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Barra PJ, Duran P, Delgado M, Viscardi S, Claverol S, Larama G, Dumont M, Mora MDLL. Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils. iScience 2023; 26:107910. [PMID: 37790272 PMCID: PMC10543181 DOI: 10.1016/j.isci.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/27/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.
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Affiliation(s)
- Patricio Javier Barra
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Paola Duran
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 4811230, Chile
| | - Mabel Delgado
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sharon Viscardi
- Escuela de la Salud, Campus San Francisco, Universidad Católica de Temuco, Temuco 4811230, Chile
| | - Stéphane Claverol
- Plateforme Protéome, Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Marc Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
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MacLean A, Legendre F, Appanna VD. The tricarboxylic acid (TCA) cycle: a malleable metabolic network to counter cellular stress. Crit Rev Biochem Mol Biol 2023; 58:81-97. [PMID: 37125817 DOI: 10.1080/10409238.2023.2201945] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The tricarboxylic acid (TCA) cycle is a primordial metabolic pathway that is conserved from bacteria to humans. Although this network is often viewed primarily as an energy producing engine fueling ATP synthesis via oxidative phosphorylation, mounting evidence reveals that this metabolic hub orchestrates a wide variety of pivotal biological processes. It plays an important part in combatting cellular stress by modulating NADH/NADPH homeostasis, scavenging ROS (reactive oxygen species), producing ATP by substrate-level phosphorylation, signaling and supplying metabolites to quell a range of cellular disruptions. This review elaborates on how the reprogramming of this network prompted by such abiotic stress as metal toxicity, oxidative tension, nutrient challenge and antibiotic insult is critical for countering these conditions in mostly microbial systems. The cross-talk between the stressors and the participants of TCA cycle that results in changes in metabolite and nucleotide concentrations aimed at combatting the abiotic challenge is presented. The fine-tuning of metabolites mediated by disparate enzymes associated with this metabolic hub is discussed. The modulation of enzymatic activities aimed at generating metabolic moieties dedicated to respond to the cellular perturbation is explained. This ancient metabolic network has to be recognized for its ability to execute a plethora of physiological functions beyond its well-established traditional roles.
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Affiliation(s)
- Alex MacLean
- School of Natural Sciences, Laurentian University, Sudbury, Canada
| | - Felix Legendre
- School of Natural Sciences, Laurentian University, Sudbury, Canada
| | - Vasu D Appanna
- School of Natural Sciences, Laurentian University, Sudbury, Canada
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Legendre F, MacLean A, Tharmalingam S, Appanna VD. Metabolic adaptation and ATP homeostasis in Pseudomonas fluorescens exposed to phosphate stress. World J Microbiol Biotechnol 2022; 38:255. [DOI: 10.1007/s11274-022-03432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
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Legendre F, MacLean A, Tharmalingam S, Appanna VD. A Metabolic Network Mediating the Cycling of Succinate, a Product of ROS Detoxification into α-Ketoglutarate, an Antioxidant. Antioxidants (Basel) 2022; 11:antiox11030560. [PMID: 35326210 PMCID: PMC8945261 DOI: 10.3390/antiox11030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Sulfur is an essential element for life. However, the soil microbe Pseudomonas (P.) fluorescens can survive in a low sulfur environment. When cultured in a sulfur-deficient medium, the bacterium reprograms its metabolic pathways to produce α-ketoglutarate (KG) and regenerate this keto-acid from succinate, a by-product of ROS detoxification. Succinate semialdehyde dehydrogenase (SSADH) and KG decarboxylase (KGDC) work in partnership to synthesize KG. This process is further aided by the increased activity of the enzymes glutamate decarboxylase (GDC) and γ-amino-butyrate transaminase (GABAT). The pool of succinate semialdehyde (SSA) generated is further channeled towards the formation of the antioxidant. Spectrophotometric analyses, HPLC experiments and electrophoretic studies with intact cells and cell-free extracts (CFE) pointed to the metabolites (succinate, SSA, GABA) and enzymes (SSADH, GDC, KGDC) contributing to this KG-forming metabolic machinery. Real-time polymerase chain reaction (RT-qPCR) revealed significant increase in transcripts of such enzymes as SSADH, GDC and KGDC. The findings of this study highlight a novel pathway involving keto-acids in ROS scavenging. The cycling of succinate into KG provides an efficient means of combatting an oxidative environment. Considering the central role of KG in biological processes, this metabolic network may be operative in other living systems.
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Affiliation(s)
- Félix Legendre
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada; (F.L.); (A.M.); (S.T.)
| | - Alex MacLean
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada; (F.L.); (A.M.); (S.T.)
| | - Sujeenthar Tharmalingam
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada; (F.L.); (A.M.); (S.T.)
- Northern Ontario School of Medicine, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Vasu D. Appanna
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada; (F.L.); (A.M.); (S.T.)
- Correspondence:
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MacLean A, Legendre F, Tharmalingam S, Appanna VD. Phosphate stress triggers the conversion of glycerol into l-carnitine in Pseudomonas fluorescens. Microbiol Res 2021; 253:126865. [PMID: 34562839 DOI: 10.1016/j.micres.2021.126865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/26/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022]
Abstract
Glycerol, a by-product of the biofuel industry is transformed into l-carnitine when the soil microbe Pseudomonas fluorescens is cultured in a phosphate-limited mineral medium (LP). Although the biomass yield was similar to that recorded in phosphate-sufficient cultures (HP), the rate of growth was slower. Phosphate was completely consumed in the LP cultures while in the HP media, approximately 35 % of the initial phosphate was detected at stationary phase of growth. The enhanced production of α-ketoglutarate (KG) in HP cultures supplemented with manganese was recently reported (Alhasawi et al., 2017). l-carnitine appeared to be a prominent metabolite in the spent fluid while the soluble cellular-free extract was characterized with peaks attributable to lysine, γ-butyrobetaine (GB), acetate and succinate in the LP cultures. Upon incubation with glycerol and NH4Cl, the resting cells readily secreted l-carnitine and revealed the presence of such precursors like GB, lysine and methionine involved in the synthesis of this trimethylated moiety. Functional proteomic studies of select enzymes participating in tricarboxylic acid cycle (TCA), oxidative phosphorylation (OP), glyoxylate cycle and l-carnitine synthesis revealed a major metabolic reconfiguration evoked by phosphate stress. While isocitrate dehydrogenase-NAD+ dependent (ICDH-NAD+) and Complex I were markedly diminished, the activities of γ-butyrobetaine aldehyde dehydrogenase (GBADH) and l-carnitine dehydrogenase (CDH) were enhanced. Real-time quantitative polymerase chain reaction (RT-qPCR) analyses pointed to an increase in transcripts of the enzymes γ-butyrobetaine dioxygenase (bbox1), S-adenosylmethionine synthase (metK) and l-carnitine dehydrogenase (lcdH). The l-carnitine/γ-butyrobetaine antiporter (caiT) was enhanced more than 400-fold in the LP cultures compared to the HP controls. This metabolic reprogramming modulated by phosphate deprivation may provide an effective technology to transform glycerol, an industrial waste into valuable l-carnitine.
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Affiliation(s)
- A MacLean
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - F Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - S Tharmalingam
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada; Northern Ontario School of Medicine, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - V D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada.
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Legendre F, MacLean A, Appanna VP, Appanna VD. Biochemical pathways to α-ketoglutarate, a multi-faceted metabolite. World J Microbiol Biotechnol 2020; 36:123. [PMID: 32686016 DOI: 10.1007/s11274-020-02900-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
α-Ketoglutarate (AKG) also known as 2-oxoglutarate is an essential metabolite in virtually all organisms as it participates in a variety of biological processes including anti-oxidative defence, energy production, signalling modules, and genetic modification. This keto-acid also possesses immense commercial value as it is utilized as a nutritional supplement, a therapeutic agent, and a precursor to a variety of value-added products such as ethylene and heterocyclic compounds. Hence, the generation of KG in a sustainable and environmentally-neutral manner is a major ongoing research endeavour. In this mini-review, the enzymatic systems and the metabolic networks mediating the synthesis of AKG will be described. The importance of such enzymes as isocitrate dehydrogenase (ICDH), glutamate dehydrogenase (GDH), succinate semialdehyde dehydrogenase (SSADH) and transaminases that directly contribute to the formation of KG will be emphasized. The efficacy of microbial systems in providing an effective platform to generate this moiety and the molecular strategies involving genetic manipulation, abiotic stress and nutrient supplementation that result in the optimal production of AKG will be evaluated. Microbial systems and their components acting via the metabolic networks and the resident enzymes are well poised to provide effective biotechnological tools that can supply renewable AKG globally.
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Affiliation(s)
- F Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - A MacLean
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - V P Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - V D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
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MacLean A, Bley AM, Appanna VP, Appanna VD. Metabolic manipulation by Pseudomonas fluorescens: a powerful stratagem against oxidative and metal stress. J Med Microbiol 2020; 69:339-346. [PMID: 31961786 DOI: 10.1099/jmm.0.001139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Metabolism is the foundation of all living organisms and is at the core of numerous if not all biological processes. The ability of an organism to modulate its metabolism is a central characteristic needed to proliferate, to be dormant and to survive any assault. Pseudomonas fluorescens is bestowed with a uniquely versatile metabolic framework that enables the microbe to adapt to a wide range of conditions including disparate nutrients and toxins. In this mini-review we elaborate on the various metabolic reconfigurations evoked by this microbial system to combat reactive oxygen/nitrogen species and metal stress. The fine-tuning of the NADH/NADPH homeostasis coupled with the production of α-keto-acids and ATP allows for the maintenance of a reductive intracellular milieu. The metabolic networks propelling the synthesis of metabolites like oxalate and aspartate are critical to keep toxic metals at bay. The biochemical processes resulting from these defensive mechanisms provide molecular clues to thwart infectious microbes and reveal elegant pathways to generate value-added products.
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Affiliation(s)
- Alex MacLean
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada
| | - Anondo Michel Bley
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada
| | - Varun P Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada
| | - Vasu D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada
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Alhasawi AA, Thomas SC, Tharmalingam S, Legendre F, Appanna VD. Isocitrate Lyase and Succinate Semialdehyde Dehydrogenase Mediate the Synthesis of α-Ketoglutarate in Pseudomonas fluorescens. Front Microbiol 2019; 10:1929. [PMID: 31507554 PMCID: PMC6716453 DOI: 10.3389/fmicb.2019.01929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/05/2019] [Indexed: 01/04/2023] Open
Abstract
Glycerol is an important by-product of the biodiesel industry and its transformation into value-added products like keto acids is being actively pursued in order to improve the efficacy of this renewable energy sector. Here, we report that the enhanced production of α-ketoglutarate (KG) effected by Pseudomonas fluorescens in a mineral medium supplemented with manganese (Mn) is propelled by the increased activities of succinate semialdehyde dehydrogenase (SSADH), γ-aminobutyric acid aminotransaminase (GABAT), and isocitrate lyase (ICL). The latter generates glyoxylate and succinate two key metabolites involved in this process. Fumarate reductase (FRD) also aids in augmenting the pool of succinate, a precursor of succinate semialdehyde (SSA). The latter is then carboxylated to KG with the assistance of α-ketoglutarate decarboxylase (KDC). These enzymes work in tandem to ensure copious secretion of the keto acid. When incubated with glycerol in the presence of bicarbonate (HCO3−), cell-free extracts readily produce KG with a metabolite fingerprint attributed to glutamate, γ-aminobutyric acid (GABA), succinate and succinate semialdehyde. Further targeted metabolomic and functional proteomic studies with high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and gel electrophoresis techniques provided molecular insights into this KG-generating machinery. Real-time quantitative polymerase chain reaction (RT-qPCR) analyses revealed the transcripts responsible for ICL and SSADH were elevated in the Mn-supplemented cultures. This hitherto unreported metabolic network where ICL and SSADH orchestrate the enhanced production of KG from glycerol, provides an elegant means of converting an industrial waste into a keto acid with wide-ranging application in the medical, cosmetic, and chemical sectors.
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Affiliation(s)
- Azhar A Alhasawi
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sean C Thomas
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sujeethar Tharmalingam
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada.,Department of Biology, Laurentian University, Sudbury, ON, Canada.,Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada.,Northern Ontario School of Medicine, Laurentian University, Sudbury, ON, Canada
| | - Felix Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Vasu D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
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Sańko-Sawczenko I, Łotocka B, Mielecki J, Rekosz-Burlaga H, Czarnocka W. Transcriptomic Changes in Medicago truncatula and Lotus japonicus Root Nodules during Drought Stress. Int J Mol Sci 2019; 20:E1204. [PMID: 30857310 PMCID: PMC6429210 DOI: 10.3390/ijms20051204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Abstract
Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research, we focused on plants from the Fabaceae family, which has a unique ability for the establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We have presented the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results proved a decrease in the efficiency of nitrogen fixation, as well as extensive changes in plant and bacterial transcriptomes, shortly after watering cessation. We showed for the first time that not only symbiotic plant components but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrated that both M. truncatula and L. japonicus root nodules were susceptible to water deprivation, they indicated significant differences in plant and bacterial response to drought between the tested species, which might be related to the various types of root nodules formed by these species.
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Affiliation(s)
- Izabela Sańko-Sawczenko
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Barbara Łotocka
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Jakub Mielecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Hanna Rekosz-Burlaga
- Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Weronika Czarnocka
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Barra PJ, Viscardi S, Jorquera MA, Duran PA, Valentine AJ, de la Luz Mora M. Understanding the Strategies to Overcome Phosphorus-Deficiency and Aluminum-Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria. Front Microbiol 2018; 9:1155. [PMID: 29910787 PMCID: PMC5992465 DOI: 10.3389/fmicb.2018.01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/14/2018] [Indexed: 11/20/2022] Open
Abstract
Phosphobacteria, secreting organic acids and phosphatases, usually favor plant performance in acidic soils by increasing phosphorus (P) availability and aluminum (Al) complexing. However, it is not well-known how P-deficiency and Al-toxicity affect the phosphobacteria physiology. Since P and Al problems often co-occur in acidic soils, we have therefore proposed the evaluation of the single and combined effects of P-deficiency and Al-toxicity on growth, organic acids secretion, malate dehydrogenase (mdh) gene expression, and phosphatase activity of five Al-tolerant phosphobacteria previously isolated from ryegrass. These phosphobacteria were identified as Klebsiella sp. RC3, Stenotrophomona sp. RC5, Klebsiella sp. RCJ4, Serratia sp. RCJ6, and Enterobacter sp. RJAL6. The strains were cultivated in mineral media modified to obtain (i) high P in absence of Al–toxicity, (ii) high P in presence of Al–toxicity, (iii) low P in absence of Al–toxicity, and (iv) low P in presence of Al–toxicity. High and low P were obtained by adding KH2PO4 at final concentration of 1.4 and 0.05 mM, respectively. To avoid Al precipitation, AlCl3 × 6H2O was previously complexed to citric acid (sole carbon source) in concentrations of 10 mM. The secreted organic acids were identified and quantified by HPLC, relative mdh gene expression was determined by qRT-PCR and phosphatase activity was colorimetrically determined using p-nitrophenyl phosphate as substrate. Our results revealed that although a higher secretion of all organic acids was achieved under P–deficiency, the patterns of organic acids secretion were variable and dependent on treatment and strain. The organic acid secretion is exacerbated when Al was added into media, particularly in the form of malic and citric acid. The mdh gene expression was significantly up–regulated by the strains RC3, RC5, and RCJ6 under P–deficiency and Al–toxicity. In general, Al–tolerant phosphobacteria under P deficiency increased both acid and alkaline phosphatase activity with respect to the control, which was deepened when Al was present. The knowledge of this bacterial behavior in vitro is important to understand and predict the behavior of phosphobacteria in vivo. This knowledge is essential to generate smart and efficient biofertilizers, based in Al–tolerant phosphobacteria which could be expansively used in acidic soils.
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Affiliation(s)
- Patricio J Barra
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Sharon Viscardi
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.,Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco, Chile
| | - Milko A Jorquera
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Paola A Duran
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Alexander J Valentine
- Department of Botany and Zoology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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Tharmalingam S, Alhasawi A, Appanna VP, Lemire J, Appanna VD. Reactive nitrogen species (RNS)-resistant microbes: adaptation and medical implications. Biol Chem 2017. [PMID: 28622140 DOI: 10.1515/hsz-2017-0152] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nitrosative stress results from an increase in reactive nitrogen species (RNS) within the cell. Though the RNS - nitric oxide (·NO) and peroxynitrite (ONOO-) - play pivotal physiological roles, at elevated concentrations, these moieties can be poisonous to both prokaryotic and eukaryotic cells alike due to their capacity to disrupt a variety of essential biological processes. Numerous microbes are known to adapt to nitrosative stress by elaborating intricate strategies aimed at neutralizing RNS. In this review, we will discuss both the enzymatic systems dedicated to the elimination of RNS as well as the metabolic networks that are tailored to generate RNS-detoxifying metabolites - α-keto-acids. The latter has been demonstrated to nullify RNS via non-enzymatic decarboxylation resulting in the production of a carboxylic acid, many of which are potent signaling molecules. Furthermore, as aerobic energy production is severely impeded during nitrosative stress, alternative ATP-generating modules will be explored. To that end, a holistic understanding of the molecular adaptation to nitrosative stress, reinforces the notion that neutralization of toxicants necessitates significant metabolic reconfiguration to facilitate cell survival. As the alarming rise in antimicrobial resistant pathogens continues unabated, this review will also discuss the potential for developing therapies that target the alternative ATP-generating machinery of bacteria.
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Identification of cypermethrin induced protein changes in green algae by iTRAQ quantitative proteomics. J Proteomics 2016; 139:67-76. [DOI: 10.1016/j.jprot.2016.03.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/26/2022]
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A. Alhasawi A, D. Appanna V. Manganese orchestrates a metabolic shift leading to the increased bioconversion of glycerol into α-ketoglutarate. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2017.1.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Thomas SC, Alhasawi A, Auger C, Omri A, Appanna VD. The role of formate in combatting oxidative stress. Antonie van Leeuwenhoek 2015; 109:263-71. [PMID: 26626058 DOI: 10.1007/s10482-015-0629-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/28/2015] [Indexed: 01/14/2023]
Abstract
The interaction of keto-acids with reactive oxygen species (ROS) is known to produce the corresponding carboxylic acid with the concomitant formation of CO2. Formate is liberated when the keto-acid glyoxylate neutralizes ROS. Here we report on how formate is involved in combating oxidative stress in the nutritionally-versatile Pseudomonas fluorescens. When the microbe was subjected to hydrogen peroxide (H2O2), the levels of formate were 8 and two-fold higher in the spent fluid and the soluble cell-free extracts obtained in the stressed cultures compared to the controls respectively. Formate was subsequently utilized as a reducing force to generate NADPH and succinate. The former is mediated by formate dehydrogenase (FDH-NADP), whose activity was enhanced in the stressed cells. Fumarate reductase that catalyzes the conversion of fumarate into succinate was also markedly increased in the stressed cells. These enzymes were modulated by H2O2. While the stressed whole cells produced copious amounts of formate in the presence of glycine, the cell-free extracts synthesized ATP and succinate from formate. Although the exact role of formate in anti-oxidative defence has to await further investigation, the data in this report suggest that this carboxylic acid may be a potent reductive force against oxidative stress.
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Affiliation(s)
- Sean C Thomas
- Faculty of Science, Engineering and Architecture, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - Azhar Alhasawi
- Faculty of Science, Engineering and Architecture, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - Christopher Auger
- Faculty of Science, Engineering and Architecture, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - Abdelwahab Omri
- Faculty of Science, Engineering and Architecture, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - Vasu D Appanna
- Faculty of Science, Engineering and Architecture, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
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15
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Jeon JM, Lee HI, Sadowsky MJ, Sugawara M, Chang WS. Characterization of a Functional Role of the Bradyrhizobium japonicum Isocitrate Lyase in Desiccation Tolerance. Int J Mol Sci 2015. [PMID: 26204840 PMCID: PMC4519974 DOI: 10.3390/ijms160716695] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bradyrhizobium japonicum is a nitrogen-fixing symbiont of soybean. In previous studies, transcriptomic profiling of B. japonicum USDA110, grown under various environmental conditions, revealed the highly induced gene aceA, encoding isocitrate lyase (ICL). The ICL catalyzes the conversion of isocitrate to succinate and glyoxylate in the glyoxylate bypass of the TCA cycle. Here, we evaluated the functional role of B. japonicum ICL under desiccation-induced stress conditions. We purified AceA (molecular mass = 65 kDa) from B. japonicum USDA110, using a His-tag and Ni-NTA column approach, and confirmed its ICL enzyme activity. The aceA mutant showed higher sensitivity to desiccation stress (27% relative humidity (RH)), compared to the wild type. ICL activity of the wild type strain increased approximately 2.5-fold upon exposure to 27% RH for 24 h. The aceA mutant also showed an increased susceptibility to salt stress. Gene expression analysis of aceA using qRT-PCR revealed a 148-fold induction by desiccation, while other genes involved in the glyoxylate pathway were not differentially expressed in this condition. Transcriptome analyses revealed that stress-related genes, such as chaperones, were upregulated in the wild-type under desiccating conditions, even though fold induction was not dramatic (ca. 1.5-2.5-fold).
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Affiliation(s)
- Jeong-Min Jeon
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
| | - Hae-In Lee
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
| | - Michael J Sadowsky
- Department of Soil, Water & Climate, and The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Masayuki Sugawara
- Department of Soil, Water & Climate, and The BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
| | - Woo-Suk Chang
- Department of Biology, University of Texas, Arlington, TX 76019, USA.
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 570-752, Korea.
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16
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Auger C, Appanna ND, Alhasawi A, Appanna VD. Deciphering metabolic networks by blue native polyacrylamide gel electrophoresis: A functional proteomic exploration. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Alhasawi A, Castonguay Z, Appanna ND, Auger C, Appanna VD. Glycine metabolism and anti-oxidative defence mechanisms in Pseudomonas fluorescens. Microbiol Res 2015; 171:26-31. [PMID: 25644949 DOI: 10.1016/j.micres.2014.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 11/25/2014] [Accepted: 12/07/2014] [Indexed: 12/22/2022]
Abstract
The role of metabolism in anti-oxidative defence is only now beginning to emerge. Here, we show that the nutritionally-versatile microbe, Pseudomonas fluorescens, reconfigures its metabolism in an effort to generate NADPH, ATP and glyoxylate in order to fend off oxidative stress. Glyoxylate was produced predominantly via the enhanced activities of glycine dehydrogenase-NADP(+) (GDH), glycine transaminase (GTA) and isocitrate lyase (ICL) in a medium exposed to hydrogen peroxide (H₂O₂). This ketoacid was utilized to produce ATP by substrate-level phosphorylation and to neutralize reactive oxygen species with the concomitant formation of formate. The latter was also a source of NADPH, a process mediated by formate dehydrogenase-NADP(+) (FDH). The increased activities of phosphoenolpyruvate carboxylase (PEPC) and pyruvate orthophosphate dikinase (PPDK) worked in tandem to synthesize ATP in the H₂O₂-challenged cells that had markedly diminished capacity for oxidative phosphorylation. These metabolic networks provide an effective means of combating ROS and reveal therapeutic targets against microbes resistant to oxidative stress.
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Affiliation(s)
- Azhar Alhasawi
- Faculty of Science and Engineering, Laurentian University, Sudbury, ON, Canada
| | - Zachary Castonguay
- Faculty of Science and Engineering, Laurentian University, Sudbury, ON, Canada
| | - Nishma D Appanna
- Faculty of Science and Engineering, Laurentian University, Sudbury, ON, Canada
| | - Christopher Auger
- Faculty of Science and Engineering, Laurentian University, Sudbury, ON, Canada
| | - Vasu D Appanna
- Faculty of Science and Engineering, Laurentian University, Sudbury, ON, Canada.
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18
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Alhasawi A, Auger C, Appanna VP, Chahma M, Appanna VD. Zinc toxicity and ATP production in Pseudomonas fluorescens. J Appl Microbiol 2014; 117:65-73. [PMID: 24629129 DOI: 10.1111/jam.12497] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/28/2014] [Accepted: 03/08/2014] [Indexed: 01/15/2023]
Abstract
AIMS To identify the molecular networks in Pseudomonas fluorescens that convey resistance to toxic concentrations of Zn, a common pollutant and hazard to biological systems. METHODS AND RESULTS Pseudomonas fluorescens strain ATCC 13525 was cultured in growth medium with millimolar concentrations of Zn. Enzymatic activities and metabolite levels were monitored with the aid of in-gel activity assays and high-performance liquid chromatography, respectively. As oxidative phosphorylation was rendered ineffective, the assimilation of citric acid mediated sequentially by citrate lyase (CL), phosphoenolpyruvate carboxylase (PEPC) and pyruvate phosphate dikinase (PPDK) appeared to play a key role in ATP synthesis via substrate-level phosphorylation (SLP). Enzymes generating the antioxidant, reduced nicotinamide adenine dinucleotide phosphate (NADPH) were enhanced, while metabolic modules mediating the formation of the pro-oxidant, reduced nicotinamide adenine dinucleotide (NADH) were downregulated. CONCLUSIONS Pseudomonas fluorescens reengineers its metabolic networks to generate ATP via SLP, a stratagem that allows the microbe to compensate for an ineffective electron transport chain provoked by excess Zn. SIGNIFICANCE AND IMPACT OF THE STUDY The molecular insights described here are critical in devising strategies to bioremediate Zn-polluted environments.
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Affiliation(s)
- A Alhasawi
- Department Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada
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19
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Wang C, Wang CY, Zhao XQ, Chen RF, Lan P, Shen RF. Proteomic analysis of a high aluminum tolerant yeast Rhodotorula taiwanensis RS1 in response to aluminum stress. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1969-75. [DOI: 10.1016/j.bbapap.2013.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 11/25/2022]
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20
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Luque-Almagro VM, Merchán F, Blasco R, Igeño MI, Martínez-Luque M, Moreno-Vivián C, Castillo F, Roldán MD. Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate:quinone oxidoreductase and an associated cyanide-insensitive electron transfer chain. MICROBIOLOGY-SGM 2010; 157:739-746. [PMID: 21178163 DOI: 10.1099/mic.0.045286-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to grow with cyanide as the sole nitrogen source. Membrane fractions from cells grown under cyanotrophic conditions catalysed the production of oxaloacetate from L-malate. Several enzymic activities of the tricarboxylic acid and glyoxylate cycles in association with the cyanide-insensitive respiratory pathway seem to be responsible for the oxaloacetate formation in vivo. Thus, in cyanide-grown cells, citrate synthase and isocitrate lyase activities were significantly higher than those observed with other nitrogen sources. Malate dehydrogenase activity was undetectable, but a malate:quinone oxidoreductase activity coupled to the cyanide-insensitive alternative oxidase was found in membrane fractions from cyanide-grown cells. Therefore, oxaloacetate production was linked to the cyanide-insensitive respiration in P. pseudoalcaligenes CECT5344. Cyanide and oxaloacetate reacted chemically inside the cells to produce a cyanohydrin (2-hydroxynitrile), which was further converted to ammonium. In addition to cyanide, strain CECT5344 was able to grow with several cyano derivatives, such as 2- and 3-hydroxynitriles. The specific system required for uptake and metabolization of cyanohydrins was induced by cyanide and by 2-hydroxynitriles, such as the cyanohydrins of oxaloacetate and 2-oxoglutarate.
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Affiliation(s)
- Victor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Faustino Merchán
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Rafael Blasco
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - M Isabel Igeño
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Manuel Martínez-Luque
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Francisco Castillo
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - M Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
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21
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Lemire J, Mailloux R, Auger C, Whalen D, Appanna VD. Pseudomonas fluorescens orchestrates a fine metabolic-balancing act to counter aluminium toxicity. Environ Microbiol 2010; 12:1384-90. [PMID: 20353438 DOI: 10.1111/j.1462-2920.2010.02200.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Aluminium (Al), an environmental toxin, is known to disrupt cellular functions by perturbing iron (Fe) homeostasis. However, Fe is essential for such metabolic processes as the tricarboxylic acid (TCA) cycle and oxidative phosphorylation, the two pivotal networks that mediate ATP production during aerobiosis. To counter the Fe conundrum induced by Al toxicity, Pseudomonas fluorescens utilizes isocitrate lyase and isocitrate dehydrogenase-NADP dependent to metabolize citrate when confronted with an ineffective aconitase provoked by Al stress. By invoking fumarase C, a hydratase devoid of Fe, this microbe is able to generate essential metabolites. To compensate for the severely diminished enzymes like Complex I, Complex II and Complex IV, the upregulation of a H(2)O-generating NADH oxidase enables the metabolism of citrate, the sole carbon source via a modified TCA cycle. The overexpression of succinyl-CoA synthetase affords an effective route to ATP production by substrate-level phosphorylation in the absence of O(2). This fine metabolic balance enables P. fluorescens to survive the dearth of bioavailable Fe triggered by an Al environment, a feature that may have potential applications in bioremediation technologies.
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Affiliation(s)
- Joseph Lemire
- Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
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22
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Singh R, Lemire J, Mailloux RJ, Chénier D, Hamel R, Appanna VD. An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in Pseudomonas fluorescens. PLoS One 2009; 4:e7344. [PMID: 19809498 PMCID: PMC2752808 DOI: 10.1371/journal.pone.0007344] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 09/11/2009] [Indexed: 01/05/2023] Open
Abstract
Although the tricarboxylic acid (TCA) cycle is essential in almost all aerobic organisms, its precise modulation and integration in global cellular metabolism is not fully understood. Here, we report on an alternative TCA cycle uniquely aimed at generating ATP and oxalate, two metabolites critical for the survival of Pseudomonas fluorescens. The upregulation of isocitrate lyase (ICL) and acylating glyoxylate dehydrogenase (AGODH) led to the enhanced synthesis of oxalate, a dicarboxylic acid involved in the immobilization of aluminum (Al). The increased activity of succinyl-CoA synthetase (SCS) and oxalate CoA-transferase (OCT) in the Al-stressed cells afforded an effective route to ATP synthesis from oxalyl-CoA via substrate level phosphorylation. This modified TCA cycle with diminished efficacy in NADH production and decreased CO(2)-evolving capacity, orchestrates the synthesis of oxalate, NADPH, and ATP, ingredients pivotal to the survival of P. fluorescens in an Al environment. The channeling of succinyl-CoA towards ATP formation may be an important function of the TCA cycle during anaerobiosis, Fe starvation and O(2)-limited conditions.
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Affiliation(s)
- Ranji Singh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Joseph Lemire
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ryan J. Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Daniel Chénier
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Robert Hamel
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Vasu D. Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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23
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Gene expression of halophyte Kosteletzkya virginica seedlings under salt stress at early stage. Genetica 2009; 137:189-99. [PMID: 19588254 DOI: 10.1007/s10709-009-9384-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
Gene differential expression of Kosteletzkya virginica seedlings under salt stress at two time points (2, 24 h) in roots and leaves was analyzed using the cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. Polymorphic transcript-derived fragments (TDFs) among control plants and salt-treated plants were grouped into four main differential expression patterns: repression (A), de novo induction (B), up-regulation (C) and down-regulation (D). Among them, 34 differentially expressed gene fragments were homologous to known genes from other species and 4 were sequences with unknown functions. These differentially expressed genes can be classified into four groups according to their putative functions: (1) genes for re-establishing ion homeostasis and protecting the plant from stress damage; (2) genes involved in metabolism or energy and resuming plant growth and development under salt stress; (3) genes involved in regulation of gene expression; (4) genes for signal transduction. Changes of eight differentially expressed genes were confirmed by quantitative real time RT-PCR.
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24
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Lemire J, Kumar P, Mailloux R, Cossar K, Appanna VD. Metabolic adaptation and oxaloacetate homeostasis inP. fluorescensexposed to aluminum toxicity. J Basic Microbiol 2008; 48:252-9. [DOI: 10.1002/jobm.200800007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Bakermans C, Tollaksen SL, Giometti CS, Wilkerson C, Tiedje JM, Thomashow MF. Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures. Extremophiles 2006; 11:343-54. [PMID: 17123128 DOI: 10.1007/s00792-006-0042-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 10/22/2006] [Indexed: 10/23/2022]
Abstract
It is crucial to examine the physiological processes of psychrophiles at temperatures below 4 degrees C, particularly to facilitate extrapolation of laboratory results to in situ activity. Using two dimensional electrophoresis, we examined patterns of protein abundance during growth at 16, 4, and -4 degrees C of the eurypsychrophile Psychrobacter cryohalolentis K5 and report the first identification of cold inducible proteins (CIPs) present during growth at subzero temperatures. Growth temperature substantially reprogrammed the proteome; the relative abundance of 303 of the 618 protein spots detected (approximately 31% of the proteins at each growth temperature) varied significantly with temperature. Five CIPs were detected specifically at -4 degrees C; their identities (AtpF, EF-Ts, TolC, Pcryo_1988, and FecA) suggested specific stress on energy production, protein synthesis, and transport during growth at subzero temperatures. The need for continual relief of low-temperature stress on these cellular processes was confirmed via identification of 22 additional CIPs whose abundance increased during growth at -4 degrees C (relative to higher temperatures). Our data suggested that iron may be limiting during growth at subzero temperatures and that a cold-adapted allele was employed at -4 degrees C for transport of iron. In summary, these data suggest that low-temperature stresses continue to intensify as growth temperatures decrease to -4 degrees C.
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Affiliation(s)
- Corien Bakermans
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
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26
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Mailloux RJ, Singh R, Appanna VD. In-gel activity staining of oxidized nicotinamide adenine dinucleotide kinase by blue native polyacrylamide gel electrophoresis. Anal Biochem 2006; 359:210-5. [PMID: 17083911 DOI: 10.1016/j.ab.2006.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 10/24/2022]
Abstract
Oxidized nicotinamide adenine dinucleotide (NAD(+)) kinase (NADK, E.C. 2.7.1.23) plays an instrumental role in cellular metabolism. Here we report on a blue native polyacrylamide gel electrophoretic technique that allows the facile detection of this enzyme. The product, oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)), formed following the reaction of NADK with NAD(+) and adenosine 5'-triphosphate was detected with the aid of glucose-6-phosphate dehydrogenase or NADP(+)-isocitrate dehydrogenase, iodonitrotetrazolium chloride, and phenazine methosulfate. The bands at the respective activity sites were excised and subjected to native and denaturing two-dimensional electrophoresis for the determination of protein levels. Hence this novel electrophoretic method allows the easy detection of NADK, a critical enzyme involved in pyridine homeostasis. Furthermore, this technique allowed the monitoring of the activity and expression of this kinase in various biological systems.
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Affiliation(s)
- Ryan J Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada P3E 2C6
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27
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Krause F. Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. Electrophoresis 2006; 27:2759-81. [PMID: 16817166 DOI: 10.1002/elps.200600049] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.
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Affiliation(s)
- Frank Krause
- Department of Chemistry, Physical Biochemistry, Darmstadt University of Technology, Germany.
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28
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Singh R, Chénier D, Bériault R, Mailloux R, Hamel RD, Appanna VD. Blue native polyacrylamide gel electrophoresis and the monitoring of malate- and oxaloacetate-producing enzymes. ACTA ACUST UNITED AC 2005; 64:189-99. [PMID: 16154636 DOI: 10.1016/j.jbbm.2005.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2005] [Revised: 07/05/2005] [Accepted: 07/19/2005] [Indexed: 11/20/2022]
Abstract
We demonstrate a facile blue native polyacrylamide gel electrophoresis (BN-PAGE) technique to detect two malate-generating enzymes, namely fumarase (FUM), malate synthase (MS) and four oxaloacetate-forming enzymes, namely pyruvate carboxylase (PC), phosphoenolpyruvate carboxykinase (PEPCK), citrate lyase (CL) and aspartate aminotransferase (AST). Malate dehydrogenase (MDH) was utilized as a coupling enzyme to detect either malate or oxaloacetate in the presence of their respective substrates and cofactors. The latter four oxaloacetate-forming enzymes were identified by 2,6-dichloroindophenol (DCIP) and p-iodonitrotetrazolium (INT) while the former two malate-producing enzymes were visualized by INT and phenazine methosulfate (PMS) in the reaction mixtures, respectively. The band formed at the site of enzymatic activity was easily quantified, while Coomassie staining provided information on the protein concentration. Hence, the expression and the activity of these enzymes can be readily evaluated. A two-dimensional (2D) BN-PAGE or SDS-PAGE enabled the rapid purification of the enzyme of interest. This technique also provides a quick and inexpensive means of quantifying these enzymatic activities in normal and stressed biological systems.
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Affiliation(s)
- R Singh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada P3E 2C6
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29
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Singh R, Beriault R, Middaugh J, Hamel R, Chenier D, Appanna VD, Kalyuzhnyi S. Aluminum-tolerant Pseudomonas fluorescens: ROS toxicity and enhanced NADPH production. Extremophiles 2005; 9:367-73. [PMID: 15970995 DOI: 10.1007/s00792-005-0450-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Accepted: 04/07/2005] [Indexed: 11/27/2022]
Abstract
Aluminum (Al) triggered a marked increase in reactive oxygen species (ROS) such as O(2) (-) and H(2)O(2) in Pseudomonas fluorescens. Although the Al-stressed cells were characterized with higher amounts of oxidized lipids and proteins than controls, NADPH production was markedly increased in these cells. Blue native polyacrylamide gel electrophoresis (BN-PAGE) analyses coupled with activity and Coomassie staining revealed that NADP(+) -dependent isocitrate dehydrogenase (ICDH, E.C. 1.1.1.42) and glucose-6-phosphate dehydrogenase (G6PDH, E.C. 1.1.1.49) played a pivotal role in diminishing the oxidative environment promoted by Al. These enzymes were overexpressed in the Al-tolerant microbes and were modulated by the presence of either Al or hydrogen peroxide (H(2)O(2)) or menadione. The activity of superoxide dismutase (SOD, E.C. 1.15.1.1), an enzyme known to combat ROS stress was also increased in the cells cultured in millimolar amounts of Al. Hence, Al-tolerant P. fluorescens invokes an anti-oxidative defense strategy in order to survive.
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Affiliation(s)
- Ranji Singh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E2C6, Canada
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30
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Middaugh J, Hamel R, Jean-Baptiste G, Beriault R, Chenier D, Appanna VD. Aluminum triggers decreased aconitase activity via Fe-S cluster disruption and the overexpression of isocitrate dehydrogenase and isocitrate lyase: a metabolic network mediating cellular survival. J Biol Chem 2004; 280:3159-65. [PMID: 15548528 DOI: 10.1074/jbc.m411979200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although aluminum is known to be toxic to most organisms, its precise biochemical interactions are not fully understood. In the present study, we demonstrate that aluminum promotes the inhibition of aconitase (Acn) activity via the perturbation of the Fe-S cluster in Pseudomonas fluorescens. Despite the significant decrease in citrate isomerization activity, cellular survival is assured by the overexpression of isocitrate lyase and isocitrate dehydrogenase (IDH)-NADP+. 13C NMR spectroscopic studies, Blue Native PAGE, and Western blot analyses indicated that although the decrease in Acn activity is concomitant with the increase of aluminum in the culture, the amount of Acn expressed is not sensitive to the concentration of the trivalent metal. A 6-fold decrease in Acn activity and no discernable change in protein content in aluminum-stressed cultures were observed. The addition of Fe(NH4)2(SO4)2 in a reducing environment led to a significant recovery in Acn activity. This enzymatic activity reverted to normal levels when aluminum-stressed cells were transferred to either a control or an iron-supplemented medium. The overexpression of the two isocitrate-metabolizing enzymes isocitrate lyase and IDH-NADP+ appears to mitigate the deficit in Acn activity. The levels of these enzymes are dependent on the aluminum content of the culture and appear to be under transcriptional control. Hence, the regulation of the enzymes involved in the homeostasis of isocitrate constitutes a pivotal component of the global metabolic strategy that ensures the survival of this organism in an aluminum citrate environment.
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Affiliation(s)
- Jeffrey Middaugh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario P3E 2C6, Canada
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