Identification of differentially expressed proteins of Arthrospira (Spirulina) plantensis-YZ under salt-stress conditions by proteomics and qRT-PCR analysis

Abstract Background Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp. in ARD was further clarified. Methods In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis. Results A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P< 0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P< 0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. Conclusions This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

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ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers

10.21203/rs.3.rs-16641/v2 ◽

2020 ◽

Author(s):

Rong Zhang ◽

Weitao Jiang ◽

Xin Liu ◽

Yanan Duan ◽

Li Xiang ◽

...

Keyword(s):

Fusarium Moniliforme ◽

Abiotic Factors ◽

Fusarium Verticillioides ◽

Protein Profile ◽

Sugar Metabolism ◽

Differentially Expressed ◽

Pcr Analysis ◽

Differentially Expressed Proteins ◽

Apple Replant Disease ◽

Qrt Pcr

Abstract Background: Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp in ARD was further clarified.Methods: In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis.Results: A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P<0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P<0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways.Conclusions: This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

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Microtubule Dynamics Plays a Vital Role in Plant Adaptation and Tolerance to Salt Stress

International Journal of Molecular Sciences ◽

10.3390/ijms22115957 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5957

Author(s):

Hyun Jin Chun ◽

Dongwon Baek ◽

Byung Jun Jin ◽

Hyun Min Cho ◽

Mi Suk Park ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Salt Stress ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Related Gene ◽

Plant Adaptation ◽

Salt Stress Response ◽

Network Analyses ◽

Cell Wall Biogenesis

Although recent studies suggest that the plant cytoskeleton is associated with plant stress responses, such as salt, cold, and drought, the molecular mechanism underlying microtubule function in plant salt stress response remains unclear. We performed a comparative proteomic analysis between control suspension-cultured cells (A0) and salt-adapted cells (A120) established from Arabidopsis root callus to investigate plant adaptation mechanisms to long-term salt stress. We identified 50 differentially expressed proteins (45 up- and 5 down-regulated proteins) in A120 cells compared with A0 cells. Gene ontology enrichment and protein network analyses indicated that differentially expressed proteins in A120 cells were strongly associated with cell structure-associated clusters, including cytoskeleton and cell wall biogenesis. Gene expression analysis revealed that expressions of cytoskeleton-related genes, such as FBA8, TUB3, TUB4, TUB7, TUB9, and ACT7, and a cell wall biogenesis-related gene, CCoAOMT1, were induced in salt-adapted A120 cells. Moreover, the loss-of-function mutant of Arabidopsis TUB9 gene, tub9, showed a hypersensitive phenotype to salt stress. Consistent overexpression of Arabidopsis TUB9 gene in rice transgenic plants enhanced tolerance to salt stress. Our results suggest that microtubules play crucial roles in plant adaptation and tolerance to salt stress. The modulation of microtubule-related gene expression can be an effective strategy for developing salt-tolerant crops.

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Circular RNA Expression Profiling Identifies Prostate Cancer- Specific circRNAs in Prostate Cancer

Cellular Physiology and Biochemistry ◽

10.1159/000494870 ◽

2018 ◽

Vol 50 (5) ◽

pp. 1903-1915 ◽

Cited By ~ 18

Author(s):

Qianlin Xia ◽

Tao Ding ◽

Guihong Zhang ◽

Zehuan Li ◽

Ling Zeng ◽

...

Keyword(s):

Prostate Cancer ◽

Polymerase Chain Reaction Analysis ◽

Circular Rna ◽

Differentially Expressed ◽

Pcr Analysis ◽

High Morbidity ◽

Qrt Pcr ◽

Diagnosis And Prognosis ◽

Novel Biomarkers ◽

Rna Expression Profiling

Background/Aims: Prostate cancer (PCa) is one of the main cancers that damage males’ health severely with high morbidity and mortality, but there is still no ideal molecular marker for the diagnosis and prognosis of prostate cancer. Methods: To determine whether the differentially expressed circRNAs in prostate cancer can serve as novel biomarkers for prostate cancer diagnosis, we screened differentially expressed circRNAs using SBC-ceRNA array in 4 pairs of prostate tumor and paracancerous tissues. A circRNA-miRNA-mRNA regulatory network for the differential circRNAs and their host genes was constructed by Cytoscape3.5.1 software. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) was performed to confirm the microarray data. Results: We found 1021 differentially expressed circRNAs in PCa tumor using SBC-ceRNA array and confirmed the expression of circ_0057558, circ_0062019 and SLC19A1 in PCa cell lines and tumor tissues through qRT-PCR analysis. We demonstrated that combination of PSA level and two differentially expressed circRNAs showed significantly increased AUC, sensitivity and specificity (0.938, 84.5% and 90.9%, respectively) than PSA alone (AUC of serum PSA was 0.854). Moreover, circ_0057558 was correlated positively with total cholesterol. The functional network of circRNA-miRNA-mRNA analysis showed that circ_0057558 and circ_0034467 regulated miR-6884, and circ_0062019 and circ_0060325 regulated miR-5008. Conclusion: Our results demonstrated that differentially expressed circRNAs (circ_0062019 and circ_0057558) and host gene SLC19A1 of circ_0062019 could be used as potential novel biomarkers for prostate cancer.

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Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon)

Plants ◽

10.3390/plants8120614 ◽

2019 ◽

Vol 8 (12) ◽

pp. 614

Author(s):

Jibiao Fan ◽

Yanhong Lou ◽

Haiyan Shi ◽

Liang Chen ◽

Liwen Cao

Keyword(s):

Leaf Senescence ◽

Plant Hormone ◽

Bioinformatics Analysis ◽

Cynodon Dactylon ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Pcr Analysis ◽

Aesthetic Quality ◽

Qrt Pcr

Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.

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Physiological and Proteomic Analyses Reveal Adaptive Mechanisms of Ryegrass (Annual vs. Perennial) Seedlings to Salt Stress

Agronomy ◽

10.3390/agronomy9120843 ◽

2019 ◽

Vol 9 (12) ◽

pp. 843 ◽

Cited By ~ 1

Author(s):

Xiaoyuan Peng ◽

Dafu Yu ◽

Junxin Yan ◽

Na Zhang ◽

Jixiang Lin ◽

...

Keyword(s):

Salt Stress ◽

Perennial Ryegrass ◽

Differentially Expressed ◽

Molecular Response ◽

Differentially Expressed Proteins ◽

Annual Ryegrass ◽

Solute Content ◽

Inorganic Ion ◽

Salt Affected Soils ◽

K Concentration

Ryegrass has a relatively high salt tolerance and is considered to be a promising species for both foraging and turf purposes in salt-affected soils in China. While annual ryegrass and perennial ryegrass are two different species, they have similar genomes. However, little is known about their physiological and molecular response mechanisms to salinity stress. Here, biomass, chlorophyll fluorescence, and inorganic ion and organic solute content were measured. 2-DE-based proteomic technology was then used to identify the differentially expressed proteins in the salt-treated seedlings. The results showed that salt stress reduced growth and photosynthesis in the seedlings of both species, but much more so in annual ryegrass. With increasing salinity, the Na+ concentration increased while the K+ concentration decreased in both species, and the sugars and proline increased as the primary organic solutes used to cope with osmotic stress. Additionally, proteomic analysis revealed 33 and 37 differentially expressed proteins in annual and perennial ryegrass, respectively. Most of the identified proteins were involved in carbohydrate and energy metabolism, photosynthesis, genetic information processes, amino acid metabolism, stress defense, and protein synthesis and folding. The results suggest that the two-ryegrass species had different physiological and proteomic responses. These findings can provide new insights into physiological mechanisms by which ryegrass species respond to salt stress.

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Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions

PeerJ ◽

10.7717/peerj.5631 ◽

2018 ◽

Vol 6 ◽

pp. e5631 ◽

Cited By ~ 14

Author(s):

Haolong Wang ◽

Haishen Wen ◽

Yun Li ◽

Kaiqiang Zhang ◽

Yang Liu

Keyword(s):

Salinity Stress ◽

Reference Genes ◽

18S Rrna ◽

Sea Bass ◽

Stress Conditions ◽

Pcr Analysis ◽

Stable Gene ◽

Qrt Pcr ◽

Lateolabrax Maculatus ◽

Suitable Reference

The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species.

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Differentially expressed proteins in canola leaf induced by salt stress- a proteomic approach

International Journal of Biosciences (IJB) ◽

10.12692/ijb/5.9.433-442 ◽

2014 ◽

Vol 5 (9) ◽

pp. 433-442

Keyword(s):

Salt Stress ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Proteomic Approach

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Differential Transcription Profiling in Bone Marrow Mononuclear Cells Between Myasthenia Gravis Patients With or Without Thymoma

10.21203/rs.3.rs-837123/v1 ◽

2021 ◽

Author(s):

Jingqun Tang ◽

Ziming Ye ◽

Yi Liu ◽

Mengxiao Zhou ◽

chao qin

Keyword(s):

Stem Cells ◽

Bone Marrow ◽

Myasthenia Gravis ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Mononuclear Cells ◽

Differentially Expressed ◽

Pcr Analysis ◽

Bone Marrow Mononuclear Cells ◽

Qrt Pcr

Abstract PurposeDefective stem cells have been recognized as being associated with autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, autoimmune cytopenias and myasthenia gravis (MG). However, the differential gene expression profile of bone marrow mononuclear cells (BMMCs) and the molecular mechanisms underlying MG pathogenesis have not been fully elucidated. Therefore, we investigated the abnormal expression and potential roles and mechanisms of mRNAs in BMMCs among patients with MG with or without thymoma.MethodsTranscription profiling of BMMCs in patients with MG without thymoma (M2) and patients with thymoma-associated MG (M1) was undertaken by using high-throughput RNA sequencing (RNA-Seq), and disease-related differentially expressed genes were validated by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsRNA-Seq demonstrated 60 significantly upregulated and 65 significantly downregulated genes in M2 compared with M1. Five disease-related differentially expressed genes were identified and validated by qRT-PCR analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to predict the functions of aberrantly expressed genes. Recombination activating 1 (RAG1), RAG2, BCL2-like 11, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and repressor element-1-silencing transcription factor might play roles in MG pathogenesis involving the primary immunodeficiency signaling pathway, signaling pathways regulating pluripotency of stem cells and forkhead box O signaling pathway.ConclusionThe aberrantly expressed genes of BMMCs in M1 or M2 patients demonstrate the underlying mechanisms governing the pathogenesis of MG.

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Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

10.21203/rs.3.rs-121953/v1 ◽

2020 ◽

Author(s):

Jingping Yuan ◽

Changwei Shen ◽

Jingjing Xin ◽

Zhenxia Li ◽

Xinzheng Li ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Expression Analysis ◽

Expression Patterns ◽

Pcr Analysis ◽

Abiotic Stress Response ◽

Element Analysis ◽

Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

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