Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Degradation pathway”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed1977

Degradation pathway of fibrinogen by plasmin.

The molecular weights of derivatives obtained from chemical and enzymatic degradation of fibrinogen and fibrin support a model in which the two halves of the fibrinogen molecule are covalently linked by a set of disulfide bonds at the amino-terminal region. The 2 asymmetric cleavages caused by plasmin in the fibrinogen molecule occur according to the reactions: X leads to Y + D Y leads to E + D. The quantitative analysis of the amino-terminal amino acids in fragments D (from fibrinogen) and DD (from crosslinked fibrin) yields a total of 3.0 and 6.9 moles of amino acids per mole of protein, indicating three and six polypeptide chain structures, respectively. The data on molecular weights, polypeptide chain composition and immunologic properties of fibrinogen degradation products support the hypothesis on the asymmetric pathway of fibrinogen degradation by plasmin and the formation of two fragment D and one fragment E molecules from each molecule of fibrinogen.

Chemical Phenomena↗
PubMed1977

Different degradation pathways for glucose and fructose in Rhodopseudomonas capsulata.

In Rhodopseudomonas capsulata the enzymes of the Entner-Doudoroff pathway and the Embden-Meyerhof pathway have been examined. Fructose-grown cells contained inducible activities of phosphoenolpyruvate-fructosephospho-transferase and 1-phosphofructokinase and only low levels of fructokinase and 6-phosphofructokinase. Although fructose-grown cells contained, in addition, all the enzymes of the Entner-Doudoroff pathway together with fructose-1,6-diphosphatase and phosphoglucose isomerase, the Entner-Doudoroff pathway was not operative in fructose catabolism and served only the degradation of glucose. The functional separation of glucose and fructose catabolism via the Entner-Doudoroff and a modified Embden-Meyerhof pathway, respectively, was confirmed by different approaches: 1. Radiorespirometric experiments with glucose and fructose labelled in positions 1, 2, 3, 3+4 and 6 have been carried out. The pattern of 14CO2-evolution from position-labelled glucose was characteristic for the Entner-Doudoroff pathway, that from position-labelled fructose for the Embden-Meyerhof pathway. 2. In the presence of arsenite up to 50% of glucose- and fructose-carbon was excreted as pyruvate. Using 1-14C-glucose, 86% of the pyruvate was labelled in the carboxyl group, whereas using 1-14C-fructose only 19% of the pyruvate was labelled in the carboxyl group. 3. A glucose-6-phosphate dehydrogenase-deficient mutant was isolated which lacked a functional Entner-Doudoroff pathway but which was unaltered in its ability to grow on fructose.

Fructose↗
PubMed1976

[Carbohydrate and pyruvic acid degradation pathways in Fusidium coccineum strains with varying levels of antibiotic synthesis].

A number of enzymes and reactions of glycolysis, pentose-phosphate cycle and degradation of pyruvic acid in strains of F. coccineum with various levels of antibiotic production was studied comparatively. The experiments showed that highly productive strains were characterized by higher activity of the NADP-deficient enzymes of the pentoze-phosphate cycle as compared to the low active strains. The activity levels of glycolytic enzymes, such as fructose-diphosphate-aldolase and 3-phosphoglycerolaldehydehydrogenase did not practically differ. Significant differences were found in the reactions of puryvic acid degradation: the activity of cytoplasmic pyruvatedecarboxylase in the mutant with high antibiotic production level was lower than that in the low productive strain, while oxidation of the pyruvate of the mitochondrial fraction was on the contrary more intensive than in the highly productive strain. Therefore, metabilism in the strains studied was characterized by ever-increasing biochemical changes with an increase in their antibiotic productivity. Lowering of the growth rate of the mutants as their capacity for antibiotic supersynthesis increased and subsequently the anabolic processes became more intensive was accompanied by increasing derepression of the key enzymes of carbohydrate metabolism and in particular NADR-deficient dehydrogenase of the pentose cycle and pyruvatedehydrogenase, significant for fusidin biosynthesis and providing production of the antibiotic of steroid nature by cofactor NADP-H and acetyl-KoA, the primary precursor.

Anti-Bacterial Agents↗
PubMed2026

Parent-of-origin specific allelic expression in outbreeding Arabidopsis arenosa identifies antagonistic parental enrichment in protein degradation pathways.

In plants, the epigenetic phenomenon of parent-of-origin allele-specific expression occurs mainly in the triploid endosperm. Although well studied in inbreeding Arabidopsis thaliana, genomic imprinting has been less investigated in outcrossers. In order to investigate a wider role of parental-specific allelic expression, we have analyzed imprinting in whole seeds of the obligate outbreeder Arabidopsis arenosa. High-throughput analysis of imprinting in outbreeding species is hampered by the lack of reference genomes and available sequenced accessions. High degree of allelic variation in outbreeding species may also limit the analysis to loci with less variation. We developed a reference-independent pipeline to detect parental-specific reads. Using different accessions in reciprocal crosses, we detected more than 70 paternally biased imprinted genes and > 500 maternally biased genes. Paternally biased genes showed major enrichment for proteins with ubiquitin protein transferase and ligase activity. Maternally biased genes were enriched for protein pathways directly counteracting paternally enriched genes. Here, we demonstrate an alignment-free protocol to identify imprinted genes that may be successfully applied for imprinting studies in other highly heterozygous outcrossing species. Our results suggest a unique role of genomic imprinting affecting post-transcriptional gene regulation in outbreeding A. arenosa.

Arabidopsis arenosa↗
PubMed2024

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater.

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Groundwater↗
PubMed1979

Genetics and physiology of proline utilization in Saccharomyces cerevisiae: enzyme induction by proline.

Proline is converted to glutamate in the yeast Saccharomyces cerevisiae by the sequential action of two enzymes, proline oxidase and delta 1-pyrroline-5-carboxylate (P5C) dehydrogenase. The levels of these enzymes appear to be controlled by the amount of proline in the cell. The capacity to transport proline is greatest when the cell is grown on poor nitrogen sources, such as proline or urea. Mutants have been isolated which can no longer utilize proline as the sole source of nitrogen. Mutants in put1 are deficient in proline oxidase, and those in put2 lack P5C dehydrogenase. The put1 and put2 mutations are recessive, segregate 2:2 in tetrads, and appear to be unlinked to one another. Proline induces both proline oxidase and P5C dehydrogenase. The arginine-degradative pathway intersects the proline-degradative pathway at P5C. The P5C formed from the breakdown of arginine or ornithine can induce both proline-degradative enzymes by virtue of its conversion to proline.

Enzyme Induction↗
PubMed2026

Chaperone-mediated autophagy as a regulator of hallmarks of cancer.

Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation pathway that maintains cellular homeostasis by degrading soluble proteins containing KFERQ-like motifs. Although CMA has traditionally been recognized for its role in protein quality control and cellular stress adaptation, increasing evidence shows that it is frequently altered in cancer, where it regulates multiple processes that promote tumor initiation, progression, and therapy resistance. The growing number of identified CMA substrates involved in cell proliferation, apoptosis, metabolism, DNA damage response, immune regulation, inflammation, and cellular plasticity suggests that CMA is much more than a protein degradation pathway; it is an important regulator of tumor adaptation. In this review, we bring together current evidence to provide a comprehensive understanding of how CMA contributes to the Hallmarks of Cancer, including sustained proliferative signaling, resistance to cell death, metabolic reprogramming, invasion and metastasis, immune evasion, and the enabling characteristics of genome instability and tumor-promoting inflammation. We further explore the emerging roles of CMA in cellular plasticity and cancer stem cell maintenance, two interconnected processes that drive tumor progression, metastasis, and therapeutic resistance. By integrating evidence from diverse tumor types, this review provides a comprehensive understanding of how CMA shapes multiple hallmarks of cancer by selectively degrading key regulatory proteins. Finally, we highlight the context-dependent roles of CMA, identify key gaps in our current understanding, and discuss the opportunities and challenges of targeting CMA for cancer therapy. Overall, this hallmark-based perspective provides an integrated understanding of how CMA contributes to multiple hallmarks of cancer and supports its potential as a therapeutic target.

autophagy↗
PubMed2025

The mhqPOD gene cluster in lignin-degrading Paenibacillus sp. B2 encodes a pathway for the degradation of lignin-derived 5,5'-di(dehydrovanillic acid) (DDVA).

Lignin-degrading bacteria Paenibacillus sp. B2, Agrobacterium sp. B1, and Ochrobactrum sp. each contain mhqO genes encoding ring cleavage dioxygenase enzymes whose biochemical function is unknown. Each of these strains was found to degrade the biphenyl-containing lignin fragment 5,5'-di(dehydrovanillic acid) (DDVA) on solid media. An operon of five mhq genes in Paenibacillus sp. B2 was analysed via gene expression using quantitative PCR, and all five genes were highly induced (400-1000-fold overexpression) by the presence of DDVA. Recombinant azoreductase MhqP was found to demethylate DDVA to its monodemethylated derivative. Hence, these genes are proposed to be responsible for DDVA degradation, via a pathway involving the same biochemical steps as that studied in Sphingobium lignivorans SYK-6, but using several unrelated genes. Decarboxylation of later pathway intermediate 5-carboxyvanillic acid in Paenibacillus sp. B2 is proposed to be catalysed by decarboxylase UbiD, whose gene is also upregulated in the presence of DDVA. Degradation of the other fragment 4-carboxy-2-hydroxypentadienoic acid is proposed to occur via hydratase UxuA, whose gene is also upregulated by DDVA, and 4-hydroxy-4-methyl-2-oxoglutarate aldolase.

Paenibacillus↗
PubMed1977

Ultrastructure of the degradation of erythrocytes by thyroid epithelial cells in vivo.

The ultrastructure of the degradation of red blood cells (RBCs) in vivo by rat thyroid epithelial cells was studied. Two morphologically distinct degradative pathways appeared evident. The granular pathway was characterized by a finely mottled appearance of RBC phagosomes, first observed about the RBC periphery and later extending to the entire RBC matrix. Such phagosomes became gradually smaller, less electron dense, and indistinguishable from cellular lysosomes. The hemolytic degrative pathway was characterized by a progessive, usually homogenous decrease in the density of the RBC matrix except at the periphery of the RBC, where a thin, dense layer persisted for some time. Such phagosomes often appeared swollen relative to freshly ingested RBCs and resembled RBC ghosts. In later stages, they became irregular, smaller, and gradually indistinguishable from cellular lysosomes. Both degradative pathways were associated with ferritin-like particles. The earliest visualization of ferritin was in the cytoplasm, but in later stages it was also found to be concentrated within lysosomes and phagolysosomes.

Animals↗
PubMed1977

Diurnal variation of autophagy in rod visual cells in the rat.

In the process of autophagy, parts of the cell's own cytoplasm are enclosed by membranes and subsequently digested by enzymes. Autophagy is a well-known process found in various tissues under different conditions (See Refs.). Autophagy in visual cells was first documented by Remé and Young (1977) and Remé (1977), and was considered to be a general and important degradative pathway in visual cell metabolism. Recently, La Vail (1976) demonstrated that the shedding of disks from the tips of rod outer segments followed a circadian rhythm in rats. The peak period of disk shedding occurred shortly after the onset of the lighting period. In this study we have demonstrated, by quantitative analysis, that autophagy in rod inner segments follows a diurnal variation. The peak period of autophagic activity occurs about 3 h after the peak period of disk-shedding. Both peak periods take place in daytime, when the animals are less active. This finding further supports our assumption of autophagy being an important pathway in visual cell degradative mechanisms.

Adaptation, Physiological↗
PubMed1975

Novel pathway for degradation of protocatechuic acid in Bacillus species.

A species of Bacillus, tentatively identified as B. circulans, degrades protocatechuic acid by a novel reaction involving meta-fission between C2 and C3 of the benzene nucleus. 2-Hydroxymuconic semialdehyde is then degraded to pyruvate and acetaldehyde by enzymatic reactions described in previous work. Protocatechuate 2,3-oxygenase exhibits a rather narrow substrate specificity; the methyl and ethyl esters of protocatechuic acid are oxidized, but other substrates for ring-fission oxygenases, notably catechol, gallic acid, and homoprotocatechuic acid, are not attached.

Acetaldehyde↗
PubMed1977

The degradation of cartilage proteoglycans by tissue proteinases. Proteoglycan heterogeneity and the pathway of proteolytic degradation.

1. CaCl2-extracted proteoglycan from bovine nasal cartilage was degraded by four tissue proteinases till no further decrease in hydroynamic size was obtained. The proteoglycan and its final degradation products were then fractionated by Sepharose 2B chromatography. 2. The average size of the degradation products was least for cathepsin B and lysosomal elastase, and greatest for cathepsin D and cathepsin G. The latter two proteinases also produced degradation products that showed the widest range of sizes. 3. The structure of the degradation products ranged from peptides containing a single glycosaminoglycan chain to those containing twelve or more chains. Of the four proteinases, only cathepsin B produced peptides that contained a single chondroitin sulphate chain. 4. The proteoglycan was very heterogeneous with respect to size and chemical composition. Its behaviour on electrophoresis suggested that at least two genetically distinct core proteins might exist. 5. Irrespective of their structural variations, all proteoglycan molecules were able to interact with hyaluronic acid. In contrast, none of the degradation products were capable of this type of interaction. 6. A pathway for the proteolytic degradation of proteoglycans is postulated in which the sites of initial cleavage may be common to the majority of proteinases, whereas the production of the final clusters is dependent on the specificity of the proteinase. Only those proteinases of broadest specificity can produce single-chain chondroitin sulphate-peptides.

Animals↗
PubMed1977

Metabolism of uracil-containing DNA: degradation of bacteriophage PBS2 DNA in Bacillus subtilis.

When Bacillus subtilis is infected by the uracil-containing DNA phage PBS2, the parental DNA labeled with radioactive uracil and cytosine remains acid insoluble. If the synthesis of the phage-induced uracil-DNA N-glycosidase inhibitor is prevented, the parental DNA is completely degraded to acid-soluble products beginning at about 6 min after infection. The host N-glycosidase probably initiates the degradation pathway, with nucleases being responsible for the remaining degradation of the DNA.

Bacillus subtilis↗
PubMed2026

Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.

Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.

Humans↗
PubMed2026

Identifying the regulatory network of the key lipid metabolism transcription factor peroxisome proliferator-activated receptor in oysters.

Rising seawater temperatures driven by global warming have led to summer mass mortality events that pose significant challenges for the oyster industry. Peroxisome proliferator-activated receptor (PPAR) serves as a key transcriptional regulator of lipid metabolism and plays an essential role in thermal adaptation. However, the upstream regulatory mechanisms of PPAR remain poorly understood in marine organisms. In this study, we identified two PPAR subtypes (PPARα and PPARβ/δ) in oysters and compared transcriptomic data in different tissues and under various environmental stressors, with PPARα exhibiting higher expression levels and responsiveness to environmental stresses. We observed significantly higher PPARα gene expression levels and promoter activity in the relatively cold-tolerant Crassostrea gigas compared to C. angulata. The low expression of the inhibitory transcription factor CTNNB1 in C. gigas may contribute to higher gene expression of PPARα. Additionally, the expression genome-wide association study (eGWAS) identified 9 significant SNPs and 124 candidate regulatory genes associated with PPARα expression, including ubiquitination, phosphorylation, signaling pathways, lipid metabolism, and glucose metabolism. We provided the first experimental validation of the PPARα ubiquitination-degradation pathway in marine organisms via Co-IP, which was mediated by the E3 ligase RFWD3. The protein kinase SNF1 and signaling-related proteins PIKA and KCNK2 indirectly modulated PPARα downstream pathway activation to varying degrees. This study presents the first systematic investigation of PPARα expression regulation in marine organisms. It identifies key molecular regulators and provides novel insights into lipid metabolic regulation and molecular targets for genetic improvement of heat tolerance in oysters under global warming.

Animals↗
PubMed2026

Flavoromics-based profiling reveals taste and aroma differences between infant formula and breast milk.

Flavor differences between infant formula (IF) and breast milk (BM) are considered a potential factor affecting infants' acceptance of IF. This experiment employs flavoromics combined with multivariate statistical analysis to systematically compare the flavor profiles of IF and BM. Electronic tongue analysis and amino acid correlation revealed that IF was characterised by pronounced saltiness and umami richness, whereas BM exhibited greater bitterness and astringency. Volatile compound profiling identified five key flavor constituents in IF, predominantly aldehydes such as hexanal and pentanal. In contrast, BM contained a broader array of compounds-including acids, aldehydes, and esters-resulting in a more complex flavor profile. Kyoto Encyclopedia of Genes and Genomes (KEGG)-based metabolic pathway annotation, together with fatty acid profiling, suggested that some volatiles may be associated with lipid oxidation, Maillard reaction and sulfur-containing amino acid degradation pathways, offering a theoretical basis for the targeted optimisation of IF flavor.

Humans↗