Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus

Background Ananas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood. Methods Comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed. Results In total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves.

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

10.21203/rs.3.rs-36055/v4 ◽

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 ◽

Chlorophyll Synthesis ◽

Phenylpropanoid Pathway ◽

Chlorophyll Metabolism ◽

Phenylpropanoid Biosynthesis ◽

Proteomic Study

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 enriched proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially enriched 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.

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

BMC Plant Biology ◽

10.1186/s12870-020-02671-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Hao Sun ◽

Jie Yu ◽

Fan Zhang ◽

Junmei Kang ◽

Mingna Li ◽

...

Keyword(s):

Leaf Development ◽

Proteomic Analysis ◽

Regulatory Networks ◽

Carbon Fixation ◽

Chlorophyll Biosynthesis ◽

Chlorophyll Synthesis ◽

Phenylpropanoid Pathway ◽

Chlorophyll Metabolism ◽

Phenylpropanoid Biosynthesis ◽

Proteomic Study

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 enriched proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially enriched 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.

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

10.21203/rs.3.rs-36055/v2 ◽

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.

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

10.21203/rs.3.rs-36055/v3 ◽

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 ◽

Chlorophyll Synthesis ◽

Phenylpropanoid Pathway ◽

Chlorophyll Metabolism ◽

Phenylpropanoid Biosynthesis ◽

Proteomic Study

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 enriched 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.

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iTRAQ-based Comparative Proteomic Analysis of Differences in the Protein Profiles of Stems and Leaves From Two Alfalfa Genotypes

10.21203/rs.3.rs-36055/v1 ◽

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.

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iTRAQ-based Proteomic Analysis of a Chlorophyll-Deficient Mutant Caused by Single Base Change in RPS4 of Chinese Cabbage (Brassica Campestris L. ssp. Pekinensis)

10.21203/rs.3.rs-56863/v1 ◽

2020 ◽

Author(s):

Xiaoyan Tang ◽

Fengyan Shi ◽

Yiheng Wang ◽

Shengnan Huang ◽

Ying Zhao ◽

...

Keyword(s):

Chinese Cabbage ◽

Proteomic Analysis ◽

Ribosomal Proteins ◽

Carbon Fixation ◽

Chlorophyll Biosynthesis ◽

Multiple Reaction Monitoring ◽

Base Substitution ◽

Deficient Mutant ◽

Chlorophyll Metabolism ◽

A Genome

Abstract Background: Plastids are important plant-cell organelles containing a genome and bacterial-type 70S ribosomes—primarily composed of plastid ribosomal proteins and ribosomal RNAs. In this study, a chlorophyll-deficient mutant (cdm) obtained from double-haploid Chinese cabbage ‘FT’ was identified as a plastome mutant with an A-to-C base substitution in the plastid gene encoding the ribosomal protein RPS4. To further elucidate the function and regulatory mechanisms of RPS4, a comparative proteomic analysis was conducted between cdm and ‘FT’ plants using isobaric tags and a relative and absolute quantitation by (iTRAQ)-based strategy.Results: A total of 6,245 proteins were identified, 540 of which were differentially expressed (DEPs) in the leaves of cdm as compared to those of ‘FT’—including 233 upregulated and 307 downregulated proteins. Upregulated DEPs were mainly involved in translation, organic nitrogen synthesis, ribosomes, and spliceosomes. Meanwhile, downregulated DEPs were mainly involved in photosynthesis, photosynthetic reaction centres, photosynthetic light harvesting, carbon fixation, and chlorophyll binding. Our findings indicate an important role of RPS4 in the regulation of growth and development of Chinese cabbage, possibly by regulating plastid translation activity by affecting the expression of specific photosynthesis- and cold stress-related proteins. Moreover, a multiple reaction monitoring test and quantitative real time polymerase chain reaction analysis confirmed our iTRAQ results.Conclusions: Quantitative proteomic analysis allowed us to confirm diverse changes in the metabolic pathways between cdm and ‘FT’ plants. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that DEPs were significantly associated with photosynthesis, chlorophyll metabolism, carbon metabolism, RNA transport, glucosinolate biosynthesis, and gene splicing. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in Chinese cabbage.

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Transcriptomic Analysis of the Photosynthetic, Respiration, and Aerenchyma Adaptation Strategies in Bermudagrass (Cynodon dactylon) under Different Submergence Stress

International Journal of Molecular Sciences ◽

10.3390/ijms22157905 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7905

Author(s):

Zhongxun Yuan ◽

Xilu Ni ◽

Muhammad Arif ◽

Zhi Dong ◽

Limiao Zhang ◽

...

Keyword(s):

Carbon Fixation ◽

Cynodon Dactylon ◽

Chlorophyll Biosynthesis ◽

Tca Cycle ◽

Ethylene Signaling ◽

Physiological Mechanisms ◽

Cell Wall Modification ◽

Aerenchyma Formation ◽

Submergence Stress ◽

Photosynthesis And Respiration

Submergence impedes photosynthesis and respiration but facilitates aerenchyma formation in bermudagrass. Still, the regulatory genes underlying these physiological responses are unclear in the literature. To identify differentially expressed genes (DEGs) related to these physiological mechanisms, we studied the expression of DEGs in aboveground and underground tissues of bermudagrass after a 7 d treatment under control (CK), shallow submergence (SS), and deep submergence (DS). Results show that compared with CK, 12276 and 12559 DEGs were identified under SS and DS, respectively. Among them, the DEGs closely related to the metabolism of chlorophyll biosynthesis, light-harvesting, protein complex, and carbon fixation were down-regulated in SS and DS. Meanwhile, a large number of DEGs involved in starch and sucrose hydrolase activities, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation were down-regulated in aboveground tissues of bermudagrass in SS and DS. Whereas in underground tissues of bermudagrass these DEGs were all up-regulated under SS, only beta-fructofuranosidase and α-amylase related genes were up-regulated under DS. In addition, we found that DEGs associated with ethylene signaling, Ca2+-ROS signaling, and cell wall modification were also up-regulated during aerenchyma formation in underground tissues of bermudagrass under SS and DS. These results provide the basis for further exploration of the regulatory and functional genes related to the adaptability of bermudagrass to submergence.

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Molecular mechanism underlying the effect of maleic hydrazide treatment on starch accumulation in S. polyrrhiza 7498 fronds

Biotechnology for Biofuels ◽

10.1186/s13068-021-01932-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yerong Zhu ◽

Xiaoxue Li ◽

Xuan Gao ◽

Jiqi Sun ◽

Xiaoyuan Ji ◽

...

Keyword(s):

Plant Growth ◽

Carbon Fixation ◽

Maleic Hydrazide ◽

Starch Content ◽

Vegetative Reproduction ◽

Photosynthetic Pigment ◽

Starch Accumulation ◽

Chlorophyll Fluorescence Parameters ◽

Significant Difference ◽

Starch Production

Abstract Background Duckweed is considered a promising feedstock for bioethanol production due to its high biomass and starch production. The starch content can be promoted by plant growth regulators after the vegetative reproduction being inhibited. Maleic hydrazide (MH) has been reported to inhibit plant growth, meantime to increase biomass and starch content in some plants. However, the molecular explanation on the mechanism of MH action is still unclear. Results To know the effect and action mode of MH on the growth and starch accumulation in Spirodela polyrrhiza 7498, the plants were treated with different concentrations of MH. Our results showed a substantial inhibition of the growth in both fronds and roots, and increase in starch contents of plants after MH treatment. And with 75 µg/mL MH treatment and on the 8th day of the experiment, starch content was the highest, about 40 mg/g fresh weight, which is about 20-fold higher than the control. The I2-KI staining and TEM results confirmed that 75 µg/mL MH-treated fronds possessed more starch and big starch granules than that of the control. No significant difference for both in the photosynthetic pigment content and the chlorophyll fluorescence parameters of PII was found. Differentially expressed transcripts were analyzed in S. polyrrhiza 7498 after 75 µg/mL MH treatment. The results showed that the expression of some genes related to auxin response reaction was down-regulated; while, expression of some genes involved in carbon fixation, C4 pathway of photosynthesis, starch biosynthesis and ABA signal transduction pathway was up-regulated. Conclusion The results provide novel insights into the underlying mechanisms of growth inhibition and starch accumulation by MH treatment, and provide a selective way for the improvement of starch production in duckweed.

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A novel mechanism of Ha-ras oncogene action: regulation of fibronectin mRNA levels by a nuclear posttranscriptional event

Molecular and Cellular Biology ◽

10.1128/mcb.14.5.3085-3093.1994 ◽

1994 ◽

Vol 14 (5) ◽

pp. 3085-3093

Author(s):

L A Chandler ◽

C P Ehretsmann ◽

S Bourgeois

Keyword(s):

Posttranscriptional Regulation ◽

Tail Length ◽

Common Mechanism ◽

Osteosarcoma Cell ◽

Mrna Levels ◽

Ras Oncogene ◽

Down Regulation ◽

Regulate Gene Expression ◽

Protein Levels ◽

Human Osteosarcoma Cell

Although loss of cell surface fibronectin (FN) is a hallmark of many oncogenically transformed cells, the mechanisms responsible for this phenomenon remain poorly understood. The present study utilized the nontumorigenic human osteosarcoma cell line TE-85 to investigate the effects of induced Ha-ras oncogene expression on FN biosynthesis. TE-85 cells were stably transfected with metallothionein-Ha-ras fusion genes, and the effects of metal-induced ras expression on FN biosynthesis were determined. Induction of the ras oncogene, but not proto-oncogene, was accompanied by a decrease in total FN mRNA and protein levels. Transfection experiments indicated that these oncogene effects were not due to reduced FN promoter activity, suggesting that a posttranscriptional mechanism was involved. The most common mechanism of posttranscriptional regulation affects cytoplasmic mRNA stability. However, in this study the down-regulation of FN was identified as a nuclear event. A component of the ras effect was due to a mechanism affecting accumulation of processed nuclear FN RNA. Mechanisms that would generate such an effect include altered RNA processing and altered stability of the processed message in the nucleus. There was no effect of ras on FN mRNA poly(A) tail length or site of polyadenylation. There was also no evidence for altered splicing at the ED-B domain of FN mRNA. This demonstration of nuclear posttranscriptional down-regulation of FN by the Ha-ras oncogene identifies a new level at which ras oncoproteins can regulate gene expression and thus contribute to development of the malignant phenotype.

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Interferon-gamma downregulates CFTR gene expression in epithelial cells

AJP Cell Physiology ◽

10.1152/ajpcell.1994.267.5.c1398 ◽

1994 ◽

Vol 267 (5) ◽

pp. C1398-C1404 ◽

Cited By ~ 75

Author(s):

F. Besancon ◽

G. Przewlocki ◽

I. Baro ◽

A. S. Hongre ◽

D. Escande ◽

...

Keyword(s):

Gene Expression ◽

Interferon Gamma ◽

Posttranscriptional Regulation ◽

Bacterial Infections ◽

Cftr Gene ◽

Mrna Levels ◽

Dependent Manner ◽

Necrosis Factor Alpha ◽

Ifn Gamma ◽

Cl Transport

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, resulting in defective transepithelial Cl- transport. The regulation of CF gene expression is not fully understood. We report that interferon-gamma (IFN-gamma), but not IFN-alpha or -beta, downregulates CFTR mRNA levels in two colon-derived epithelial cell lines, HT-29 and T84, in a time- and concentration (from 0.1 IU/ml)-dependent manner. IFN-gamma has no effect on the transcription rate of the CFTR gene but reduces CFTR mRNA half-life, indicating that it exerts a posttranscriptional regulation of CFTR expression, at least partly, through destabilization of the transcripts. Cells treated with IFN-gamma contain subnormal amounts of 165-kDa CFTR protein. Assays of adenosine 3',5'-cyclic monophosphate-stimulated 36Cl- efflux and whole cell currents show that CFTR function is diminished in IFN-gamma-treated cells. IFN-gamma and tumor necrosis factor-alpha synergistically reduce CFTR gene expression. Our results suggest that production of these cytokines in response to bacterial infections and inflammatory disorders may alter transmembrane Cl- transport.

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