scholarly journals Molecular insights into the functional role of nitric oxide (NO) as a signal for plant responses in chickpea

2018 ◽  
Vol 45 (2) ◽  
pp. 267 ◽  
Author(s):  
Parankusam Santisree ◽  
Pooja Bhatnagar-Mathur ◽  
Kiran K. Sharma
Keyword(s):  
Nitric Oxide ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Lipid Transfer Protein ◽  
Positive Impact ◽  
Large Subunit ◽  
Plant Responses ◽  
Acid Oxidase ◽  
No Donor ◽  
Bisphosphate Carboxylase

The molecular mechanisms and targets of nitric oxide (NO) are not fully known in plants. Our study reports the first large-scale quantitative proteomic analysis of NO donor responsive proteins in chickpea. Dose response studies carried out using NO donors, sodium nitroprusside (SNP), diethylamine NONOate (DETA) and S-nitrosoglutathione (GSNO) in chickpea genotype ICCV1882, revealed a dose dependent positive impact on seed germination and seedling growth. SNP at 0.1 mM concentration proved to be most appropriate following confirmation using four different chickpea genotypes. while SNP treatment enhanced the percentage of germination, chlorophyll and nitrogen contents in chickpea, addition of NO scavenger, cPTIO reverted its impact under abiotic stresses. Proteome profiling revealed 172 downregulated and 76 upregulated proteins, of which majority were involved in metabolic processes (118) by virtue of their catalytic (145) and binding (106) activity. A few crucial proteins such as S-adenosylmethionine synthase, dehydroascorbate reductase, pyruvate kinase fragment, 1-aminocyclopropane-1-carboxylic acid oxidase, 1-pyrroline-5-carboxylate synthetase were less abundant whereas Bowman-Birk type protease inhibitor, non-specific lipid transfer protein, chalcone synthase, ribulose-1-5-bisphosphate carboxylase oxygenase large subunit, PSII D2 protein were highly abundant in SNP treated samples. This study highlights the protein networks for a better understanding of possible NO induced regulatory mechanisms in plants.

scholarly journals Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

2020 ◽  
Author(s):  
Liang Chen ◽  
Huihui Zhu ◽  
Honglian Ai ◽  
Zhengrong Hu ◽  
Dongyun Du ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Stress Response ◽  
Secondary Metabolites ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
Antioxidant Activities ◽  
Cadmium Stress ◽  
Glutathione Metabolism ◽  
Cd Stress ◽  
No Donor

Abstract Background It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches. Results The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with c-PTIO together with L-NAME (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were involved in antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism. Conclusions In general, the results revealed that there are three major mechanisms regulated by NO in Cd stress response in tall fescue: (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.

scholarly journals Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat.

2021 ◽  
Author(s):  
Vijayendran Chandran ◽  
Mei-Ling Bermudez ◽  
Mert Koka ◽  
Dhanashri Pawale ◽  
Ramana Vishnubhotla ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Immune Response ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Positive Impact ◽  
Core Network ◽  
Protein Protein Interaction ◽  
Genomic Study ◽  
Meditation Retreat ◽  
Significant Expression

The positive impact of meditation on human wellbeing is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole blood gene expression profiling combined with multi-level bioinformatic analyses to characterize the co-expression, transcriptional, and protein-protein interaction networks to identify meditation-specific core network after an advanced 8-day Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were downregulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon (IFN) signaling were upregulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and potential implications to voluntarily and non-pharmacologically improve the immune response before immunotherapy for many conditions, including multiple sclerosis and COVID-19 vaccination.

scholarly journals Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat

2021 ◽  
Vol 118 (51) ◽  
pp. e2110455118
Author(s):  
Vijayendran Chandran ◽  
Mei-Ling Bermúdez ◽  
Mert Koka ◽  
Brindha Chandran ◽  
Dhanashri Pawale ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Positive Impact ◽  
Well Being ◽  
Core Network ◽  
Protein Protein Interaction ◽  
Genomic Study ◽  
Meditation Retreat

The positive impact of meditation on human well-being is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole-blood gene expression profiling combined with multilevel bioinformatic analyses to characterize the coexpression, transcriptional, and protein–protein interaction networks to identify a meditation-specific core network after an advanced 8-d Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were down-regulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon signaling, were up-regulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and suggests that meditation as a behavioral intervention can voluntarily and nonpharmacologically improve the immune response for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.

scholarly journals Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

2020 ◽  
Author(s):  
Huihui Zhu ◽  
Honglian Ai ◽  
Zhengrong Hu ◽  
Dongyun Du ◽  
Jie Sun ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Secondary Metabolites ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
Antioxidant Activities ◽  
Profile Analysis ◽  
Cadmium Stress ◽  
Metabolite Profile ◽  
Glutathione Metabolism ◽  
No Donor

Abstract Background: It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches. Results: The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with Carboxy-PTIO (c-PTIO) together with Nitro-L-arginine methyl ester (L-NAME) (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd (only Cd treatment) and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism.Conclusions: In general, the results revealed that there are three major mechanisms involved in NO-mediated Cd detoxification in tall fescue, including (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.

scholarly journals Evolution of Cyanobacteria by Exchange of Genetic Material among Phyletically Related Strains

1998 ◽  
Vol 180 (13) ◽  
pp. 3453-3461 ◽  
Author(s):  
Knut Rudi ◽  
Olav M. Skulberg ◽  
Kjetill S. Jakobsen
Keyword(s):  
16S Rdna ◽  
Molecular Mechanisms ◽  
Large Subunit ◽  
Genetic Material ◽  
The Other ◽  
Small Subunit Rrna ◽  
Nucleotide Substitutions ◽  
Bisphosphate Carboxylase ◽  
Other Hand ◽  
Conserved Gene

ABSTRACT The cyanobacterial radiation consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts. To investigate the molecular mechanisms responsible for stabilizing or homogenizing cyanobacterial characters, we compared the evolutionary rates and phylogenetic origins of the small-subunit rRNA-encoding DNA (16S rDNA), the conserved gene rbcL(encoding d-ribulose 1,5-bisphosphate carboxylase-oxygenase large subunit), and the less conserved gene rbcX. This survey includes four categories of phyletically related organisms: 16 strains of Microcystis, 6 strains of Tychonema, 10 strains of Planktothrix, and 12 strains ofNostoc. Both rbcL and rbcX can be regarded as neutrally evolving genes, with 95 to 100% and 50 to 80% synonymous nucleotide substitutions, respectively. There is generally low sequence divergence within the Microcystis,Tychonema, and Planktothrix categories both forrbcLX and 16S rDNA. The Nostoc category, on the other hand, consists of three genetically clustered lineages for these loci. The 16S rDNA and rbcLX phylogenies are not congruent for strains within the clustered groups. Furthermore, analysis of the phyletic structure for rbcLX indicates recombinational events between the informative sites within this locus. Thus, our results are best explained by a model involving both intergenic and intragenic recombinations. This evolutionary model explains the DNA sequence clustering for the modern species as a result of sequence homogenization (concerted evolution) caused by exchange of genetic material for neutrally evolving genes. The morphological clustering, on the other hand, is explained by structural and functional stability of these characters. We also suggest that exchange of genetic material for neutrally evolving genes may explain the apparent stability of cyanobacterial morphological characters, perhaps over billions of years.

scholarly journals Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

2016 ◽  
Vol 113 (29) ◽  
pp. E4161-E4169 ◽  
Author(s):  
Xinshuai Zhang ◽  
Michael S. Carter ◽  
Matthew W. Vetting ◽  
Brian San Francisco ◽  
Suwen Zhao ◽  
...  
Keyword(s):  
Unknown Function ◽  
Large Scale ◽  
Large Subunit ◽  
Class Ii ◽  
Dihydroxyacetone Phosphate ◽  
Catabolic Pathways ◽  
Bisphosphate Carboxylase ◽  
Domain Of Unknown Function ◽  
Class Ii Aldolase ◽  
Carbon Acid

Using a large-scale “genomic enzymology” approach, we (i) assigned novel ATP-dependent four-carbon acid sugar kinase functions to members of the DUF1537 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and (ii) discovered novel catabolic pathways for d-threonate, l-threonate, and d-erythronate. The experimentally determined ligand specificities of several solute binding proteins (SBPs) for TRAP (tripartite ATP-independent permease) transporters for four-carbon acids, including d-erythronate and l-erythronate, were used to constrain the substrates for the catabolic pathways that degrade the SBP ligands to intermediates in central carbon metabolism. Sequence similarity networks and genome neighborhood networks were used to identify the enzyme components of the pathways. Conserved genome neighborhoods encoded SBPs as well as permease components of the TRAP transporters, members of the DUF1537 family, and a member of the 4-hydroxy-l-threonine 4-phosphate dehydrogenase (PdxA) oxidative decarboxylase, class II aldolase, or ribulose 1,5-bisphosphate carboxylase/oxygenase, large subunit (RuBisCO) superfamily. Because the characterized substrates of members of the PdxA, class II aldolase, and RuBisCO superfamilies are phosphorylated, we postulated that the members of the DUF1537 family are novel ATP-dependent kinases that participate in catabolic pathways for four-carbon acid sugars. We determined that (i) the DUF1537/PdxA pair participates in a pathway for the conversion of d-threonate to dihydroxyacetone phosphate and CO2 and (ii) the DUF1537/class II aldolase pair participates in pathways for the conversion of d-erythronate and l-threonate (epimers at carbon-3) to dihydroxyacetone phosphate and CO2. The physiological importance of these pathways was demonstrated in vivo by phenotypic and genetic analyses.

scholarly journals Nitric oxide donor sodium nitroprusside-induced transcriptional changes and hypocrellin biosynthesis of Shiraia sp. S9

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yan Jun Ma ◽  
Xin Ping Li ◽  
Yue Wang ◽  
Jian Wen Wang
Keyword(s):  
Nitric Oxide ◽  
Sodium Nitroprusside ◽  
Large Scale ◽  
Unsaturated Fatty Acids ◽  
Major Facilitator Superfamily ◽  
Nitric Oxide Donor ◽  
Total Production ◽  
No Donor ◽  
Transporter Protein ◽  
Major Facilitator

Abstract Background Nitric oxide (NO) is a ubiquitous signaling mediator in various physiological processes. However, there are less reports concerning the effects of NO on fungal secondary metabolites. Hypocrellins are effective anticancer photodynamic therapy (PDT) agents from fungal perylenequinone pigments of Shiraia. NO donor sodium nitroprusside (SNP) was used as a chemical elicitor to promote hypocrellin biosynthesis in Shiraia mycelium cultures. Results SNP application at 0.01–0.20 mM was found to stimulate significantly fungal production of perylenequinones including hypocrellin A (HA) and elsinochrome A (EA). SNP application could not only enhance HA content by 178.96% in mycelia, but also stimulate its efflux to the medium. After 4 days of SNP application at 0.02 mM, the highest total production (110.34 mg/L) of HA was achieved without any growth suppression. SNP released NO in mycelia and acted as a pro-oxidant, thereby up-regulating the gene expression and activity of reactive oxygen species (ROS) generating NADPH oxidase (NOX) and antioxidant enzymes, leading to the increased levels of superoxide anion (O2−) and hydrogen peroxide (H2O2). Gene ontology (GO) analysis revealed that SNP treatment could up-regulate biosynthetic genes for hypocrellins and activate the transporter protein major facilitator superfamily (MFS) for the exudation. Moreover, SNP treatment increased the proportion of total unsaturated fatty acids in the hypha membranes and enhanced membrane permeability. Our results indicated both cellular biosynthesis of HA and its secretion could contribute to HA production induced by SNP. Conclusions The results of this study provide a valuable strategy for large-scale hypocrellin production and can facilitate further understanding and exploration of NO signaling in the biosynthesis of the important fungal metabolites.

scholarly journals Molecular Mechanisms Underlying the Acclimation of Chlamydomonas reinhardtii Against Nitric Oxide Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Eva YuHua Kuo ◽  
Tse-Min Lee
Keyword(s):  
Nitric Oxide ◽  
Nadph Oxidase ◽  
Chlamydomonas Reinhardtii ◽  
Protein Trafficking ◽  
Molecular Mechanisms ◽  
Antioxidant Defense System ◽  
No Donor ◽  
Dynamic Regulation ◽  
Translational Activity ◽  
Photosynthesis Inhibition

The acclimation mechanism of Chlamydomonas reinhardtii to nitric oxide (NO) was studied by exposure to S-nitroso-N-acetylpenicillamine (SNAP), a NO donor. Treatment with 0.1 or 0.3 mM SNAP transiently inhibited photosynthesis within 1 h, followed by a recovery, while 1.0 mM SNAP treatment caused irreversible photosynthesis inhibition and mortality. The SNAP effects are avoided in the presence of the NO scavenger, 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-l-oxyl-3-oxide (cPTIO). RNA-seq, qPCR, and biochemical analyses were conducted to decode the metabolic shifts under NO stress by exposure to 0.3 mM SNAP in the presence or absence of 0.4 mM cPTIO. These findings revealed that the acclimation to NO stress comprises a temporally orchestrated implementation of metabolic processes: (1). modulation of NADPH oxidase (respiratory burst oxidase-like 2, RBOL2) and ROS signaling pathways for downstream mechanism regulation, (2). trigger of NO scavenging elements to reduce NO level; (3). prevention of photo-oxidative risk through photosynthesis inhibition and antioxidant defense system induction; (4). acclimation to nitrogen and sulfur shortage; (5). attenuation of transcriptional and translational activity together with degradation of damaged proteins through protein trafficking machinery (ubiquitin, SNARE, and autophagy) and molecular chaperone system for dynamic regulation of protein homeostasis. In addition, the expression of the gene encoding NADPH oxidase, RBOL2, showed a transient increase while that of RBOL1 was slightly decreased after NO challenge. It reflects that NADPH oxidase, a regulator in ROS-mediated signaling pathway, may be involved in the responses of Chlamydomonas to NO stress. In conclusion, our findings provide insight into the molecular events underlying acclimation mechanisms in Chlamydomonas to NO stress.

scholarly journals Insights into Nitric Oxide-Mediated Water Balance, Antioxidant Defence and Mineral Homeostasis in Rice (Oryza sativa L.) under Chilling Stress

2020 ◽  
Author(s):  
Abdullah Al Mamun Sohag ◽  
Md Tahjib-Ul-Arif ◽  
Sonya Afrin ◽  
Md Kawsar Khan ◽  
Md. Abdul Hannan ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Oryza Sativa ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Chilling Stress ◽  
Soluble Sugar ◽  
Chilling Injury ◽  
Chilling Tolerance ◽  
No Donor ◽  
Mineral Homeostasis

Being a chilling-sensitive staple crop, rice (Oryza sativa L.) is vulnerable to climate change. The competence of rice to withstand chilling stress should, therefore, be enhanced through technological tools. The present study employed chemical intervention like application of sodium nitroprusside (SNP) as nitric oxide (NO) donor and elucidated the underlying molecular mechanisms of NO-mediated chilling tolerance in rice. At germination stage, germination indicators were interrupted by chilling stress (5.0 ± 1.0°C for 8 h day‒1), while pretreatment with 100 μM SNP markedly improved the indicators. At seedling stage (14-day-old), chilling stress caused stunted growth with visible toxicity along with alteration of biochemical markers, for example, increase in oxidative stress markers (superoxide, hydrogen peroxide, and malondialdehyde) and osmolytes (total soluble sugar; proline and soluble protein content, SPC), and decrease in chlorophyll (Chl), relative water content (RWC), and antioxidants. However, NO application attenuated toxicity symptoms with improving growth performance which might be attributed to enhanced activities of antioxidants, mineral contents, Chl, RWC and SPC. Furthermore, principal component analysis indicated that water imbalance and increased oxidative damage were the main contributors to chilling injury, whereas NO-mediated mineral homeostasis and antioxidant defense were the critical determinants for chilling tolerance in rice. Collectively, our findings revealed that NO protects against chilling stress through valorizing cellular defense mechanisms, suggesting that exogenous application of NO could be a potential tool to evolve cold tolerance as well as climate resilience in rice.

scholarly journals Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

2020 ◽  
Author(s):  
Huihui Zhu ◽  
Honglian Ai ◽  
Zhengrong Hu ◽  
Dongyun Du ◽  
Jie Sun ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Secondary Metabolites ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
Antioxidant Activities ◽  
Profile Analysis ◽  
Cadmium Stress ◽  
Metabolite Profile ◽  
Glutathione Metabolism ◽  
No Donor

Abstract Background: It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches. Results: The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with Carboxy-PTIO (c-PTIO) together with Nitro-L-arginine methyl ester (L-NAME) (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd (only Cd treatment) and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism.Conclusions: In general, the results revealed that there are three major mechanisms involved in NO-mediated Cd detoxification in tall fescue, including (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.

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