Label-free microscopy and stress responses reveal the functional organization of Pseudodiaptomus marinus copepod myofibrils

2015 ◽  
Vol 191 (2) ◽  
pp. 224-235 ◽  
Author(s):  
Ali Ibrahim ◽  
Charles Henri Hage ◽  
Anissa Souissi ◽  
Aymeric Leray ◽  
Laurent Héliot ◽  
...  
Keyword(s):  
Stress Responses ◽  
Functional Organization ◽  
Label Free ◽  
Pseudodiaptomus Marinus

scholarly journals Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels

2020 ◽  
Vol 21 (4) ◽  
pp. 1369
Author(s):  
Quanquan Chen ◽  
Ran Huang ◽  
Zhenxiang Xu ◽  
Yaxin Zhang ◽  
Li Li ◽  
...  
Keyword(s):  
Laser Capture Microdissection ◽  
Stress Responses ◽  
Label Free ◽  
Kernel Development ◽  
Flight Mass Spectrometry ◽  
Specific Proteins ◽  
Response To Stress ◽  
Black Layer ◽  
Maize Kernels ◽  
Laser Capture

The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.

scholarly journals Quantitative Proteome and PTMome Analysis of Arabidopsis Thaliana Root Responses to Persistent Osmotic and Salinity Stress.

2021 ◽  
Author(s):  
M C Rodriguez ◽  
D Mehta ◽  
M Tan ◽  
R G Uhrig
Keyword(s):  
Arabidopsis Thaliana ◽  
Salt Stress ◽  
Stress Responses ◽  
Protein Level ◽  
Economic Losses ◽  
Plant Responses ◽  
Protein Abundance ◽  
Lysine Acetylation ◽  
Label Free ◽  
Proteome Level

ABSTRACT Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h - days) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM Mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while PTMs do not. Further, we find significant changes in PTMs and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulphur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.

scholarly journals Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins

Proteomes ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 48 ◽  
Author(s):  
Tony Cijsouw ◽  
Austin Ramsey ◽  
TuKiet Lam ◽  
Beatrice Carbone ◽  
Thomas Blanpied ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Functional Organization ◽  
Neuronal Cell ◽  
Super Resolution ◽  
Synaptic Cleft ◽  
Surface Proteins ◽  
Mammalian Brain ◽  
Label Free ◽  
Edge Zone ◽  
Cultured Cortical Neurons

Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons. This reporter marked excitatory synapses as measured by confocal microcopy and was targeted to the edge zone of the synaptic cleft as determined using 3D dSTORM super-resolution imaging. Proximity labeling with a membrane-impermeant biotin-phenol compound restricted labeling to the cell surface, and Label-Free Quantitation (LFQ) mass spectrometry combined with ratiometric HRP tagging of membrane vs. synaptic surface proteins was used to identify the proteomic content of excitatory clefts. Novel cleft candidates were identified, and Receptor-type tyrosine-protein phosphatase zeta was selected and successfully validated. This study supports the robust applicability of peroxidase-mediated proximity labeling for synaptic cleft proteomics and its potential for understanding synapse heterogeneity in health and changes in diseases such as psychiatric disorders and addiction.

scholarly journals Methyl-Arginine Profile of Brain from Aged PINK1-KO+A53T-SNCA Mice Suggests Altered Mitochondrial Biogenesis

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Georg Auburger ◽  
Suzana Gispert ◽  
Nadine Brehm
Keyword(s):  
Mitochondrial Biogenesis ◽  
Posttranslational Modifications ◽  
Stress Responses ◽  
Autosomal Recessive ◽  
Oxygen Sensor ◽  
Alpha Synuclein ◽  
Label Free ◽  
Brain Hemispheres ◽  
Mrna Decapping ◽  
Dopaminergic Differentiation

Hereditary Parkinson’s disease can be triggered by an autosomal dominant overdose of alpha-Synuclein (SNCA) or the autosomal recessive deficiency of PINK1. We recently showed that the combination of PINK1-knockout with overexpression of A53T-SNCA in double mutant (DM) mice potentiates phenotypes and reduces survival. Now we studied brain hemispheres of DM mice at age of 18 months in a hypothesis-free approach, employing a quantitative label-free global proteomic mass spectrometry scan of posttranslational modifications focusing on methyl-arginine. The strongest effects were documented for the adhesion modulator CMAS, the mRNA decapping/deadenylation factor PATL1, and the synaptic plasticity mediator CRTC1/TORC1. In addition, an intriguing effect was observed for the splicing factor PSF/SFPQ, known to interact with the dopaminergic differentiation factor NURR1 as well as with DJ-1, the protein responsible for the autosomal recessive PARK7 variant of PD. CRTC1, PSF, and DJ-1 are modulators of PGC1alpha and of mitochondrial biogenesis. This pathway was further stressed by dysregulations of oxygen sensor EGLN3 and of nuclear TMPO. PSF and TMPO cooperate with dopaminergic differentiation factors LMX1B and NURR1. Further dysregulations concerned PRR18, TRIO, HNRNPA1, DMWD, WAVE1, ILDR2, DBNDD1, and NFM. Thus, we report selective novel endogenous stress responses in brain, which highlight early dysregulations of mitochondrial homeostasis and midbrain vulnerability.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of Saccharomyces cerevisiae

2016 ◽  
Vol 2016 ◽  
pp. 1-12
Author(s):  
Chiranjit Panja ◽  
Rakesh K.S. Setty ◽  
Gopal Vaidyanathan ◽  
Sanjay Ghosh
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Responses ◽  
Nitrosative Stress ◽  
Nitrogen Compound ◽  
Nuclear Gene ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Differential Proteomics ◽  
Go Terms

Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. To better understand the physiological function of flavohemoglobin in yeast, in the present study a label-free differential proteomics study has been carried out in wild-type and YHB1 deleted strains of S. cerevisiae grown under fermentative conditions. From the analysis, 417 proteins in Y190 and 392 proteins in ΔYHB1 were identified with high confidence. Interestingly, among the differentially expressed identified proteins, 40 proteins were found to be downregulated whereas 41 were found to be upregulated in ΔYHB1 strain of S. cerevisiae (p value < 0.05). The differentially expressed proteins were also classified according to gene ontology (GO) terms. The most enriched and significant GO terms included nitrogen compound biosynthesis, amino acid biosynthesis, translational regulation, and protein folding. Interactions of differentially expressed proteins were generated using Search Tool for the Retrieval of Interacting Genes (STRING) database. This is the first report which offers a more complete view of the proteome changes in S. cerevisiae in the absence of flavohemoglobin.

scholarly journals Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Agronomic Traits ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. Results Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

scholarly journals Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

2020 ◽  
Author(s):  
Daoping Wang ◽  
Yongying Mu ◽  
Xiaojiao Hu ◽  
Bo Ma ◽  
Zhibo Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Label Free ◽  
Maize Production ◽  
Maize Hybrids ◽  
Comparative Proteomic Analysis

Abstract BackgroundMaize is a major crop worldwide and heterotic hybrids play important roles in global maize production. Heterosis refers hybrid progeny of species or varieties exhibiting superior traits compared with those of their parents and much attention has been paid to heterosis associated genes recently. The hybridization between parents can change the expression pattern of some proteins such as non-additive proteins which might lead to heterosis, so that comparative proteomic analysis of maize hybrid and its parents is helpful for understanding the mechanism of heterosis.ResultsSecond seedling leaves of maize hybrids "Zhongdan 808" and "Zhongdan 909" and their parents were collected at three-leaf stage for protein extractions. Over 2,000 protein groups were accurately assessed in the two hybrids and their parents by label-free quantification. Quantitative data analyses of the proteomes revealed that the two hybrids were more similar to their female parents. Additionally, pathway enrichment analysis showed that most non-additive proteins in Zhongdan 808 were mainly enriched in stress-related pathways, while those in Zhongdan 909 were mainly enriched in photosynthesis. ConclusionsIn comparison with their parents, the excellent agronomic traits of hybrid Zhongdan 808 was correlated with the high expression levels of some proteins related to stress responses and and metabolic functions, while those of Zhongdan 909 was correlated with photosynthesis. Our proteomics results supported previous physiological and morphological research. This work may provide useful information for understanding of the molecular mechanisms involved in the heterosis of hybrid maize.

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