scholarly journals Transcriptomic and proteomic analysis reveals mechanisms of  low pollen-pistil compatibility  during water lily cross breeding

2019 ◽  
Author(s):  
Chun-Qing Sun ◽  
Fa-Di Chen ◽  
Nian-Jun Teng ◽  
Yue-Mei Yao ◽  
Xi Shan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Label Free ◽  
Water Lily ◽  
Ros Metabolism ◽  
Cell Wall Organization ◽  
Phenylpropanoid Biosynthesis ◽  
Viable Seeds

Abstract Background: In water lily ( Nymphaea ) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea . The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results: RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism , hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions: Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

scholarly journals Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding

2019 ◽  
Author(s):  
Chun-Qing Sun ◽  
Fa-Di Chen ◽  
Nian-Jun Teng ◽  
Yue-Mei Yao ◽  
Xi Shan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Label Free ◽  
Water Lily ◽  
Ros Metabolism ◽  
Cell Wall Organization ◽  
Phenylpropanoid Biosynthesis ◽  
Viable Seeds

Abstract Background: In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results: RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism , hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions: Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

scholarly journals Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding

2019 ◽  
Author(s):  
Chun-Qing Sun ◽  
Fa-Di Chen ◽  
Nian-Jun Teng ◽  
Yue-Mei Yao ◽  
Xi Shan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Label Free ◽  
Water Lily ◽  
Ros Metabolism ◽  
Cell Wall Organization ◽  
Phenylpropanoid Biosynthesis ◽  
Viable Seeds

Abstract Background: In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results: RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism , hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions: Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

scholarly journals Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Chun-Qing Sun ◽  
Fa-Di Chen ◽  
Nian-Jun Teng ◽  
Yue-Mei Yao ◽  
Xi Shan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Label Free ◽  
Water Lily ◽  
Ros Metabolism ◽  
Cell Wall Organization ◽  
Phenylpropanoid Biosynthesis ◽  
Viable Seeds

Abstract Background In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 h after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8789 (4680 were up-regulated), 6401 (3020 were up-regulated), and 11,284 (6148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism, hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

scholarly journals Transcriptomic and proteomic analysis reveals mechanisms of pre-fertilization barriers during water lily cross breeding

2019 ◽  
Author(s):  
Chun-Qing Sun ◽  
Fa-Di Chen ◽  
Nian-Jun Teng ◽  
Yue-Mei Yao ◽  
Xi Shan ◽  
...  
Keyword(s):  
Stress Response ◽  
Early Stage ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Label Free ◽  
Water Lily ◽  
Peroxide Decomposition ◽  
Ros Metabolism ◽  
Phenylpropanoid Biosynthesis ◽  
Viable Seeds

Abstract Background In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause pre-fertilization barriers in Nymphaea were identified. Results RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism, hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions These results indicated that genes involved in regulation and gene pathways involved in stress response might overlap in the process of pollination process forming the hybridization barrier in Nymphaea. These results indicate that the pollen tube entering stigma tissue was very similar to the process of external injury, further suggesting that these genes involved in defense and stress response were necessary in the early stage of interaction between the pollen and stigma. This study strengthens our understanding of the mechanism of pre-fertilization barriers in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

scholarly journals iTRAQ-based comparative proteomic analysis of differences in the protein profiles of stems and leaves from two alfalfa genotypes

2020 ◽  
Author(s):  
Hao Sun ◽  
Jie Yu ◽  
Fan Zhang ◽  
Junmei Kang ◽  
Mingna Li ◽  
...  
Keyword(s):  
Leaf Development ◽  
Proteomic Analysis ◽  
Regulatory Networks ◽  
Carbon Fixation ◽  
Chlorophyll Biosynthesis ◽  
Phenylpropanoid Pathway ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Chlorophyll Metabolism ◽  
Phenylpropanoid Biosynthesis

Abstract Background: To explore the molecular regulatory mechanisms of early stem and leaf development, proteomic analysis was performed on leaves and stems of F genotype alfalfa, with thin stems and small leaves, and M genotype alfalfa, with thick stems and large leaves. Results: Based on fold-change thresholds of >1.20 or <0.83 ( p <0.05), a large number of proteins were identified as being differentially enriched between the M and F genotypes: 249 downregulated and 139 upregulated in stems and 164 downregulated and 134 upregulated in leaves. The differentially expressed proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially expressed proteins in leaves were mainly involved in porphyrin and chlorophyll metabolism, phenylpropanoid biosynthesis, starch and sucrose metabolism, and carbon fixation in photosynthetic organisms. Six differentially enriched proteins were mapped onto the porphyrin and chlorophyll metabolism pathway in leaves of the M genotype, including five upregulated proteins involved in chlorophyll biosynthesis and one downregulated protein involved in chlorophyll degradation. Eleven differentially enriched proteins were mapped onto the phenylpropanoid pathway in stems of the M genotype, including two upregulated proteins and nine downregulated proteins. Conclusion: Enhanced chlorophyll synthesis and decreased lignin synthesis provided a reasonable explanation for the larger leaves and lower levels of stem lignification in M genotype alfalfa. This proteomic study aimed to classify the functions of differentially enriched proteins and to provide information on the molecular regulatory networks involved in stem and leaf development.

scholarly journals Comparative proteomic analysis of thick-walled ray formation of Haloxylon ammodendron in the Gurbantunggut Desert, China

2020 ◽  
Author(s):  
Chaobin Zhou ◽  
Junjie Ding ◽  
Xiaojing Hu ◽  
Wei Gong
Keyword(s):  
Cell Wall ◽  
Wall Thickness ◽  
Carbon Metabolism ◽  
Proteomic Analysis ◽  
Metabolic Pathways ◽  
Cell Wall Biosynthesis ◽  
Haloxylon Ammodendron ◽  
Ray Cells ◽  
Phenylpropanoid Biosynthesis ◽  
Ray Cell

Abstract Background The thick-walled ray cells have been reported in Haloxylon ammodendron for the first time. This study measured the wall thickness of ray cells and performed a proteomic analysis of ray cell wall formation in the xylem of H. ammodendron using isobaric tags for relative and absolute quantitation. Results The wall thickness of ray cells in Jinghe (2.85 ± 0.42 µm) was significantly lower than that in Shihezi (3.08 ± 0.44 µm) (P < 0.01). In Shihezi, which has a thicker wall of ray cells than that in Jinghe, 795 differentially expressed proteins were upregulated. Phenylpropanoid biosynthesis, photosynthesis, glycolysis/gluconeogenesis, carbon metabolism, starch and sucrose metabolism, metabolic pathways, etc. promote ray cell wall biosynthesis of the xylem of H. ammodendron by providing substrates or energy. During the process of cell wall biosynthesis in the xylem of H. ammodendron, the nonspecific lipid-transfer protein and beta expansin EXPB2.1 (Mirabilis jalapa] first loosens the cell wall, followed by extension and expansion, and the xyloglucan endotransglycosylase/hydrolase 1 cleaves and links the xyloglucan chains. Then, photosystem I P700 apoprotein A1, reversibly glycosylated polypeptide 1 and GDP-mannose-3′, 5′-epimerase, etc., are involved in cellulose, hemicellulose and pectin biosynthesis of the cell wall by providing components or energy. Finally, the proteins in phenylpropanoid biosynthesis promote the lignification of the ray cell wall and complete the biosynthetic process of the cell wall. Conclusions Phenylpropanoid biosynthesis, photosynthesis, glycolysis/gluconeogenesis, carbon metabolism, starch and sucrose metabolism, metabolic pathways, etc. promote ray cell wall biosynthesis of the xylem of H. ammodendron by providing substrates or energy. The results are important for improving the wood mechanical properties of timber plantations.

scholarly journals Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 488 ◽  
Author(s):  
Baiquan Ma ◽  
Yuduan Ding ◽  
Cuiying Li ◽  
Mingjun Li ◽  
Fengwang Ma ◽  
...  
Keyword(s):  
Organic Acids ◽  
Organic Acid ◽  
Proteomic Analysis ◽  
Soluble Sugar ◽  
Soluble Sugars ◽  
Sugar Metabolism ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Malus Species

Soluble sugars and organic acids are the main determinants of fruit organoleptic quality. To investigate the genes responsible for the soluble sugar and organic acid contents of apple fruits, a label-free proteomic analysis involving liquid chromatography (LC)-mass spectrometry (MS)/MS was conducted with the fruits of two Malus species, M. sargentii and M. niedzwetzkyana, which exhibit significant differences in soluble sugar and organic acid contents. A total of 13,036 unique peptides and 1,079 differentially-expressed proteins were identified. To verify the LC-MS/MS results, five candidate proteins were further analyzed by parallel reaction monitoring. The results were consistent with the LC-MS/MS data, which confirmed the reliability of the LC-MS/MS analysis. The functional annotation of the differentially-expressed proteins, based on the gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, revealed that they were mainly related to biological processes and cellular components. Additionally, the main enriched KEGG pathways were related to metabolic processes. Moreover, 31 proteins involved in soluble sugar metabolism, organic acid metabolism, and H+-transport were identified. The results of this study may be useful for the comprehensive characterization of the complex mechanism regulating apple fruit-soluble sugar and organic acid contents.

Sign in / Sign up

Export Citation Format

Share Document