scholarly journals Integration of Transcriptomic And Proteomic Analyses Reveals Several Levels of Metabolic Regulation In The Excess Starch And Early Senescent Leaf Mutant lses1 In Rice

2021 ◽  
Author(s):  
Zhiming Chen ◽  
Yongsheng Wang ◽  
Rongyu Huang ◽  
Zesen Zhang ◽  
Jinpeng Huang ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Metabolic Regulation ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Starch Biosynthesis ◽  
Regulation Mechanism ◽  
Aba Signaling ◽  
Significant Differential Expression ◽  
Premature Leaf Senescence ◽  
Proteomic Analyses

Abstract Background: The normal metabolism of transitory starch in leaves plays an important role in ensuring photosynthesis, delaying senescence and maintaining high yield in crops. OsCKI1 (casein kinase I1) plays crucial regulatory roles in multiple important physiological processes, including root development, hormonal signaling and low temperature-treatment adaptive growth in rice; however, its potential role in regulating temporary starch metabolism or premature leaf senescence remains unclear. To reveal the molecular regulatory mechanism of OsCKI1 in rice leaves, physiological, transcriptomic and proteomic analyses of leaves of the mutant lses1 (leaf starch excess and senescence 1), allelic to osckI1, and its wild-type variety (WT) were performed. Results: Phenotypic identification and physiological measurements showed that the lses1 mutant exhibited starch excess in the leaves and an obvious leaf tip withering phenotype as well as high ROS and MDA contents, low chlorophyll content and protective enzyme activities compared to WT. Transcriptomic and proteomic analyses showed that the correlations of most genes at the transcription and translation levels were limited. However, the changes of several important genes related to carbohydrate metabolism and apoptosis at the mRNA and protein levels were consistent. The protein-protein interaction (PPI) network might play accessory roles in promoting premature senescence of lses1 leaves. Comprehensive transcriptomic and proteomic analysis indicated that multiple key genes/proteins related to starch and sugar metabolism, apoptosis and ABA signaling exhibited significant differential expression. Abnormal increase in temporary starch was highly correlated with the expression of starch biosynthesis-related genes, which might be the main factor that causes premature leaf senescence and changes in multiple metabolic levels in leaves of lses1. In addition, significant up regulation of four proteins associated with ABA accumulation and signaling were detected in the lses1 mutant, suggesting that ABA may involve in multiple metabolic regulation via LSES1/OsCKI1 and the formation of mutant phenotype in lses1 leaves.Conclusion: The current study established the high correlation between the changes in physiological characteristics and mRNA and protein expression profiles in lses1 leaves, and emphasized the positive effect of excessive starch on accelerating premature leaf senescence. The expression patterns of genes/proteins related to starch biosynthesis and ABA signaling were analyzed via transcriptomes and proteomes, which provided a novel direction and research basis for the subsequent exploration of the regulation mechanism of temporary starch and apoptosis via LSES1/OsCKI1 in rice.

scholarly journals Abiotic Stresses Intervene with ABA Signaling to Induce Destructive Metabolic Pathways Leading to Death: Premature Leaf Senescence in Plants

2019 ◽  
Vol 20 (2) ◽  
pp. 256 ◽  
Author(s):  
Muhammad Asad ◽  
Shamsu Zakari ◽  
Qian Zhao ◽  
Lujian Zhou ◽  
Yu Ye ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Abiotic Stresses ◽  
Inhibitory Effect ◽  
Signal Molecules ◽  
Aba Signaling ◽  
Endogenous Factors ◽  
Premature Leaf Senescence ◽  
Signaling Receptors ◽  
Future Outcomes ◽  
Senescence Associated Genes

Abiotic stresses trigger premature leaf senescence by affecting some endogenous factors, which is an important limitation for plant growth and grain yield. Among these endogenous factors that regulate leaf senescence, abscisic acid (ABA) works as a link between the oxidase damage of cellular structure and signal molecules responding to abiotic stress during leaf senescence. Considering the importance of ABA, we collect the latest findings related to ABA biosynthesis, ABA signaling, and its inhibitory effect on chloroplast structure destruction, chlorophyll (Chl) degradation, and photosynthesis reduction. Post-translational changes in leaf senescence end with the exhaustion of nutrients, yellowing of leaves, and death of senescent tissues. In this article, we review the literature on the ABA-inducing leaf senescence mechanism in rice and Arabidopsis starting from ABA synthesis, transport, signaling receptors, and catabolism. We also predict the future outcomes of investigations related to other plants. Before changes in translation occur, ABA signaling that mediates the expression of NYC, bZIP, and WRKY transcription factors (TFs) has been investigated to explain the inducing effect on senescence-associated genes. Various factors related to calcium signaling, reactive oxygen species (ROS) production, and protein degradation are elaborated, and research gaps and potential prospects are presented. Examples of gene mutation conferring the delay or induction of leaf senescence are also described, and they may be helpful in understanding the inhibitory effect of abiotic stresses and effective measures to tolerate, minimize, or resist their inducing effect on leaf senescence.

scholarly journals The Developmental Transcriptome of Ae. albopictus, a Major Worldwide Human Disease Vector

2019 ◽  
Author(s):  
Stephanie Gamez ◽  
Igor Antoshechkin ◽  
Stelia C. Mendez-Sanchez ◽  
Omar S. Akbari
Keyword(s):  
Aedes Aegypti ◽  
Aedes Albopictus ◽  
Human Disease ◽  
Control Strategies ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Significant Differential Expression ◽  
Disease Vector ◽  
Biological Studies ◽  
Similarities And Differences

AbstractAedes albopictus mosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacing Aedes aegypti populations, it adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies for Aedes albopictus mosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterized Aedes albopictus mRNA expression profiles at 47 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. Moreover, to illuminate the similarities and differences between Aedes aegypti, a related human disease vector, we performed a comparative analysis using the two developmental transcriptomes. We identify life stages were the two species exhibited significant differential expression among orthologs. These findings provide insights into the similarities and differences between Aedes albopictus and Aedes aegypti mosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology of Aedes albopictus mosquitoes and provide a goldmine resource for the development of transgene-based vector control strategies.

scholarly journals Gene expression profiling of adp-glucose pyrophosphorylase (AGPase) in sink and source organs of some cassava varieties with different starch contents in Vietnam

2018 ◽  
Vol 14 (4) ◽  
pp. 673-682
Author(s):  
Nguyen Thi Minh Hong ◽  
Le Thu Ngoc ◽  
Nguyen Mau Hung ◽  
Pham Bich Ngoc ◽  
Chu Hoang Ha
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Transcript Level ◽  
Starch Biosynthesis ◽  
Storage Roots ◽  
Genes Encoding ◽  
Adp Glucose Pyrophosphorylase ◽  
Level Analysis ◽  
Starch Production ◽  
Cassava Varieties

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bio-ethanol production. Starch is stored in the form of osmotically inactive, water-insoluble granules in amyloplasts (storage starch) and chloroplasts (transitory starch). The biosynthesis of starch involves not only the production of the composite glucans but also their arrangement into an organized form within the starch granule. Understanding the specific functions played by individual isoforms of enzymes involved in starch biosynthesis pathways will provide important basis for regulation of starch production in plant. A transcript-level analysis of the genes which encode starch-synthesis enzymes is fundamental for assessment of enzyme function and the regulatory mechanism for starch biosynthesis in source and sink organs. In this work, the expression level of the genes encoding ADP-glucose pyrophosphorylase (AGPase) in two local varieties Do Dia Phuong (Do DF) and Trang Hoa Binh (Trang HB) as well as two imported varieties KM94 (Rayong1 X Rayong 90) and KM140 (KM98-1 x KM36) with different starch contents were evaluated by quantitative real-time PCR method. The result of transcript level analysis made the expression profiles of cassava AGPS and AGPL genes (encoding AGPase small and large subunits) during three development periods, 90, 180 and 270 DAP (day after planting). The transcriptional activities of these genes exhibited tissue-specific expression patterns. In particular, AGPS2 and AGPL1 transcripts were predominant in leaves, whereas expression of AGPS1, AGPL2, and AGPL3 appeared to be mostly confined to storage roots. Despite of having disparities between development stages, expression patterns of both AGPS2 and AGPL1 in leaves did not show significant differences amongst investigated cassava varieties. In contrast, transcriptional activities of AGPS1 and AGPL3 in tubers had patterns directly related to the starch contents of the cultivars. These results indicated that AGPS1 and AGPL3 genes likely play an important role in the starch biosynthesis pathway and have potential for regulation of starch production in cassava.

scholarly journals Integrative Analyses of Biochemical Properties and Transcriptome Reveal the Dynamic Changes in Leaf Senescence of Tobacco (Nicotiana tabacum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Binghui Zhang ◽  
Jiahan Yang ◽  
Gang Gu ◽  
Liao Jin ◽  
Chengliang Chen ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Biochemical Properties ◽  
Dynamic Changes ◽  
Software Analysis ◽  
Nicotiana Tabacum L ◽  
Series Expression ◽  
Functional Investigation ◽  
Short Time

Leaf senescence is an important process of growth and development in plant, and it is a programmed decline controlled by a series of genes. In this study, the biochemical properties and transcriptome at five maturity stages (M1∼M5) of tobacco leaves were analyzed to reveal the dynamic changes in leaf senescence of tobacco. A total of 722, 1,534, 3,723, and 6,933 genes were differentially expressed (DEG) between M1 and M2, M1 and M3, M1 and M4, and M1 and M5, respectively. Significant changes of nitrogen, sugars, and the DEGs related to metabolite accumulation were identified, suggesting the importance of energy metabolism during leaf senescence. Gene Ontology (GO) analysis found that DEGs were enriched in biosynthetic, metabolic, photosynthesis, and redox processes, and especially, the nitrogen metabolic pathways were closely related to the whole leaf senescence process (M1∼M5). All the DEGs were grouped into 12 expression profiles according to their distinct expression patterns based on Short Time-series Expression Miner (STEM) software analysis. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that these DEGs were enriched in pathways of carbon metabolism, starch and sucrose metabolism, nitrogen metabolism, and photosynthesis among these expression profiles. A total of 30 core genes were examined by Weight Gene Co-expression Network Analysis (WGCNA), and they appeared to play a crucial role in the regulatory of tobacco senescence. Our results provided valuable information for further functional investigation of leaf senescence in plants.

scholarly journals Characterization and Mapping of a Novel Premature Leaf Senescence Mutant in Common Tobacco (Nicotiana tabacum L.)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 415 ◽  
Author(s):  
Xiaoming Gao ◽  
Xinru Wu ◽  
Guanshan Liu ◽  
Zenglin Zhang ◽  
Jiangtao Chao ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Leaf Senescence ◽  
Genetic Manipulation ◽  
Recessive Gene ◽  
Marker Genes ◽  
Regulation Mechanism ◽  
Nicotiana Tabacum L ◽  
Genes Expression ◽  
Leaf Yellowing ◽  
Premature Leaf Senescence

As the last stage of plant development, leaf senescence has a great impact on plant’s life cycle. Genetic manipulation of leaf senescence has been used as an efficient approach in improving the yield and quality of crop plants. Here we describe an ethyl methane sulfonate (EMS) mutagenesis induced premature leaf senescence mutant yellow leaf 1 (yl1) in common tobacco (Nicotiana tabacum L.). The yl1 plants displayed early leaf yellowing. Physiological parameters and marker genes expression indicated that the yl1 phenotype was caused by premature leaf senescence. Genetic analyses indicated that the yl1 phenotype was controlled by a single recessive gene that was subsequently mapped to a specific interval of tobacco linkage group 11 using simple sequence repeat (SSR) markers. Exogenous plant hormone treatments of leaves showed that the yl1 mutant was more sensitive to ethylene and jasmonic acid than the wild type. No similar tobacco premature leaf senescence mutants have been reported. This study laid a foundation for finding the gene controlling the mutation phenotype and revealing the molecular regulation mechanism of tobacco leaf senescence in the next stage.

scholarly journals Study on cyanidin metabolism in petals of pink-flowered strawberry based on transcriptome sequencing and metabolite analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Li Xue ◽  
Jian Wang ◽  
Jun Zhao ◽  
Yang Zheng ◽  
Hai-Feng Wang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Anthocyanin Synthesis ◽  
Integrated Analysis ◽  
Intergeneric Hybridization ◽  
Significant Differential Expression

Abstract Background Pink-flowered strawberry is a promising new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, a prolonged flowering period and edible fruits. Its flower color ranges from light pink to red. Pigment compounds accumulated in its fruits were the same as in cultivated strawberry fruits, but different from that in its flowers. However, the transcriptional events underlying the anthocyanin biosynthetic pathway have not been fully characterized in petal coloration. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify the key genes, we performed an integrated analysis of the transcriptome and metabolome in petals of pink-flowered strawberry. Results The main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compound. There were no anthocyanins detected in the white-flowered hybrids. A total of 50,285 non-redundant unigenes were obtained from the transcriptome databases involved in red petals of pink-flowered strawberry cultivar Sijihong at three development stages. Amongst the unigenes found to show significant differential expression, 57 were associated with anthocyanin or other flavonoid biosynthesis, in which they were regulated by 241 differentially expressed members of transcription factor families, such as 40 MYBs, 47 bHLHs, and 41 NACs. Based on a comprehensive analysis relating pigment compounds to gene expression profiles, the mechanism of flower coloration was examined in pink-flowered strawberry. A new hypothesis was proposed to explain the lack of color phenotype of the white-flowered strawberry hybrids based on the transcriptome analysis. The expression patterns of FpDFR and FpANS genes corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the major factors that led to the absence of anthocyanins in the white petals of pink-flowered strawberry hybrids. Meanwhile, the competitive effect of FpFLS and FpDFR genes might further inhibit anthocyanin synthesis. Conclusions The data presented herein are important for understanding the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating novel potential target genes to breed valuable pink-flowered strawberry cultivars.

The Predominant microRNAs in β-cell Clusters for Insulin Regulation and Diabetic Control

2020 ◽  
Vol 21 (7) ◽  
pp. 722-734
Author(s):  
Adele Soltani ◽  
Arefeh Jafarian ◽  
Abdolamir Allameh
Keyword(s):  
Mirna Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Diabetic Control ◽  
In Vitro Proliferation ◽  
Cell Functions ◽  
Mirna Expression Profiles ◽  
Multiple Processes ◽  
The Impact

micro (mi)-RNAs are vital regulators of multiple processes including insulin signaling pathways and glucose metabolism. Pancreatic β-cells function is dependent on some miRNAs and their target mRNA, which together form a complex regulative network. Several miRNAs are known to be directly involved in β-cells functions such as insulin expression and secretion. These small RNAs may also play significant roles in the fate of β-cells such as proliferation, differentiation, survival and apoptosis. Among the miRNAs, miR-7, miR-9, miR-375, miR-130 and miR-124 are of particular interest due to being highly expressed in these cells. Under diabetic conditions, although no specific miRNA profile has been noticed, the expression of some miRNAs and their target mRNAs are altered by posttranscriptional mechanisms, exerting diverse signs in the pathobiology of various diabetic complications. The aim of this review article is to discuss miRNAs involved in the process of stem cells differentiation into β-cells, resulting in enhanced β-cell functions with respect to diabetic disorders. This paper will also look into the impact of miRNA expression patterns on in vitro proliferation and differentiation of β-cells. The efficacy of the computational genomics and biochemical analysis to link the changes in miRNA expression profiles of stem cell-derived β-cells to therapeutically relevant outputs will be discussed as well.

scholarly journals Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1312
Author(s):  
Jia Liu ◽  
Weicong Qi ◽  
Haiying Lu ◽  
Hongbo Shao ◽  
Dayong Zhang
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Early Gene ◽  
Plant Responses ◽  
Constitutive Overexpression ◽  
Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

scholarly journals Low Light/Darkness as Stressors of Multifactor-Induced Senescence in Rice Plants

2021 ◽  
Vol 22 (8) ◽  
pp. 3936
Author(s):  
Ahmed G. Gad ◽  
Habiba ◽  
Xiangzi Zheng ◽  
Ying Miao
Keyword(s):  
Leaf Senescence ◽  
Crop Yields ◽  
Crop Improvement ◽  
Light Response ◽  
Development Stage ◽  
Regulatory Mechanisms ◽  
Economic Losses ◽  
Low Light ◽  
Chlorophyll Breakdown ◽  
Premature Leaf Senescence

Leaf senescence, as an integral part of the final development stage for plants, primarily remobilizes nutrients from the sources to the sinks in response to different stressors. The premature senescence of leaves is a critical challenge that causes significant economic losses in terms of crop yields. Although low light causes losses of up to 50% and affects rice yield and quality, its regulatory mechanisms remain poorly elucidated. Darkness-mediated premature leaf senescence is a well-studied stressor. It initiates the expression of senescence-associated genes (SAGs), which have been implicated in chlorophyll breakdown and degradation. The molecular and biochemical regulatory mechanisms of premature leaf senescence show significant levels of redundant biomass in complex pathways. Thus, clarifying the regulatory mechanisms of low-light/dark-induced senescence may be conducive to developing strategies for rice crop improvement. This review describes the recent molecular regulatory mechanisms associated with low-light response and dark-induced senescence (DIS), and their effects on plastid signaling and photosynthesis-mediated processes, chloroplast and protein degradation, as well as hormonal and transcriptional regulation in rice.

scholarly journals Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaoqian Zhang ◽  
Chang Li ◽  
Bingzhou Zhang ◽  
Zhonghua Li ◽  
Wei Zeng ◽  
...  
Keyword(s):  
Differential Expression ◽  
Porcine Epidemic Diarrhea Virus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Bacterial Invasion ◽  
Sequencing Data ◽  
Diarrhea Virus ◽  
Comparison Groups ◽  
Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

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