scholarly journals Changes in Fruit pigment accumulation, chloroplast development, and Transcriptome analysis in the CRISPR/Cas9-Mediated Knockout of Stay-green 1 (slsgr1) Mutant

2021 ◽  
Author(s):  
Liqun Ma ◽  
Ni Zeng ◽  
Ke Cheng ◽  
Jinyan Li ◽  
Keru Wang ◽  
...  
Keyword(s):  
Color Change ◽  
Tomato Fruit ◽  
Carotenoid Biosynthesis ◽  
Carotenoid Content ◽  
Rna Seq ◽  
Loss Of Function ◽  
Stay Green ◽  
Pigment Accumulation ◽  
Brown Color

Abstract The tomato fruit of green-flesh (gf) mutant ripen to a muddy brown color and has been demonstrated previously to be a loss-of-function mutant. Here, we provide more evidence to support this view that SlSGR1 involved in color change in ripening tomato fruits. Knocking out SlSGR1 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy showed obviously a muddy brown color with significantly higher chlorophyll and carotenoid content compared with WT fruits. To further verify the role of SlSGR1 in fruit color change, we performed RNA-seq analysis, where a total of 354 differentially expressed genes (124/230 down-/upregulated) were identified between WT and slsgr1. Additionally, the expression of numerous genes associated with photosynthesis and chloroplast function changed significantly when SlSGR1 was knocked out. Taken together, these results indicate that SlSGR1 is involved color change in ripening fruit via chlorophyll degradation and carotenoid biosynthesis.

scholarly journals MBRS-17. EXAMINING THE ROLE OF LHX9 IN GROUP 3 MEDULLOBLASTOMA

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii401-iii401
Author(s):  
Sarah Injac ◽  
L Frank Huang ◽  
Stephen Mack ◽  
Frank Braun ◽  
Yuchen Du ◽  
...  
Keyword(s):  
Drug Repositioning ◽  
Single Agent ◽  
Xenograft Model ◽  
Cell Killing ◽  
Rna Seq ◽  
Loss Of Function ◽  
Novel Treatments ◽  
Novel Approach ◽  
Group 3

Abstract Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Despite major advances in our understanding of the biology of MB, novel treatments remain urgently needed. Using a chemical-genomics driven drug repositioning strategy, we identified the cardiac glycoside family of compounds as potential treatments for Group 3 MB. We subsequently demonstrated that single-agent treatment with digoxin prolongs survival in a patient-derived xenograft model (PDOX) of Group 3 MB to a degree comparable to radiation therapy, a mainstay in the treatment of MB. Finally, we examined the mechanism of digoxin-mediated cell killing using RNA-seq. This work identified LHX9, a member of the LIM homeobox family of transcription factors, as the gene most significantly down-regulated following treatment (Huang and Injac et al, Sci Trans Medicine, 2018). Homologs of LHX9 play key roles in cerebellar development via spatially and temporally restricted expression and LHX9 has been proposed as a core transcription factor (TF) in the regulatory circuitry of Group 3 tumors. Loss of function of other core TFs has been shown to impact MB growth. The role of LHX9 in MB, however, has not been previously experimentally evaluated. We now report that knockdown of LHX9 in MB-derived cell lines results in marked growth inhibition raising the possibility that loss of LHX9 plays a major role in digoxin-mediated cell killing and that LHX9 represents a key dependency required for the growth of Group 3 MB. Clinical targeting of core TFs would represent a novel approach to targeting this devastating disease.

scholarly journals Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

2018 ◽  
Vol 19 (12) ◽  
pp. 4006 ◽  
Author(s):  
Xi Li ◽  
Dongqin Tang ◽  
Hui Du ◽  
Yimin Shi
Keyword(s):  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Carotenoid Content ◽  
Rna Seq ◽  
Color Formation ◽  
Light Yellow ◽  
Color Fading ◽  
Narcissus Pseudonarcissus ◽  
Bulbous Plant ◽  
Β Carotene

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

scholarly journals Transcriptome Analysis of Orange Head Chinese Cabbage (Brassica rapaL. ssp.pekinensis) and Molecular Marker Development

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Jingjuan Li ◽  
Yihui Zhang ◽  
Qian Ding ◽  
Huayin Li ◽  
Lifeng Liu ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Carotenoid Biosynthesis ◽  
Underlying Mechanism ◽  
Indel Marker ◽  
Carotenoid Content ◽  
Nucleotide Polymorphisms ◽  
Visual Appearance ◽  
Carotenoid Biosynthesis Pathway ◽  
Molecular Marker Development ◽  
Pigment Accumulation

Due to the visual appearance and high carotenoid content, orange inner leaves are a desirable trait for the Chinese cabbage. To understand the molecular mechanism underlying the formation of orange inner leaves, theBrCRTISO(Bra031539) gene, as theBr-orcandidate gene, was analyzed among the white and orange varieties, and 7 single nucleotide polymorphisms (SNPs) were identified. However, only one SNP (C952to T952) altered the amino acid sequence, resulting in a mutation from Leu318to Phe318in the orange varieties. Additionally, we analyzed differentially expressed genes (DEGs) between the orange and white F2individuals (14-401 × 14-490) and found four downregulated genes were involved in the carotenoid biosynthesis pathway, which may lead to the accumulation of prolycopene and other carotenoid pigments in the orange inner leaves. In addition, we developed a novel InDel marker in the first intron, which cosegregates with the phenotypes of orange color inner leaves. In conclusion, these findings enhance our understanding of the underlying mechanism of pigment accumulation in the inner leaves of the Chinese cabbage. Additionally, the SNP (C952to T952) and the InDel marker will facilitate the marker-assisted selection during Chinese cabbage breeding.

scholarly journals Brassinosteroid signaling component SlBES1 promotes tomato fruit softening through transcriptional repression of PMEU1

2021 ◽  
Author(s):  
Haoran Liu ◽  
Lihong Liu ◽  
Dongyi Liang ◽  
Min Zhang ◽  
Chengguo Jia ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Tomato Fruit ◽  
Fruit Softening ◽  
Loss Of Function ◽  
Postharvest Storage ◽  
Nutrition Quality ◽  
Transcriptional Inhibition ◽  
Tomato Fruit Ripening ◽  
Brassinosteroid Signaling

ABSTRACTFirmness is one of the most important factors that affect postharvest properties of tomato fruit. However, the regulatory mechanism underlying firmness formation in tomato fruit is poorly understood. Here, we report a novel role of SlBES1, a transcriptional factor (TF) mediating brassinosteroid (BR) signaling, in tomato fruit softening. We first found that SlBES1 promotes fruit softening during tomato fruit ripening and postharvest storage. RNA-seq analysis suggested that PMEU1, which encodes a pectin de-methylesterification protein, might participate in SlBES1-mediated fruit softening. Biochemical and immunofluorescence assays in SlBES1 transgenic fruits indicated that SlBES1 inhibited PMEU1-related pectin de-methylesterification. Further molecular and genetic evidence verified that SlBES1 directly binds to the E-box in the promoter of PMEU1 to repress its expression, leading to the softening of the tomato fruits. Loss-of-function SlBES1 mutant generated by CRISPR/cas9 showed firmer fruits and longer shelf life during postharvest storage without the color, size and nutritional quality alteration. Collectively, our results indicated the potential of manipulating SlBES1 to regulate fruit firmness via transcriptional inhibition of PMEU1 without negative consequence on visual and nutrition quality.

scholarly journals Effect of Fluridone on Some Physiological and Qualitative Features of Ripening Tomato Fruit

2017 ◽  
Vol 59 (2) ◽  
pp. 41-49
Author(s):  
Justyna Góraj-Koniarska ◽  
Marian Saniewski ◽  
Ryszard Kosson ◽  
Wiesław Wiczkowski ◽  
Marcin Horbowicz
Keyword(s):  
Ethylene Production ◽  
Tomato Fruit ◽  
Carotenoid Biosynthesis ◽  
Tomato Fruits ◽  
Tomato Plants ◽  
Tomato Fruit Ripening ◽  
Chlorophyll Production ◽  
Carotenoid Biosynthesis Pathway ◽  
Metabolic Significance

AbstractIn tomato fruits, chlorophyll, lycopene and ß-carotene are mostly responsible for the color. During ripening of tomato fruits, the color of the pericarp changes from green to red as chlorophyll is degraded and carotenoids accumulate. These changes are associated with an increase in respiration and ethylene production. Carotenoid biosynthesis pathway in plants can be disturbed by herbicide fluridone (1-methyl-3-phenyl-5-[3-trifluoromethyl(phenyl)]- 4(1H)-pyridinone), which inhibits the activity of phytoene desaturase, an enzyme responsible for conversion of phytoene to phytofluene. Fluridone is also used as an inhibitor of biosynthesis of abscisic acid (ABA) and strigolactones, and it reduces chlorophyll production in plants. In our research we studied the effect of fluridone on some physiological parameters, such as color, firmness, ethylene production, lycopene and chlorophyll content during ripening of the tomato fruit. Tomato plants cv. Altadena (Syngenta) were cultivated in a greenhouse in controlled temperature and both immature and mature fruits were used for the experiments, performed between August and November 2016. Fluridone at concentrations of 0.1% and 1.0% in lanolin paste was applied as a 2-3 mm stripe from the top to the base of tomato fruits, and as a control a stripe of lanolin was applied in the same way on the opposite side of the fruits. Fluridone at a concentration of 1.0% greatly inhibited lycopene accumulation in the pericarp of tomato fruits from the treated side. The measurements of fruit firmness have shown no significant differences between firmness of the part of the tomato fruits treated with fluridone, and the non-treated ones. Tomato fruits treated with fluridone produced amounts of ethylene similar to those found in control tissues on the opposite side of the same fruit. Fluridone delayed chlorophyll degradation in tomato fruits. The metabolic significance of these findings is discussed with the role of carotenogenesis inhibition in tomato fruit ripening.

scholarly journals Carotenoid biosynthesis during tomato fruit development: regulatory role of 1-deoxy-D-xylulose 5-phosphate synthase

2000 ◽  
Vol 22 (6) ◽  
pp. 503-513 ◽  
Author(s):  
Luisa Maria Lois ◽  
Manuel Rodriguez-Concepcion ◽  
Francesca Gallego ◽  
Narciso Campos ◽  
Albert Boronat
Keyword(s):  
Fruit Development ◽  
Tomato Fruit ◽  
Carotenoid Biosynthesis ◽  
Regulatory Role ◽  
Phosphate Synthase

scholarly journals Periostin loss-of-function protects mice from post-traumatic and age-related osteoarthritis

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Mukundan Attur ◽  
Xin Duan ◽  
Lei Cai ◽  
Tianzhen Han ◽  
Weili Zhang ◽  
...  
Keyword(s):  
Serum Levels ◽  
Cartilage Degeneration ◽  
Rna Seq ◽  
Loss Of Function ◽  
Age Related ◽  
Synovial Lining Cell ◽  
Bone Changes ◽  
Post Traumatic ◽  
Old Mice

Abstract Background Elevated levels of periostin (Postn) in the cartilage and bone are associated with osteoarthritis (OA). However, it remains unknown whether Postn loss-of-function can delay or prevent the development of OA. In this study, we sought to better understand the role of Postn in OA development and assessed the functional impact of Postn deficiency on post-traumatic and age-related OA in mice. Methods The effects of Postn deficiency were studied in two murine experimental OA models using Postn−/− (n = 32) and littermate wild-type (wt) mice (n = 36). Post-traumatic OA was induced by destabilization of the medial meniscus (DMM) in 10-week-old mice (n = 20); age-related OA was analyzed in 24-month-old mice (n = 13). Cartilage degeneration was assessed histologically using the OARSI scoring system, and synovitis was evaluated by measuring the synovial lining cell layer and the cells density in the synovial stroma. Bone changes were measured by μCT analysis. Serum levels of Postn were determined by ELISA. Expression of Postn and collagenase-3 (MMP-13) was measured by immunostaining. RNA-seq was performed on chondrocytes isolated from 21-day old Postn−/− (n = 3) and wt mice (n = 3) to discover genes and pathways altered by Postn knockout. Results Postn−/− mice exhibited significantly reduced cartilage degeneration and OARSI score relative to wt mice in post-traumatic OA after 8 weeks (maximum: 2.37 ± 0.74 vs. 4.00 ± 1.20, P = 0.011; summed: 9.31 ± 2.52 vs. 21.44 ± 6.01, P = 0.0002) and spontaneous OA (maximum: 1.93 ± 0.45 vs. 3.58 ± 1.16, P = 0.014; summed: 6.14 ± 1.57 vs. 11.50 ± 3.02, P = 0.003). Synovitis was significantly lower in Postn−/− mice than wt only in the DMM model (1.88 ± 1.01 vs. 3.17 ± 0.63; P = 0.039). Postn−/− mice also showed lower trabecular bone parameters such as BV/TV, vBMD, Tb.Th, and Tb.N and high Tb. Sp in both models. Postn−/− mice had negligible levels of serum Postn compared with wt. Immunofluorescent studies of cartilage indicated that Postn−/− mice expressed lower MMP-13 levels than wt mice. RNA-seq revealed that cell-cell-adhesion and cell-differentiation processes were enriched in Postn−/− mice, while those related to cell-cycle and DNA-repair were enriched in wt mice. Conclusions Postn deficiency protects against DMM-induced post-traumatic and age-related spontaneous OA. RNA-seq findings warrant further investigations to better understand the mechanistic role of Postn and its potential as a therapeutic target in OA.

scholarly journals KLF5-mediated EPPK1 Expression Promotes Cell Proliferation in Cervical Cancer via the P38 Signaling Pathway

2020 ◽  
Author(s):  
Zhe Pan ◽  
Xiao Liu ◽  
Quan Chang ◽  
Jin-jin Zhang ◽  
Na Hua ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Proliferation ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Immunofluorescence Staining ◽  
Rna Seq ◽  
Loss Of Function ◽  
Cytoskeleton Reorganization ◽  
Direct Binding

Abstract Background: Epiplakin1 (Eppk1) is part of the EGF signal and is involved in cytoskeleton reorganization and cell proliferation. However, the role of Eppk1 in cervical cancer remains unknown. Methods: The expression of Eppk1 and KLF5 as well as their correlation were assessed by RNA-seq, qRT-PCR, TCGA database and immunofluorescence staining. In CC cell lines, adenovirus-mediated overexpression or knockdown of KLF5 and Eppk1 as well as corresponding assessment of cell proliferation and signaling were determined by western blot and CCK8 experiments. Assays of lucifase reporter gene and CHIP were used to investigate mechanism between KLF5 and Eppk1. Results: Eppk1 expression was markedly in CC tissues and cell lines companied by KLF5 upregulation. The results of immunofluorescence staining further showed that the increased expression of Eppk1 and KLF5 correlated with progression of cervical tumorigenesis. Overexpression of KLF5 significantly increased Eppk1 expression at transcription and translation levels. Conversely, the knockdown of KLF5 by siRNA against KLF5 decreased Eppk1 expression. Mechanical studies showed that KLF5 activated Eppk1 transcription by direct binding to the Eppk1 promoter. Gain- and loss-of-function experiments showed that KLF5 promoted cell proliferation in Hela by upregulating Eppk1 expression. Moreover, KLF5-mediated the activation of EGFR and p38 signaling significantly decreased after Eppk1 knockdown companied with reduction of proliferating activity, suggesting that Eppk1 lies upstream of p38 signaling affecting cell proliferation in CC. Finally, the expression of Eppk1 positively correlated with tumor size. Conclusions: Eppk1 may be an effective therapeutic target on affecting EGFR-associated p38 signaling pathway and cell proliferation in cervical cancer.

scholarly journals KLF5-mediated Eppk1 expression promotes cell proliferation in cervical cancer via the  p38 signaling pathway

2020 ◽  
Author(s):  
Zhe Pan ◽  
Xiao Liu ◽  
Quan Chang ◽  
Jin-jin Zhang ◽  
Na Hua ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Proliferation ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Immunofluorescence Staining ◽  
Rna Seq ◽  
Loss Of Function ◽  
Cytoskeleton Reorganization ◽  
Direct Binding

Abstract Background: Epiplakin1 (Eppk1) is part of the EGF signal and is involved in cytoskeleton reorganization and cell proliferation. However, the role of Eppk1 in cervical cancer remains unknown. Objective: To determine the role of EPPK1 on cell proliferation in cervical cancer. Methods: The expression of Eppk1 and KLF5 as well as their correlation were assessed by RNA-seq, qRT-PCR, TCGA database and immunofluorescence staining. In CC cell lines, adenovirus-mediated overexpression or knockdown of KLF5 and Eppk1 as well as corresponding assessment of cell proliferation and signaling were determined by western blot and CCK8 experiments. Assays of lucifase reporter gene and CHIP were used to investigate mechanism between KLF5 and Eppk1 . Results: Eppk1 expression was markedly in CC tissues and cell lines companied by KLF5 upregulation. The results of immunofluorescence staining further showed that the increased expression of Eppk1 and KLF5 correlated with progression of cervical tumorigenesis. Overexpression of KLF5 significantly increased Eppk1 expression at transcription and translation levels. Conversely, the knockdown of KLF5 by siRNA against KLF5 decreased Eppk1 expression. Mechanical studies showed that KLF5 activated Eppk1 transcription by direct binding to the Eppk1 promoter. Gain- and loss-of-function experiments showed that KLF5 promoted cell proliferation in Hela by upregulating Eppk1 expression. Moreover, KLF5-mediated the activation of EGFR and p38 signaling significantly decreased after Eppk1 knockdown companied with reduction of proliferating activity, suggesting that Eppk1 lies upstream of p38 signaling affecting cell proliferation in CC. Finally, the expression of Eppk1 positively correlated with tumor size. Conclusions: Eppk1 may be an effective therapeutic target on affecting EGFR-associated p38 signaling pathway and cell proliferation in cervical cancer.

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