Alternative Biosynthetic Pathway Research Articles

Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli.

Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthesis of commercially attractive molecules often involves promiscuous enzymes or lacks well-established routes. To address these challenges, we developed a computational workflow integrating enumeration/retrosynthesis algorithms, a toolbox for pathway analysis, enzyme selection tools, and a gene discovery pipeline, supported by manual curation and literature review. Our focus has been on implementing biosynthetic pathways for tyrosine-derived compounds, specifically L-3,4-dihydroxyphenylalanine (L-DOPA) and dopamine, with significant applications in health and nutrition. We selected one pathway to produce L-DOPA and two different pathways for dopamine-one already described in the literature and a novel pathway. Our goal was either to identify the most suitable gene candidates for expression in Escherichia coli for the known pathways or to discover innovative pathways. Although not all implemented pathways resulted in the accumulation of target compounds, in our shake-flask experiments we achieved a maximum L-DOPA titer of 0.71g/L and dopamine titers of 0.29 and 0.21g/L for known and novel pathways, respectively. In the case of L-DOPA, we utilized, for the first time, a mutant version of tyrosinase from Ralstonia solanacearum. Production of dopamine via the known biosynthesis route was accomplished by coupling the L-DOPA pathway with the expression of DOPA decarboxylase from Pseudomonas putida, resulting in a unique biosynthetic pathway never reported in literature before. In the context of the novel pathway, dopamine was produced using tyramine as the intermediate compound. To achieve this, tyrosine was initially converted into tyramine by expressing TDC from Levilactobacillus brevis, which, in turn, was converted into dopamine through the action of the enzyme encoded by ppoMP from Mucuna pruriens. This marks the first time that an alternative biosynthetic pathway for dopamine has been validated in microbes. These findings underscore the effectiveness of our computational workflow in facilitating pathway enumeration and selection, offering the potential to uncover novel biosynthetic routes, thus paving the way for other target compounds of biotechnological interest.

Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution

Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7’s genome.

Over-expression of GGP1 and GPP genes enhances ascorbate content and nutritional quality of tomato

L-Ascorbic acid (AsA), a strong antioxidant, serves as an enzyme cofactor and redox status marker, modulating a plethora of biological processes. As tomato commercial varieties and hybrids possess relatively low amounts of AsA, the improvement of fruit AsA represents a strategic goal for enhanced human health. Previously, we have suggested that GDP-L-Galactose phosphorylase (GGP) and L-galactose-1-phosphate phosphatase (GPP) can serve as possible targets for AsA manipulation in tomato (Solanum lycopersicon L.) fruit. To this end, we produced and evaluated T3 transgenic tomato plants carrying these two genes under the control of CaMV-35S and two fruit specific promoters, PPC2 and PG-GGPI. The transgenic lines had elevated levels of AsA, with the PG-GGP1 line containing 3-fold more AsA than WT, without affecting fruit characteristics. Following RNA-Seq analysis, 164 and 13 DEGs were up- or down-regulated, respectively, between PG-GGP1 and WT pink fruits. PG-GGP1 fruit had a distinct number of up-regulated transcripts associated with cell wall modification, ethylene biosynthesis and signaling, pollen fertility and carotenoid metabolism. The elevated AsA accumulation resulted in the up regulation of AsA associated transcripts and alternative biosynthetic pathways suggesting that the entire metabolic pathway was influenced, probably via master regulation. We show here that AsA-fortification of tomato ripe fruit via GGP1 overexpression under the action of a fruit specific promoter PG affects fruit development and ripening, reduces ethylene production, and increased the levels of sugars, and carotenoids, supporting a robust database to further explore the role of AsA induced genes for agronomically important traits, breeding programs and precision gene editing approaches.

A mathematical model for strigolactone biosynthesis in plants.

Strigolactones mediate plant development, trigger symbiosis with arbuscular mycorrhizal fungi, are abundant in 80% of the plant kingdom and help plants gain resistance to environmental stressors. They also induce germination of parasitic plant seeds that are endemic to various continents, such as Orobanche in Europe or Asia and Striga in Africa. The genes involved in the early stages of strigolactones biosynthesis are known in several plants. The regulatory structure and the latter parts of the pathway, where flux branching occurs to produce alternative strigolactones, are less well-understood. Here we present a computational study that collects the available experimental evidence and proposes alternative biosynthetic pathways that are consistent with that evidence. Then, we test the alternative pathways through in silico simulation experiments and compare those experiments to experimental information. Our results predict the differences in dynamic behavior between alternative pathway designs. Independent of design, the analysis suggests that feedback regulation is unlikely to exist in strigolactone biosynthesis. In addition, our experiments suggest that engineering the pathway to modulate the production of strigolactones could be most easily achieved by increasing the flux of β-carotenes going into the biosynthetic pathway. Finally, we find that changing the ratio of alternative strigolactones produced by the pathway can be done by changing the activity of the enzymes after the flux branching points.

Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets.

Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.

Amino Acid Metabolism Controls Fatty Acid Structure in Staphylococcus aureus

Staphylococcus aureus produces a combination of branched and straight chain fatty acids to maintain membrane homeostasis. Recently, we showed that the branched:straight chain ratio in fatty acids is controlled by amino acid metabolism that supplies the branched‐chain acyl‐CoA primers for fatty acid biosynthesis. The fatty acid composition is determined when FabH catalyzes the initial condensation using the available short‐chain acyl‐CoA primers with malonyl‐acyl carrier protein. Branched‐chain ketoacid dehydrogenase (Bkd) is recognized as the primary enzyme responsible for the formation of branched‐chain acyl‐CoA primers. Most experiments with S. aureus are carried out in media with an abundant supply of branched‐chain amino acids where the Bkd pathway for the utilization of Ile dominates. However, branched‐chain fatty acids are still produced in bkd knockout strains and the enzyme(s) responsible for this alternate biosynthetic pathway is unknown. It is important to understand how S. aureus copes with limited availability of Ile because multiple laboratories conclude that isoleucine is a limiting nutrient at S. aureus infection sites that regulates metabolism and virulence.Mass tracing experiments with heavy amino acids show that Bkd is the key step in a pathway that selectively converts extracellular Ile into 2‐methyl‐butyryl‐CoA (anteiso‐C5‐CoA) that FabH uses to initiate anteiso fatty acid synthesis. The phosphatidylglycerol (PG) molecular species in wild‐type strains consists of a mixture of anteiso‐17:0 and ‐19:0 and 18:0 and 20:0 straight chain fatty acids in the 1‐position paired with anteiso‐15:0 in the 2‐position. If Ile is removed from the medium, Leu metabolism results in the introduction of iso‐15:0 into the 2‐position. Val is not significantly metabolized by the Bkd pathway. The analysis of the PG molecular species in strains lacking an active Bkd complex have a straight chain fatty acid in the 1‐position paired with either iso‐14:0 or anteiso‐15:0 in the 2‐position. This same switch in PG molecular species composition is observed when wild‐type strains are grown in defined medium lacking both Ile and Leu. Our metabolomics analyses show that C5‐CoA derived from the Bkd pathway is the most abundant acyl‐CoA primer available for FabH in wild‐type strains; however, when Ile and Leu are not present in the medium, iso‐C4‐CoA increases and anateiso‐C5‐CoA decreases. In the bkd knockout strains, the C4‐CoA pool is even more elevated, and the C5‐CoA pool is substantially lower. This means that in the absence of Bkd, a second pathway creates a supply of iso‐C4‐CoA for FabH to prime fatty acid synthesis and produce iso‐14:0 for the 2‐position. Thus, there are two pathways for the formation of branched‐chain acyl‐CoA substrates for FabH. The Bkd pathway is responsible for the utilization of extracellular Ile (and to a lesser extent, Leu) to initiate fatty acid synthesis, whereas the alternate, de novo biosynthetic pathway makes a significant contribution in wild‐type strain growth without exogenous Ile and is the only process operating in the bkd knockout strains. We are testing the hypothesis that the key enzyme in the de novo pathway to iso‐C4‐CoA is CidC, an enzyme related to pyruvate oxidase.

Bioinformatic comparison of three Embleya species and description of steffimycins production by Embleya sp. NF3.

The Embleya genus is a new member of the Streptomycetaceae family formed by only two species isolated from soil (Embleya scabrispora and Embleya hyalina). Strain NF3 is an endophytic actinobacterium obtained from the medicinal tree Amphipterygium adstringens. By 16S rRNA gene analysis, NF3 strain was identified as Embleya sp., closely related to E. hyalina. In our interest to deep into the NF3 strain features, a bioinformatic study was performed on the Embleya genus based on their genome information to produce secondary metabolites. A comparative analysis of the biosynthetic gene clusters (BGCs) of NF3 with the two released Embleya genomes revealed that NF3 has 49 BGCs, E. scabrispora DSM41855 has 50 BGCs, and E. hyalina NBRC13850 has 46 BGCs. Although bearing similar cluster numbers, the three strains shared only 25% of the BGCs information. NF3 encoded the nybomycin cluster detected in E. hyalina NBRC13850 and lacked the hitachimycin cluster present in E. scabrispora DSM41855. On the contrary, strain NF3 contained a cluster for the anthracycline steffimycin, neither encoded by E. hyalina NBRC13850 nor by E. scabrispora DSM41855. Our results and previous characterization studies supported strain NF3 as a new member of the genus Embleya. The chemical analysis of the steffimycins produced by strain NF3 showed the production of eight compounds of the steffimycins and steffimycinone families. Four of these molecules have already been described: steffimycin B, steffimycin C, 8-demethoxy-10-deoxysteffimycinone, and 7-deoxiesteffimycinone, and four are new natural products: 8-demethoxysteffimycin B, 8-demethoxy-10-deoxysteffimycin B, 7-deoxy-8-demethoxysteffimycinone, and 7-deoxy-10-deoxysteffimycinone. With this information, we proposed an alternative pathway to produce StefB. Among steffimycins, StefB was the main compound produced by this strain (29.8%) and showed the best cytotoxic activity. KEY POINTS: • The Embleya genus and its biosynthetic potential • An alternative biosynthetic pathway for steffimycins biosynthesis • Four new natural products of the steffimycin family.

Discovery and Biomimetic Synthesis of a Polycyclic Polymethylated Phloroglucinol Collection from Rhodomyrtus tomentosa.

Inspired by a previously reported biomimetic synthesis study, four new naturally occurring phloroglucinol trimers 1-4 with unusual 6/5/5/6/6/6-fused hexacyclic ring systems, along with two known analogues (5 and 6) and two known biogenetically related dimers (10 and 11), were isolated from Rhodomyrtus tomentosa. Their structures and absolute configurations were unambiguously elucidated by spectroscopic analysis, X-ray diffraction, and electronic circular dichroism calculation. By mimicking two potentially alternative biosynthetic pathways, the first asymmetric syntheses of 1-4 and the racemic syntheses of 5 and 6 were achieved in only five to six steps without the need for protecting groups. Furthermore, phloroglucinol dimers 10 and 11 exhibited significant in vitro antiviral activity against the respiratory syncytial virus.

Acetyl-CoA-Mediated Post-Biosynthetic Modification of Desferrioxamine B Generates N- and N-O-Acetylated Isomers Controlled by a pH Switch.

Biosynthesis of the hydroxamic acid siderophore desferrioxamine D1 (DFOD1, 6), which is the N-acetylated analogue of desferrioxamine B (DFOB, 5), has been delineated. Enzyme-independent Ac-CoA-mediated N-acetylation of 5 produced 6, in addition to three constitutional isomers containing an N-O-acetyl group installed at either one of the three hydroxamic acid groups of 5. The formation of N-Ac-DFOB (DFOD1, 6) and the composite of N-O-acetylated isomers N-O-Ac-DFOB[001] (6a), N-O-Ac-DFOB[010] (6b), and N-O-Ac-DFOB[100] (6c) (defined as the N-O-Ac motif positioned within the terminal amine, internal, or N-acetylated region of 5, respectively), was pH-dependent, with 6a-6c dominant at pH < 8.5 and 6 dominant at pH > 8.5. The trend in the pH dependence was consistent with the pKa values of the NH3+ (pKa ∼ 10) and N-OH (pKa ∼ 8.5-9) groups in 5. The N- and N-O-acetyl motifs can be conceived as a post-biosynthetic modification (PBM) of a nonproteinaceous secondary metabolite, akin to a post-translational modification (PTM) of a protein. The pH-labile N-O-acetyl group could act as a reversible switch to modulate the properties and functions of secondary metabolites, including hydroxamic acid siderophores. An alternative (most likely minor) biosynthetic pathway for 6 showed that the nonribosomal peptide synthetase-independent siderophore synthetase DesD was competent in condensing N'-acetyl-N-succinyl-N-hydroxy-1,5-diaminopentane (N'-Ac-SHDP, 7) with the dimeric hydroxamic acid precursor (AHDP-SHDP, 4) native to 5 biosynthesis to generate 6. The strategy of diversifying protein structure and function using PTMs could be paralleled in secondary metabolites with the use of PBMs.

Progress toward a biomimetic synthesis of pegaharmaline A.

Efforts towards a biomimetic synthesis of the alkaloid pegaharmaline A began with attempted validation of the putative biosynthesis described in the isolation report. The reaction between vasicinone-derived pyrroloquinazoline 1 and tryptamines 2 and 9 proceeded under aqueous conditions at ambient temperature, forming the 1,6,10-triazaspiro[4.5]dec-7-anes 7 and 8. Alternative pyrroloquinazoline precursors were subsequently investigated; the reaction between dehydrodimethylisovasicinone (10) and tryptamine (9) led to the ring-opened product 13 that could not be converted into pegaharmaline A scaffold under Bischler-Napieralski conditions. The Pictet-Spengler reaction between a model isovasicinone (22) and tryptamine (9) was successful, but the resulting tetrahydro-β-carboline could not be converted into the natural product. These studies suggest an alternative biosynthetic pathway is potentially operating, while structural revision of the natural product cannot be ruled out at this time. As vasicinones and tryptamines are widely distributed throughout Nature, the novel scaffolds reported herein may be undiscovered natural products.

Defining Color Change in Pitaya: A Close Look at Betacyanin Synthesis Genes in Stenocereus queretaroensis

Betalains are tyrosine-derived plant pigments present in several species of the Caryophyllales order. Betalains are classified in red betacyanins and yellow betaxanthins and are implicated in plant stress tolerance and visual attraction for pollinators. The compounds are used as natural colorants in many industries. Today, there is little information on betalain biosynthesis with several key enzymes that remain unknown on plants of the Caryophyllales order. Omic tools have proven to be very useful in gaining insights into various molecular mechanisms. In this study, we used suspension cells from fruits of the cactus Stenocereus queretaroensis. Two growing conditions were used to perform RNA-seq and differential expression analysis to help identify betalain biosynthesis-related genes. We found 98 differential expressed genes related to aromatic amino acids and betalain biosynthesis pathways. Interestingly, we found that only one gene of the betalain synthesis pathway was differentially expressed. The rest of the genes belong to the aromatic amino acid pathway, including hydroxy phenylpyruvate-related genes, suggesting the possibility of an alternative biosynthetic pathway similar to that observed in legumes.

Kynurenine pathway as alternative biosynthetic pathway for fusaric acid in Fusarium oxysporum f.sp. cubense

Banana fusarium wilt caused by Fusarium. oxysporum f.sp. cubense race 4, has already become one of the main diseases in banana production. Previous research suggests that Foc can secrete two phytotoxins, respectively, fusaric acid and beauvericin, to contribute to its pathogenicity when it infects bananas. A gene cluster FUB consisting of 12 genes has been identified for fusaric acid biosynthesis in several Fusarium spp, including Fusarium. oxysporum f.sp. cubense race 4, F. oxysporum f.sp. lycopersici etc. In the present study, using reverse genetic research methods, we report the evidence for the kynurenine pathway as alternative biosynthetic pathways of fusaric acid in F. oxysporum f.sp. cubense 4. In the meanwhile, our experiments suggests that the beauvericin might not directly contribute to the pathogenicity to banana of F. oxysporum f.sp. cubense 4.

Flavonoids from Woodfordia fruticosa as potential SmltD inhibitors in the alternative biosynthetic pathway of peptidoglycan

SmltD is an ATP-dependent ligase that catalyzes the condensation of UDP-MurNAc-l-Ala and l-Glu to form UDP-MurNAc-l-Ala-l-Glu, in the newly discovered peptidoglycan biosynthesis pathway of a Gram-negative multiple-drug-resistant pathogen, Stenotrophomonas maltophilia. Phytochemical investigation of the 70% ethanol extract from Woodfordia fruticosa flowers collected in Myanmar led to the identification of anti-SmltD active flavonoids, kaempferol 3-O-(6′′-galloyl)-β-d-glucopyranoside (1), astragalin (2), and juglalin (3). Among them, 1 showed the most potent SmltD inhibitory activity. An enzyme steady-state kinetic study revealed that 1 exerted competitive inhibition with respect to ATP. The results of this study provided an attractive foundation for the further development of novel inhibitors of SmltD.

Chemical Basis of Floral Color Signals in Gesneriaceae: The Effect of Alternative Anthocyanin Pathways.

Changes in floral pigmentation can have dramatic effects on angiosperm evolution by making flowers either attractive or inconspicuous to different pollinator groups. Flower color largely depends on the type and abundance of pigments produced in the petals, but it is still unclear whether similar color signals rely on same biosynthetic pathways and to which extent the activation of certain pathways influences the course of floral color evolution. To address these questions, we investigated the physical and chemical aspects of floral color in the Neotropical Gesnerioideae (ca. 1,200 spp.), in which two types of anthocyanins, hydroxyanthocyanins, and deoxyanthocyanins, have been recorded as floral pigments. Using spectrophotometry, we measured flower reflectance for over 150 species representing different clades and pollination syndromes. We analyzed these reflectance data to estimate how the Gesnerioideae flowers are perceived by bees and hummingbirds using the visual system models of these pollinators. Floral anthocyanins were further identified using high performance liquid chromatography coupled to mass spectrometry. We found that orange/red floral colors in Gesnerioideae are produced either by deoxyanthocyanins (e.g., apigenidin, luteolinidin) or hydroxyanthocyanins (e.g., pelargonidin). The presence of deoxyanthocyanins in several lineages suggests that the activation of the deoxyanthocyanin pathway has evolved multiple times in the Gesnerioideae. The hydroxyanthocyanin-producing flowers span a wide range of colors, which enables them to be discriminated by hummingbirds or bees. By contrast, color diversity among the deoxyanthocyanin-producing species is lower and mainly represented at longer wavelengths, which is in line with the hue discrimination optima for hummingbirds. These results indicate that Gesnerioideae have evolved two different biochemical mechanisms to generate orange/red flowers, which is associated with hummingbird pollination. Our findings also suggest that the activation of the deoxyanthocyanin pathway has restricted flower color diversification to orange/red hues, supporting the potential constraining role of this alternative biosynthetic pathway on the evolutionary outcome of phenotypical and ecological diversification.

Mammalian-Like Inflammatory and Pro-Resolving Oxylipins in Marine Algae.

Oxylipins constitute a family of oxidized fatty acids, that are well known as tissue hormones in mammals. They contribute to inflammation and its resolution. The major classes of these lipid mediators are inflammatory prostaglandins (PGs) and leukotrienes (LTs) as well as pro‐resolving resolvins (Rvs). Understanding their biosynthetic pathways and modes of action is important for anti‐inflammatory interventions. Besides mammals, marine algae also biosynthesize mammalian‐like oxylipins and thus offer new opportunities for oxylipin research. They provide prolific sources for these compounds and offer unique opportunities to study alternative biosynthetic pathways to the well‐known lipid mediators. Herein, we discuss recent findings on the biosynthesis of oxylipins in mammals and algae including an alternative pathway to prostaglandin E2, a novel pathway to a precursor of leukotriene B4, and the production of resolvins in algae. We evaluate the pharmacological potential of the algal metabolites with implications in health and disease.

Characterization of Miharamycin Biosynthesis Reveals a Hybrid NRPS-PKS to Synthesize High-Carbon Sugar from a Complex Nucleoside.

Miharamycins are peptidyl nucleoside antibiotics with a unique branched C9 pyranosyl amino acid core and a rare 2-aminopurine moiety. Inactivation of 19 genes in the biosynthetic gene cluster and identification of several unexpected intermediates suggest an alternative biosynthetic pathway, which is further supported by feeding experiments and in vitro characterization of an unusual adenylation domain recognizing a complex nucleoside derivative as the substrate. These results thereby provide an unprecedented biosynthetic route of high-carbon sugar catalyzed by atypical hybrid nonribosomal peptide synthetase-polyketide synthase.

Reductive tricarboxylic acid cycle enzymes and reductive amino acid synthesis pathways contribute to electron balance in a Rhodospirillum rubrum Calvin-cycle mutant.

Purple non-sulfur bacteria (PNSB) use light for energy and organic substrates for carbon and electrons when growing photoheterotrophically. This lifestyle generates more reduced electron carriers than are required for biosynthesis, even during consumption of some of the most oxidized organic substrates like malate and fumarate. Reduced electron carriers not used in biosynthesis must still be oxidized for photoheterotrophic growth to occur. Diverse PNSB commonly rely on the CO2-fixing Calvin cycle to oxidize reduced electron carriers. Some PNSB also produce H2 or reduce terminal electron acceptors as alternatives to the Calvin cycle. Rhodospirillum rubrum Calvin-cycle mutants defy this trend by growing phototrophically on malate or fumarate without H2 production or access to terminal electron acceptors. We used 13C-tracer experiments to examine how a Rs. rubrum Calvin-cycle mutant maintains electron balance under such conditions. We detected the reversal of some tricarboxylic acid cycle enzymes, carrying reductive flux from malate or fumarate to αKG. This pathway and the reductive synthesis of αKG-derived amino acids are likely important for electron balance, as supplementing the growth medium with αKG-derived amino acids prevented Rs. rubrum Calvin-cycle-mutant growth unless a terminal electron acceptor was provided. Flux estimates also suggested that the Calvin-cycle mutant preferentially synthesized isoleucine using the reductive threonine-dependent pathway instead of the less-reductive citramalate-dependent pathway. Collectively, our results suggest that alternative biosynthetic pathways can contribute to electron balance within the constraints of a relatively constant biomass composition.

15‐Hydroperoxy‐PGE2: Intermediate in Mammalian and Algal Prostaglandin Biosynthesis

AbstractArachidonic‐acid‐derived prostaglandins (PGs), specifically PGE2, play a central role in inflammation and numerous immunological reactions. The enzymes of PGE2 biosynthesis are important pharmacological targets for anti‐inflammatory drugs. Besides mammals, certain edible marine algae possess a comprehensive repertoire of bioactive arachidonic‐acid‐derived oxylipins including PGs that may account for food poisoning. Described here is the analysis of PGE2 biosynthesis in the red macroalga Gracilaria vermiculophylla that led to the identification of 15‐hydroperoxy‐PGE2, a novel precursor of PGE2 and 15‐keto‐PGE2. Interestingly, this novel precursor is also produced in human macrophages where it represents a key metabolite in an alternative biosynthetic PGE2 pathway in addition to the well‐established arachidonic acid‐PGG2‐PGH2‐PGE2 route. This alternative pathway of mammalian PGE2 biosynthesis may open novel opportunities to intervene with inflammation‐related diseases.

15-Hydroperoxy-PGE2 : Intermediate in Mammalian and Algal Prostaglandin Biosynthesis.

Arachidonic‐acid‐derived prostaglandins (PGs), specifically PGE2, play a central role in inflammation and numerous immunological reactions. The enzymes of PGE2 biosynthesis are important pharmacological targets for anti‐inflammatory drugs. Besides mammals, certain edible marine algae possess a comprehensive repertoire of bioactive arachidonic‐acid‐derived oxylipins including PGs that may account for food poisoning. Described here is the analysis of PGE2 biosynthesis in the red macroalga Gracilaria vermiculophylla that led to the identification of 15‐hydroperoxy‐PGE2, a novel precursor of PGE2 and 15‐keto‐PGE2. Interestingly, this novel precursor is also produced in human macrophages where it represents a key metabolite in an alternative biosynthetic PGE2 pathway in addition to the well‐established arachidonic acid‐PGG2‐PGH2‐PGE2 route. This alternative pathway of mammalian PGE2 biosynthesis may open novel opportunities to intervene with inflammation‐related diseases.

Dysregulated transmethylation leading to hepatocellular carcinoma compromises redox homeostasis and glucose formation

ObjectiveThe loss of liver glycine N-methyltransferase (GNMT) promotes liver steatosis and the transition to hepatocellular carcinoma (HCC). Previous work showed endogenous glucose production is reduced in GNMT-null mice with gluconeogenic precursors being used in alternative biosynthetic pathways that utilize methyl donors and are linked to tumorigenesis. This metabolic programming occurs before the appearance of HCC in GNMT-null mice. The metabolic physiology that sustains liver tumor formation in GNMT-null mice is unknown. The studies presented here tested the hypothesis that nutrient flux pivots from glucose production to pathways that incorporate and metabolize methyl groups in GNMT-null mice with HCC. Methods2H/13C metabolic flux analysis was performed in conscious, unrestrained mice lacking GNMT to quantify glucose formation and associated nutrient fluxes. Molecular analyses of livers from mice lacking GNMT including metabolomic, immunoblotting, and immunochemistry were completed to fully interpret the nutrient fluxes. ResultsGNMT knockout (KO) mice showed lower blood glucose that was accompanied by a reduction in liver glycogenolysis and gluconeogenesis. NAD+ was lower and the NAD(P)H-to-NAD(P)+ ratio was higher in livers of KO mice. Indices of NAD+ synthesis and catabolism, pentose phosphate pathway flux, and glutathione synthesis were dysregulated in KO mice. ConclusionGlucose precursor flux away from glucose formation towards pathways that regulate redox status increase in the liver. Moreover, synthesis and scavenging of NAD+ are both impaired resulting in reduced concentrations. This metabolic program blunts an increase in methyl donor availability, however, biosynthetic pathways underlying HCC are activated.