Fatty Acid Alpha-oxidation Research Articles

Identification of an at-risk subpopulation with high immune infiltration based on the peroxisome pathway and TIM3 in colorectal cancer

BackgroundPeroxisomes are pivotal metabolic organelles that exist in almost all eukaryote cells. A reduction in numbers and enzymatic activities of peroxisomes was found in colon adenocarcinomas. However, the role of peroxisomes or the peroxisome pathway in colorectal cancer (CRC) is not defined.MethodsIn the current study, a peroxisome score was calculated to indicate the activity of the peroxisome pathway using gene set variant analysis based on transcriptomic datasets. CIBERSORTx was chosen to infer enriched immune cells for tumors among subgroups. The SubMap algorithm was applied to predict its sensitivity to immunotherapy.ResultsThe patients with a relatively low peroxisome score and high level of T-cell immunoglobulin and mucin domain 3 (TIM-3) presented the worse overall survival than others. Moreover, low peroxisome scores were associated with high infiltration of lymphocytes and poor prognosis in those CRC patients. Thus, a PERLowTIM3High CRC risk subpopulation was identified and characterized by high immune infiltration. The results also showed that CD8 T cells and macrophages highly infiltrated tumors of the PERLowTIM3High group, regardless of consortium molecular subtype and microsatellite instability status. This subgroup had the highest tumor mutational burden and overexpression of immune checkpoint genes. Further, the PERLowTIM3High group showed a higher probability of responding to programmed cell death protein-1-based immunotherapy. In addition, genes involved in peroxisomal metabolic processes in CRC were also investigated since peroxisome is a rather pleiotropic and highly metabolic organelle in cell. The results indicated that only those genes involved in fatty acid alpha oxidation could be used to stratify CRC patients as similar as peroxisome pathway genes.ConclusionsWe revealed the favorable prognostic value of the peroxisome pathway in CRC and provided a new CRC stratification based on peroxisomes and TIM3, which might be helpful for CRC diagnostics and personalized treatment.

Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle.

Simple SummaryIn this study, we investigated the association between single nucleotide polymorphisms (SNPs) and reproductive traits in order to identify candidate genes and biological pathways associated with these traits in Nelore beef cattle. The genome-wide association analysis revealed genomic regions that could explain part of the genetic variance of the studied traits. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, being important for reproductive efficiency. The identification of candidate genes that were associated with the studied traits as well as genes enriched in the functional terms and pathways may be useful for exploring the genetic architecture underlying reproductive traits and may be used in Nelore breeding programs.The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.

Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum.

Peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways which include: (1.) etherphospholipid biosynthesis; (2.) fatty acid beta-oxidation; (3.) bile acid synthesis; (4.) docosahexaenoic acid (DHA) synthesis; (5.) fatty acid alpha-oxidation; (6.) glyoxylate metabolism; (7.) amino acid degradation, and (8.) ROS/RNS metabolism. The importance of peroxisomes for human health and development is exemplified by the existence of a large number of inborn errors of peroxisome metabolism in which there is an impairment in one or more of the metabolic functions of peroxisomes. Although the clinical signs and symptoms of affected patients differ depending upon the enzyme which is deficient and the extent of the deficiency, the disorders involved are usually (very) severe diseases with neurological dysfunction and early death in many of them. With respect to the role of peroxisomes in metabolism it is clear that peroxisomes are dependent on the functional interplay with other subcellular organelles to sustain their role in metabolism. Indeed, whereas mitochondria can oxidize fatty acids all the way to CO2 and H2O, peroxisomes are only able to chain-shorten fatty acids and the end products of peroxisomal beta-oxidation need to be shuttled to mitochondria for full oxidation to CO2 and H2O. Furthermore, NADH is generated during beta-oxidation in peroxisomes and beta-oxidation can only continue if peroxisomes are equipped with a mechanism to reoxidize NADH back to NAD+, which is now known to be mediated by specific NAD(H)-redox shuttles. In this paper we describe the current state of knowledge about the functional interplay between peroxisomes and other subcellular compartments notably the mitochondria and endoplasmic reticulum for each of the metabolic pathways in which peroxisomes are involved.

Metabolic functions of peroxisomes in health and disease

Peroxisomes are subcellular organelles which are present in virtually every eukaryotic cell and catalyze a large number of metabolic functions. The importance of peroxisomes for humans is stressed by the existence of a large group of genetic diseases in which either the biogenesis of peroxisomes is impaired or one of its metabolic functions. Thanks to the work on Zellweger syndrome which is the prototype of the group of peroxisomal disorders, much has been learned about the metabolism and biogenesis of peroxisomes in humans. These metabolic functions include: (1.) fatty acid beta-oxidation; (2.) etherphospholipid biosynthesis; (3.) fatty acid alpha-oxidation, and (4.) glyoxylate detoxification. Since peroxisomes lack a citric acid cycle and a respiratory chain, peroxisomes are relatively helpless organelles which rely heavily on their cross-talk with other subcellular organelles in order to metabolize the end products of metabolism as generated in peroxisomes. The metabolic functions of peroxisomes in humans will be briefly described in this review with emphasis on the cross-talk with other subcellular organelles as well as the peroxisomal disorders in which one or more peroxisomal functions are impaired.

Fatty acid 2-Hydroxylation in mammalian sphingolipid biology

2-Hydroxy fatty acids (hFA) are important components of a subset of mammalian sphingolipids. The presence of hFA in sphingolipids is best described in the nervous system, epidermis, and kidney. However, the literature also indicates that various hFA-sphingolipids are present in additional tissues and cell types, as well as in tumors. Biosynthesis of hFA-sphingolipids requires fatty acid 2-hydroyxlase, and degradation of hFA-sphingolipids depends, at least in part, on lysosomal acid ceramidase and the peroxisomal fatty acid alpha-oxidation pathway. Mutations in the fatty acid 2-hydroxylase gene, FA2H, have been associated with leukodystrophy and spastic paraparesis in humans, underscoring the importance of hFA-sphingolipids in the nervous system. In the epidermis, hFA-ceramides are essential for the permeability barrier function. Physiological function of hFA-sphingolipids in other organs remains largely unknown. Recent evidence indicates that hFA-sphingolipids have specific roles in cell signaling.

Mutasynthesis‐Derived Myxalamids and Origin of the Isobutyryl‐CoA Starter Unit of Myxalamid B

Myxalamids are potent inhibitors of the eukaryotic electron transport chain produced by different myxobacteria. Here, we describe the identification of the myxalamid biosynthesis gene cluster from Myxococcus xanthus. Additionally, new myxalamids (5-13) have been obtained by mutasynthesis from bkd mutants of M. xanthus and Stigmatella aurantiaca. Moreover, as these bkd mutants are still able to produce myxalamid B (2), the origin of the isobutyryl-CoA (IB-CoA) starter unit required for its biosynthesis has been determined. In a M. xanthus bkd mutant, IB-CoA originates from valine, but in S. aurantiaca this starter unit is derived from alpha-oxidation of iso-odd fatty acids, thereby connecting primary and secondary metabolism.

Degenerative Disorders of the Central Nervous System

Degenerative Disorders of the Central Nervous System

Identification and Characterization of HAOX1, HAOX2, and HAOX3, Three Human Peroxisomal 2-Hydroxy Acid Oxidases

Computer-based approaches identified three distinct human 2-hydroxy acid oxidase genes, HAOX1, HAOX2, and HAOX3, that encode proteins with significant sequence similarity to plant glycolate oxidase, a prototypical 2-hydroxy acid oxidase. The products of these genes are targeted to peroxisomes and have 2-hydroxy acid oxidase activities. Each gene displays a distinct tissue-specific pattern of expression, and each enzyme exhibits distinct substrate preferences. HAOX1 is expressed primarily in liver and pancreas and is most active on the two-carbon substrate, glycolate, but is also active on 2-hydroxy fatty acids. HAOX2 is expressed predominantly in liver and kidney and displays highest activity toward 2-hydroxypalmitate. HAOX3 expression was detected only in pancreas, and this enzyme displayed a preference for the medium chain substrate 2-hydroxyoctanoate. These results indicate that all three human 2-hydroxy acid oxidases are involved in the oxidation of 2-hydroxy fatty acids and may also contribute to the general pathway of fatty acid alpha-oxidation. Primary hyperoxaluria type 1 (PH1) is caused by defects in peroxisomal alanine-glyoxylate aminotransferase, the enzyme that normally eliminates intraperoxisomal glyoxylate. The presence of HAOX1 in liver and kidney peroxisomes and the ability of HAOX1 to oxidize glyoxylate to oxalate implicate HAOX1 as a mediator of PH1 pathophysiology.

Intermediates and products formed during fatty acid alpha-oxidation in cucumber (Cucumis sativus).

Fatty acid alpha-oxidation is an essential metabolic pathway both in plants and in mammals which is still not completely understood. We previously described and purified an alpha-oxidation enzyme in cucumber which has been used in the present investigation of the alpha-oxidation reaction mechanism. Free fatty acids, and not the CoA thioesters, were found to undergo alpha-oxidation in cucumber. 2-Hydroxy- and 2-oxopalmitic acids were identified as palmitic acid alpha-oxidation intermediates by high-performance liquid chromatography and gas chromatography-mass spectrometry analysis in cucumber subcellular 150,000 x g(max) pellets obtained by differential centrifugation. Incubation of purified alpha-oxidation enzyme with [1-14C]palmitic acid resulted in the formation of both the above-described intermediates and the Cn-1 product, pentadecanal, and 14CO2. Besides 14CO2, 14C-formate was identified as an alpha-oxidation product from [1-14C]palmitic acid in cucumber subcellular fractions. Fe2+ stimulated the 14CO2 and 14C-formate production, and the addition of ascorbate and 2-oxoglutarate together with Fe2+ resulted in optimal alpha-oxidation activities, suggesting a dioxygenase reaction mechanism, as previously shown in mammals. NADPH and, to a lesser extent, NADH stimulated the total 14C-formate plus 14CO2 production but had only slight or no effects on 14CO2 production. H2O2 showed concentration-dependent inhibitory effects, while FAD had neither effect on 14CO2 nor 14CO2 plus 14C-formate production. The results in the present study demonstrate that an alpha-oxidation enzyme in cucumber is capable of oxidizing palmitic acid via 2-hydroxy- and 2-oxo-palmitic acid to produce pentadecanal and CO2. In contrast to the subcellular 150,000 x g(max) fraction, the purified alpha-oxidation enzyme could neither produce formate nor convert 14C-formate into 14C02, indicating two possible alpha-oxidation routes in cucumber.

Alpha-oxidation of fatty acids in fasted or diabetic rats

Induction of α-oxidation, a possible gluconeogenic process, which should produce odd-chain fatty acids from even-chain fatty acids, was studied in rats fasted or made diabetic with streptozotocin. When a ω-phenylated even-chain fatty acid, phenylbutyric acid (1.2 mmol/kg), was administered to rats under these conditions, a significant increase in the urinary excretion of benzoic acid, the metabolic end-product of ω-phenylated odd-chain fatty acids, was observed in fasted (3.54 ± 0.46 μmol/day) and diabetic (6.73 ± 2.10) rats (control, 0.58 ± 0.43; P < 0.001). Phenylated longer chain fatty acids, phenylhexanoic and phenyldecanoic acid, did not produce significantly more benzoic acid than did phenylbutryic acid. Although the rate of α-oxidation was very low compared to that of β-oxidation, these results suggested that α-oxidation of fatty acids was induced under fasting or diabetic conditions, and that α-oxidation might take place at the butyric acid stage.

Studies on fatty acid α-oxidation in cucumber

Alpha-oxidation of fatty acids was studied in cucumber. Both differential centrifugation and average sedimentation coefficient determination suggested that the α-oxidation was particle bound and mainly localized to the mitochondrial fraction. A partly purified α-oxidation system was obtained by fast protein liquid chromatography. The activity of the α-oxidation system determined as release of 14CO 2 was characterized with respect to inhibitors and reductant requirements. The results from this study suggest a similarity between the α-oxidation system in cucumber and that of pea leaf and cotyledons of germinating peanuts.

Inactivation of alcohol dehydrogenase in rice seedlings is related to a microsomal fatty acid alpha-oxidation system.

The selective inactivation of alcohol dehydrogenase by the inactivator found in the microsomal fraction of rice (Oryza sativa) seedlings growing in air (Shimomura, S. & Beevers, H. (1983) Plant Physiol. 71, 736-741; 742-746) was further studied. This inactivation was found to be essentially dependent on the presence of free fatty acids. The specificity for fatty acids and the inhibitory effects of imidazole, 2-hydroxyfatty acids and dithiothreitol on the inactivation were all consistent with the properties of the fatty acid alpha-oxidation system in plants. Both O2 consumption and decarboxylation of fatty acid due to alpha-oxidation were also demonstrated in rice microsomes. When purified rice alcohol dehydrogenase was added to the alpha-oxidation system in rice microsomes, the decarboxylation of fatty acid was inhibited, and the cysteinyl residues of alcohol dehydrogenase were oxidized. The oxidation of two cysteinyl residues per monomer resulted in the complete inactivation of the enzyme. The activity of the inactivator in the isolated microsomes was gradually lost during storage and was rapidly lost upon heating. The inactivation of alcohol dehydrogenase was observed even when the enzyme was separated from microsomes by a dialysis membrane. These results indicate that the inactivation of alcohol dehydrogenase is closely related to fatty acid alpha-oxidation. We postulate that an intermediate of alpha-oxidation is the inactivator.

On the formation of alpha-hydroxy fatty acids. Evidence for a direct hydroxylation of nonhydroxy fatty acid-containing sphingolipids.

When Tetrahymena pyriformis, strain NT-1, was warmed from a growth temperature of 15 degrees C to 39 degrees C, there was a rapid conversion of its sphingolipids from the nonhydroxy fatty acid-containing ceramide aminoethylphosphonate (NCAEP) predominant at low temperature to the alpha-hydroxy fatty acid-containing analog (HCAEP). The fatty acid composition of the freshly formed HCAEP strongly resembled that of the original NCAEP pool. An extensive utilization of NCAEP long chain bases for HCAEP formation was shown by prelabeling the NCAEP bases with [14C]serine. The specific radioactivities of both fatty acids and long chain bases of the two sphingolipid classes of cells prelabeled with [3H]palmitic acid at 15 degrees C and then warmed to 39 degrees C were compatible with a direct hydroxylation of the intact ceramide aminoethylphosphonate or free ceramide formed from it. Exogenously added alpha-hydroxypalmitic acid was not incorporated into the sphingolipids intact, but there was an active alpha-oxidation of alpha-hydroxy fatty acids, yielding nonhydroxy fatty acids one carbon atom shorter in length. In vitro experiments failed to demonstrate a direct hydroxylation of NCAEP, and nonhydroxy fatty acid-containing free ceramides were hydroxylated only sparingly. This inefficient hydroxylation is attributed to the rapid enzymatic hydrolysis of these substrates in vitro and to a limited availability of the added ceramides to the hydroxylating enzymes. The weight of the evidence from this study strongly favors the alpha-hydroxylation of fatty acids only when they are bound as elements of sphingolipids.

The stereochemistry of alpha-oxidation of fatty acids in plants: the configuration of biosynthetic long-chain 2-hydroxy acids.

The stereochemistry of alpha-oxidation of fatty acids in plants: the configuration of biosynthetic long-chain 2-hydroxy acids.

The Stereochemistry of α‐Oxidation of Fatty Acids in Leaves

When [U‐14C]palmitic acid is incubated with a particulate fraction obtained from young pea leaves, [14C]pentadecanal accumulates. L‐[U‐14C, 2‐3H]Palmitic acid similarly yields [14C]pentadecanal which retains the tritium (90% retention). D‐[U‐14C, 2‐3H]Palmitic acid gives [14C]‐pentadecanal with loss of tritium (13% retention). These results suggest that D‐2‐hydroxypalmitic acid is an intermediate in this reaction, but that L‐2‐hydroxypalmitic acid and 2‐ketopalmitic acid are not. The mechanism of α‐oxidation of palmitic acid in leaves is discussed.

Alpha-oxidation of Fatty Acids in Various Mammals, and a Phytanic Acid Feeding Experiment in an Animal with a Low Alpha-oxidation Capacity

Patients with Refsum's disease, who accumulate phytanic acid, have a reduced capacity for α-oxidation of branched chain fatty acids. To try to elucidate the role of phytanic acid in the symptomatology of this disease, a phytanic acid feeding experiment in animals has been performed. In vitro studies with 3,6-dimethyloctanoic acid showed that carnivorous animals had lower α-oxidation capacities than herbivorous animals. Polecats (Mustela putorius) were chosen for the phytanic acid feeding, which was started in utero, before the main myelination had occurred, and continued until they had reached maturity weights.During the feeding period the animals increased their tolerance for phytanic acid by increasing their α-oxidation capacity. Large amounts of phytanic acid had acute toxic effects, but no symptoms of myelin disorders occurred during the experiment. Based upon these findings, compared with the clinical improvements of the patients on a phytanic acid lowering diet, the pathogenic role of phytanic acid is discussed.

Alpha oxidation of the brain fatty acids

Alpha oxidation of the brain fatty acids