Genes For Pathway Enzymes Research Articles

Kynurenine 3-monooxygenase limits de novo NAD+ synthesis through dietary tryptophan in renal proximal tubule epithelial cell models.

Nicotinamide adenine dinucleotide (NAD+) is a pivotal coenzyme, essential for cellular reactions, metabolism, and mitochondrial function. Depletion of kidney NAD+ levels and reduced de novo NAD+ synthesis through the tryptophan-kynurenine pathway are linked to acute kidney injury (AKI), whereas augmenting NAD+ shows promise in reducing AKI. We investigated de novo NAD+ biosynthesis using in vitro, ex vivo, and in vivo models to understand its role in AKI. Two-dimensional (2-D) cultures of human primary renal proximal tubule epithelial cells (RPTECs) and HK-2 cells showed limited de novo NAD+ synthesis, likely due to low pathway enzyme gene expression. Using three-dimensional (3-D) spheroid culture model improved the expression of tubular-specific markers and enzymes involved in de novo NAD+ synthesis. However, de novo NAD+ synthesis remained elusive in the 3-D spheroid culture, regardless of injury conditions. Further investigation revealed that 3-D cultured cells could not metabolize tryptophan (Trp) beyond kynurenine (KYN). Intriguingly, supplementation of 3-hydroxyanthranilic acid into RPTEC spheroids was readily incorporated into NAD+. In a human precision-cut kidney slice (PCKS) ex vivo model, de novo NAD+ synthesis was limited due to substantially downregulated kynurenine 3-monooxygenase (KMO), which is responsible for KYN to 3-hydroxykynurenine conversion. KMO overexpression in RPTEC 3-D spheroids successfully reinstated de novo NAD+ synthesis from Trp. In addition, in vivo study demonstrated that de novo NAD+ synthesis is intact in the kidney of the healthy adult mice. Our findings highlight disrupted tryptophan-kynurenine NAD+ synthesis in in vitro cellular models and an ex vivo kidney model, primarily attributed to KMO downregulation.NEW & NOTEWORTHY Nicotinamide adenine dinucleotide (NAD+) is essential in regulating mitochondrial function. Reduced NAD+ synthesis through the de novo pathway is associated with acute kidney injury (AKI). Our study reveals a disruption in de novo NAD+ synthesis in proximal tubular models, but not in vivo, attributed to downregulation of enzyme kynurenine 3-monooxygenase (KMO). These findings highlight a crucial role of KMO in governing de novo NAD+ biosynthesis within the kidney, shedding light on potential AKI interventions.

Construction of an engineered Escherichia coli for effective synthesis of 2′-fucosyllactose via the salvage pathway

2′-Fucosyllactose (2′-FL) is one of the important functional oligosaccharides in breast milk. So far, few attempts on biosynthesis of 2′-FL by the salvage pathway have been reported. Herein, the salvage pathway enzyme genes were introduced into the E. coli BL21star(DE3) for synthesis of 2′-FL. The 2′-FL titer increased from 1.56 to 2.13 g/L by deleting several endogenous genes on competitive pathways. The α-1,2-fucosyltransferase (WbgL) was selected, and improved the 2′-FL titer to 2.88 g/L. Additionally, the expression level of pathway enzyme genes was tuned through optimizing the plasmid copy number. Furthermore, the spatial distribution of WbgL was enhanced by fusing with the MinD C-tag. After optimizing the fermentation conditions, the 2′-FL titer reached to 7.13 g/L. The final strain produced 59.22 g/L of 2′-FL with 95% molar conversion rate of lactose and 92% molar conversion rate of fucose in a 5 L fermenter. These findings will contribute to construct a highly efficient microbial cell factory to produce 2′-FL or other HMOs.

Tryptophan Metabolism in Obesity: The Indoleamine 2,3-Dioxygenase-1 Activity and Therapeutic Options.

Obesity activates both innate and adaptive immune responses in adipose tissue. Adipose tissue macrophages are functional antigen-presenting cells that promote the proliferation of interferon-gamma (IFN-γ)-producing cluster of differentiation (CD)4+ T cells in adipose tissue of obese subjects. The increased formation of neopterin and degradation of tryptophan may result in decreased T-cell responsiveness and lead to immunodeficiency. The activity of inducible indoleamine 2,3-dioxygenase-1 (IDO1) plays a major role in pro-inflammatory, IFN-γ-dominated settings. The expression of several kynurenine pathway enzyme genes is significantly increased in obesity. IDO1 in obesity shifts tryptophan metabolism from serotonin and melatonin synthesis to the formation of kynurenines and increases the ratio of kynurenine to tryptophan as well as with neopterin production. Reduction in serotonin (5-hydroxytryptamine; 5-HT) production provokes satiety dysregulation that leads to increased caloric uptake and obesity. According to the monoamine-deficiency hypothesis, a deficiency of cerebral serotonin is involved in neuropsychiatric symptomatology of depression, mania, and psychosis. Indeed, bipolar disorder (BD) and related cognitive deficits are accompanied by a higher prevalence of overweight and obesity. Furthermore, the accumulation of amyloid-β in Alzheimer's disease brains has several toxic effects as well as IDO induction. Hence, abdominal obesity is associated with vascular endothelial dysfunction. kynurenines and their ratios are prognostic parameters in coronary artery disease. Increased kynurenine/tryptophan ratio correlates with increased intima-media thickness and represents advanced atherosclerosis. However, after bariatric surgery, weight reduction does not lead to the normalization of IDO1 activity and atherosclerosis. IDO1 is involved in the mechanisms of immune tolerance and in the concept of tumor immuno-editing process in cancer development. Serum IDO1 activity is still used as a parameter in cancer development and growth. IDO-producing tumors show a high total IDO immunostaining score, and thus, using IDO inhibitors, such as Epacadostat, Navoximod, and L isomer of 1-methyl-tryptophan, seems an important modality for cancer treatment. There is an inverse correlation between serum folate concentration and body mass index, thus folate deficiency leads to hyperhomocysteinemia-induced oxidative stress. Immune checkpoint blockade targeting cytotoxic T-lymphocyte-associated protein-4 synergizes with imatinib, which is an inhibitor of mitochondrial folate-mediated one-carbon (1C) metabolism. Antitumor effects of imatinib are enhanced by increasing T-cell effector function in the presence of IDO inhibition. Combining IDO targeting with chemotherapy, radiotherapy and/or immunotherapy, may be an effective tool against a wide range of malignancies. However, there are some controversial results regarding the efficacy of IDO1 inhibitors in cancer treatment.

Persicaria minor F-box Gene Pmf-box1 Indirectly Affects Arabidopsis thaliana LOX-HPL Pathway for Green Leaf Volatile Production

Green leaf volatiles (GLVs) play an essential role in plant defence, plant-plant interaction and plant-insect interaction. The plant releases GLVs and inhibits the growth and propagation of plant pathogens. In this study, overexpression of PmF-box1 in wild type A. thaliana showed the downregulation of genes involved in the lipoxygenase-hydroperoxide lyase (LOX-HPL) pathway, which contributes to the biosynthesis of GLVs. It resulted in a marked reduction of hexanal production in the PmF-box1-overexpressing plant. The expression pattern of LOX-HPL branch genes in the kelch-repeat modified PmF-box1 (KMF)-overexpressing plant showed a pattern much closer to the expression of LOX-HPL branch genes in the vector control (VC) plant. It was shown that the functional KMF protein sequence was not responsible for the significant reduction of all GLVs including hexanal, 1-hexanol, (Z)-3-hexen-1-ol, and the carbon 5 (C5) volatile, 1-penten-3-ol, in plants overexpressing KMF. Furthermore, this study also showed that the relative proportion of production of 1-penten-3-ol to hexanal was higher in the PmF-box1-overexpressing plant. Based on the current comparative literature search, PmF-box1 does not appear to interact directly with the proteins or transcription factors of the LOX-HPL pathway. On the other hand, PmF-box1 interacts with SAMS1, which subsequently influences the HPL pathway enzyme genes. Thus, this study highlights the potential roles of PmF-box1 in the manipulation of GLV productions.

Prevalence of Polymorphisms of Genes Responsible for Coagulation System and Folate Metabolism and Their Predictive Value for Thrombosis Development in MINOCA Patients: Immediate and Long-Term Prognoses

(1) Background. One of the causes of myocardial infarction (MI) with nonobstructive coronary arteries (MINOCA) is thrombus formation in situ followed by lysis, resulting in a morphologically normal angiogram but with an underlying prothrombotic state that is potentially predisposed to recurrence. Recent studies have shown that a subset of MINOCA patients may have thrombophilic conditions at screening. Objective: To compare the prothrombotic trend in MINOCA patients with that of subjects with MI and obstructive coronary arteries (MIOCA) by testing for known congenital thrombophilias and markers of coagulation activation. (2) Materials and methods. Screening included congenital thrombophilias (factor V Leiden; assessment of protein C, protein S, and antithrombin III) and eight genes. Of these, four genes represented the folate pathway enzymes: MTHFR 677 C>T (rs1801133), MTHFR 1298 A>C (rs1801131), MTR 2756 A>G (rs1805087), and MTRR 66 A>G (rs1801394). The other four genes represented the blood coagulation system: F13 (163 G>T) rs5985, F1 (−455 G>A) rs1800790, GP IIb–IIIa (1565 T>C) rs5918, and PAI-I (−675 5G>4G) rs1799889. Additionally, we examined the levels of homocysteine and lipoprotein (LP) (a). (3) Results. Our study included 269 patients: 114 MINOCA patients and 155 MIOCA patients with lesions of one coronary artery. The frequencies of polymorphisms in the genes of the blood coagulation system and the folate pathway did not differ between the groups. The following genes were associated with in-hospital mortality in the MINOCA group: MTHFR 1298 A>C rs1801131 (OR 8.5; 95% CI 1.67–43.1) and F1 (−455 G>A) rs1800790 (OR 5.8; 95% CI 1.1–27.8). In the MIOCA group, the following genes were associated with in-hospital mortality: MTHFR 1298 A>C rs1801131 (OR 9.1; 95% CI 2.8–28.9), F1 (−455 G>A) rs1800790 (OR 11.4; 95% CI 3.6–35.9), GP IIb–IIIa (1565 T>C) rs5918 (OR 10.5; 95% CI 3.5–30.8), and PAI-I (−675 5G>4G) rs1799889 (OR 12.9; 95% CI 4.2–39.7). We evaluated long-term outcomes (case fatality rate, recurrent MI, and stroke) over a period of 12 months in both groups. The variables associated with these outcomes were laboratory parameters, such as protein C deficiency, hyperhomocysteinemia, and a content of LP (a) > 30 mg/dL. However, we did not reveal the prognostic value of polymorphisms of the studied genes representing the blood coagulation system and the folate pathway. (4) Conclusion. We established no statistically significant differences between the MINOCA and MIOCA groups in the prevalence of congenital thrombophilias and the prevalence of folate pathway enzyme genes and blood coagulation system genes. The MTHFR 1298 A>C (rs1801131) and F1 (−455 G>A) rs1800790 genes were associated with in-hospital mortality in both groups. More significant prognostic factors in both groups during the one-year period were protein C deficiency, hyperhomocysteinemia, and LP (a) > 30 mg/dL.

Light plays a critical role in the accumulation of chlorogenic acid in Lonicera macranthoides Hand.-Mazz

Light has important effects on plant metabolism. However, the relationship between the chlorogenic acid (CGA) content and light in plants remains unclear. Here, we investigated the effects of shading treatment on gene expression and CGA content in Lonicera macranthoides Hand.-Mazz. (LM), a widely used medicinal plant. A total of 1891 differentially expressed genes (DEGs) were obtained in flower buds and 819 in leaves in response to light in shading treatment compared to the control sample by RNA-Seq. After shading treatment, the content of CGA in LM leaves decreased significantly by 1.78-fold, the carotenoid content increased, and the soluble sugar and starch contents significantly decreased. WGCNA and the expression of related genes verified by qRT‒PCR revealed that CGA synthesis pathway enzyme genes form a co-expression network with genes for carbohydrate synthesis, photosynthesis, light signalling elements, and transcription factor genes (TFs) that affect the accumulation of CGA. Through a virus-induced gene silencing (VIGS) system and CGA assay in Nicotiana benthamiana (NB), we determined that downregulation of NbHY5 expression decreased the CGA content in NB leaves. In this study, we found that light provides energy and material for the accumulation of CGA in LM, and light affects the expression of CGA accumulation-related genes. Our results show that different light intensities have multiple effects on leaves and flower buds in LM and are able to coregulate LmHY5 expression and CGA synthesis.

Effects of itol A on the larval growth and development of Spodoptera frugiperda (Lepidoptera: Noctuidae).

Itol A, extracted from Itoa orientalis Hemsl. (Flacourtiaceae), possesses bioactivity on Spodoptera litura (Lepidoptera: Noctuidae) and Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). Our previous study showed that the effects on Spodoptera frugiperda, a destructive pest found worldwide, were similar to those of fenoxycarb (FC), a juvenile hormone analog. Thus, we speculate that itol A could have growth-regulating effects. The current work explored juvenile hormone (JH) levels and mRNA levels of crucial JH signaling pathway enzyme genes in S. frugiperda larvae treated with itol A and FC. Itol A caused severe growth obstacles in S. frugiperda, extended the larval duration and reduced the mean worm weight and body length rates. Three and 7 days after exposure to a sublethal concentration of itol A (500 mg L-1 ), the JH level of the larvae significantly decreased by 36.59% and 22.70%, respectively. qPCR inferred that the mRNA expression levels of crucial JH metabolism enzymes (SfJHE and SfJHEH) significantly increased by 6.58-fold and 2.12-fold, respectively, relative to the control group 3 days after treatment. Itol A adversely affects the development of S. frugiperda. We propose that this effect was caused by decreasing JH levels and disrupting the JH signaling pathway via mediating its synthetic and metabolic crucial enzymes. © 2021 Society of Chemical Industry.

Physiological function analysis of Lactobacillus plantarum Y44 based on genotypic and phenotypic characteristics

In our previous studies, Lactobacillus plantarum Y44 showed antioxidant activity and favorable gastric and intestinal transit tolerance. In the current study, we investigated the physiological function of L. plantarum Y44 based on an analysis of its genotype and phenotype. The complete genome of L. plantarum Y44 contained a single circular chromosome of 3,255,555 bp, with a GC content of 44.6%, and a single circular plasmid of 51,167 bp, with a GC content of 38.8%. The L. plantarum Y44 genome contained 3,293 genes including 3,112 protein coding sequences, 16 rRNAs, 66 tRNAs, 4 small (s)RNAs, and 95 pseudo genes. Lactobacillus plantarum Y44 could metabolize 24 different carbohydrate sources. Nineteen complete phosphoenolpyruvate-dependent sugar phosphotransferase system complex genes and intact Embden-Meyerhof-Parnas pathway and hexose monophosphate pathway enzyme genes, as well as abundant carbohydrate active enzyme genes, were identified in the L. plantarum Y44 genome. We also identified genes related to the biosynthesis of exopolysaccharide and surface proteins. Surface proteins played an important role in the L. plantarum Y44 adhesion to HT-29 cell monolayers, as evidenced by the removal of cell surface proteins leading to decreased adhesion capacity. The L. plantarum Y44 genome contained genes encoding chaperones, intracellular proteases, and 2-component systems, which were associated with the general stress response. Genes encoding bile salt hydrolase, F0F1-ATPase, Na+/H+-antiporter, H+/Cl- exchange transporter, cyclopropane-fatty acyl-phospholipid synthase, and alkaline shock protein were identified in the L. plantarum Y44 genome, which might explain the strain's favorable gastric and intestinal transit tolerance. Some genes associated with encoding the NADH system, glutathione system, and thioredoxin system were predicted via in silico analysis and might account for the strain's ability to scavenge reactive oxygen species. Lactobacillus plantarum Y44 was susceptive to 7 antibiotics and did not produce biogenic amines, likely due to the absence of acquired antibiotic resistance genes and amino acid decarboxylase genes. The phenotype profile of L. plantarum Y44 was associated with its genetic characteristics, indicating that strains with certain physiological functions can be screened by analyzing their phenotypic and genotypic characteristics. Lactobacillus plantarum Y44 has the potential to be used as a starter culture in fermented dairy products.

SmGRAS3 negatively responds to GA signaling while promotes tanshinones biosynthesis in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge is the origin plant of traditional Chinese medicine, Danshen. Demand of high-quality S. miltiorrhiza is increasing because of its excellent pharmaceutical value. Tanshinones and salvianolic acids (SAs) are the main active ingredients of S. miltiorrhiza. GA was reported to induce tanshinones and SAs accumulation, however, its mechanism was unclear. Here, we got a GA responsive protein, SmGRAS3. SmGRAS3 expressed highest in the periderm where tanshinones produced and accumulated. Results of SmGRAS3 over and antisense expression indicated that SmGRAS3 is a positive regulator of tanshinones biosynthesis in S. miltiorrhiza hairy roots. But overexpression of SmGRAS3 depressed SAs and GA biosynthesis as well as hairy roots growth, and application of GA could partially recover these depressions. Pathway enzyme genes expressions of tanshinones, SAs and GA biosynthesis were comprehensively changed in SmGRAS3 transgenic hairy roots. SmGRAS3 acted as a transcription factor that located in nucleus and has the transcription activation activity. Yeast one-hybrid (Y1H) and electrophoretic mobility shift assay (EMSA) showed that SmGRAS3 directly bound to GARE-motif in promoter of KSL1 and activated KSL1 transcription. Our study suggested that the SmGRAS3 may be a good potential target for further metabolic engineering of bioactive components biosynthesis in S. miltiorrhiza.

Effects of 1-MCP and storage temperature on transcription of mevalonate (MVA) enzyme genes of α-farnesene in ‘White Winter Pearmain’ apples fruit

The effects of 1-methylcylopropene (1-MCP) and storage temperature on the transcription of key mevalonate pathway enzyme genes in relation to α-farnesene and the conjugated trienols of apples (cv. White Winter Pearmain) were studied. Fruit samples were treated with 0.7 M 1-MCP and stored at 0 °C along with a control fruit were stored at 0 °C (Control@0 °C) and another group stored at 5 °C (Temp@5 °C) for 113 d. Results indicated that Temp@5 °C improved the α-farnesene and CTols content, ethylene production rate, and fruit scald compared with Control@0 °C, and 1-MCP@0 °C was significantly lower than Control@0 °C during storage. Flesh firmness and soluble solid contents of fruit remained unchanged by either treatment in the later period of storage. In response to 1-MCP treatment and storage temperature, qRT-PCR analysis revealed changes in the transcript level of the α-farnesene-related genes (HMGR family genes, MdMVK, MdFPPS, and MdAFS) during storage. Thus, the results of this study indicated that 1-MCP treatment and storage temperature could facilitate fruit storage by decreasing the expression of α-farnesene-related genes.

Two R2R3-MYB proteins are broad repressors of flavonoid and phenylpropanoid metabolism in poplar.

The phenylpropanoid pathway leads to the production of many important plant secondary metabolites including lignin, chlorogenic acids, flavonoids, and phenolic glycosides. Early studies have demonstrated that flavonoid biosynthesis is transcriptionally regulated, often by a MYB, bHLH, and WDR transcription factor complex. In poplar, several R2R3 MYB transcription factors are known to be involved in flavonoid biosynthesis. Previous work determined that poplar MYB134 and MYB115 are major activators of the proanthocyanidin pathway, and also induce the expression of repressor-like MYB transcription factors. Here we characterize two new repressor MYBs, poplar MYB165 and MYB194, paralogs which comprise a subgroup of R2R3-MYBs distinct from previously reported poplar repressors. Both MYB165 and MYB194 repressed the activation of flavonoid promoters by MYB134 in transient activation assays, and both interacted with a co-expressed bHLH transcription factor, bHLH131, in yeast two-hybrid assays. Overexpression of MYB165 and MYB194 in hybrid poplar resulted in greatly reduced accumulation of several phenylpropanoids including anthocyanins, proanthocyanidins, phenolic glycosides, and hydroxycinnamic acid esters. Transcriptome analysis of MYB165- and MYB194-overexpressing poplars confirmed repression of many phenylpropanoid enzyme genes. In addition, other MYB genes as well as several shikimate pathway enzyme genes were downregulated by MYB165-overexpression. By contrast, leaf aromatic amino acid concentrations were greater in MYB165-overexpressing poplars. Our findings indicate that MYB165 is a major repressor of the flavonoid and phenylpropanoid pathway in poplar, and may also affect the shikimate pathway. The coordinated action of repressor and activator MYBs could be important for the fine tuning of proanthocyanidin biosynthesis during development or following stress.

Inhibiting mevalonate pathway enzymes increases stromal cell resilience to a cholesterol-dependent cytolysin

Animal health depends on the ability of immune cells to kill invading pathogens, and on the resilience of tissues to tolerate the presence of pathogens. Trueperella pyogenes causes tissue pathology in many mammals by secreting a cholesterol-dependent cytolysin, pyolysin (PLO), which targets stromal cells. Cellular cholesterol is derived from squalene, which is synthesized via the mevalonate pathway enzymes, including HMGCR, FDPS and FDFT1. The present study tested the hypothesis that inhibiting enzymes in the mevalonate pathway to reduce cellular cholesterol increases the resilience of stromal cells to PLO. We first verified that depleting cellular cholesterol with methyl-β-cyclodextrin increased the resilience of stromal cells to PLO. We then used siRNA to deplete mevalonate pathway enzyme gene expression, and used pharmaceutical inhibitors, atorvastatin, alendronate or zaragozic acid to inhibit the activity of HMGCR, FDPS and FDFT1, respectively. These approaches successfully reduced cellular cholesterol abundance, but mevalonate pathway enzymes did not affect cellular resilience equally. Inhibiting FDFT1 was most effective, with zaragozic acid reducing the impact of PLO on cell viability. The present study provides evidence that inhibiting FDFT1 increases stromal cell resilience to a cholesterol-dependent cytolysin.

Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study.

Despite many developed experimental and computational approaches, functional gene annotation remains challenging. With the rapidly growing number of sequenced genomes, the concept of phylogenetic profiling, which predicts functional links between genes that share a common co-occurrence pattern across different genomes, has gained renewed attention as it promises to annotate gene functions based on presence/absence calls alone. We applied phylogenetic profiling to the problem of metabolic pathway assignments of plant genes with a particular focus on secondary metabolism pathways. We determined phylogenetic profiles for 40,960 metabolic pathway enzyme genes with assigned EC numbers from 24 plant species based on sequence and pathway annotation data from KEGG and Ensembl Plants. For gene sequence family assignments, needed to determine the presence or absence of particular gene functions in the given plant species, we included data of all 39 species available at the Ensembl Plants database and established gene families based on pairwise sequence identities and annotation information. Aside from performing profiling comparisons, we used machine learning approaches to predict pathway associations from phylogenetic profiles alone. Selected metabolic pathways were indeed found to be composed of gene families of greater than expected phylogenetic profile similarity. This was particularly evident for primary metabolism pathways, whereas for secondary pathways, both the available annotation in different species as well as the abstraction of functional association via distinct pathways proved limiting. While phylogenetic profile similarity was generally not found to correlate with gene co-expression, direct physical interactions of proteins were reflected by a significantly increased profile similarity suggesting an application of phylogenetic profiling methods as a filtering step in the identification of protein-protein interactions. This feasibility study highlights the potential and challenges associated with phylogenetic profiling methods for the detection of functional relationships between genes as well as the need to enlarge the set of plant genes with proven secondary metabolism involvement as well as the limitations of distinct pathways as abstractions of relationships between genes.

A multifunctional lipoxygenase from Pyropia haitanensis— The cloned and functioned complex eukaryotic algae oxylipin pathway enzyme

Lipoxygenases (LOXs) are critical starting biocatalysts for the synthesis of signaling compounds derived from lipid peroxidation. However, LOXs from prokaryotes or lower eukaryotes always show nonspecific and multifunctional properties. Here, an oxylipin pathway enzyme gene of eukaryotic algae, Pyropia haitanensis of Bangiaceae (Rhodophyta), named PhLOX was cloned and characterized; a phylogenetic analysis was also performed. This unique LOX isoform is a multifunctional enzyme, combined unusually high hydroperoxidelyase (HPL), lipoxygenase, and allene oxide synthase (AOS) three catalytic activities within one catalytic domain of the protein, which may explain the observed diversity of P. haitanensis oxylipins. Phylogenetic analysis indicated that red algae LOXs separated from the LOX clades of the ancestor of higher plant and animal in the early stages of evolution. The substrate flexibility, oxygenation position flexibility, and functional versatility of PhLOX represented typical properties of lower organisms. These results indicated that the origin of the oxylipin biosynthetic gene and the oxylipin biosynthetic pathway of some red algae are unique, which may shed light on the specific defense strategies of these red algae and the evolution of the oxylipin pathway as well as the compact genome of red algae.

The Histone H3 Methyltransferase G9A Epigenetically Activates the Serine-Glycine Synthesis Pathway to Sustain Cancer Cell Survival and Proliferation

Increased activation of the serine-glycine biosynthetic pathway is an integral part of cancer metabolism that drives macromolecule synthesis needed for cell proliferation. Whether this pathway is under epigenetic control is unknown. Here we show that the histone H3 lysine 9 (H3K9) methyltransferase G9A is required for maintaining the pathway enzyme genes in an active state marked by H3K9 monomethylation and for the transcriptional activation of this pathway in response to serine deprivation. G9A inactivation depletes serine and its downstream metabolites, triggering cell death with autophagy in cancer cell lines of different tissue origins. Higher G9A expression, which is observed in various cancers and is associated with greater mortality in cancer patients, increases serine production and enhances the proliferation and tumorigenicity of cancer cells. These findings identify a G9A-dependent epigenetic program in the control of cancer metabolism, providing a rationale for G9A inhibition as a therapeutic strategy for cancer.

Development of a strain for efficient degradation of polychlorinated biphenyls by patchwork assembly of degradation pathways

Rhodococcus jostii RHA1 accumulates chlorobenzoates (CBA) during the degradation of polychlorinated biphenyls (PCBs). CBA degradation is considered one of the rate-limiting steps in the complete degradation of PCBs. To reduce the accumulation of CBAs, the upper pathway enzyme genes for PCB degradation of RHA1 were introduced into a CBA-degrading bacterium, Burkholderia sp. NK8. The resulting recombinant strain exhibited no biphenyl 2,3-dioxygenase (BphA) activity encoded by bphAaAbAcAd genes, which encode the large and small subunits of the terminal oxygenase component and the ferredoxin and reductase subunits responsible for electron transfer from NADH to the large subunit. The remaining enzyme genes involved in the transformation of biphenyl to benzoate, bphB2C1D1, which encode dehydrogenase, ring-cleavage dioxygenase and hydrolase, conferred activities to NK8. To obtain the BphA activity of RHA1 in NK8, sets of BphA genes were constructed by combining the bphAaAbAcAd genes of RHA1 and bphA3A4 of Pseudomonas pseudoalcaligenes KF707, encoding the ferredoxin and reductase subunits. Hybrid derivatives of BphA containing the KF707 bphA3 conferred BphA activity to NK8, and a derivative containing the RHA1 bphAaAb and KF707 bphA3A4 genes exhibited the highest BphA activity. A plasmid containing the RHA1 bphAaAb and KF707 bphA3A4 genes plus the RHA1 bphB2C1D1 genes was constructed and introduced into NK8. The resulting recombinant strain efficiently degraded 2-, 3- and 4-chlorobiphenyls with an apparent reduction in CBA accumulation in comparison to the recombinant mutant strain, which had an insertion in the cbeA gene to inactivate CBA dioxygenase.

Effect of a High-Fat Diet on 24-Hour Pattern in Expression of Prolactin and Redox Pathway Enzymes in the Rat Adenohypophysis~!2009-06-24~!2009-10-09~!2010-06-09~!

The effect of a high-fat diet (35% fat) on 24-h changes in expression of prolactin and redox pathway enzyme genes was examined in the anterior pituitary of male rats. When body weight of high-fat fed rats attained values about 20- 25 % higher than controls (after 66 days of treatment) animals were sacrificed at 6 different time intervals throughout a 24-h cycle. Anterior pituitary mRNA levels were measured by real-time PCR analysis. In control rats expression of the prolactin gene peaked in anterior pituitary at early scotophase, 3 h in advance to the peak in plasma prolactin levels. In high-fat fed rats this correlation was lost. A disruption of 24-h rhythmicity of pituitary gene expression of heme oxygenase (HO)-2, Cu/Zn- superoxide dismutases (SOD), Mn-SOD, catalase, glutathione peroxidase (GPx) and glutathione reductase (GR) was apparent in high-fat fed rats. Anterior pituitary mRNA levels for nitric oxide synthase (NOS)-2 and HO-2, Cu/Zn- and Mn- SOD and catalase augmented in high-fat fed rats, whereas those of GPx and GR decreased. The results indicate a disrupted coordination between prolactin gene expression and prolactin release in high- fat fed rats that comes along with a disturbed expression of redox enzyme genes in the anterior pituitary.

Folate Pathway Enzyme Gene Polymorphisms and the Efficacy and Toxicity of Methotrexate in Psoriatic Arthritis

To determine the association between folate pathway gene polymorphisms and the effectiveness, toxicity, and drug survival of methotrexate (MTX) in psoriatic arthritis (PsA). Data were obtained from a longitudinal cohort of PsA patients evaluated according to a standard protocol. Data on duration of drug therapy, dose, side effects, and reasons for discontinuation are systematically recorded. Patients treated with MTX after clinic admission who had > or = 3 swollen joints prior to initiating MTX therapy were selected for evaluation of effectiveness. Response to MTX treatment was assessed at 6 months. Data from all patients treated in the clinic with MTX were used in evaluation of toxicity and drug survival. The following single-nucleotide polymorphisms (SNP) were measured using the Sequenom platform: MTHFR 677C>T (rs1801133), MTHFR 1298A>C (rs1801131), DHFR -473T>C (rs1650697), DHFR 35289A>G (rs1232027), and RFC 80G>A (rs1051266). Fisher's exact test, logistic regression, and Cox proportional hazard analyses were used to determine association. Two hundred eighty-one patients were identified from the database. All patients were included in the analysis for side effects and drug survival, and 119 patients were included in the effectiveness analysis. The minor A allele of DHFR gene at +35289 was the only SNP demonstrating association with response to MTX therapy (OR 2.99, p = 0.02). Patients homozygous for the minor allele of MTHFR 677C/T (677TT) had more liver toxicity (Fisher exact test, p = 0.04). Polymorphisms of the DHFR gene may be associated with MTX efficacy. MTHFR 677TT may have a relationship with MTX-induced liver toxicity in PsA.

Expression profiling of genes involved in paclitaxel biosynthesis for targeted metabolic engineering

Taxus plant suspension cell cultures provide a sustainable source of paclitaxel (Taxol ®) for the treatment of many cancers. To develop an optimal bioprocess for paclitaxel supply, taxane biosynthetic pathway regulation must be better understood. Here we examine the expression profile of paclitaxel biosynthetic pathway genes by RNA gel blot analysis and RT-PCR in the Taxus cuspidata cell line P991 and compare with taxane metabolite levels. Upon methyl jasmonate (MJ) elicitation (100 μM), paclitaxel accumulates to 3.3 mg/L and cephalomannine to 2.2 mg/L 7 days after elicitation but neither are observed before this time. 10-deacetylbaccatin III accumulates to 3.3 mg/L and baccatin III to 1.2 mg/L by day 7 after elicitation. The early pathway enzyme genes GGPPS, TASY, and T5αH are up-regulated by MJ elicitation within 6 h and continue through 24 h before their abundances decrease. This study reveals the preference for one side of the biosynthetic pathway branch in early taxane synthesis, where transcripts coding for T αH are abundant after elicitation with MJ but transcripts encoding the two enzymes for the alternative branch ( TDAT and T10βH) are not highly expressed following elicitation. Transcripts encoding the enzymes DBBT and DBAT are up-regulated upon MJ elicitation. Their products, 10-deacetylbaccatin III and baccatin III, respectively, accumulate within 6 h of the initial increase in transcript abundance. Importantly, the steady-state levels of the two terminal enzyme transcripts ( BAPT and DBTNBT) are much lower than transcripts of early pathway steps. These are potential steps in the pathway for targeted metabolic engineering to increase accumulation of paclitaxel in suspension cell culture.

Ethylene suppresses jasmonate-induced gene expression in nicotine biosynthesis.

In Nicotiana sylvestris, a set of nicotine biosynthesis genes were activated by exogenous application of methyl jasmonate, but the activation was effectively suppressed by simultaneous treatment with ethylene. When N. sylvestris transgenic hairy roots were treated with a natural ethylene precursor, the jasmonate-responsive expression of the promoter from a nicotine pathway enzyme gene was completely suppressed, and this suppressive effect was abolished when ethylene perception was blocked with silver cation. These and additional immunoblot results suggest that ethylene signal antagonizes jasmonate signal in nicotine biosynthesis.