New insights into the role of cyanide in the promotion of seed germination in tomato

Abstract Background Cyanide is a natural metabolite that exists widely in plants, and it is speculated to be involved in the regulation of various growth and development processes of plants in addition to being regarded as toxic waste. Previous studies have shown that exogenous cyanide treatment helps to improve seed germination, but the mechanism is still unclear. In this study, tomato (Solanum lycopersicum cv. Alisa Craig) was used as the material, and the effects of cyanide pretreatment at different concentrations on tomato seed germination were investigated. Results The results showed that exogenous application of a lower concentration of cyanide (10 μmol/L KCN) for 12 h strongly increased the tomato seed germination rate. RNA-Seq showed that compared with the control, a total of 15,418 differentially expressed genes (P<0.05) were obtained after pretreatment with KCN for 12 h, and in the next 12 h, a total of 13,425 differentially expressed genes (P<0.05) were regulated. GO and KEGG analyses demonstrated that exogenous KCN pretreatment was involved in regulating the expression (mainly downregulation) of seed storage proteins, thereby accelerating the degradation of stored proteins for seed germination. In addition, KCN pretreatment was also involved in stimulating glycolysis, the TCA cycle and oxidative phosphorylation. Notably, it is shown that KCN acted on the regulation of plant hormone biosynthesis and perception, i.e., down-regulated the gene expression of ABA biosynthesis and signal transduction, but up-regulated the expression of genes related to GA biosynthesis and response. Consistent with this, plant hormone measurements confirmed that the levels of ABA were reduced, but GA levels were induced after pretreatment with KCN. Conclusion These findings provide new insights into the regulation of seed germination by cyanide, that is cyanide-mediated seed germination occurs in a time- and dose-dependent manner, and is related to the mobilization of energy metabolism and the regulation of some plant hormone signals.

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Dihydroartemisinin Inhibits Proliferation and Induces Apoptosis of Human Hepatocellular Carcinoma Cell by Upregulating Tumor Necrosis Factor via JNK/NF-κB Pathways

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2019/9581327 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Long Wu ◽

Yanlei Cheng ◽

Junjian Deng ◽

Weiping Tao ◽

Junjie Ye

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Proliferation ◽

Differentially Expressed Genes ◽

Carcinoma Cell ◽

Expression Profiles ◽

Human Hepatocellular Carcinoma ◽

Differentially Expressed ◽

Venn Diagram ◽

Dependent Manner ◽

Hepatocellular Carcinoma Cell

Background. Dihydroartemisinin (DHA) is a predominant compound in Artemisia annua L., and it has been shown to inhibit tumorigenesis. Methods. In this study, the antitumor potential of DHA was investigated in the MHCC97-L hepatocellular carcinoma cell line. Cells were treated at various concentrations of DHA, and then the cell cycle, viability, and DNA synthesis were measured to evaluate cell proliferation. Furthermore, the expression of genes and proteins related to proliferation and apoptosis was measured to determine the effects of DHA. Finally, the mechanism was investigated using RNA-sequencing to identify differentially expressed genes and signaling pathways, and JNK/NF-κB pathways were evaluated with Western blotting. Results. Cells were treated with a concentration range of DHA from 1 to 100 μM, and cell proliferation was suppressed in a dose-dependent manner. In addition, the genes and proteins involved in typical cellular functions of MHCC97-L cells were significantly inhibited. DHA treatment downregulated the angiogenic gene ANGPTL2 and the cell proliferation genes CCND1, E2F1, PCNA, and BCL2. DHA treatment significantly upregulated the apoptotic genes CASP3, CASP8, CASP9, and TNF. Global gene expression profiles identified 2064 differentially expressed genes (DEGs). Among them, 744 were upregulated and 1320 were downregulated. Furthermore, MAPK, NF-kappa B, and TNF pathways were enriched based on the DEGs, and the consensus DEG was identified as TNF using a Venn diagram of those pathways. DHA promoted phosphorylation of JNK, inhibited nuclear p65, and then significantly induced TNF-α synthesis. Conclusion. DHA inhibited cell proliferation and induced apoptosis in human hepatocellular carcinoma cells by upregulating TNF expression via JNK/NF-κB pathways.

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Detrimental Effects of Blood Meal and Feather Meal on Tomato (Solanum lycopersicon L.) Seed Germination

HortScience ◽

10.21273/hortsci11192-16 ◽

2017 ◽

Vol 52 (1) ◽

pp. 138-141 ◽

Cited By ~ 2

Author(s):

Juan Carlos Diaz-Perez ◽

W. Keith Jenkins ◽

Dharmalingam Pitchay ◽

Gunawati Gunawan

Keyword(s):

Seed Germination ◽

Blood Meal ◽

Germination Rate ◽

Ammonia Concentration ◽

Organic Fertilizers ◽

Organic Substrates ◽

Limited Information ◽

Feather Meal ◽

Tomato Seed ◽

N Concentration

There is limited information on the effect of organic fertilizers on seed germination and subsequent transplant growth. The objective of this study was to determine the effects of application rate of blood meal (BM) and feather meal (FM) fertilizers on germination of tomato seeds. Both organic fertilizers were applied as amendments to peat-based organic substrates at rates ranging from 0 to over 50 g·kg−1 N. Tomato ‘Brandywine’ seed were sown in trays. Seed germination was recorded daily until the germination percentage remained unchanged. Ammonia concentration in the substrates (Pro-Mix and Miracle-Gro) increased with increasing rate of substrate N concentration. Ammonia concentration also increased with increasing time after incorporation of BM and FM reaching maximum values (16 ppm) at day 9. Tomato seed germination was little affected at BM and FM rates lower than ≈3 g·kg−1 N (4% w/w for BM or FM), but declined above 3 g·kg−1 N reaching 0% germination rate at ≈14 g·kg−1 N for both BM and FM. Substrates pH was 5.9 in the absence of BM or FM and increased to about pH 7 with addition of low rates of BM (2.7 g·kg−1 N) and FM (2.6 g·kg−1 N). Substrate electrical conductivity (EC) increased with increasing substrate N concentration as supplied by BM and FM; FM, however, had a stronger effect on increasing EC compared with BM. In conclusion, BM and FM had inhibitory effects on tomato seed germination when applied at more than 3 g·kg−1 N (4% w/w for BM or FM). High ammonia concentration in the substrates for the first 2 weeks after incorporation of BM or FM likely caused, at least partially, inhibition of tomato seed germination. Thus, substrate mixed with BM or FM should be allowed to incubate for at least 2 weeks before planting tomato seed.

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Identification and fine mapping of a novel qGR6.2 locus controlling rice salt tolerance during seed germination

10.21203/rs.3.rs-24631/v1 ◽

2020 ◽

Author(s):

Peng Zeng ◽

Peiwen Zhu ◽

Luofeng Qian ◽

Xumei Qian ◽

Yuxin Mi ◽

...

Keyword(s):

Salt Tolerance ◽

Seed Germination ◽

Candidate Genes ◽

Fine Mapping ◽

Developmental Stages ◽

Indica Rice ◽

Germination Rate ◽

Differentially Expressed ◽

Germination Ability ◽

Germination Traits

Abstract Background Rice growth is frequently affected by salinity. When rice plants are exposed to high salinity, seed germination and seedling establishment are significantly inhibited. In particular, with the promotion of rice direct-seeding in Asia, improving rice salt tolerance during seed germination is of strong importance for rice breeding. Results In this study, we found that the indica rice landrace Wujiaozhan (WJZ) showed a high capability of seed germination under both water (H 2 O) and salt (NaCl) conditions, particularly under high salt stress. The BC 1 F 2 population produced by crossing WJZ with japonica Nipponbare (Nip) was used to evaluate the germination traits under water (H 2 O) and salt (300 mM NaCl) conditions using germination rate (GR) and germination index (GI). A total of 13 quantitative trait loci (QTLs) were identified, including eight QTLs of GR, two QTLs of GI under H 2 O conditions, six QTLs of GR, and three QTLs of GI under 300 mM NaCl conditions. Six QTLs ( qGR6.1 , qGR8.1 , qGR8.2 , qGR10.1 , qGR10.2 and qGI10.1 ) contributed to GR under both H 2 O and 300 mM NaCl conditions. Three QTLs ( qGR6.2 , qGR10.1 and qGR10.2 ) under 300 mM NaCl conditions were identified at different time points of seed germination and shared the same region with qGI6 , qGI10.1 and qGI10.2 for GI. These QTLs could be used to improve seed germination ability via marker-assisted selection (MAS). One major effective salt-tolerance-specific QTL, qGR6.2, on chromosome 6 was further confirmed via the BC 2 F 2 population, which explained more than 20% of the phenotypic variation. Fine mapping results showed that qGR6.2 was narrowed to a 65.9-kb region between the Z654 and Z619 molecular markers, with eleven candidate genes being predicted. Based on the microarray database, there were high transcript abundances of six genes ( LOC_Os06g10650 , LOC_Os06g10660 , LOC_Os06g10690 , LOC_Os06g10710 , LOC_Os06g10730 and LOC_Os06g10750 ) at all developmental stages, and only LOC_Os06g10750 was differentially expressed after salt incubation. RT-qPCR showed that two genes ( LOC_Os06g10650 and LOC_Os06g10750 ) were significantly differentially expressed at 300 mM NaCl during seed germination. This result suggested that LOC_Os06g10650 and LOC_Os06g10750 might be the causal candidate genes for the major effective salt-tolerance-specific QTL qGR6.2 identified in WJZ, which may facilitate map-based cloning and help to elucidate the molecular mechanism underlying salt tolerance during seed germination. Conclusions In our study, we identified 13 QTLs from indica landrace WJZ that confer seed germination traits under water and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was confirmed and fine mapped to a 65.9-kb region flanked by the Z654 and Z619 markers. Our results provide information on the genetic basis of improving salt tolerance during seed germination by MAS.

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Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

BMC Genomics ◽

10.1186/s12864-019-6201-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Lihang Qiu ◽

Rongfa Chen ◽

Yegeng Fan ◽

Xing Huang ◽

Hanmin Luo ◽

...

Keyword(s):

Signal Transduction ◽

Nitrogen Metabolism ◽

Differentially Expressed Genes ◽

Small Rna ◽

Plant Hormone ◽

Expression Profiles ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Internode Elongation ◽

Mirna Regulation

Abstract Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

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Multiomics Combined Analysis of Low-Phosphorus and Drought Stresses in Lotus Japonicus

10.21203/rs.3.rs-942639/v2 ◽

2021 ◽

Author(s):

Ma Peijie+ ◽

Li Yajiao+ ◽

Shu Jianhong ◽

Wang Ziyuan ◽

Chen Xi ◽

...

Keyword(s):

Drought Stress ◽

Differentially Expressed Genes ◽

Plant Hormone ◽

Signal Transmission ◽

Lotus Japonicus ◽

Sucrose Metabolism ◽

Differentially Expressed ◽

Kegg Pathways ◽

Low Phosphorus ◽

Transmission Pathways

Abstract BackgroundLotus japonicus is a perennial herb in Leguminosae. It is a good feed source and improves soil. It is also an excellent honey source and medicinal plant. Low-phosphorus and drought stresses are among the main abiotic stress factors limiting the production of pulse roots. MethodsIn this experiment, the effects of low-phosphorus and drought stresses on Baimai roots were analyzed under three treatments: control (zl1), low-phosphorus stress (zl2) and drought stress (zl3). Results A total of 2176, 3026 and 2980 differentially expressed genes were screened in zl1 vs. zl2, zl1 vs. zl3 and zl2 vs. zl3, respectively. The differentially expressed genes were enriched in functions related to cells, membranes, ion binding, enzyme activity and resistance to low-phosphorus and drought stresses. The enriched KEGG pathways included the MAPK signaling pathway-plant, flavor biosynthesis, starch and sucrose metabolism and plant hormone signal transmission. In particular, a large number of differentially expressed genes were enriched in the response to plant hormone signal transmission pathways among different treatments, and gene expression changes were analyzed. In addition, the differentially expressed genes identified under drought stress and the phase response genes identified under osmotic stress were upregulated. Differential metabolites were mainly enriched in the important metabolic pathways of flavonoid biosynthesis, arginine and proline metabolism and starch and sucrose metabolism. Differentially expressed proteins were mainly enriched in GO terms related to cell, membrane, ion binding and enzyme activity functions, and the main enriched KEGG pathways included the ribosome, starch and sucrose metabolism and plant hormone signal transmission pathways. ConclusionIn conclusion, these results of transcriptome, metabolome and proteome sequencing are helpful for understanding the response mechanisms, gene changes, metabolite changes and protein changes in Baimai roots under low-phosphorus and drought stress conditions to lay a foundation for future research on Lotus japonicus.

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Common QTL Affect the Rate of Tomato Seed Germination under Different Stress and Nonstress Conditions

International Journal of Plant Genomics ◽

10.1155/2007/97386 ◽

2007 ◽

Vol 2007 ◽

pp. 1-10 ◽

Cited By ~ 19

Author(s):

Majid R. Foolad ◽

Prakash Subbiah ◽

Liping Zhang

Keyword(s):

Seed Germination ◽

Germination Rate ◽

Wild Accession ◽

Tomato Seed ◽

Physiological Mechanisms ◽

Related Condition ◽

Common Qtl ◽

Salt And Drought Stress ◽

Molecular Marker Analysis ◽

Germinating Seeds

The purpose of this study was to determine whether the rates of tomato seed germination under different stress and nonstress conditions were under common genetic controls by examining quantitative trait loci (QTL) affecting such traits. Seeds of BC1 progeny of a cross between a slow-germinating tomato breeding line and a rapid-germinating tomato wild accession were evaluated for germination under nonstress as well as cold, salt, and drought stress conditions. In each treatment, the most rapidly-germinating seeds were selected, grown to maturity, and subjected to molecular marker analysis. A selective genotyping approach detected between 6 and 9 QTL affecting germination rate under each of the four conditions, with a total of 14 QTL identified. Ten QTL affected germination rate under 2 or 3 conditions, which were considered germination-related common QTL. Four QTL affected germination rate only in one treatment, which were considered germination-related, condition-specific QTL . The results indicated that mostly the same QTL affected seed germination under different stress and nonstress conditions, supporting a previous suggestion that similar physiological mechanisms contribute to rapid seed germination under different conditions. Marker-assisted selection for the common QTL may result in progeny with rapid seed germinability under different conditions.

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Identifying the p65-Dependent Effect of Sulforaphene on Esophageal Squamous Cell Carcinoma Progression via Bioinformatics Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms22010060 ◽

2020 ◽

Vol 22 (1) ◽

pp. 60

Author(s):

Sichong Han ◽

Zhe Wang ◽

Jining Liu ◽

Qipeng Yuan

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Differentially Expressed Genes ◽

Squamous Cell ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Differentially Expressed ◽

Dependent Manner

Understanding the mechanism by which sulforaphene (SFE) affects esophageal squamous cell carcinoma (ESCC) contributes to the application of this isothiocyanate as a chemotherapeutic agent. Thus, we attempted to investigate SFE regulation of ESCC characteristics more deeply. We performed gene set enrichment analysis (GSEA) on microarray data of SFE-treated ESCC cells and found that differentially expressed genes are enriched in TNFα_Signaling_via_the_NFκB_Pathway. Coupled with the expression profile data from the GSE20347 and GSE75241 datasets, we narrowed the set to 8 genes, 4 of which (C-X-C motif chemokine ligand 10 (CXCL10), TNF alpha induced protein 3 (TNFAIP3), inhibin subunit beta A (INHBA), and plasminogen activator, urokinase (PLAU)) were verified as the targets of SFE. RNA-sequence (RNA-seq) data of 182 ESCC samples from The Cancer Genome Atlas (TCGA) were grouped into two phenotypes for GSEA according to the expression of CXCL10, TNFAIP3, INHBA, and PLAU. The enrichment results proved that they were all involved in the NFκB pathway. ChIP-seq analyses obtained from the Cistrome database indicated that NFκB-p65 is likely to control the transcription of CXCL10, TNFAIP3, INHBA, and PLAU, and considering TNFAIP3 and PLAU are the most significantly differentially expressed genes, we used chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) to verify the regulation of p65 on their expression. The results demonstrated that SFE suppresses ESCC progression by down-regulating TNFAIP3 and PLAU expression in a p65-dependent manner.

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Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

Biochemistry Research International ◽

10.1155/2016/1049462 ◽

2016 ◽

Vol 2016 ◽

pp. 1-6 ◽

Cited By ~ 4

Author(s):

Pramod Kumar Singh ◽

Nidhi Shrivastava ◽

Krishna Chaturvedi ◽

Bechan Sharma ◽

Sameer S. Bhagyawant

Keyword(s):

Mass Spectrometry ◽

Storage Proteins ◽

Seed Storage Protein ◽

Expression Patterns ◽

Seed Storage ◽

Seed Storage Proteins ◽

Differentially Expressed ◽

2D Electrophoresis ◽

Differentially Expressed Proteins ◽

Amino Acid Homology

Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins withArabidopsis thaliana.

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Identification And Validation of A Cigarette Smoke-Related Five-Gene Signature As A Prognostic Biomarker In Kidney Renal Clear Cell Carcinoma

10.21203/rs.3.rs-593776/v1 ◽

2021 ◽

Author(s):

Yefei Huang ◽

Qinzhi Wang ◽

Yu Tang ◽

Zixuan Liu ◽

Guixiang Sun ◽

...

Keyword(s):

Cell Carcinoma ◽

Cigarette Smoke ◽

Differentially Expressed Genes ◽

Clear Cell ◽

Clear Cell Carcinoma ◽

Gene Signature ◽

Renal Clear Cell Carcinoma ◽

Differentially Expressed ◽

Dependent Manner ◽

Rna Seq

Abstract Cigarette smoking greatly promotes the progression of kidney renal clear cell carcinoma (KIRC), however, the underlying molecular events has not been fully established. In this study, RCC cells were exposed to the tobacco specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, nicotine-derived nitrosamine ketone) for 120 days, and then the soft agar colony formation, wound healing and transwell assays were used to explore characteristics of RCC cells. RNA-seq was used to explore differentially expressed genes. We found that NNK promoted RCC cell growth and migration in a dose-dependent manner, and RNA-seq explored 14 differentially expressed genes. In TCGA-KIRC cohort, Lasso regression and multivariate COX regression models screened and constructed a five-gene signature containing ANKRD1, CYB5A, ECHDC3, MT1E, and AKT1S1. This novel gene signature significantly associated with TNM stage, invasion depth, metastasis, and tumor grade. Moreover, when compared with individual genes, the gene signature contained a higher hazard ratio and therefore had a more powerful value for the prognosis of KIRC. A nomogram was also developed based on clinical features and the gene signature, which showed good application. Finally, AKT1S1, the most crucial component of the gene signature, was significantly induced after NNK exposure and its related AKT-mTOR signaling pathway was dramatically activated. Our findings supported that NNK exposure would promote the KIRC progression, and the novel cigarette smoke-related five-gene signature might serve as a highly efficient biomarker to identify progression of KIRC patients, AKT1S1 might play an important role in cigarette smoke exposure-induced KIRC progression.

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