Browsing by Author "Fernie, Alisdair R."

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Establishment of a photoautotrophic cell suspension culture of Arabidopsis thaliana for photosynthetic, metabolic, and signaling studies
(Oxford University Press, 2012) Hampp, Christine; Richter, Andreas; Osorio, Sonia; Zellnig, Gunther; Sinha, Alok Krishna; Jammer, Alexandra; Fernie, Alisdair R.; Grimm, Bernhard; Roitsch, Thomas
Plant cell suspension cultures have been used as model sys- tems to circumvent the problems associated with the analyses of a multi-factorial plant that is composed of multiple tissue and cell types exposed to diverse signals. A number of plant suspension cultures have proven to be valuable to study vari- ous topics including defense response, secondary metabolite formation, ion transport, gene regulation, and signal trans- duction (Roitsch and Sinha, 2002 and references therein). How- ever, most cultures reported to date, including the cultures from model species such as Arabidopsis (Christie and Jenkins, 1996), require the presence of sugar in the medium and are characterized by no or negligible photosynthetic activity (Roitsch and Sinha, 2002). For only a very limited number of species, such as Chenopodium rubrum, have true photoauto- trophic (PA) cultures been established (see references in Roitsch and Sinha, 2002). Such cultures combine the advan- tages of plant suspension cultures with carbon autotrophy and represent very powerful model systems for plant research. Unfortunately, for as-yet unknown reasons, it is very difficult to establish PA cultures (Widholm, 1992); hence, PA cultures from only a few crop species have been established. PA cul- tures have, however, been used to address various aspects of photosynthesis, herbicide effects, and secondary product formation from exclusively chloroplast localized pathways as well as in characterization of the metabolic changes occurring during the source–sink transition (Roitsch et al., 1995) and the coordinated regulation of primary metabolism and defense responses (Ehness et al., 1997). In parallel, a large number of mutant and transgenic Arabidopsis plants have been char- acterized with respect to their physiology, biochemistry, and molecular biology. That said, the establishment of a PA cell culture of Arabidopsis has, to date, proven elusive.
The multifaceted metabolic role of lactate dehydrogenase in submergence tolerance
(John Wiley & Sons, 2026) Swain, Jagannath; Fernie, Alisdair R.; Foyer, Christine H.; Gupta, Kapuganti Jagadis
In this commentary, we highlight the importance of LDH in the modulation of several crucial metabolic pathways for submergence tolerance in rice. Lactate Dehydrogenase (LDH), a tetrameric enzyme that catalyses the reversible interconversion of pyruvate and lactate during fermentation induced by hypoxia in plants and animals. Catalysing an important rate-limiting step in the glyco-metabolism pathway, the increased expression and activity of this enzyme are required for the maintenance of glycolysis under hypoxia, protecting energy homeostasis by maintaining NADH/NAD+ ratios (Ha et al. 2024). Recent evidence demonstrated the importance of LDH in the modulation of several metabolic pathways for submergence tolerance in rice (Chatterjee et al. 2025).
Nitrate nutrition influences multiple factors in order to increase energy efficiency under hypoxia in Arabidopsis
(Oxford University Press, 2019) Wany, Aakanksha; Gupta, Alok Kumar; Kumari, Aprajita; Mishra, Sonal; Singh, Namrata; Pandey, Sonika; Vanvari, Rhythm; Igamberdiev, Abir U.; Fernie, Alisdair R.; Gupta, Kapuganti Jagadis
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.
Nitrite and nitric oxide are important in the adjustment of primary metabolism during the hypersensitive response in tobacco
(Oxford University Press, 2019) Mur, Luis A. J.; Kumari, Aprajita; Brotman, Yariv; Zeier, Jurgen; Mandon, Julien; Cristescu, Simona M.; Harren, Frans; Kaiser, Werner M.; Fernie, Alisdair R.; Gupta, Kapuganti Jagadis
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.
The role of nitrite and nitric oxide under low oxygen conditions in plants
(Oxford University Press, 2020) Gupta, Kapuganti Jagadis; Mur, Luis A.J.; Wany, Aakanksha; Kumari, Aprajita; Fernie, Alisdair R.; Ratcliffe, R. George
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 extensively described. 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. Whilst 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, is also 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 non-symbiotic 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.
Serine hydroxymethyltransferase6 is involved in growth and resistance against pathogens via ethylene and lignin production in Arabidopsis
(John Wiley & Sons, 2024) Singh, Pooja; Kumari, Aprajita; Khaladhar, Vemula Chandra; Singh, Namrata; Pathak, Pradeep Kumar; Kumar, Vinod; Kumar, Ritika Jantu; Jain, Priyanka; Thakur, Jitendra K.; Fernie, Alisdair R.; Bauwe, Hermann; Raghavendra, A.S.; Gupta, Kapuganti Jagadis
Photorespiratory serine hydroxymethyltransferases (SHMTs) are important enzymes of cellular one-carbon metabolism. In this study, we investigated the potential role of SHMT6 in Arabidopsis thaliana. We found that SHMT6 is localized in the nucleus and expressed in different tissues during development. Interestingly SHMT6 is inducible in response to avirulent, virulent Pseudomonas syringae and to Fusarium oxysporum infection. Overexpression of SHMT6 leads to larger flowers, siliques, seeds, roots, and consequently an enhanced overall biomass. This enhanced growth was accompanied by increased stomatal conductance and photosynthetic capacity as well as ATP, protein, and chlorophyll levels. By contrast, a shmt6 knockout mutant displayed reduced growth. When challenged with Pseudomonas syringae pv tomato (Pst) DC3000 expressing AvrRpm1, SHMT6 overexpression lines displayed a clear hypersensitive response which was characterized by enhanced electrolyte leakage and reduced bacterial growth. In response to virulent Pst DC3000, the shmt6 mutant developed severe disease symptoms and becomes very susceptible, whereas SHMT6 overexpression lines showed enhanced resistance with increased expression of defense pathway associated genes. In response to Fusarium oxysporum, overexpression lines showed a reduction in symptoms. Moreover, SHMT6 overexpression lead to enhanced production of ethylene and lignin, which are important components of the defense response. Collectively, our data revealed that SHMT6 plays an important role in development and defense against pathogens.
The uncoupling of respiration in plant mitochondria: keeping reactive oxygen and nitrogen species under control
(Oxford University Press, 2021) Popov, Vasily N.; Syromyatnikov, Mikhail Y.; Fernie, Alisdair R.; Chakraborty, Subhra; Gupta, Kapuganti Jagadis; Igamberdiev, Abir U.
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.