• The Plant Pathology Journal
• /
• v.35 no.6
• /
• pp.609-622
• /
• 2019

Sound vibration (SV) treatment can trigger various molecular and physiological changes in plants. Previously, we showed that pre-exposure of Arabidopsis plants to SV boosts its defense response against Botrytis cinerea fungus. The present study was aimed to investigate the changes in the proteome states in the SV-treated Arabidopsis during disease progression. Proteomics analysis identified several upregulated proteins in the SV-infected plants (i.e., SV-treated plants carrying Botrytis infection). These upregulated proteins are involved in a plethora of biological functions, e.g., primary metabolism (i.e., glycolysis, tricarboxylic acid cycle, ATP synthesis, cysteine metabolism, and photosynthesis), redox homeostasis, and defense response. Additionally, our enzyme assays confirmed the enhanced activity of antioxidant enzymes in the SV-infected plants compared to control plants. Broadly, our results suggest that SV pre-treatment evokes a more efficient defense response in the SV-infected plants by modulating the primary metabolism and reactive oxygen species scavenging activity.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.9 no.6
• /
• pp.506-513
• /
• 2004

Spirulina produces $\gamma$-linolenic acid (GLA), an important pharmaceutical substance, in a relatively low level compared with fungi and plants, prompting more research to improve its GLA yield. In this study, metabolic flux analysis was applied to determine the cellular metabolic flux distributions in the GLA synthetic pathways of two Spiru/ina strains, wild type BP and a high­GLA producing mutant Z19/2. Simplified pathways involving the GLA synthesis of S. platensis formulated comprise of photosynthesis, gluconeogenesis, the pentose phosphate pathway, the anaplerotic pathway, the tricarboxylic cycle, the GLA synthesis pathway, and the biomass syn­thesis pathway. A stoichiometric model reflecting these pathways contains 17 intermediates and 22 reactions. Three fluxes - the bicarbonate (C-source) uptake rate, the specific growth rate, and the GLA synthesis rate - were measured and the remaining fluxes were calculated using lin­ear optimization. The calculation showed that the flux through the reaction converting acetyl­CoA into malonyl-CoA in the mutant strain was nearly three times higher than that in the wild­type strain. This finding implies that this reaction is rate controlling. This suggestion was sup­ported by experiments, in which the stimulating factors for this reaction $(NADPH\;and\;MgCl_{2})$ were added into the culture medium, resulting in an increased GLA-synthesis rate in the wild type strain.

• Microbiology and Biotechnology Letters
• /
• v.51 no.1
• /
• pp.37-42
• /
• 2023

Neutral and non-essential amino acid, glutamine (Gln), plays an essential role in supplying nitrogen to all the amino acids and nucleotides in the mammalian body. Gln is also the most important carbon source that provides intermediates for gluconeogenesis and fatty acid synthesis and supplements the tricarboxylic acid cycle in fast-growing cancer cells. Among the known 14 Gln transporter genes, soluted carrier family 1 member 5 (SLC1A5) has been reported to be closely associated with cancer cell growth. Three variants (v1, v2, and v3) have been derived from SLC1A5. Here, we established a heterologous gene expression system for the active form of human SLC1A5 variant-2 (hSLC1A5v2) in Escherichia coli. v2 is the smallest variant that has not yet been studied. Four expression systems were investigated: pBAD, pCold, pET, and pQE. We also addressed the problem of codon usage bias. Although pCold and pET overexpressed hSLC1A5v2 in E. coli, they were functionally inactive. hSLC1A5v2 using the pBAD system was able to catalyze the successful transport of Gln, even if it was not highly expressed. Initial activity of hSLC1A5v2 for [¹⁴C] Gln uptake in E. coli reached up to 6.73 μmole·min^-1·gDW^-1 when the cell was induced with 80 mM L-arabinose. In this study, we demonstrated a heterologous expression system for the human membrane protein, SLC1A5, in E. coli. Our results can be used for the functional comparison of SLC1A5 variants (v1, v2, and v3) in future studies, to facilitae the developement of SLC1A5 inhibitors as effective anticancer drugs.

• Korean Journal of Environmental Biology
• /
• v.40 no.4
• /
• pp.398-404
• /
• 2022

Bis(2-ethylhexyl) phthalate (DEHP) is one of the plasticizers used in the polyvinyl chloride(PVC) industry. It is known to be easily released into the environment. In this study, we investigated effects of DEHP on growth, metabolic pathway, and virulence gene expression in soil-borne bacterial plant pathogen, Pectobacterium carotovorum SCC1 using in vitro assays. As a result, DEHP at 20 ㎍ mL^-1 did not affect the growth, cell membrane permeability, or ATPase activity of P. carotovorum SCC1. However, it decreased succinyl-CoA synthase (SCS) activity in the tricarboxylic acid (TCA) cycle. Relative expression levels of virulence genes encoding pectate lyase and pectin were differentially influenced by DEHP treatment. These results suggest that biological characteristics of P. carotovorum might be influenced by DEHP in soil.

• Journal of Microbiology and Biotechnology
• /
• v.34 no.8
• /
• pp.1609-1616
• /
• 2024

The Burkholderia cepacia complex (Bcc) consists of opportunistic pathogens known to cause pneumonia in immunocompromised individuals, especially those with cystic fibrosis. Treating Bcc pneumonia is challenging due to the pathogens' high multidrug resistance. Therefore, inhalation therapy with tobramycin powder, which can achieve high antibiotic concentrations in the lungs, is a promising treatment option. In this study, we investigated potential mechanisms that could compromise the effectiveness of tobramycin therapy. By selecting for B. cenocepacia survivors against tobramycin, we identified three spontaneous mutations that disrupt a gene encoding a key enzyme in the biosynthesis of cobalamin (Vitamin B₁₂). This disruption may affect the production of succinyl-CoA by methylmalonyl-CoA mutase, which requires adenosylcobalamin as a cofactor. The depletion of cellular succinyl-CoA may impact the tricarboxylic acid (TCA) cycle, which becomes metabolically overloaded upon exposure to tobramycin. Consequently, the mutants exhibited significantly reduced reactive oxygen species (ROS) production. Both the wild-type and mutants showed tolerance to tobramycin and various other bactericidal antibiotics under microaerobic conditions. This suggests that compromised ROS-mediated killing, due to the impacted TCA cycle, underlies the mutants' tolerance to bactericidal antibiotics. The importance of ROS-mediated killing and the potential emergence of mutants that evade it through the depletion of cobalamin (Vitamin B₁₂) provide valuable insights for developing strategies to enhance antibiotic treatments of Bcc pneumonia.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.12
• /
• pp.2106-2115
• /
• 2016

To identify the global effects of (p)ppGpp in the gram-positive bacterium Deinococcus radiodurans, which exhibits remarkable resistance to radiation and other stresses, RelA/SpoT homolog (RSHs) mutants were constructed by direct deletion mutagenesis. The results showed that RelA has both synthesis and hydrolysis domains of (p)ppGpp, whereas RelQ only synthesizes (p)ppGpp in D. radiodurans. The growth assay for mutants and complementation analysis revealed that deletion of relA and relQ sensitized the cells to $H_2O_2$, heat shock, and amino acid limitation. Comparative proteomic analysis revealed that the bifunctional RelA is involved in DNA repair, molecular chaperone functions, transcription, the tricarboxylic acid cycle, and metabolism, suggesting that relA maintains the cellular (p)ppGpp levels and plays a crucial role in oxidative resistance in D. radiodurans. The D. radiodurans relA and relQ genes are responsible for (p)ppGpp synthesis/hydrolysis and (p)ppGpp hydrolysis, respectively. (p)ppGpp integrates a general stress response with a targeted re-programming of gene regulation to allow bacteria to respond appropriately towards heat shock, oxidative stress, and starvation. This is the first identification of RelA and RelQ involvement in response to oxidative, heat shock, and starvation stresses in D. radiodurans, which further elucidates the remarkable resistance of this bacterium to stresses.

• Journal of Life Science
• /
• v.31 no.8
• /
• pp.778-785
• /
• 2021

The germination of cucumber seeds begins with the degradation of reserved oil to fatty acids within the lipid body, which are then further metabolized to acyl-CoA. The acyl-CoA moves from the lipid body to the glyoxysome following β-oxidation for the production of acetyl-CoA. As an initial carbon source supplier, acetyl-CoA is an essential molecule in the glyoxylate cycle within the glyoxysome, which produces the metabolic intermediates of citrate and malate, among others. The glyoxylate cycle is a necessary metabolic pathway for oil seed plant germination because it produces the metabolic intermediates for the tricarboxylic acid (TCA) cycle and for gluconeogenesis, such as the oxaloacetate, which moves to the cytosol for the initiation of gluconeogenesis by phophoenolpyruvate carboxykinase (PEPCK). Following reserved oil mobilization, the production and transport of various metabolic intermediates are involved in the coordinated operation and activation of multiple metabolic pathways to supply directly usable carbohydrate in the form of glucose. Furthermore, corresponding gene expression regulation compatibly transforms the microbody to glyoxysome, which contains the organelle-specific malate synthase (MS) and isocitrate lyase (ICL) enzymes during oil seed germination. Together with glyoxylate cycle, carnitine, which mediates the supplementary route of the acetyl-CoA transport mechanism via the mitochondrial BOU (A BOUT DE SOUFFLE) system, possibly plays a secondary role in lipid metabolism for enhanced plant development.

• Microbiology and Biotechnology Letters
• /
• v.38 no.4
• /
• pp.349-361
• /
• 2010

In this review, the current knowledge of the carbon metabolism and global carbon regulation in Corynebacterium glutamicum are summarized. C. gluamicum has phosphotransferase system (PTS) for the utilization of sucrose, glucose, and fructose. C. glutamicum does not show any preference for glucose when various sugars or organic acids are present with glucose, and thus cometabolizes glucose with other sugars or organic acids. The molecular mechanism of global carbon regulation such as carbon catabolite repression (CCR) in C. glutamicum is quite different to that in Gram-negative or low-GC Gram-positive bacteria. GlxR (glyoxylate bypass regulator) in C. glutamicum is the cyclic AMP receptor protein (CRP) homologue of E. coli. GlxR has been reported to regulate genes involved in not only glyoxylate bypass, but also central carbon metabolism and CCR including glycolysis, gluconeogenesis, and tricarboxylic acid (TCA) cycle. Therefore, GlxR has been suggested as a global transcriptional regulator for the regulation of diverse physiological processes as well as carbon metabolism. Adenylate cyclase of C. glutamicum is a membrane protein belonging to class III adenylate cyclases, thus it could possibly be a sensor for some external signal, thereby modulating cAMP level in response to environmental stimuli. In addition to GlxR, three additional transcriptional regulators like RamB, RamA, and SugR are also involved in regulating the expression of many genes of carbon metabolism. Finally, recent approaches for constructing new pathways for the utilization of new carbon sources, and strategies for enhancing amino acid production through genetic modification of carbon metabolism or regulatory network are described.

• BMB Reports
• /
• v.45 no.7
• /
• pp.419-424
• /
• 2012

High-fat diets (HFD) and high-carbohydrate diets (HCD)-induced obesity through different pathways, but the metabolic differences between these diets are not fully understood. Therefore, we applied proton nuclear magnetic resonance ($^1H$ NMR)-based metabolomics to compare the metabolic patterns between C57BL/6 mice fed HCD and those fed HFD. Principal component analysis derived from $^1H$ NMR spectra of urine showed a clear separation between the HCD and HFD groups. Based on the changes in urinary metabolites, the slow rate of weight gain in mice fed the HCD related to activation of the tricarboxylic acid cycle (resulting in increased levels of citrate and succinate in HCD mice), while the HFD affected nicotinamide metabolism (increased levels of 1-methylnicotineamide, nicotinamide-N-oxide in HFD mice), which leads to systemic oxidative stress. In addition, perturbation of gut microflora metabolism was also related to different metabolic patterns of those two diets. These findings demonstrate that $^1H$ NMR-based metabolomics can identify diet-dependent perturbations in biological pathways.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.11
• /
• pp.1943-1950
• /
• 2016

Polycyclic aromatic hydrocarbons (PAHs) are commonly present xenobiotics in natural and contaminated soils. We studied three (phenanthrene, naphthalene, and biphenyl) xenobiotics, catabolism, and associated proteins in Sphingobium chungbukense DJ77 by two-dimensional gel electrophoresis (2-DE) analysis. Comparative analysis of the growth-dependent 2-DE results revealed that the intensity of 10 protein spots changed identically upon exposure to the three xenobiotics. Among the upregulated proteins, five protein spots, which were putative dehydrogenase, dioxygenase, and hydrolase and involved in the catabolic pathway of xenobiotic degradation, were induced. Identification of these major multifunctional proteins allowed us to map the multiple catabolic pathway for phenanthrene, naphthalene, and biphenyl degradation. A part of the initial diverse catabolism was converged into the catechol degradation branch. Detection of intermediates from 2,3-dihydroxy-biphenyl degradation to pyruvate and acetyl-CoA production by LC/MS analysis showed that ring-cleavage products of PAHs entered the tricarboxylic acid cycle, and were mineralized in S. chungbukense DJ77. These results suggest that S. chungbukense DJ77 completely degrades a broad range of PAHs via a multiple catabolic pathway.