GAMYB TF modulates bHLH142 and is homeostatically regulated by TDR TF during rice anther tapetal and pollen development

2021 ◽  
Author(s):  
Swee-Suak Ko ◽  
Min-Jeng Li ◽  
Yi-Cheng Ho ◽  
Chun-Ping Yu ◽  
Ting-Ting Yang ◽  
...  
Keyword(s):  
Pollen Development ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Specific Binding ◽  
Biological Functions ◽  
Altered Expression ◽  
Regulatory Pathways ◽  
E Box ◽  
And Function ◽  
Different Tissues

Abstract GAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a “hub” in these two pollen pathways. We show that GAMYB modulates bHLH142 expression through specific binding to the MYB motif of bHLH142 promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation of bHLH142 by binding to the E-box close to the MYB motif on the promoter. The altered expression of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely on bHLH142 in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development.

scholarly journals GAMYB modulates bHLH142 and is homeostatically regulated by TDR during rice anther tapetal and pollen development

2020 ◽  
Author(s):  
Swee-Suak Ko ◽  
Min-Jeng Li ◽  
Yi-Cheng Ho ◽  
Chun-Ping Yu ◽  
Ting-Ting Yang ◽  
...  
Keyword(s):  
Pollen Development ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Specific Binding ◽  
Biological Functions ◽  
Regulatory Pathways ◽  
Normal Pollen ◽  
E Box ◽  
And Function ◽  
Different Tissues

AbstractGAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a “hub” in these two pollen pathways. We show that GAMYB modulates bHLH142 expression through specific binding to the MYB motif of bHLH142 promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation of bHLH142 by binding to the E-box close to the MYB motif on the promoter. The up- and down-regulation of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely on bHLH142 in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development.HighlightGAMYB can directly modulate the transactivation of the bHLH142, but the modulation is repressed by TDR to keep the homeostasis of bHLH142 gene expression to ensure normal pollen development.

scholarly journals Ion Channels: New Actors Playing in Chemotherapeutic Resistance

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 376 ◽  
Author(s):  
Philippe Kischel ◽  
Alban Girault ◽  
Lise Rodat-Despoix ◽  
Mohamed Chamlali ◽  
Silviya Radoslavova ◽  
...  
Keyword(s):  
Ion Channels ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Breast Cancers ◽  
Altered Expression ◽  
Acquired Drug Resistance ◽  
Therapeutic Modalities ◽  
Channel Expression ◽  
Systemic Agents ◽  
Resistance To Chemotherapy

In the battle against cancer cells, therapeutic modalities are drastically limited by intrinsic or acquired drug resistance. Resistance to therapy is not only common, but expected: if systemic agents used for cancer treatment are usually active at the beginning of therapy (i.e., 90% of primary breast cancers and 50% of metastases), about 30% of patients with early-stage breast cancer will have recurrent disease. Altered expression of ion channels is now considered as one of the hallmarks of cancer, and several ion channels have been linked to cancer cell resistance. While ion channels have been associated with cell death, apoptosis and even chemoresistance since the late 80s, the molecular mechanisms linking ion channel expression and/or function with chemotherapy have mostly emerged in the last ten years. In this review, we will highlight the relationships between ion channels and resistance to chemotherapy, with a special emphasis on the underlying molecular mechanisms.

scholarly journals Mechanisms underlying gut microbiota–host interactions in insects

2021 ◽  
Vol 224 (2) ◽  
pp. jeb207696 ◽  
Author(s):  
Konstantin Schmidt ◽  
Philipp Engel
Keyword(s):  
Gut Microbiota ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Molecular Processes ◽  
General Introduction ◽  
Host Interactions ◽  
Host Nutrition ◽  
Insect Gut ◽  
Almost All ◽  
And Function

ABSTRACTInsects are the most diverse group of animals and colonize almost all environments on our planet. This diversity is reflected in the structure and function of the microbial communities inhabiting the insect digestive system. As in mammals, the gut microbiota of insects can have important symbiotic functions, complementing host nutrition, facilitating dietary breakdown or providing protection against pathogens. There is an increasing number of insect models that are experimentally tractable, facilitating mechanistic studies of gut microbiota–host interactions. In this Review, we will summarize recent findings that have advanced our understanding of the molecular mechanisms underlying the symbiosis between insects and their gut microbiota. We will open the article with a general introduction to the insect gut microbiota and then turn towards the discussion of particular mechanisms and molecular processes governing the colonization of the insect gut environment as well as the diverse beneficial roles mediated by the gut microbiota. The Review highlights that, although the gut microbiota of insects is an active field of research with implications for fundamental and applied science, we are still in an early stage of understanding molecular mechanisms. However, the expanding capability to culture microbiomes and to manipulate microbe–host interactions in insects promises new molecular insights from diverse symbioses.

scholarly journals Molecular Mechanisms and Function Prediction of Long Noncoding RNA

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Handong Ma ◽  
Yun Hao ◽  
Xinran Dong ◽  
Qingtian Gong ◽  
Jingqi Chen ◽  
...  
Keyword(s):  
Computational Methods ◽  
Genetic Information ◽  
Noncoding Rna ◽  
Recent Progress ◽  
Molecular Mechanisms ◽  
Noncoding Rnas ◽  
Whole Genome ◽  
Biological Functions ◽  
Large Numbers ◽  
And Function

The central dogma of gene expression considers RNA as the carrier of genetic information from DNA to protein. However, it has become more and more clear that RNA plays more important roles than simply being the information carrier. Recently, whole genome transcriptomic analyses have identified large numbers of dynamically expressed long noncoding RNAs (lncRNAs), many of which are involved in a variety of biological functions. Even so, the functions and molecular mechanisms of most lncRNAs still remain elusive. Therefore, it is necessary to develop computational methods to predict the function of lncRNAs in order to accelerate the study of lncRNAs. Here, we review the recent progress in the identification of lncRNAs, the molecular functions and mechanisms of lncRNAs, and the computational methods for predicting the function of lncRNAs.

scholarly journals Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo Xiong ◽  
Xia Qiu ◽  
Shengjia Huang ◽  
Xiaojia Wang ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Chlorophyll Biosynthesis ◽  
Expression Patterns ◽  
Sequencing Error ◽  
Sequencing Data ◽  
Chlorophyll Metabolism ◽  
Regulatory Pathways ◽  
Chlorophyll Contents ◽  
Kegg Pathways ◽  
And Function

Abstract Citrus species are among the most economically important fruit crops. Physiological characteristics and molecular mechanisms associated with de-etiolation have been partially revealed. However, little is known about the mechanisms controlling the expression and function of genes associated with photosynthesis and chlorophyll biosynthesis in variegated citrus seedlings. The lower biomass, chlorophyll contents, and photosynthetic parameter values recorded for the variegated seedlings suggested that chlorophyll biosynthesis was partially inhibited. Additionally, roots of the variegated seedlings were longer than the roots of green seedlings. We obtained 567.07 million clean reads and 85.05 Gb of RNA-sequencing data, with more than 94.19% of the reads having a quality score of Q30 (sequencing error rate = 0.1%). Furthermore, we detected 4,786 and 7,007 differentially expressed genes (DEGs) between variegated and green Shiranuhi and Huangguogan seedlings. Thirty common pathways were differentially regulated, including pathways related to photosynthesis (GO: 0015979) and the chloroplast (GO: 0009507). Photosynthesis (44 and 63 DEGs), photosynthesis-antenna proteins (14 and 29 DEGs), and flavonoid biosynthesis (16 and 29 DEGs) pathways were the most common KEGG pathways detected in two analyzed libraries. Differences in the expression patterns of PsbQ, PetF, PetB, PsaA, PsaN, PsbP, PsaF, Cluster-2274.8338 (ZIP1), Cluster-2274.38688 (PTC52), and Cluster-2274.78784 might be responsible for the variegation in citrus seedlings. We completed a physiological- and transcriptome-level comparison of the Shiranuhi and Huangguogan cultivars that differ in terms of seedling variegation. We performed mRNA-seq analyses of variegated and green Shiranuhi and Huangguogan seedlings to explore the genes and regulatory pathways involved in the inhibition of chlorophyll biosynthesis and decreases in Chl a and Chl b contents. The candidate genes described herein should be investigated in greater detail to further characterize variegated citrus seedlings.

scholarly journals Combined Proteomic and Physiological Analysis of Chloroplasts Reveals Drought and Recovery Response Mechanisms in Nicotiana benthamiana

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1127
Author(s):  
Silin Chen ◽  
Ping Li ◽  
Shunling Tan ◽  
Xiaojun Pu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Responses ◽  
Nicotiana Benthamiana ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Early Stage ◽  
Repair Process ◽  
Altered Expression ◽  
Subsequent Recovery ◽  
Recovery Response

Chloroplasts play essential roles in plant metabolic processes and stress responses by functioning as environmental sensors. Understanding chloroplast responses to drought stress and subsequent recovery will help the ability to improve stress tolerance in plants. Here, a combined proteomic and physiological approach was used to investigate the response mechanisms of Nicotiana benthamiana chloroplasts to drought stress and subsequent recovery. Early in the stress response, changes in stomatal movement were accompanied by immediate changes in protein synthesis to sustain the photosynthetic process. Thereafter, increasing drought stress seriously affected photosynthetic efficiency and led to altered expression of photosynthesis- and carbon-fixation-related proteins to protect the plants against photo-oxidative damage. Additional repair mechanisms were activated at the early stage of recovery to restore physiological functions and repair drought-induced damages, even while the negative effects of drought stress were still ongoing. Prolonging the re-watering period led to the gradual recovery of photosynthesis at both physiological and protein levels, indicating that a long repair process is required to restore plant function. Our findings provide a precise view of drought and recovery response mechanisms in N. benthamiana and serve as a reference for further investigation into the physiological and molecular mechanisms underlying plant drought tolerance.

scholarly journals Review of the Isolation, Characterization, Biological Function, and Multifarious Therapeutic Approaches of Exosomes

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 307 ◽  
Author(s):  
Sangiliyandi Gurunathan ◽  
Min-Hee Kang ◽  
Muniyandi Jeyaraj ◽  
Muhammad Qasim ◽  
Jin-Hoi Kim
Keyword(s):  
Molecular Mechanisms ◽  
Cell Communication ◽  
Biological Functions ◽  
Research Attention ◽  
Diagnosis And Prognosis ◽  
Imaging Probes ◽  
Health And Disease ◽  
The Stability ◽  
And Function ◽  
Invasive Diagnostics

Exosomes are extracellular vesicles that contain a specific composition of proteins, lipids, RNA, and DNA. They are derived from endocytic membranes and can transfer signals to recipient cells, thus mediating a novel mechanism of cell-to-cell communication. They are also thought to be involved in cellular waste disposal. Exosomes play significant roles in various biological functions, including the transfer of biomolecules such as RNA, proteins, enzymes, and lipids and the regulation of numerous physiological and pathological processes in various diseases. Because of these properties, they are considered to be promising biomarkers for the diagnosis and prognosis of various diseases and may contribute to the development of minimally invasive diagnostics and next generation therapies. The biocompatible nature of exosomes could enhance the stability and efficacy of imaging probes and therapeutics. Due to their potential use in clinical applications, exosomes have attracted much research attention on their roles in health and disease. To explore the use of exosomes in the biomedical arena, it is essential that the basic molecular mechanisms behind the transport and function of these vesicles are well-understood. Herein, we discuss the history, biogenesis, release, isolation, characterization, and biological functions of exosomes, as well as the factors influencing their biogenesis and their technical and biological challenges. We conclude this review with a discussion on the future perspectives of exosomes.

scholarly journals Identifying biological pathways that underlie primordial short stature using network analysis

2014 ◽  
Vol 52 (3) ◽  
pp. 333-344 ◽  
Author(s):  
Dan Hanson ◽  
Adam Stevens ◽  
Philip G Murray ◽  
Graeme C M Black ◽  
Peter E Clayton
Keyword(s):  
Molecular Mechanisms ◽  
Growth Failure ◽  
Mrna Splicing ◽  
Hek293 Cells ◽  
Growth Disorders ◽  
Biological Functions ◽  
Altered Expression ◽  
Signalling Molecules ◽  
Cellular Pathways ◽  
Exon 11

Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M ‘interactome’, to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.

scholarly journals DICER Inactivation Identifies Pancreatic β-Cell “Disallowed” Genes Targeted by MicroRNAs

2015 ◽  
Vol 29 (7) ◽  
pp. 1067-1079 ◽  
Author(s):  
Aida Martinez-Sanchez ◽  
Marie-Sophie Nguyen-Tu ◽  
Guy A. Rutter
Keyword(s):  
Molecular Mechanisms ◽  
Early Stage ◽  
Cell Mass ◽  
Noncoding Rnas ◽  
Sole Source ◽  
Rnase Iii ◽  
Β Cells ◽  
Β Cell ◽  
Small Noncoding Rnas ◽  
And Function

Abstract Pancreatic β-cells are the body's sole source of circulating insulin and essential for the maintenance of blood glucose homeostasis. Levels of up to 66 “disallowed” genes, which are strongly expressed and play housekeeping roles in most other mammalian tissues, are unusually low in β-cells. The molecular mechanisms involved in repressing these genes are largely unknown. Here, we explore the role in gene disallowance of microRNAs (miRNAs), a type of small noncoding RNAs that silence gene expression at the posttranscriptional level and are essential for β-cell development and function. To selectively deplete miRNAs from adult β-cells, the miRNA-processing enzyme DICER was inactivated by deletion of the RNase III domain with a tamoxifen-inducible Pdx1CreER transgene. In this model, β-cell dysfunction was apparent 2 weeks after recombination and preceded a decrease in insulin content and loss of β-cell mass. Of the 14 disallowed genes studied, quantitative RT-quantitative real-time PCR revealed that 6 genes (Fcgrt, Igfbp4, Maf, Oat, Pdgfra, and Slc16a1) were up-regulated (1.4- to 2.1-fold, P < .05) at this early stage. Expression of luciferase constructs bearing the 3′-untranslated regions of the corresponding mRNAs in wild-type or DICER-null β-cells demonstrated that Fcgrt, Oat, and Pdgfra are miRNA direct targets. We thus reveal a role for miRNAs in the regulation of disallowed genes in β-cells and provide evidence for a novel means through which noncoding RNAs control the functional identity of these cells independently of actions on β-cell mass.

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