Publications by authors named "Kapuganti Jagadis Gupta"

53 Publications

ROS/RNS Balancing, Aerobic Fermentation Regulation and Cell Cycle Control - a Complex Early Trait ('CoV-MAC-TED') for Combating SARS-CoV-2-Induced Cell Reprogramming.

Front Immunol 2021 7;12:673692. Epub 2021 Jul 7.

Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil.

In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for -scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension. In the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to 'RegroVirus' complemented by alternative oxidase (AOX) genes during programming under SE-inducing conditions with corona virus-induced transcriptome profiles. This approach enabled identifying a jor omplex rait for arly programming during SARS-CoV-2 infection, called 'CoV-MAC-TED'. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle. We conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target 'CoV-MAC-TED' in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants. Furthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that 'de-stressing' disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.
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http://dx.doi.org/10.3389/fimmu.2021.673692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293103PMC
August 2021

From Plant Survival Under Severe Stress to Anti-Viral Human Defense - A Perspective That Calls for Common Efforts.

Front Immunol 2021;12:673723. Epub 2021 Jun 15.

Non-Institutional Competence Focus (NICFocus) 'Functional Cell Reprogramming and Organism Plasticity' (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal.

Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.
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http://dx.doi.org/10.3389/fimmu.2021.673723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240590PMC
July 2021

Gaining Acceptance of Novel Plant Breeding Technologies.

Trends Plant Sci 2021 06 20;26(6):575-587. Epub 2021 Apr 20.

School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK. Electronic address:

Ensuring the sustainability of agriculture under climate change has led to a surge in alternative strategies for crop improvement. Advances in integrated crop breeding, social acceptance, and farm-level adoption are crucial to address future challenges to food security. Societal acceptance can be slow when consumers do not see the need for innovation or immediate benefits. We consider how best to address the issue of social licence and harmonised governance for novel gene technologies in plant breeding. In addition, we highlight optimised breeding strategies that will enable long-term genetic gains to be achieved. Promoted by harmonised global policy change, innovative plant breeding can realise high and sustainable productivity together with enhanced nutritional traits.
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http://dx.doi.org/10.1016/j.tplants.2021.03.004DOI Listing
June 2021

Sensing and signalling in plant stress responses: ensuring sustainable food security in an era of climate change.

New Phytol 2020 11;228(3):823-827

Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK.

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http://dx.doi.org/10.1111/nph.16893DOI Listing
November 2020

The uncoupling of respiration in plant mitochondria: keeping reactive oxygen and nitrogen species under control.

J Exp Bot 2021 02;72(3):793-807

Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada.

Plant mitochondrial respiration involves the operation of various alternative pathways. These pathways participate, both directly and indirectly, in the maintenance of mitochondrial functions though they do not contribute to energy production, being uncoupled from the generation of an electrochemical gradient across the mitochondrial membrane and thus from ATP production. Recent findings suggest that uncoupled respiration is involved in reactive oxygen species (ROS) and nitric oxide (NO) scavenging, regulation, and homeostasis. Here we discuss specific roles and possible functions of uncoupled mitochondrial respiration in ROS and NO metabolism. The mechanisms of expression and regulation of the NDA-, NDB- and NDC-type non-coupled NADH and NADPH dehydrogenases, the alternative oxidase (AOX), and the uncoupling protein (UCP) are examined in relation to their involvement in the establishment of the stable far-from-equilibrium state of plant metabolism. The role of uncoupled respiration in controlling the levels of ROS and NO as well as inducing signaling events is considered. Secondary functions of uncoupled respiration include its role in protection from stress factors and roles in biosynthesis and catabolism. It is concluded that uncoupled mitochondrial respiration plays an important role in providing rapid adaptation of plants to changing environmental factors via regulation of ROS and NO.
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http://dx.doi.org/10.1093/jxb/eraa510DOI Listing
February 2021

The power of the phytoglobin-NO cycle in the regulation of nodulation and symbiotic nitrogen fixation.

New Phytol 2020 07 9;227(1):5-7. Epub 2020 May 9.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India.

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http://dx.doi.org/10.1111/nph.16615DOI Listing
July 2020

Regulating the regulator: nitric oxide control of post-translational modifications.

New Phytol 2020 09 23;227(5):1319-1325. Epub 2020 May 23.

Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.

Nitric oxide (NO) is perfectly suited for the role of a redox signalling molecule. A key route for NO bioactivity occurs via protein S-nitrosation, and involves the addition of a NO moiety to a protein cysteine (Cys) thiol (-SH) to form an S-nitrosothiol (SNO). This process is thought to underpin a myriad of cellular processes in plants that are linked to development, environmental responses and immune function. Here we collate emerging evidence showing that NO bioactivity regulates a growing number of diverse post-translational modifications including SUMOylation, phosphorylation, persulfidation and acetylation. We provide examples of how NO orchestrates these processes to mediate plant adaptation to a variety of cellular cues.
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http://dx.doi.org/10.1111/nph.16622DOI Listing
September 2020

An Efficient Method of Mitochondrial DNA Isolation from Vigna radiata for Genomic Studies.

Methods Mol Biol 2020 ;2107:305-315

National Institute of Plant Genome Research, New Delhi, India.

Isolation of mitochondrial DNA from root tissues of mung bean (Vigna radiata) is quite tedious, complex, and often results in low yield. Hence here we show a simple, rapid, and improved protocol for isolation of mitochondrial DNA from root tissues of hydroponically grown mung bean plants. This method involves purification of mitochondria and subsequent isolation of DNA from obtained purified mitochondria. For this purpose, mitochondria were isolated using a discontinuous Percoll gradient centrifugation followed by RNase I treatment to the isolated DNA to remove any traces of RNA contamination. The mitochondrial DNA was isolated from mitochondrial samples by commonly used CTAB method. The specificity of isolated mitochondrial DNA was confirmed using mtDNA-specific genes (NAD1 and COX3). β-Actin primer was used to check the nuclear DNA contamination. PCR amplification was observed in mtDNA specific genes NAD1 and COX3 except nuclear encoded β-actin gene suggesting that mitochondrial DNA was not contaminated by nuclear DNA.
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http://dx.doi.org/10.1007/978-1-0716-0235-5_16DOI Listing
January 2021

The PHYTOGLOBIN-NO Cycle Regulates Plant Mycorrhizal Symbiosis.

Trends Plant Sci 2019 11 14;24(11):981-983. Epub 2019 Oct 14.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India; http://www.nipgr.res.in/research/dr_jagadis.php. Electronic address:

The production of the redox-active signaling molecule, NO, has long been associated with interactions between microbes and their host plants. Emerging evidence now suggests that specific NO signatures and cognate patterns of PHYTOGLOBIN1 (PHYTOGB1) expression, a key regulator of cellular NO homeostasis, may help determine either symbiosis or pathogenicity.
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http://dx.doi.org/10.1016/j.tplants.2019.09.007DOI Listing
November 2019

Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis-A Role Relevant for Seed Vigor Prediction and Plant Robustness.

Front Plant Sci 2019 20;10:1134. Epub 2019 Sep 20.

Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal.

Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)-stressed, and endophyte-treated seeds. studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing and propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.
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http://dx.doi.org/10.3389/fpls.2019.01134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776121PMC
September 2019

Using Foldscope to Monitor Superoxide Production and Cell Death During Pathogen Infection in Arabidopsis Under Different Nitrogen Regimes.

Methods Mol Biol 2020 ;2057:93-102

National Institute of Plant Genome Research, Aurna Asaf Ali Marg, New Delhi, India.

Nitrogen nutrition plays a role in plant growth development and resistance against biotic and abiotic stress. During pathogen infection various signal molecules such as reactive oxygen species, calcium, reactive nitrogen species, salicylic acid, and ethylene plays an important role. The form of nitrogen nutrition such as nitrate or ammonium plays a role in production of these molecules. Under nitrate nutrition NO is predominant. The produced NO plays a role in reacting with superoxide to generate peroxynitrite to induce cell death during hypersensitive response elicited by avirulent pathogens. Excess of ROS is also detrimental to plants and NO plays a role in regulating ROS. Hence it is important to observe superoxide production during infection. By using an avirulent Pseudomonas syringae and Arabidopsis differential N nutrition we show superoxide production in leaves using a paper microscope called Foldscope, which can be applied as a simple microscope to observe objects. The data also compared with root system infected with pathogenic Fusarium oxysporum. Taken together here we show that Foldscope is a cost-effective and powerful technique to visualize superoxide and cell death in plants during infection.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_9DOI Listing
November 2020

Using Different Forms of Nitrogen to Study Hypersensitive Response Elicited by Avirulent Pseudomonas syringae.

Methods Mol Biol 2020 ;2057:79-92

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitrate, ammonium, or a combination of both is the form of N available for nitrogen assimilation from soil by the plants. Nitrogen is an important and integral part of amino acids, nucleotides, and defense molecules. Hence it is very important to study the role of nitrate and ammonium nutrition in plant defense via hypersensitive response (HR). Shifting plants from ammonium nitrate Hoagland solution to nitrate Hoagland nutrition slightly enhances root length and leaf area. HR phenotype is different in nitrate and ammonium grown plants when challenged with avirulent Pseudomonas syringae DC3000 avrRpm1. HR is also associated with increased production of reactive oxygen species (ROS) and nitric oxide (NO). Hence to understand HR development it is essential to measure HR lesions, cell death, ROS, NO, and bacterial growth. Here we provide a stepwise protocol of various parameters to study HR in Arabidopsis in response to nitrate and ammonium nutrition.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_8DOI Listing
November 2020

Expression Analysis of Important Genes Involved in Nitrogen Metabolism Under Hypoxia.

Methods Mol Biol 2020 ;2057:61-69

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Hypoxia or anoxia condition can occurs during flooding or waterlogging and can cause intense damage to the plants. Since oxygen is important for active operation of electron transport chain in mitochondria to generate energy production (ATP) any drop in oxygen can cause an energy crisis during flooding/waterlogging. To cope with this energy crisis plants have developed various anatomical, physiological, and biochemical adaptations. Perception of signals and induction of genes are required for initiation of these adaptive responses. Various genes involved in nitrogen, carbon, and fermentative metabolism play a role in hypoxic tolerance. Regulation of genes involved in nitrogen metabolism also plays a role under hypoxia. Hence in this present chapter we describe the expression of nitrate reductase-1 (NIA1), nitrate reductase-2 (NIA2), and glutamine synthetase-1 (GLN-1) during hypoxia in Arabidopsis.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_6DOI Listing
November 2020

Measurement of Nitrate Reductase Activity in Tomato (Solanum lycopersicum L.) Leaves Under Different Conditions.

Methods Mol Biol 2020 ;2057:27-35

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitrogen is one of the crucial macronutrients essential for plant growth, development, and survival under stress conditions. Depending on cellular requirement, plants can absorb nitrogen mainly in multiple forms such as nitrate (NO ) or ammonium (NH ) or combination of both via efficient and highly regulated transport systems in roots. In addition, nitrogen-fixing symbiotic bacteria can fix atmospheric nitrogen in to NH via highly regulated complex enzyme system and supply to the roots in nodules of several species of leguminous plants. If NO is a primary source, it is transported from roots and then it is rapidly converted to nitrite (NO ) by nitrate reductase (NR) (EC 1.6.6.1) which is a critical and very important enzyme for this conversion. This key reaction is mediated by transfer of two electrons from NAD(P)H to NO . This occurs via the three redox centers comprised of two prosthetic groups (FAD and heme) and a MoCo cofactor. NR activity is greatly influenced by factors such as developmental stage and various stress conditions such as hypoxia, salinity and pathogen infection etc. In addition, light/dark dynamics plays crucial role in modulating NR activity. NR activity can be easily detected by measuring the conversion of NO to NO under optimized conditions. Here, we describe a detailed protocol for measuring relative NR enzyme activity of tomato crude extracts. This protocol offers an efficient and straightforward procedure to compare the NR activity of various plants under different conditions.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_3DOI Listing
November 2020

Methods for Measuring Nitrate Reductase, Nitrite Levels, and Nitric Oxide from Plant Tissues.

Methods Mol Biol 2020 ;2057:15-26

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitrogen (N) is one of the most important nutrients which exist in both inorganic and organic forms. Plants assimilate inorganic form of N [nitrate (NO ), nitrite (NO ) or ammonium (NH )] and incorporate into amino acids. The metabolism of N involves a series of events such as sensing, uptake, and assimilation. The initial stage is sensing, triggered by nitrate or ammonium signals initiating signal transduction processes in N metabolism. The assimilation pathway initiates with NO /NH transport to roots via specific high and low affinity (HATs and LATs) nitrate transporters or directly via ammonium transporters (AMTs). In cytosol the NO is reduced to NO by cytosolic nitrate reductase (NR) and the produced NO is further reduced to NH by nitrite reductase (NiR) in plastids. NR has capability to reduce NO to nitric oxide (NO) under specific conditions such as hypoxia, low pH, and pathogen infection. The produced NO acts as a signal for wide range of processes such as plant growth development and stress. Here, we provide methods to measure NR activity, NO levels, and NO production in plant tissues.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_2DOI Listing
November 2020

An Overview of Important Enzymes Involved in Nitrogen Assimilation of Plants.

Methods Mol Biol 2020 ;2057:1-13

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitrogen (N) is a macro-nutrient that is essential for growth development and resistance against biotic and abiotic stresses of plants. Nitrogen is a constituent of amino acids, proteins, nucleic acids, chlorophyll, and various primary and secondary metabolites. The atmosphere contains huge amounts of nitrogen but it cannot be taken up directly by plants. Plants can take up nitrogen in the form of nitrate, ammonium, urea, nitrite, or a combination of all these forms. In addition, in various leguminous rhizobia, bacteria can convert atmospheric nitrogen to ammonia and supply it to the plants. The form of nitrogen nutrition is also important in plant growth and resistance against pathogens. Nitrogen content has an important function in crop yield. Nitrogen deficiency can cause reduced root growth, change in root architecture, reduced plant biomass, and reduced photosynthesis. Hence, understanding the function and regulation of N metabolism is important. Several enzymes and intermediates are involved in nitrogen assimilation. Here we provide an overview of the important enzymes such as nitrate reductase, nitrite reductase, glutamine synthase, GOGAT, glutamate dehydrogenase, and alanine aminotransferase that are involved in nitrogen metabolism.
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http://dx.doi.org/10.1007/978-1-4939-9790-9_1DOI Listing
November 2020

Does the alternative respiratory pathway offer protection against the adverse effects resulting from climate change?

J Exp Bot 2020 01;71(2):465-469

National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Elevated greenhouse gases (GHGs) induce adverse conditions directly and indirectly, causing decreases in plant productivity. To deal with climate change effects, plants have developed various mechanisms including the fine-tuning of metabolism. Plant respiratory metabolism is highly flexible due to the presence of various alternative pathways. The mitochondrial alternative oxidase (AOX) respiratory pathway is responsive to these changes, and several lines of evidence suggest it plays a role in reducing excesses of reactive oxygen species (ROS) and reactive nitrogen species (RNS) while providing metabolic flexibility under stress. Here we discuss the importance of the AOX pathway in dealing with elevated carbon dioxide (CO2), nitrogen oxides (NOx), ozone (O3), and the main abiotic stresses induced by climate change.
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http://dx.doi.org/10.1093/jxb/erz428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6946008PMC
January 2020

Polyamine Induction in Postharvest Banana Fruits in Response to NO Donor SNP Occurs via l-Arginine Mediated Pathway and Not via Competitive Diversion of S-Adenosyl-l-Methionine.

Antioxidants (Basel) 2019 Sep 1;8(9). Epub 2019 Sep 1.

Plant Cell Biotechnology Department, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore 570020, India.

Nitric oxide (NO) is known to antagonize ethylene by various mechanisms; one of such mechanisms is reducing ethylene levels by competitive action on S-adenosyl-L-methionine (SAM)-a common precursor for both ethylene and polyamines (PAs) biosynthesis. In order to investigate whether this mechanism of SAM pool diversion by NO occur towards PAs biosynthesis in banana, we studied the effect of NO on alterations in the levels of PAs, which in turn modulate ethylene levels during ripening. In response to NO donor sodium nitroprusside (SNP) treatment, all three major PAs viz. putrescine, spermidine and spermine were induced in control as well as ethylene pre-treated banana fruits. However, the gene expression studies in two popular banana varieties of diverse genomes, Nanjanagudu rasabale (NR; AAB genome) and Cavendish (CAV; AAA genome) revealed the downregulation of SAM decarboxylase, an intermediate gene involved in ethylene and PA pathway after the fifth day of NO donor SNP treatment, suggesting that ethylene and PA pathways do not compete for SAM. Interestingly, arginine decarboxylase belonging to arginine-mediated route of PA biosynthesis was upregulated several folds in response to the SNP treatment. These observations revealed that NO induces PAs via l-arginine-mediated route and not via diversion of SAM pool.
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http://dx.doi.org/10.3390/antiox8090358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769871PMC
September 2019

Recommendations on terminology and experimental best practice associated with plant nitric oxide research.

New Phytol 2020 03 26;225(5):1828-1834. Epub 2019 Sep 26.

Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK.

Nitric oxide (NO) emerged as a key signal molecule in plants. During the last two decades impressive progress has been made in plant NO research. This small, redox-active molecule is now known to play an important role in plant immunity, stress responses, environmental interactions, plant growth and development. To more accurately and robustly establish the full spectrum of NO bioactivity in plants, it will be essential to apply methodological best practice. In addition, there are some instances of conflicting nomenclature within the field, which would benefit from standardization. In this context, we attempt to provide some helpful guidance for best practice associated with NO research and also suggestions for the cognate terminology.
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http://dx.doi.org/10.1111/nph.16157DOI Listing
March 2020

Nitrite and nitric oxide are important in the adjustment of primary metabolism during the hypersensitive response in tobacco.

J Exp Bot 2019 08;70(17):4571-4582

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitrate and ammonia deferentially modulate primary metabolism during the hypersensitive response in tobacco. In this study, tobacco RNAi lines with low nitrite reductase (NiRr) levels were used to investigate the roles of nitrite and nitric oxide (NO) in this process. The lines accumulate NO2-, with increased NO generation, but allow sufficient reduction to NH4+ to maintain plant viability. For wild-type (WT) and NiRr plants grown with NO3-, inoculation with the non-host biotrophic pathogen Pseudomonas syringae pv. phaseolicola induced an accumulation of nitrite and NO, together with a hypersensitive response (HR) that resulted in decreased bacterial growth, increased electrolyte leakage, and enhanced pathogen resistance gene expression. These responses were greater with increases in NO or NO2- levels in NiRr plants than in the WT under NO3- nutrition. In contrast, WT and NiRr plants grown with NH4+ exhibited compromised resistance. A metabolomic analysis detected 141 metabolites whose abundance was differentially changed as a result of exposure to the pathogen and in response to accumulation of NO or NO2-. Of these, 13 were involved in primary metabolism and most were linked to amino acid and energy metabolism. HR-associated changes in metabolism that are often linked with primary nitrate assimilation may therefore be influenced by nitrite and NO production.
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http://dx.doi.org/10.1093/jxb/erz161DOI Listing
August 2019

Nitric oxide accelerates germination via the regulation of respiration in chickpea.

J Exp Bot 2019 08;70(17):4539-4555

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India.

Seed germination is crucial for the plant life cycle. We investigated the role of nitric oxide (NO) in two chickpea varieties that differ in germination capacity: Kabuli, which has a low rate of germination and germinates slowly, and Desi, which shows improved germination properties. Desi produced more NO than Kabuli and had lower respiratory rates. As a result of the high respiration rates, Kabuli had higher levels of reactive oxygen species (ROS). Treatment with the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) reduced respiration in Kabuli and decreased ROS levels, resulting in accelerated germination rates. These findings suggest that NO plays a key role in the germination of Kabuli. SNAP increased the levels of transcripts encoding enzymes involved in carbohydrate metabolism and the cell cycle. Moreover, the levels of amino acids and organic acids were increased in Kabuli as a result of SNAP treatment. 1H-nuclear magnetic resonance analysis revealed that Kabuli has a higher capacity for glucose oxidation than Desi. An observed SNAP-induced increase in 13C incorporation into soluble alanine may result from enhanced oxidation of exogenous [13C]glucose via glycolysis and the pentose phosphate pathway. A homozygous hybrid that originated from a recombinant inbred line population of a cross between Desi and Kabuli germinated faster and had increased NO levels and a reduced accumulation of ROS compared with Kabuli. Taken together, these findings demonstrate the importance of NO in chickpea germination via the control of respiration and ROS accumulation.
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http://dx.doi.org/10.1093/jxb/erz185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735774PMC
August 2019

The role of nitrite and nitric oxide under low oxygen conditions in plants.

New Phytol 2020 02 11;225(3):1143-1151. Epub 2019 Jul 11.

Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.

Plant tissues, particularly roots, can be subjected to periods of hypoxia due to environmental circumstances. Plants have developed various adaptations in response to hypoxic stress and these have been described extensively. Less well-appreciated is the body of evidence demonstrating that scavenging of nitric oxide (NO) and the reduction of nitrate/nitrite regulate important mechanisms that contribute to tolerance to hypoxia. Although ethylene controls hyponasty and aerenchyma formation, NO production apparently regulates hypoxic ethylene biosynthesis. In the hypoxic mitochondrion, cytochrome c oxidase, which is a major source of NO, also is inhibited by NO, thereby reducing the respiratory rate and enhancing local oxygen concentrations. Nitrite can maintain ATP generation under hypoxia by coupling its reduction to the translocation of protons from the inner side of mitochondria and generating an electrochemical gradient. This reaction can be further coupled to a reaction whereby nonsymbiotic haemoglobin oxidizes NO to nitrate. In addition to these functions, nitrite has been reported to influence mitochondrial structure and supercomplex formation, as well as playing a role in oxygen sensing via the N-end rule pathway. These studies establish that nitrite and NO perform multiple functions during plant hypoxia and suggest that further research into the underlying mechanisms is warranted.
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http://dx.doi.org/10.1111/nph.15969DOI Listing
February 2020

Current approaches to measure nitric oxide in plants.

J Exp Bot 2019 08;70(17):4333-4343

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Nitric oxide (NO) is now established as an important signalling molecule in plants where it influences growth, development, and responses to stress. Despite extensive research, the most appropriate methods to measure and localize these signalling radicals are debated and still need investigation. Many confounding factors such as the presence of other reactive intermediates, scavenging enzymes, and compartmentation influence how accurately each can be measured. Further, these signalling radicals have short half-lives ranging from seconds to minutes based on the cellular redox condition. Hence, it is necessary to use sensitive and specific methods in order to understand the contribution of each signalling molecule to various biological processes. In this review, we summarize the current knowledge on NO measurement in plant samples, via various methods. We also discuss advantages, limitations, and wider applications of each method.
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http://dx.doi.org/10.1093/jxb/erz242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736158PMC
August 2019

Novel and conserved functions of S-nitrosoglutathione reductase in tomato.

J Exp Bot 2019 09;70(18):4877-4886

Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.

Nitric oxide (NO) is emerging as a key signalling molecule in plants. The chief mechanism for the transfer of NO bioactivity is thought to be S-nitrosylation, the addition of an NO moiety to a protein cysteine thiol to form an S-nitrosothiol (SNO). The enzyme S-nitrosoglutathione reductase (GSNOR) indirectly controls the total levels of cellular S-nitrosylation, by depleting S-nitrosoglutathione (GSNO), the major cellular NO donor. Here we show that depletion of GSNOR function impacts tomato (Solanum lycopersicum. L) fruit development. Thus, reduction of GSNOR expression through RNAi modulated both fruit formation and yield, establishing a novel function for GSNOR. Further, depletion of S. lycopersicum GSNOR (SlGSNOR) additionally impacted a number of other developmental processes, including seed development, which also has not been previously linked with GSNOR activity. In contrast to Arabidopsis, depletion of GSNOR function did not influence root development. Further, reduction of GSNOR transcript abundance compromised plant immunity. Surprisingly, this was in contrast to previous data in Arabidopsis that reported that reducing Arabidopsis thaliana GSNOR (AtGSNOR) expression by antisense technology increased disease resistance. We also show that increased SlGSNOR expression enhanced pathogen protection, uncovering a potential strategy to enhance disease resistance in crop plants. Collectively, our findings reveal, at the genetic level, that some but not all GSNOR activities are conserved outside the Arabidopsis reference system. Thus, manipulating the extent of GSNOR expression may control important agricultural traits in tomato and possibly other crop plants.
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http://dx.doi.org/10.1093/jxb/erz234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760305PMC
September 2019

Alternative oxidase is an important player in the regulation of nitric oxide levels under normoxic and hypoxic conditions in plants.

J Exp Bot 2019 08;70(17):4345-4354

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, Delhi, India.

Plant mitochondria possess two different pathways for electron transport from ubiquinol: the cytochrome pathway and the alternative oxidase (AOX) pathway. The AOX pathway plays an important role in stress tolerance and is induced by various metabolites and signals. Previously, several lines of evidence indicated that the AOX pathway prevents overproduction of superoxide and other reactive oxygen species. More recent evidence suggests that AOX also plays a role in regulation of nitric oxide (NO) production and signalling. The AOX pathway is induced under low phosphate, hypoxia, pathogen infections, and elicitor treatments. The induction of AOX under aerobic conditions in response to various stresses can reduce electron transfer through complexes III and IV and thus prevents the leakage of electrons to nitrite and the subsequent accumulation of NO. Excess NO under various stresses can inhibit complex IV; thus, the AOX pathway minimizes nitrite-dependent NO synthesis that would arise from enhanced electron leakage in the cytochrome pathway. By preventing NO generation, AOX can reduce peroxynitrite formation and tyrosine nitration. In contrast to its function under normoxia, AOX has a specific role under hypoxia, where AOX can facilitate nitrite-dependent NO production. This reaction drives the phytoglobin-NO cycle to increase energy efficiency under hypoxia.
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http://dx.doi.org/10.1093/jxb/erz160DOI Listing
August 2019

Senescent Hepatocytes in Decompensated Liver Show Reduced UPR and Its Key Player, CLPP, Attenuates Senescence In Vitro.

Cell Mol Gastroenterol Hepatol 2019 13;8(1):73-94. Epub 2019 Mar 13.

Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India. Electronic address:

Background And Aims: Non-dividing hepatocytes in end-stage liver disease indicates permanent growth arrest similar to senescence. Identifying senescence in vivo is often challenging and mechanisms inhibiting senescence are poorly understood. In lower organisms mitochondrial unfolded protein response (UPR) helps in increasing longevity; however, its role in senescence and liver disease is poorly understood. Aim of this study was to identify hepatocyte senescence and the role of UPR in cryptogenic cirrhosis.

Methods: Doxorubicin was used to induce senescence in non-neoplastic hepatocytes (PH5CH8) and hepatoma cells (HepG2 and Huh7). Senescence-associated markers and unfolded protein response was evaluated by fluorescence microscopy, immunoblotting and gene expression. Explants/biopsies from normal, fibrosis, compensated and decompensated cirrhosis without any known etiology were examined for presence of senescence and UPR by immunohistochemistry and gene expression.

Results: Accumulation of senescent hepatocytes in cryptogenic cirrhosis was associated with reduced proliferation, increased expression of γH2AX and p21, together with loss of LaminB1. Dysfunctional mitochondria and compromised UPR were key features of senescent hepatocytes both in vitro and also in decompensated cirrhosis. Intriguingly, compensated cirrhotic liver mounted strong UPR, with high levels of mitochondrial protease, CLPP. Overexpression of CLPP inhibited senescence in vitro, by reducing mitochondrial ROS and altering oxygen consumption.

Conclusions: Our results implicate a role of hepatocyte senescence in cryptogenic cirrhosis together with a crucial role of UPR in preventing hepatocyte senescence. A compromised UPR may shift the fate of cirrhotic liver toward decompensation by exaggerating hepatocyte senescence. Restoring CLPP levels at least in cell culture appears as a promising strategy in mitohormesis, thereby, preventing senescence and possibly improving hepatocyte function.
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http://dx.doi.org/10.1016/j.jcmgh.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520637PMC
April 2020

Nitrate nutrition influences multiple factors in order to increase energy efficiency under hypoxia in Arabidopsis.

Ann Bot 2019 03;123(4):691-705

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Background And Aims: Nitrogen (N) levels vary between ecosystems, while the form of available N has a substantial impact on growth, development and perception of stress. Plants have the capacity to assimilate N in the form of either nitrate (NO3-) or ammonium (NH4+). Recent studies revealed that NO3- nutrition increases nitric oxide (NO) levels under hypoxia. When oxygen availability changes, plants need to generate energy to protect themselves against hypoxia-induced damage. As the effects of NO3- or NH4+ nutrition on energy production remain unresolved, this study was conducted to investigate the role of N source on group VII transcription factors, fermentative genes, energy metabolism and respiration under normoxic and hypoxic conditions.

Methods: We used Arabidopsis plants grown on Hoagland medium with either NO3- or NH4+ as a source of N and exposed to 0.8 % oxygen environment. In both roots and seedlings, we investigated the phytoglobin-nitric oxide cycle and the pathways of fermentation and respiration; furthermore, NO levels were tested using a combination of techniques including diaminofluorescein fluorescence, the gas phase Griess reagent assay, respiration by using an oxygen sensor and gene expression analysis by real-time quantitative reverse transcription-PCR methods.

Key Results: Under NO3- nutrition, hypoxic stress leads to increases in nitrate reductase activity, NO production, class 1 phytoglobin transcript abundance and metphytoglobin reductase activity. In contrast, none of these processes responded to hypoxia under NH4+ nutrition. Under NO3- nutrition, a decreased total respiratory rate and increased alternative oxidase capacity and expression were observed during hypoxia. Data correlated with decreased reactive oxygen species and lipid peroxidation levels. Moreover, increased fermentation and NAD+ recycling as well as increased ATP production concomitant with the increased expression of transcription factor genes HRE1, HRE2, RAP2.2 and RAP2.12 were observed during hypoxia under NO3- nutrition.

Conclusions: The results of this study collectively indicate that nitrate nutrition influences multiple factors in order to increase energy efficiency under hypoxia.
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http://dx.doi.org/10.1093/aob/mcy202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417481PMC
March 2019

Nitrate, NO and ROS Signaling in Stem Cell Homeostasis.

Trends Plant Sci 2018 12 10;23(12):1041-1044. Epub 2018 Oct 10.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067, New Delhi, India. Electronic address:

Shoot and root growth is facilitated by stem cells in the shoot and root apical meristems (SAM and RAM). Recent reports have demonstrated a close link between nitrogen nutrition, nitric oxide (NO), and reactive oxygen species (ROS) in the regulation of SAM and RAM functions in response to nitrogen availability.
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http://dx.doi.org/10.1016/j.tplants.2018.09.010DOI Listing
December 2018

A discrete role for alternative oxidase under hypoxia to increase nitric oxide and drive energy production.

Free Radic Biol Med 2018 07 28;122:40-51. Epub 2018 Mar 28.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, 110067 New Delhi, India. Electronic address:

Alternative oxidase (AOX) is an integral part of the mitochondrial electron transport and can prevent reactive oxygen species (ROS) and nitric oxide (NO) production under non-stressed, normoxic conditions. Here we assessed the roles of AOX by imposing stress under normoxia in comparison to hypoxic conditions using AOX over expressing (AOX OE) and anti-sense (AOX AS) transgenic Arabidopsis seedlings and roots. Under normoxic conditions stress was induced with the defence elicitor flagellin (flg22). AOX OE reduced NO production whilst this was increased in AOX AS. Moreover AOX AS also exhibited an increase in superoxide and therefore peroxynitrite, tyrosine nitration suggesting that scavenging of NO by AOX can prevent toxic peroxynitrite formation under normoxia. In contrast, during hypoxia interestingly we found that AOX is a generator of NO. Thus, the NO produced during hypoxia, was enhanced in AOX OE and suppressed in AOX AS. Additionally, treatment of WT or AOX OE with the AOX inhibitor SHAM inhibited hypoxic NO production. The enhanced levels of NO correlated with expression of non-symbiotic haemoglobin, increased NR activity and ATP production. The ATP generation was suppressed in nia1,2 mutant and non symbiotic haemoglobin antisense line treated with SHAM. Taken together these results suggest that hypoxic NO generation mediated by AOX has a discrete role by feeding into the haemoglobin-NO cycle to drive energy efficiency under conditions of low oxygen tension.
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http://dx.doi.org/10.1016/j.freeradbiomed.2018.03.045DOI Listing
July 2018
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