scholarly journals Autophagy-dependent ribosomal RNA degradation is essential for maintaining nucleotide homeostasis during C. elegans development

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Yubing Liu ◽  
Wei Zou ◽  
Peiguo Yang ◽  
Li Wang ◽  
Yan Ma ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
De Novo ◽  
Normal Growth ◽  
Growth Conditions ◽  
Rna Degradation ◽  
Pyrimidine Nucleotides ◽  
C Elegans ◽  
Key Enzyme ◽  
Simultaneous Loss

Ribosome degradation through the autophagy-lysosome pathway is crucial for cell survival during nutrient starvation, but whether it occurs under normal growth conditions and contributes to animal physiology remains unaddressed. In this study, we identified RNST-2, a C. elegans T2 family endoribonuclease, as the key enzyme that degrades ribosomal RNA in lysosomes. We found that loss of rnst-2 causes accumulation of rRNA and ribosomal proteins in enlarged lysosomes and both phenotypes are suppressed by blocking autophagy, which indicates that RNST-2 mediates autophagic degradation of ribosomal RNA in lysosomes. rnst-2(lf) mutants are defective in embryonic and larval development and are short-lived. Remarkably, simultaneous loss of RNST-2 and de novo synthesis of pyrimidine nucleotides leads to complete embryonic lethality, which is suppressed by supplements of uridine or cytidine. Our study reveals an essential role of autophagy-dependent degradation of ribosomal RNA in maintaining nucleotide homeostasis during animal development.

scholarly journals Identification and Characterization of Chalcone Isomerase Genes Involved in Flavonoid Production in Dracaena cambodiana

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiahong Zhu ◽  
Wan Zhao ◽  
Rongshuang Li ◽  
Dong Guo ◽  
Huiliang Li ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Normal Growth ◽  
Growth Conditions ◽  
Ultraviolet B ◽  
Chalcone Isomerase ◽  
Enzyme Activity Assay ◽  
Dragon’S Blood ◽  
Dracaena Cambodiana ◽  
Key Enzyme

Dragon’s blood is a traditional medicine in which flavonoids are the main bioactive compounds; however, the underlying formation mechanism of dragon’s blood remains largely poorly understood. Chalcone isomerase (CHI) is the key enzyme in the flavonoid biosynthesis pathway. However, CHI family genes are not well understood in Dracaena cambodiana Pierre ex Gagnep, an important source plant of dragon’s blood. In this study, 11 CHI family genes were identified from D. cambodiana, and they were classified into three types. Evolutionary and transcriptional profiling analysis revealed that DcCHI1 and DcCHI4 might be involved in flavonoid production. Both DcCHI1 and DcCHI4 displayed low expression levels in stem under normal growth conditions and were induced by methyl jasmonate (MeJA), 6-benzyl aminopurine (6-BA, synthetic cytokinin), ultraviolet-B (UV-B), and wounding. The recombinant proteins DcCHI1 and DcCHI4 were expressed in Escherichia coli and purified by His-Bind resin chromatography. Enzyme activity assay indicated that DcCHI1 catalyzed the formation of naringenin from naringenin chalcone, while DcCHI4 lacked this catalytic activity. Overexpression of DcCHI1 or DcCHI4 enhanced the flavonoid production in D. cambodiana and tobacco. These findings implied that DcCHI1 and DcCHI4 play important roles in flavonoid production. Thus, our study will not only contribute to better understand the function and expression regulation of CHI family genes involved in flavonoid production in D. cambodiana but also lay the foundation for developing the effective inducer of dragon’s blood.

scholarly journals Overexpression of WAX INDUCER1/SHINE1 Gene Enhances Wax Accumulation under Osmotic Stress and Oil Synthesis in Brassica napus

2019 ◽  
Vol 20 (18) ◽  
pp. 4435 ◽  
Author(s):  
Ning Liu ◽  
Jie Chen ◽  
Tiehu Wang ◽  
Qing Li ◽  
Pengpeng Cui ◽  
...  
Keyword(s):  
Salt Stress ◽  
Brassica Napus ◽  
De Novo ◽  
Normal Growth ◽  
Acid Synthesis ◽  
Growth Conditions ◽  
Lipid Profiling ◽  
Intracellular Lipids ◽  
Oil Synthesis ◽  
Genes Encoding

WAX INDUCER1/SHINE1 (WIN1) belongs to the AP2/EREBP transcription factor family and plays an important role in wax and cutin accumulation in plants. Here we show that BnWIN1 from Brassica napus (Bn) has dual functions in wax accumulation and oil synthesis. Overexpression (OE) of BnWIN1 led to enhanced wax accumulation and promoted growth without adverse effects on oil synthesis under salt stress conditions. Lipid profiling revealed that BnWIN1-OE plants accumulated more waxes with elevated C29-alkanes, C31-alkanes, C28-alcohol, and C29-alcohol relative to wild type (WT) under salt stress. Moreover, overexpression of BnWIN1 also increased seed oil content under normal growth conditions. BnWIN1 directly bound to the promoter region of genes encoding biotin carboxyl carrier protein 1 (BCCP1), glycerol-3-phosphate acyltransferase 9 (GPAT9), lysophosphatidic acid acyltransferase 5 (LPAT5), and diacylglycerol acyltransferase 2 (DGAT2) involved in the lipid anabolic process. Overexpression of BnWIN1 resulted in upregulated expression of numerous genes involved in de novo fatty acid synthesis, wax accumulation, and oil production. The results suggest that BnWIN1 is a transcriptional activator to regulate the biosynthesis of both extracellular and intracellular lipids.

scholarly journals Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress

2019 ◽  
Vol 48 (4) ◽  
pp. 1954-1968 ◽  
Author(s):  
Mustafa Malik Ghulam ◽  
Mathieu Catala ◽  
Sherif Abou Elela
Keyword(s):  
Ribosomal Protein ◽  
Rna Polymerase Ii ◽  
Ribosomal Proteins ◽  
Normal Growth ◽  
Growth Conditions ◽  
Duplicated Genes ◽  
Ribosomal Protein Genes ◽  
Expression Ratio ◽  
Gene Copies ◽  
Response To Stress

Abstract In Saccharomyces cerevisiae, most ribosomal proteins are synthesized from duplicated genes, increasing the potential for ribosome heterogeneity. However, the contribution of these duplicated genes to ribosome production and the mechanism determining their relative expression remain unclear. Here we demonstrate that in most cases, one of the two gene copies generate the bulk of the active ribosomes under normal growth conditions, while the other copy is favored only under stress. To understand the origin of these differences in paralog expression and their contribution to ribosome heterogeneity we used RNA polymerase II ChIP-Seq, RNA-seq, polyribosome association and peptide-based mass-spectrometry to compare their transcription potential, splicing, mRNA abundance, translation potential, protein abundance and incorporation into ribosomes. In normal conditions a post-transcriptional expression hierarchy of the duplicated ribosomal protein genes is the product of the efficient splicing, high stability and efficient translation of the major paralog mRNA. Exposure of the cell to stress modifies the expression ratio of the paralogs by repressing the expression of the major paralog and thus increasing the number of ribosomes carrying the minor paralog. Together the data indicate that duplicated ribosomal protein genes underlie a modular network permitting the modification of ribosome composition in response to changing growth conditions.

Dynamics and thermal sensitivity of ribosomal RNA maturation paths in plants

2021 ◽  
Author(s):  
Thiruvenkadam Shanmugam ◽  
Deniz Streit ◽  
Frank Schroll ◽  
Jelena Kovacevic ◽  
Enrico Schleiff
Keyword(s):  
High Temperature ◽  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Thermal Sensitivity ◽  
Normal Growth ◽  
Growth Conditions ◽  
High Temperature Stress ◽  
High Temperature Treatment ◽  
Rrna Synthesis ◽  
Rrna Maturation

Abstract Ribosome biogenesis is a constitutive fundamental process for cellular function. Its rate of production depends on the rate of maturation of precursor ribosomal RNA (pre-rRNA). The rRNA maturation paths are marked by four dominant rate-limiting intermediates with cell-type variation of the processivity rate. We have identified that high temperature stress in plants, while halting the existing pre-rRNA maturation schemes, also transiently triggers an atypical pathway for 35S pre-rRNA processing. This pathway leads to production of an aberrant precursor rRNA, reminiscent of yeast 24S, encompassing 18S and 5.8S rRNA that do not normally co-occur together at sub-unit levels; this response is elicited specifically by high and not low temperatures. We show this response to be conserved in two other model crop plant species (Rice and Tomato). This pathway persists even after returning to normal growth conditions for 1 hour and is reset between 1-6 hours after stress treatment, likely, due to resumption of normal 35S pre-rRNA synthesis and processing. The heat-induced ITS2 cleavage-derived precursors and stalled P-A2-like precursors were heterogeneous in nature with a fraction containing polymeric (A) tails. Furthermore, high temperature treatment and subsequent fractionation resulted in polysome and precursor rRNA depletion.

scholarly journals Altered proteostasis in aging and heat shock response in C. elegans revealed by analysis of the global and de novo synthesized proteome

2014 ◽  
Vol 71 (17) ◽  
pp. 3339-3361 ◽  
Author(s):  
Vanessa Liang ◽  
Milena Ullrich ◽  
Hong Lam ◽  
Yee Lian Chew ◽  
Samuel Banister ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Heat Shock ◽  
Heat Shock Response ◽  
Ribosomal Proteins ◽  
Aging Process ◽  
De Novo ◽  
Tricarboxylic Acid Cycle ◽  
Mitochondrial Enzymes ◽  
C Elegans ◽  
Shock Response

Abstract Protein misfolding and aggregation as a consequence of impaired protein homeostasis (proteostasis) not only characterizes numerous age-related diseases but also the aging process itself. Functionally related to the aging process are, among others, ribosomal proteins, suggesting an intimate link between proteostasis and aging. We determined by iTRAQ quantitative proteomic analysis in C. elegans how the proteome changes with age and in response to heat shock. Levels of ribosomal proteins and mitochondrial chaperones were decreased in aged animals, supporting the notion that proteostasis is altered during aging. Mitochondrial enzymes of the tricarboxylic acid cycle and the electron transport chain were also reduced, consistent with an age-associated energy impairment. Moreover, we observed an age-associated decline in the heat shock response. In order to determine how protein synthesis is altered in aging and in response to heat shock, we complemented our global analysis by determining the de novo proteome. For that, we established a novel method that enables both the visualization and identification of de novo synthesized proteins, by incorporating the non-canonical methionine analogue, azidohomoalanine (AHA), into the nascent polypeptides, followed by reacting the azide group of AHA by ‘click chemistry’ with an alkyne-labeled tag. Our analysis of AHA-tagged peptides demonstrated that the decreased abundance of, for example, ribosomal proteins in aged animals is not solely due to degradation but also reflects a relative decrease in their synthesis. Interestingly, although the net rate of protein synthesis is reduced in aged animals, our analyses indicate that the synthesis of certain proteins such as the vitellogenins increases with age.

scholarly journals Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis

2021 ◽  
Vol 22 (13) ◽  
pp. 6861
Author(s):  
Hong-Hsiang Guan ◽  
Yen-Hua Huang ◽  
En-Shyh Lin ◽  
Chun-Jung Chen ◽  
Cheng-Yang Huang
Keyword(s):  
De Novo ◽  
Competitive Inhibitor ◽  
Carnivorous Plant ◽  
Binding Modes ◽  
Anticancer Activities ◽  
Pyrimidine Nucleotides ◽  
Anticancer Chemotherapy ◽  
Key Enzyme ◽  
4T1 Cells ◽  
Induced Apoptosis

Dihydroorotase (DHOase) is the third enzyme in the de novo biosynthesis pathway for pyrimidine nucleotides, and an attractive target for potential anticancer chemotherapy. By screening plant extracts and performing GC–MS analysis, we identified and characterized that the potent anticancer drug plumbagin (PLU), isolated from the carnivorous plant Nepenthes miranda, was a competitive inhibitor of DHOase. We also solved the complexed crystal structure of yeast DHOase with PLU (PDB entry 7CA1), to determine the binding interactions and investigate the binding modes. Mutational and structural analyses indicated the binding of PLU to DHOase through loop-in mode, and this dynamic loop may serve as a drug target. PLU exhibited cytotoxicity on the survival, migration, and proliferation of 4T1 cells and induced apoptosis. These results provide structural insights that may facilitate the development of new inhibitors targeting DHOase, for further clinical anticancer chemotherapies.

scholarly journals Versatile Physiological Functions of Plant GSK3-Like Kinases

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 697
Author(s):  
Juan Mao ◽  
Wenxin Li ◽  
Jing Liu ◽  
Jianming Li
Keyword(s):  
Stress Responses ◽  
Glycogen Synthase ◽  
Plant Stress ◽  
Normal Growth ◽  
Growth Conditions ◽  
Genetic Studies ◽  
Physiological Functions ◽  
Environmental Signals ◽  
Plant Stress Responses ◽  
Diverse Plant

The plant glycogen synthase kinase 3 (GSK3)-like kinases are highly conserved protein serine/threonine kinases that are grouped into four subfamilies. Similar to their mammalian homologs, these kinases are constitutively active under normal growth conditions but become inactivated in response to diverse developmental and environmental signals. Since their initial discoveries in the early 1990s, many biochemical and genetic studies were performed to investigate their physiological functions in various plant species. These studies have demonstrated that the plant GSK3-like kinases are multifunctional kinases involved not only in a wide variety of plant growth and developmental processes but also in diverse plant stress responses. Here we summarize our current understanding of the versatile physiological functions of the plant GSK3-like kinases along with their confirmed and potential substrates.

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