scholarly journals Comparative Transcriptome Analysis Provides Insights into the Seed Germination in Cotton in Response to Chilling Stress

2020 ◽  
Vol 21 (6) ◽  
pp. 2067 ◽  
Author(s):  
Qian Shen ◽  
Siping Zhang ◽  
Shaodong Liu ◽  
Jing Chen ◽  
Huijuan Ma ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Glyoxylate Cycle ◽  
Chilling Stress ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Zeatin Riboside ◽  
Cotton Species ◽  
Tolerant Variety ◽  
Cold Tolerant

Gossypium hirsutum L., is a widely cultivated cotton species around the world, but its production is seriously threatened by its susceptibility to chilling stress. Low temperature affects its germination, and the underlying molecular mechanisms are rarely known, particularly from a transcriptional perspective. In this study, transcriptomic profiles were analyzed and compared between two cotton varieties, the cold-tolerant variety KN27-3 and susceptible variety XLZ38. A total of 7535 differentially expressed genes (DEGs) were identified. Among them, the transcripts involved in energy metabolism were significantly enriched during germination based on analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as glycolysis/gluconeogenesis, tricarboxylic acid cycle (TCA cycle), and glyoxylate cycle (GAC). Results from further GO enrichment analysis show the earlier appearance of DNA integration, meristem growth, cotyledon morphogenesis, and other biological processes in KN27-3 compared with XLZ38 under chilling conditions. The synthesis of asparagine, GDP-mannose, and trehalose and the catabolic process of raffinose were activated. DEGs encoding antioxidants (spermidine) and antioxidase (CAT1, GPX4, DHAR2, and APX1) were much more up-regulated in embryos of KN27-3. The content of auxin (IAA), cis-zeatin riboside (cZR), and trans-zeatin riboside (tZR) in KN27-3 are higher than that in XLZ38 at five stages (from 12 h to 54 h). GA3 was expressed at a higher level in KN27-3 from 18 h to 54 h post imbibition compared to that in XLZ38. And abscisic acid (ABA) content of KN27-3 is lower than that in XLZ38 at five stages. Results from hormone content measurements and the related gene expression analysis indicated that IAA, CTK, and GA3 may promote germination of the cold-tolerant variety, while ABA inhibits it. These results expand the understanding of cottonseed germination and physiological regulations under chilling conditions by multiple pathways.

scholarly journals Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses

2020 ◽  
Author(s):  
Inseok Choi ◽  
Hyewon Son ◽  
Jea-Hyun Baek
Keyword(s):  
Immune Responses ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Cell Stress ◽  
Danger Signals ◽  
Cellular Processes ◽  
The Tca Cycle ◽  
Tca Cycle Intermediates

Tricarboxylic acid cycle (TCA) is a series of chemical reactions in aerobic organisms used to generate energy via the oxidation of acetyl-CoA derived from carbohydrates, fatty acids, and proteins. In the eukaryotic system, the TCA cycle completely occurs in mitochondria, while the intermediates of the TCA cycle are retained in mitochondria due to their polarity and hydrophilicity. Under conditions of cell stress, mitochondria become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss their implications for immune activation and suppression.

scholarly journals Global Proteomic Analysis Reveals Widespread Lysine Succinylation in Rice Seedlings

2019 ◽  
Vol 20 (23) ◽  
pp. 5911 ◽  
Author(s):  
Kai Zhang ◽  
Yehui Xiong ◽  
Wenxian Sun ◽  
Guo-Liang Wang ◽  
Wende Liu
Keyword(s):  
Biological Function ◽  
Tricarboxylic Acid Cycle ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Biological Processes ◽  
Rice Seedlings ◽  
Post Translational Modification ◽  
Lysine Succinylation ◽  
Rice Samples ◽  
Pathway Category

Lysine succinylation (Ksu) is a dynamic and reversible post-translational modification that plays an important role in many biological processes. Although recent research has analyzed Ksu plant proteomes, little is known about the scope and cellular distribution of Ksu in rice seedlings. Here, we report high-quality proteome-scale Ksu data for rice seedlings. A total of 710 Ksu sites in 346 proteins with diverse biological functions and subcellular localizations were identified in rice samples. About 54% of the sites were predicted to be localized in the chloroplast. Six putative succinylation motifs were detected. Comparative analysis with succinylation data revealed that arginine (R), located downstream of Ksu sites, is the most conserved amino acid surrounding the succinylated lysine. KEGG pathway category enrichment analysis indicated that carbon metabolism, tricarboxylic acid cycle (TCA) cycle, oxidative phosphorylation, photosynthesis, and glyoxylate and dicarboxylate metabolism pathways were significantly enriched. Additionally, we compared published Ksu data from rice embryos with our data from rice seedlings and found conserved Ksu sites between the two rice tissues. Our in-depth survey of Ksu in rice seedlings provides the foundation for further understanding the biological function of lysine-succinylated proteins in rice growth and development.

scholarly journals Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 69
Author(s):  
Inseok Choi ◽  
Hyewon Son ◽  
Jea-Hyun Baek
Keyword(s):  
Immune Responses ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Cell Stress ◽  
Danger Signals ◽  
Cellular Processes ◽  
The Tca Cycle ◽  
Tca Cycle Intermediates

The tricarboxylic acid cycle (TCA) is a series of chemical reactions used in aerobic organisms to generate energy via the oxidation of acetylcoenzyme A (CoA) derived from carbohydrates, fatty acids and proteins. In the eukaryotic system, the TCA cycle occurs completely in mitochondria, while the intermediates of the TCA cycle are retained inside mitochondria due to their polarity and hydrophilicity. Under cell stress conditions, mitochondria can become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss its implication for immune activation and suppression.

scholarly journals QTL mapping of physiological traits at the booting stage in rice under low temperature combined with nitrogen fertilization

2019 ◽  
Vol 55 (No. 4) ◽  
pp. 146-155
Author(s):  
Shu Ming Yang ◽  
Fei Fei Zhang ◽  
Su Hua Zhang ◽  
Gui Yong Li ◽  
Li Qiong Zeng ◽  
...  
Keyword(s):  
Composite Interval Mapping ◽  
Molecular Mechanisms ◽  
Cold Water ◽  
Flag Leaf ◽  
Chilling Stress ◽  
Interval Mapping ◽  
Physiological Traits ◽  
Environment Interaction ◽  
Nitrogen Application ◽  
Cold Tolerant

Further dissection of physiological molecular mechanisms is indispensable to alleviate rice yield losses resulting from cold injury. By using 105 near-isogenic lines (NILs) derived from a backcross between cv. Lijiangxintuanheigu (LTH) and cv. Towada, we detected quantitative trait loci (QTLs) for physiological traits of the rice flag leaf, based on polymorphic simple sequence repeat (SSR) markers, inclusive composite interval mapping (ICIM), mixed composite interval mapping (MCIM) approaches and phenotypic value subjected to combine with cold-water stress and three nitrogen application rates. By using ICIM, a total of 34 QTLs with additive effects (A-QTLs) were identified on chromosomes 1, 3, 4, 5, 6, 7 and 10, and the phenotypic variation (R<sup>2</sup>) explained by each QTL ranged from 8.46 to 29.14%. By using MCIM, 20 A-QTLs and 14 pairs of QTLs with epistatic × environment interaction effects (Epistatic QTLs) were detected, the contribution of environment interaction (H<sup>2</sup>AE) was 0.87 to 7.36%, while the contribution rates of E-QTL were from 0.97 to 3.58%. Fourteen A-QTLs were detected by ICIM and MCIM, which may serve as a basis for fine-mapping and candidate gene studies, and providing strategies for the development of cold-tolerant rice cultivars and nitrogen application to alleviate chilling stress.  

scholarly journals Comparative transcriptome profiling reveals the cold stress responsiveness in two contrasting Chinese jujube cultivars

2020 ◽  
Author(s):  
Heying Zhou(Former Corresponding Author) ◽  
Xiaoming Pang(New Corresponding Author) ◽  
Ying He ◽  
Yongsheng Zhu ◽  
Meiyu Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Freezing Stress ◽  
Comparative Transcriptome ◽  
Chinese Jujube ◽  
Cold Tolerant ◽  
C 30

Abstract Background Low temperature is a major factor influences the growth and development of Chinese jujube ( Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms for coping with different freezing stress conditions in jujube. To gain insight into the freezing-related molecular changes, we conducted comparative transcriptome analyses from the cold-sensitive cultivar ‘Dongzao’ and cold-tolerant cultivar ‘Jinsixiaozao’ using RNA-Seq. Results In our study, more than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars was 1831, 2030, 1993, 1845 and 2137 under the five treatments, respectively. Functional enrichment analysis suggested that metabolic pathway, response to stimulus and catalytic activity were significantly enriched at stronger freezing stress. Among them, nine DEGs participated in the pathway of Ca 2+ signal, thirty-two DEGs were identified to take part in sucrose metabolism, and other DEGs were identified to participate in the regulation of ROS, plant hormones and antifreeze protein. In addition, important transcription factors ( WRKY , AP2 / ERF , NAC and bZIP ) participating in the freezing stress were activated under different degrees of freezing stress. Conclusions Our research provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome levels in Z. jujuba , especially two cultivars with different cold tolerance. These results expanding our understanding on the complex molecular mechanism of jujube, which also provide new insights and candidate genes for genetic improvement of jujube tolerance to freezing stress.

scholarly journals A Transcriptional Switch in the Expression of Yeast Tricarboxylic Acid Cycle Genes in Response to a Reduction or Loss of Respiratory Function

1999 ◽  
Vol 19 (10) ◽  
pp. 6720-6728 ◽  
Author(s):  
Zhengchang Liu ◽  
Ronald A. Butow
Keyword(s):  
Binding Site ◽  
Respiratory Function ◽  
Leucine Zipper ◽  
Tricarboxylic Acid Cycle ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Helix Loop Helix ◽  
Expression Of Genes ◽  
The Glyoxylate Cycle

ABSTRACT The Hap2,3,4,5p transcription complex is required for expression of many mitochondrial proteins that function in electron transport and the tricarboxylic acid (TCA) cycle. We show that as the cells’ respiratory function is reduced or eliminated, the expression of four TCA cycle genes, CIT1, ACO1, IDH1, andIDH2, switches from HAP control to control by three genes, RTG1, RTG2, and RTG3. The expression of four additional TCA cycle genes downstream ofIDH1 and IDH2 is independent of theRTG genes. We have previously shown that theRTG genes control the retrograde pathway, defined as a change in the expression of a subset of nuclear genes, e.g., the glyoxylate cycle CIT2 gene, in response to changes in the functional state of mitochondria. We show that thecis-acting sequence controlling RTG-dependent expression of CIT1 includes an R box element, GTCAC, located 70 bp upstream of the Hap2,3,4,5p binding site in theCIT1 upstream activation sequence. The R box is a binding site for Rtg1p-Rtg3p, a heterodimeric, basic helix-loop-helix/leucine zipper transcription factor complex. We propose that in cells with compromised mitochondrial function, the RTG genes take control of the expression of genes leading to the synthesis of α-ketoglutarate to ensure that sufficient glutamate is available for biosynthetic processes and that increased flux of the glyoxylate cycle, via elevated CIT2 expression, provides a supply of metabolites entering the TCA cycle sufficient to support anabolic pathways. Glutamate is a potent repressor of RTG-dependent expression of genes encoding both mitochondrial and nonmitochondrial proteins, suggesting that it is a specific feedback regulator of the RTG system.

scholarly journals Metabolic responses to elevated pCO2 in the gills of the Pacific Oyster (Magallana gigas) using a GC-TOF-MS-based metabolomics approach

2018 ◽  
Author(s):  
Zengjie Jiang ◽  
Xiaoqin Wang ◽  
Samuel P.S. Rastrick ◽  
Jinghui Fang ◽  
Meirong Du ◽  
...  
Keyword(s):  
Atmospheric Carbon Dioxide ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Potential Effect ◽  
Metabolic Responses ◽  
Pathway Enrichment Analysis ◽  
Human Fossil ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion and cement production, are resulting in increasing absorption of CO2 by the oceans, which has led to a decline in ocean pH in a process known as ocean acidification (OA). There is a growing body of evidence demonstrating the potential effect of OA on life-history traits of marine organisms. Consequently, gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) based metabolic profiling approach was applied to examine the metabolic responses of Magallana gigas to elevated pCO2 levels, under otherwise natural field conditions. CO2. Oysters were exposed natural environmental pCO2 (~625.40 μatm) and elevated pCO2 (~1432.94 μatm) levels for 30 days. Results indicated that 36 differential metabolites with variable importance in the projection (VIP) value greater than 1 and Student's t-test lower than 0.05 were identified. Differential metabolites were mapped in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to search for the related metabolic pathways. Pathway enrichment analysis indicates that alanine, aspartate and glutamate metabolism and glycine, serine and threonine metabolism were the most statistically enriched pathways. Further analysis suggested that elevated pCO2 disturb the TCA cycle via succinate accumulation and Magallana gigas most likely adjust their energy metabolic via alanine and GABA accumulation accordingly to cope with elevated pCO2. These findings provide an understanding of the molecular mechanisms involved in modulating metabolism under elevated pCO2 levels associated with predicted OA.

scholarly journals Potential Inhibitors for Isocitrate Lyase ofMycobacterium tuberculosisand Non-M. tuberculosis: A Summary

2015 ◽  
Vol 2015 ◽  
pp. 1-20 ◽  
Author(s):  
Yie-Vern Lee ◽  
Habibah A. Wahab ◽  
Yee Siew Choong
Keyword(s):  
Isocitrate Lyase ◽  
Tricarboxylic Acid Cycle ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Natural Compounds ◽  
Multidrug Resistant ◽  
Synthetic Compound ◽  
Synthetic Compounds ◽  
Hiv Coinfection ◽  
Potential Inhibitors

Isocitrate lyase (ICL) is the first enzyme involved in glyoxylate cycle. Many plants and microorganisms are relying on glyoxylate cycle enzymes to survive upon downregulation of tricarboxylic acid cycle (TCA cycle), especiallyMycobacterium tuberculosis(MTB). In fact, ICL is a potential drug target for MTB in dormancy. With the urge for new antitubercular drug to overcome tuberculosis treat such as multidrug resistant strain and HIV-coinfection, the pace of drug discovery has to be increased. There are many approaches to discovering potential inhibitor for MTB ICL and we hereby review the updated list of them. The potential inhibitors can be either a natural compound or synthetic compound. Moreover, these compounds are not necessary to be discovered only from MTB ICL, as it can also be discovered by a non-MTB ICL. Our review is categorized into four sections, namely, (a) MTB ICL with natural compounds; (b) MTB ICL with synthetic compounds; (c) non-MTB ICL with natural compounds; and (d) non-MTB ICL with synthetic compounds. Each of the approaches is capable of overcoming different challenges of inhibitor discovery. We hope that this paper will benefit the discovery of better inhibitor for ICL.

Changes in activity of certain enzymes of the tricarboxylic acid cycle and the glyoxylate cycle during the initiation of conidiation of Aspergillus niger

1969 ◽  
Vol 15 (10) ◽  
pp. 1207-1212 ◽  
Author(s):  
J. C. Galbraith ◽  
J. E. Smith
Keyword(s):  
Life Cycle ◽  
Aspergillus Niger ◽  
Isocitrate Lyase ◽  
Tricarboxylic Acid Cycle ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Acid Cycle ◽  
Glycine Synthesis ◽  
The Glyoxylate Cycle

The activities of certain enzymes of the tricarboxylic acid (TCA) cycle and the glyoxylate cycle (GLC) varied during growth of Aspergillus niger as a function of the stage of the life cycle and of the growth medium. Isocitrate dehydrogenase (carboxylating) and isocitrate lyase each showed a marked increase in activity prior to sporulation. There were no similar increases in vegetative cultures. It is proposed that isocitrate lyase is functional in glycine synthesis and that a source of glyoxylate may be indispensable to the expression of sporulation.

scholarly journals Comparative transcriptome, physiological and biochemical analyses reveal response mechanism mediated by CBF4 and ICE2 in enhancing cold stress tolerance in Gossypium thurberi

AoB Plants ◽  
2019 ◽  
Vol 11 (6) ◽  
Author(s):  
Xiaoyan Cai ◽  
Richard Odongo Magwanga ◽  
Yanchao Xu ◽  
Zhongli Zhou ◽  
Xingxing Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Tolerance ◽  
Cold Tolerance ◽  
Molecular Mechanisms ◽  
Chilling Stress ◽  
Cold Treatment ◽  
Cold Sensitivity ◽  
Cotton Species ◽  
Wide Range ◽  
Gossypium Thurberi

Abstract Low temperature is one of the key environmental stresses that impair plant growth and significantly restricts the productivity and spatial distribution of crop plants. Gossypium thurberi, a wild diploid cotton species, has adapted to a wide range of temperatures and exhibits a better tolerance to chilling stress. Here, we compared phenotypes and physiochemical changes in G. thurberi under cold stress and found this species indeed showed better cold tolerance. Therefore, to understand the molecular mechanisms of the cold tolerance in G. thurberi, we compared transcription changes in leaves of G. thurberi under cold stress by high-throughput transcriptome sequencing. In total, 35 617 unigenes were identified in the whole-genome transcription profile, and 4226 differentially expressed genes (DEGs) were discovered in the leaves upon cold treatment. Gene Ontology (GO) classification analyses showed that the majority of DEGs belonged to categories of signal transduction, transcription factors (TFs) and carbohydrate transport and metabolism. The expression of several cold-responsive genes such as ICE1, CBF4, RAP2-7 and abscisic acid (ABA) biosynthesis genes involved in different signalling pathways were induced after G. thurberi seedlings were exposed to cold stress. Furthermore, cold sensitivity was increased in CBF4 and ICE2 virus-induced gene silencing (VIGS) plants, and high level of malondialdehyde (MDA) showed that the CBF4 and ICE2 silenced plants were under oxidative stress compared to their wild types, which relatively had higher levels of antioxidant enzyme activity, as evident by high levels of proline and superoxide dismutase (SOD) content. In conclusion, our findings reveal a new regulatory network of cold stress response in G. thurberi and broaden our understanding of the cold tolerance mechanism in cotton, which might accelerate functional genomics studies and genetic improvement for cold stress tolerance in cultivated cotton.

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