNT-4x. Eight important upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and Q40689. Among them, B8AM24 and B8ARJ0 were related to the lysine biosynthesis process. GO enrichment analysis revealed that the critical functions of DEPs exhibited little overlap between the 10, 15, and 20 DAF groups. Endosperm glutelin accumulation was regulated mainly by different DEPs during the late stage, and 15 DAF was a critical regulating point for glutelin accumulation. KEGG pathway analysis showed that ribosomal proteins were significantly higher in AJNT-4x than in AJNT-2x at 10 DAF, and the protein processing, biosynthesis, and metabolism of amino acids were higher and more active in AJNT-4x at 15 DAF, while the peroxisome was richer in AJNT-4x at 20 DAF. The PPI network showed that ribosomal proteins gradually decreased with increasing endosperm development. Conclusions: These results provide new insights into dynamic glutelin expression differences during endosperm development in autotetraploid rice, which will help in developing rice cultivars with increased yield and improved grain nutritional quality.

Toward an alignment of the actin molecule within the actin filament

1983 ◽  
Vol 41 ◽  
pp. 450-451
Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi
Keyword(s):  
Actin Filament ◽  
Diffraction Data ◽  
Quantitative Estimate ◽  
Molecular Model ◽  
Quantitative Comparison ◽  
Regulatory Proteins ◽  
Essential Information ◽  
X Ray ◽  
Maximum Resolution ◽  
Lack Of Information

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.

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