Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development

Abstract Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, and the generation of pegs and formation of subterranean pods are essential processes in peanut reproductive development. However, little information has been reported about alternative splicing (AS) in peanut peg formation and development. Results Herein, we presented a comprehensive full-length (FL) transcriptome profiling of AS isoforms during peanut peg and early pod development. We identified 1448, 1102, 832, and 902 specific spliced transcripts in aerial pegs, subterranean pegs, subterranean unswollen pegs, and early swelling pods, respectively. A total of 184 spliced transcripts related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins were identified as possibly involved in peanut peg development. For aerial pegs, spliced transcripts we got were mainly involved in gravity stimulation and cell wall morphogenetic processes. The genes undergoing AS in subterranean peg were possibly involved in gravity stimulation, cell wall morphogenetic processes, and abiotic response. For subterranean unswollen pegs, spliced transcripts were predominantly related to the embryo development and root formation. The genes undergoing splice in early swelling pods were mainly related to ovule development, root hair cells enlargement, root apex division, and seed germination. Conclusion This study provides evidence that multiple genes are related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins undergoing AS express development-specific spliced isoforms or exhibit an obvious isoform switch during the peanut peg development. AS isoforms in subterranean pegs and pods provides valuable sources to further understand post-transcriptional regulatory mechanisms of AS in the generation of pegs and formation of subterranean pods.

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Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat

Scientific Reports ◽

10.1038/s41598-019-54315-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Yanjun Zhang ◽

Lele Wang ◽

Zhen Li ◽

Dong Chen ◽

Wenjing Han ◽

...

Keyword(s):

Alternative Splicing ◽

Molecular Mechanisms ◽

Transcriptome Profiling ◽

Hair Follicles ◽

Splicing Regulation ◽

Cashmere Goat ◽

Rna Seq ◽

Three Stages ◽

Functional Pathways ◽

First Time

AbstractThe undercoat fiber of the cashmere goat, from the secondary hair follicle (HF), possesses commercial value. However, very few studies have focused on the molecular details of primary and secondary HF initiation and development in goat embryos. In this study, skin samples at embryonic day 45, 55, and 65 (E45, E55, and E65) were collected and prepared for RNA sequencing (RNA-seq). We found that the HF probably initiated from E55 to E65 by analyzing the functional pathways of differentially expressed genes (DEGs). Most key genes in canonical signaling pathways, including WNT, TGF-β, FGF, Hedgehog, NOTCH, and other factors showed clear expression changes from E55 to E65. We, for the first time, explored alternative splicing (AS) alterations, which showed distinct patterns among these three stages. Functional pathways of AS-regulated genes showed connections to HF development. By comparing the published RNA-seq samples from the E60, E120, and newborn (NB) stages, we found the majority of WNT/β-catenin signaling genes were important in the initiation of HF development, while other factors including FOXN1, GATA3, and DLX3 may have a consistent influence on HF development. Our investigation supported the time points of embryonic HF initiation and identified genes that have potential functions of embryonic HF initiation and development. We further explored the potential regulatory roles of AS in HF initiation, which extended our knowledge about the molecular mechanisms of HF development.

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Salinity stress-induced modification of pectin activates stress signaling pathways and requires HERK/THE and FER to attenuate the response

10.1101/2020.12.18.423458 ◽

2020 ◽

Author(s):

Nora Gigli-Bisceglia ◽

Eva Van Zelm ◽

Wenying Huo ◽

Jasper Lamers ◽

Christa Testerink

Keyword(s):

Cell Wall ◽

Salt Stress ◽

Signaling Pathways ◽

Stress Responses ◽

Molecular Mechanisms ◽

Structural Integrity ◽

Marker Gene ◽

Mitogen Activated Protein Kinase ◽

Growth And Yield ◽

Receptor Like Kinase

AbstractSoil salinity is an increasing worldwide problem for agriculture, affecting plant growth and yield. In our attempt to understand the molecular mechanisms activated in response to salt in plants, we investigated the Catharanthus roseus Receptor like Kinase 1 Like (CrRLK1L) family, which contains well described sensors previously shown to be involved in maintaining and sensing the structural integrity of the cell walls. We have observed that herk1the1-4 double mutants, lacking the function of the Arabidopsis thaliana Receptor like Kinase HERKULES1 combined with a gain of function allele of THESEUS1, phenocopied the phenotypes previously reported in plants lacking FERONIA (FER) function. We report that both fer-4 and herk1the1-4 mutants respond strongly to salt application, resulting in a more intense activation of early and late stress responses. We also show that salt triggers de-methyl esterification of loosely bound pectins. These cell wall modifications might be partly responsible for the activation of the signaling pathways required to activate salt stress responses. In fact, by adding calcium chloride or by chemically inhibiting pectin methyl esterase (PME) activity we observed reduced activation of the early signaling protein Mitogen Activated Protein Kinase 6 (MPK6) as well as a reduced amplitude in salt-induced marker gene induction. We show that MPK6 is required for the full induction of the salt-induced gene expression markers we tested. However, the sodium specific root halotropism response is likely regulated by a different branch of the pathway being independent of MPK6 or calcium application but influenced by the cell wall sensors FER/HERK1/THE1-4 and PME activity. We hypothesize a model where salt-triggered modification of pectin requires the functionality of FER alone or the HERK1/THE1 combination to attenuate salt responses. Collectively, our results show the complexity of salt stress responses and salt sensing mechanisms and their connection to cell wall modifications, likely being in part responsible for the response phenotypes observed in salt treated plants.

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Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat

Biology ◽

10.3390/biology10080787 ◽

2021 ◽

Vol 10 (8) ◽

pp. 787

Author(s):

Xinbo Zhang ◽

Fujian Li ◽

Yonggang Ding ◽

Quan Ma ◽

Yuan Yi ◽

...

Keyword(s):

Molecular Mechanisms ◽

Transcriptome Profiling ◽

Gene Families ◽

Crop Productivity ◽

Application Rate ◽

Metabolic Energy ◽

Genotypic Difference ◽

Transcriptional Regulatory Mechanisms ◽

Normal Nitrogen ◽

Nitrogen Conditions

Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha−1, corresponding to 1.6 g N pot−1). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.

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Wnt/beta-catenin and PI3K/Akt/mTOR Signaling Pathways in Glioblastoma: Two Main Targets for Drug Design: A Review

Current Pharmaceutical Design ◽

10.2174/1381612826666200131100630 ◽

2020 ◽

Vol 26 (15) ◽

pp. 1729-1741 ◽

Cited By ~ 4

Author(s):

Seyed H. Shahcheraghi ◽

Venant Tchokonte-Nana ◽

Marzieh Lotfi ◽

Malihe Lotfi ◽

Ahmad Ghorbani ◽

...

Keyword(s):

Signaling Pathways ◽

Molecular Mechanisms ◽

Cellular Proliferation ◽

Chemotherapy Resistance ◽

Wnt Signaling Pathway ◽

Therapeutic Interventions ◽

Beta Catenin ◽

Clinical Prognosis ◽

Invasion And Migration ◽

And Migration

: Glioblastoma (GBM) is the most common and malignant astrocytic glioma, accounting for about 90% of all brain tumors with poor prognosis. Despite recent advances in understanding molecular mechanisms of oncogenesis and the improved neuroimaging technologies, surgery, and adjuvant treatments, the clinical prognosis of patients with GBM remains persistently unfavorable. The signaling pathways and the regulation of growth factors of glioblastoma cells are very abnormal. The various signaling pathways have been suggested to be involved in cellular proliferation, invasion, and glioma metastasis. The Wnt signaling pathway with its pleiotropic functions in neurogenesis and stem cell proliferation is implicated in various human cancers, including glioma. In addition, the PI3K/Akt/mTOR pathway is closely related to growth, metabolism, survival, angiogenesis, autophagy, and chemotherapy resistance of GBM. Understanding the mechanisms of GBM’s invasion, represented by invasion and migration, is an important tool in designing effective therapeutic interventions. This review will investigate two main signaling pathways in GBM: PI3K/Akt/mTOR and Wnt/beta-catenin signaling pathways.

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Melatonin As a Modulator of Degenerative and Regenerative Signaling Pathways in Injured Retinal Ganglion Cells

Current Pharmaceutical Design ◽

10.2174/1381612825666190829151314 ◽

2019 ◽

Vol 25 (28) ◽

pp. 3057-3073 ◽

Cited By ~ 6

Author(s):

Kobra B. Juybari ◽

Azam Hosseinzadeh ◽

Habib Ghaznavi ◽

Mahboobeh Kamali ◽

Ahad Sedaghat ◽

...

Keyword(s):

Optic Nerve ◽

Mitochondrial Dysfunction ◽

Signaling Pathways ◽

Retinal Ganglion Cells ◽

Molecular Mechanisms ◽

Nitrosative Stress ◽

Ganglion Cells ◽

Axon Growth ◽

Nerve Fibers ◽

Retinal Ganglion

Optic neuropathies refer to the dysfunction or degeneration of optic nerve fibers caused by any reasons including ischemia, inflammation, trauma, tumor, mitochondrial dysfunction, toxins, nutritional deficiency, inheritance, etc. Post-mitotic CNS neurons, including retinal ganglion cells (RGCs) intrinsically have a limited capacity for axon growth after either trauma or disease, leading to irreversible vision loss. In recent years, an increasing number of laboratory evidence has evaluated optic nerve injuries, focusing on molecular signaling pathways involved in RGC death. Trophic factor deprivation (TFD), inflammation, oxidative stress, mitochondrial dysfunction, glutamate-induced excitotoxicity, ischemia, hypoxia, etc. have been recognized as important molecular mechanisms leading to RGC apoptosis. Understanding these obstacles provides a better view to find out new strategies against retinal cell damage. Melatonin, as a wide-spectrum antioxidant and powerful freeradical scavenger, has the ability to protect RGCs or other cells against a variety of deleterious conditions such as oxidative/nitrosative stress, hypoxia/ischemia, inflammatory processes, and apoptosis. In this review, we primarily highlight the molecular regenerative and degenerative mechanisms involved in RGC survival/death and then summarize the possible protective effects of melatonin in the process of RGC death in some ocular diseases including optic neuropathies. Based on the information provided in this review, melatonin may act as a promising agent to reduce RGC death in various retinal pathologic conditions.

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The Protective Effects of Green Tea Catechins in the Management of Neurodegenerative Diseases: A Review

Current Drug Discovery Technologies ◽

10.2174/1570163815666180219115453 ◽

2019 ◽

Vol 16 (1) ◽

pp. 57-65 ◽

Cited By ~ 3

Author(s):

Tahereh Farkhondeh ◽

Hanieh Shaterzadeh Yazdi ◽

Saeed Samarghandian

Keyword(s):

Neurodegenerative Diseases ◽

Signaling Pathways ◽

Green Tea ◽

Molecular Mechanisms ◽

Main Role ◽

Related Factor ◽

Protective Effects ◽

Tea Catechins ◽

Green Tea Catechins ◽

And Control

Background: The therapeutic strategies to manage neurodegenerative diseases remain limited and it is necessary to discover new agents for their prevention and control. Oxidative stress and inflammation play a main role in the pathogenesis of neurodegenerative diseases. The aim of this study is to review the effects of green tea catechins against the Neurodegenerative Diseases. Methods: In this study, we extensively reviewed all articles on the terms of Green tea, catechins, CNS disorders, and different diseases in PubMed, Science Direct, Scopus, and Google Scholar databases between the years 1990 and 2017. Results: The present study found that catechins, the major flavonoids in green tea, are powerful antioxidants and radical scavengers which possess the potential roles in the management of neurodegenerative diseases. Catechins modulate the cellular and molecular mechanisms through the inflammation-related NF-&#954;B and the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathways. Conclusion: The findings of the present review shows catechins could be effective against neurodegenerative diseases due to their antioxidation and anti-inflammation effects and the involved biochemical pathways including Nrf2 and NF-kB signaling pathways.<P>

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The Signaling Pathways in Nitric Oxide Production by Neutrophils Exposed to N-nitrosodimethylamine

Letters in Drug Design & Discovery ◽

10.2174/1570180815666180426121503 ◽

2018 ◽

Vol 16 (2) ◽

pp. 194-199

Author(s):

Wioletta Ratajczak-Wrona ◽

Ewa Jablonska

Keyword(s):

Nitric Oxide ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Polymorphonuclear Neutrophils ◽

Microbial Pathogens ◽

Human Neutrophils ◽

No Production ◽

Oxide Synthase ◽

Inducible Nitric Oxide

Background: Polymorphonuclear neutrophils (PMNs) play a crucial role in the innate immune system’s response to microbial pathogens through the release of reactive nitrogen species, including Nitric Oxide (NO). </P><P> Methods: In neutrophils, NO is produced by the inducible Nitric Oxide Synthase (iNOS), which is regulated by various signaling pathways and transcription factors. N-nitrosodimethylamine (NDMA), a potential human carcinogen, affects immune cells. NDMA plays a major part in the growing incidence of cancers. Thanks to the increasing knowledge on the toxicological role of NDMA, the environmental factors that condition the exposure to this compound, especially its precursors- nitrates arouse wide concern. Results: In this article, we present a detailed summary of the molecular mechanisms of NDMA’s effect on the iNOS-dependent NO production in human neutrophils. Conclusion: This research contributes to a more complete understanding of the mechanisms that explain the changes that occur during nonspecific cellular responses to NDMA toxicity.

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Classic and Novel Signaling Pathways Involved in Cancer: Targeting the NF-κB and Syk Signaling Pathways

Current Stem Cell Research & Therapy ◽

10.2174/1574888x13666180723104340 ◽

2019 ◽

Vol 14 (3) ◽

pp. 219-225 ◽

Cited By ~ 6

Author(s):

Cong Tang ◽

Guodong Zhu

Keyword(s):

Cancer Therapy ◽

Tyrosine Kinase ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Therapeutic Potential ◽

Cell Receptor ◽

Transmembrane Receptors ◽

Biological Responses ◽

Different Types

The nuclear factor kappa B (NF-κB) consists of a family of transcription factors involved in the regulation of a wide variety of biological responses. Growing evidence support that NF-κB plays a major role in oncogenesis as well as its well-known function in the regulation of immune responses and inflammation. Therefore, we made a review of the diverse molecular mechanisms by which the NF-κB pathway is constitutively activated in different types of human cancers and the potential role of various oncogenic genes regulated by this transcription factor in cancer development and progression. We also discussed various pharmacological approaches employed to target the deregulated NF-κB signaling pathway and their possible therapeutic potential in cancer therapy. Moreover, Syk (Spleen tyrosine kinase), non-receptor tyrosine kinase which mediates signal transduction downstream of a variety of transmembrane receptors including classical immune-receptors like the B-cell receptor (BCR), which can also activate the inflammasome and NF-κB-mediated transcription of chemokines and cytokines in the presence of pathogens would be discussed as well. The highlight of this review article is to summarize the classic and novel signaling pathways involved in NF-κB and Syk signaling and then raise some possibilities for cancer therapy.

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Inhibition of cell expansion enhances cortical microtubule stability in the root apex of Arabidopsis thaliana

Journal of Biological Research-Thessaloniki ◽

10.1186/s40709-021-00143-8 ◽

2021 ◽

Vol 28 (1) ◽

Author(s):

Veronica Giourieva ◽

Emmanuel Panteris

Keyword(s):

Arabidopsis Thaliana ◽

Cell Wall ◽

Cell Expansion ◽

Cortical Microtubule ◽

Root Apex ◽

Cellulose Synthase ◽

Cellulose Biosynthesis ◽

Cortical Microtubules ◽

Wild Type ◽

Microtubule Stability

Abstract Background Cortical microtubules regulate cell expansion by determining cellulose microfibril orientation in the root apex of Arabidopsis thaliana. While the regulation of cell wall properties by cortical microtubules is well studied, the data on the influence of cell wall to cortical microtubule organization and stability remain scarce. Studies on cellulose biosynthesis mutants revealed that cortical microtubules depend on Cellulose Synthase A (CESA) function and/or cell expansion. Furthermore, it has been reported that cortical microtubules in cellulose-deficient mutants are hypersensitive to oryzalin. In this work, the persistence of cortical microtubules against anti-microtubule treatment was thoroughly studied in the roots of several cesa mutants, namely thanatos, mre1, any1, prc1-1 and rsw1, and the Cellulose Synthase Interacting 1 protein (csi1) mutant pom2-4. In addition, various treatments with drugs affecting cell expansion were performed on wild-type roots. Whole mount tubulin immunolabeling was applied in the above roots and observations were performed by confocal microscopy. Results Cortical microtubules in all mutants showed statistically significant increased persistence against anti-microtubule drugs, compared to those of the wild-type. Furthermore, to examine if the enhanced stability of cortical microtubules was due to reduced cellulose biosynthesis or to suppression of cell expansion, treatments of wild-type roots with 2,6-dichlorobenzonitrile (DCB) and Congo red were performed. After these treatments, cortical microtubules appeared more resistant to oryzalin, than in the control. Conclusions According to these findings, it may be concluded that inhibition of cell expansion, irrespective of the cause, results in increased microtubule stability in A. thaliana root. In addition, cell expansion does not only rely on cortical microtubule orientation but also plays a regulatory role in microtubule dynamics, as well. Various hypotheses may explain the increased cortical microtubule stability under decreased cell expansion such as the role of cell wall sensors and the presence of less dynamic cortical microtubules.

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Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽

10.3390/agronomy11071328 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1328

Author(s):

Noushin Jahan ◽

Yang Lv ◽

Mengqiu Song ◽

Yu Zhang ◽

Liangguang Shang ◽

...

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Transcriptome Profiling ◽

Bhlh Transcription Factor ◽

F1 Hybrid ◽

Salt Stress Response ◽

Productivity Losses ◽

Expression Of Genes ◽

Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

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