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1
Kräutler, Bernhard. "Chlorophyll Breakdown – How Chemistry Has Helped to Decipher a Striking Biological Enigma." Synlett 30, no. 03 (October 31, 2018): 263–74. http://dx.doi.org/10.1055/s-0037-1611063.
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How the fall colors arise and how chlorophyll (Chl) breakdown occurs in higher plants has remained enigmatic until three decades ago. Fundamental insights into this fascinating puzzle have been gained, meanwhile, by basic contributions from plant biology and chemistry. This short review is a personal account of key advances from synthetic, mechanistic, and structural chemistry that led to the discovery of the bilin-type Chl catabolites and helped elucidate the metabolic processes that generated them from Chl.1 Introduction2 Discovery and Structure Elucidation of a First Non-Green Chl Catabolite3 Structure Elucidation of Fleetingly Existent Blue-Fluorescent Chl Catabolites4 The Red Chl Catabolite – Key Ring-Opened Tetrapyrrole Accessed by Partial Synthesis5 Synthesis of ‘Primary’ Fluorescent Chl Catabolites by Reduction of Red Chl Catabolite6 Nonfluorescent Chl Catabolites from Isomerization of Fluorescent Chl Catabolites7 Persistent Fluorescent Chl Catabolites and Blue-Luminescent Bananas8 Discovery, Structure Elucidation, and Biological Formation of Dioxobilin-Type Chl Catabolites9 Occurrence, Partial Synthesis, and Structure of Phyllochromobilins, the Colored Bilin-Type Chl Catabolites10 Conclusion and Outlook
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D’Alessandro, C., E. Colombini, G. Pasquariello, G. Sbragia, and A. Cupisti. "Compliance Alla Terapia Dietetica." Giornale di Clinica Nefrologica e Dialisi 22, no. 4 (January 31, 2018): 2–5. http://dx.doi.org/10.33393/gcnd.2010.1235.
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La terapia nutrizionale è uno dei cardini della terapia conservativa dell'Insufficienza Renale Cronica (IRC). È in grado di contrastare segni, sintomi e complicanze dell'insufficienza renale, di procrastinare l'inizio della dialisi e di mantenere lo stato nutrizionale. La dieta deve essere ridotta in proteine perché molte delle tossine e dei cataboliti ritenuti derivano dalle proteine esogene, e perché la restrizione proteica rappresenta una condizione necessaria, anche se non sufficiente, per la contestuale riduzione dell'apporto di sodio e fosforo che contribuisce agli effetti terapeutici. Altra caratteristica fondamentale della terapia dietetica è l'adeguatezza energetica. I due casi descritti rappresentano quello che spesso accade nella pratica clinica nel paziente con IRC cui viene prescritta una dieta ipoproteica, e sottolineano l'importanza del counselling dietetico per la sicurezza e l'efficacia della terapia nutrizionale nel paziente renale con o senza diabete mellito.
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Djapic, Nina. "Chlorophyll catabolism in Prunus serrulata autumnal leaves." Facta universitatis - series: Physics, Chemistry and Technology 10, no. 1 (2012): 21–26. http://dx.doi.org/10.2298/fupct1201021d.
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Chlorophyll catabolism in Prunus serrulata autumnal leaves was investigated. The amount of chlorophyll catabolites accumulated within the same plant species varies with the time of the leaf collection, seasonal climate and developmental stage of the plant. The chlorophyll catabolites found in P. serrulata autumnal leaves presented the tendency of the organism to decrease the level of photodynamically active chlorophyll before the programmed cell death. In the methanol extract several chlorophyll catabolites were identified. The results obtained by liquid - chromatography/mass spectrometry permitted the identification of the chlorophyll catabolites found in P. serrulata autumnal leaves. The analysis done revealed the chlorophyll catabolic pathway found in P. serrulata autumnal leaves.
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Campbell III, John, Gary R. Bender, and Robert E. Marquis. "Barotolerant variant of Streptococcus faecalis with reduced sensitivity to glucose catabolite repression." Canadian Journal of Microbiology 31, no. 7 (July 1, 1985): 644–50. http://dx.doi.org/10.1139/m85-121.
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Physiological characterization of the APR-11 variant of Streptococcus faecalis ATCC 9790 revealed that the variant has reduced sensitivity to glucose catabolite repression. This reduced sensitivity was indicated by the synthesis of enzymes for catabolism of lactose or arginine in cultures growing at 0.1, 40, or 70 MPa in media with levels of glucose highly repressive for the parent strain. Reduced catabolite repression appeared to be due to reduced activity of the glucose-specific, phosphotransferase system in APR-11 cells. Conversion of pyruvate to lactate or to acetate and ethanol did not appear to be altered in the variant. The APR-11 variant produced a greater final yield of biomass than the parent at all pressures tested, and its barotolerance was especially marked in media with low levels of glucose and high levels of lactose in which derepression of the lactose catabolic system was necessary for full growth. Overall, the greater barotolerance of the APR-11 strain appeared to be due to its enhanced capacity for catabolism related to its reduced sensitivity to catabolite repression by glucose.
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Cooper, T. G., R. Rai, and H. S. Yoo. "Requirement of upstream activation sequences for nitrogen catabolite repression of the allantoin system genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 12 (December 1989): 5440–44. http://dx.doi.org/10.1128/mcb.9.12.5440-5444.1989.
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Synthesis of the transport systems and enzymes mediating uptake and catabolism of nitrogenous compounds is sensitive to nitrogen catabolite repression. In spite of the widespread occurrence of the control process, little is known about its mechanism. We have previously demonstrated that growth of cells on repressive nitrogen sources results in a dramatic decrease in the steady-state levels of mRNA encoded by the allantoin and arginine catabolic pathway genes and of the transport systems associated with allantoin metabolism. The present study identified the upstream activation sequences in the 5'-flanking regions of the allantoin system genes as the cis-acting sites through which nitrogen catabolite repression is exerted.
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Cooper, T. G., R. Rai, and H. S. Yoo. "Requirement of upstream activation sequences for nitrogen catabolite repression of the allantoin system genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 12 (December 1989): 5440–44. http://dx.doi.org/10.1128/mcb.9.12.5440.
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Synthesis of the transport systems and enzymes mediating uptake and catabolism of nitrogenous compounds is sensitive to nitrogen catabolite repression. In spite of the widespread occurrence of the control process, little is known about its mechanism. We have previously demonstrated that growth of cells on repressive nitrogen sources results in a dramatic decrease in the steady-state levels of mRNA encoded by the allantoin and arginine catabolic pathway genes and of the transport systems associated with allantoin metabolism. The present study identified the upstream activation sequences in the 5'-flanking regions of the allantoin system genes as the cis-acting sites through which nitrogen catabolite repression is exerted.
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Bahar, Masoud, John de Majnik, Margaret Wexler, Judith Fry, Philip S. Poole, and Peter J. Murphy. "A Model for the Catabolism of Rhizopine in Rhizobium leguminosarum Involves a Ferredoxin Oxygenase Complex and the Inositol Degradative Pathway." Molecular Plant-Microbe Interactions® 11, no. 11 (November 1998): 1057–68. http://dx.doi.org/10.1094/mpmi.1998.11.11.1057.
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Rhizopines are nodule-specific compounds that confer an intraspecies competitive nodulation advantage to strains that can catabolize them. The rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) catabolic moc gene cluster mocCABRDE(F) in Rhizobium leguminosarum bv. viciae strain 1a is located on the Sym plasmid. MocCABR are homologous to the mocCABR gene products from Sinorhizobium meliloti. MocD and MocE contain motifs corresponding to a TOL-like oxygenase and a [2Fe-2S] Rieske-like ferredoxin, respectively. The mocF gene encodes a ferredoxin reductase that would complete the oxygenase system, but is not essential for rhizopine catabolism. We propose a rhizopine catabolic model whereby MocB transports rhizopine into the cell and MocDE and MocF (or a similar protein elsewhere in the genome), under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine (SI). MocA, an NAD(H)-dependent dehydrogenase, and MocC continue the catabolic process. Compounds formed then enter the inositol catabolic pathway.
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Platt, Thomas G., James D. Bever, and Clay Fuqua. "A cooperative virulence plasmid imposes a high fitness cost under conditions that induce pathogenesis." Proceedings of the Royal Society B: Biological Sciences 279, no. 1734 (November 23, 2011): 1691–99. http://dx.doi.org/10.1098/rspb.2011.2002.
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Harbouring a plasmid often imposes a fitness cost on the bacterial host. Motivated by implications for public health, the majority of studies on plasmid cost are focused on elements that impart antibiotic resistance. Plasmids, however, can provide a wide range of ecologically important phenotypes to their bacterial hosts—such as virulence, specialized catabolism and metal resistance. The Agrobacterium tumefaciens tumour-inducing (Ti) plasmid confers both the ability to infect dicotyledonous plants and to catabolize the metabolites that plants produce as a result of being infected. We demonstrate that this virulence and catabolic plasmid imposes a measurable fitness cost on host cells under resource-limiting, but not resource replete, environmental conditions. Additionally, we show that the expression of Ti-plasmid-borne pathogenesis genes necessary to initiate cooperative pathogenesis is extremely costly to the host cell. The benefits of agrobacterial pathogenesis stem from the catabolism of public goods produced by infected host plants. Thus, the virulence-plasmid-dependent costs we demonstrate constitute costs of cooperation typically associated with the ability to garner the benefits of cooperation. Interestingly, genotypes that harbour derived opine catabolic plasmids minimize this trade-off, and are thus able to freeload upon the pathogenesis initiated by other individuals.
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Berthon, Céline, Michaela Fontenay, Selim Corm, Isabelle Briche, Michel Lhermitte, and Bruno Quesnel. "Metabolites of Tryptophan Catabolism Are Elevated in Sera of Patients with Myelodysplastic Syndromes and Inhibit Hematopoietic Progenitor Amplification." Blood 120, no. 21 (November 16, 2012): 3843. http://dx.doi.org/10.1182/blood.v120.21.3843.3843.
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Abstract Abstract 3843 Introduction: Tryptophan catabolism, which is mediated by the enzymes indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO), produces kynurenine, which blocks T-cell activation and induces immunosuppression. Kynurenine itself is converted by downstream enzymes into secondary catabolites that also have toxic effects on T cells. Tryptophan catabolism is elevated in many cancers, including acute myeloid leukemia (AML). However, tryptophan catabolites that are downstream of kynurenine have never been investigated in hematological malignancies. Methods: We evaluated the serum levels of primary and secondary tryptophan catabolites in a cohort of patients with myelodysplastic syndromes (MDS). Sera were isolated from 132 adult MDS patients after informed consent was obtained in accordance with the Helsinki Declaration. The levels of tryptophan, kynurenine, kynurenic acid, 3-hydroxykynurenine, 3-hydroxyanthranilic acid, and anthranilic acid in the sera were quantified using HPLC. For erythroid cell expansion, CD34+ cells were collected and isolated from the mononuclear cell fractions of cytapheresis products from 3 healthy donors and cultured in liquid medium under erythroid conditions with tryptophan catabolites. Results: The MDS patients showed significantly lower levels of tryptophan and higher levels of kynurenine, kynurenic acid, 3-hydroxyanthranilic acid, and anthranilic acid compared with the healthy controls. We also compared the kynurenine and tryptophan levels in the MDS patients with our previous cohort of 112 patients with primary AML. The kynurenine/tryptophan ratios were significantly higher in the MDS patients (median 0.0468 vs. 0.0676). The tryptophan catabolites correlated with cytopenia; higher kynurenine levels were associated with lower hemoglobin levels and higher blast counts and were associated with presence of dysgranulopoiesis. Lower tryptophan levels were found in patients with platelet transfusion dependency. Kynurenic acid levels were higher in patients with dysmegakaryopoiesis. High 3-hydroxyanthranilic and kynurenic acid levels were associated with severe thrombopenia below 20 G/L. IPSS score, cytogenetic, and WHO diagnosis did not associated with any tryptophan catabolite level. The tryptophan catabolites inhibited progenitor expansion during the in vitro culture of hematopoietic cells and reduced the numbers of granulocytes and erythroblasts. Conclusions: Thus, MDS patients are characterized by high tryptophan catabolism resulting in elevated primary and secondary metabolites, which both have inhibitory effects on hematopoiesis. These results suggest that IDO or TDO inhibitors should be investigated in MDS. Disclosures: No relevant conflicts of interest to declare.
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Cunningham, T. S., and T. G. Cooper. "Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression." Molecular and Cellular Biology 11, no. 12 (December 1991): 6205–15. http://dx.doi.org/10.1128/mcb.11.12.6205-6215.1991.
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We have cloned the negative regulatory gene (DAL80) of the allantoin catabolic pathway, characterized its structure, and determined the physiological conditions that control DAL80 expression and its influence on the expression of nitrogen catabolic genes. Disruption of the DAL80 gene demonstrated that it regulates multiple nitrogen catabolic pathways. Inducer-independent expression was observed for the allantoin pathway genes DAL7 and DUR1,2, as well as the UGA1 gene required for gamma-aminobutyrate catabolism in the disruption mutant. DAL80 transcription was itself highly sensitive to nitrogen catabolite repression (NCR), and its promoter contained 12 sequences homologous to the NCR-sensitive UASNTR. The deduced DAL80 protein structure contains zinc finger and coiled-coil motifs. The DAL80 zinc finger motif possessed high homology to the transcriptional activator proteins required for expression of NCR-sensitive genes in fungi and the yeast GLN3 gene product required for functioning of the NCR-sensitive DAL UASNTR. It was also homologous to the three GATAA-binding proteins reported to be transcriptional activators in avian and mammalian tissues. The latter correlations raise the possibility that both positive and negative regulators of allantoin pathway transcription may bind to similar sequences.
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Cunningham, T. S., and T. G. Cooper. "Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression." Molecular and Cellular Biology 11, no. 12 (December 1991): 6205–15. http://dx.doi.org/10.1128/mcb.11.12.6205.
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We have cloned the negative regulatory gene (DAL80) of the allantoin catabolic pathway, characterized its structure, and determined the physiological conditions that control DAL80 expression and its influence on the expression of nitrogen catabolic genes. Disruption of the DAL80 gene demonstrated that it regulates multiple nitrogen catabolic pathways. Inducer-independent expression was observed for the allantoin pathway genes DAL7 and DUR1,2, as well as the UGA1 gene required for gamma-aminobutyrate catabolism in the disruption mutant. DAL80 transcription was itself highly sensitive to nitrogen catabolite repression (NCR), and its promoter contained 12 sequences homologous to the NCR-sensitive UASNTR. The deduced DAL80 protein structure contains zinc finger and coiled-coil motifs. The DAL80 zinc finger motif possessed high homology to the transcriptional activator proteins required for expression of NCR-sensitive genes in fungi and the yeast GLN3 gene product required for functioning of the NCR-sensitive DAL UASNTR. It was also homologous to the three GATAA-binding proteins reported to be transcriptional activators in avian and mammalian tissues. The latter correlations raise the possibility that both positive and negative regulators of allantoin pathway transcription may bind to similar sequences.
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LITTLE, Chris B., Carl R. FLANNERY, Clare E. HUGHES, John S. MORT, Peter J. ROUGHLEY, Colin DENT, and Bruce CATERSON. "Aggrecanase versus matrix metalloproteinases in the catabolism of the interglobular domain of aggrecan in vitro." Biochemical Journal 344, no. 1 (November 8, 1999): 61–68. http://dx.doi.org/10.1042/bj3440061.
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The importance of aggrecanase versus matrix metalloproteinase (MMP) enzymic activities in the degradation of aggrecan in normal and osteoarthritic (OA) articular cartilage in vitro was studied in order to further our understanding of the potential role of these two enzyme activities in aggrecan catabolism during the pathogenesis of cartilage degeneration. Porcine and bovine articular cartilage was maintained in explant culture for up to 20 days in the presence or absence of the catabolic stimuli retinoic acid, interleukin-1 or tumour necrosis factor-α. Release of proteoglycan from cartilage was measured as glycosaminoglycan (GAG) release using a colorimetric assay. Analysis of proteoglycan degradation products, both released into culture media and retained within the cartilage matrix, was performed by Western blotting using antibodies specific for the N- and C-terminal neoepitopes generated by aggrecanase- and MMP-related catabolism of the interglobular domain of the aggrecan core protein (IGD). In addition, studies determining the mRNA expression for MMP-3 and MMP-13 in these same cultures were undertaken. These analyses indicated that all three catabolic agents stimulated the release of > 80% of the GAG from the articular cartilage over 4 days. The degree of GAG release corresponded to an increase in aggrecanase-generated aggrecan catabolites released into the media and retained within the cartilage. Importantly, there was no evidence for the release of MMP-generated aggrecan metabolites into the medium, nor the accumulation of MMP-generated catabolites within the tissue in these same cultures. Expression of the mRNAs for two MMPs known to be capable of degrading the aggrecan IGD, MMP-3 and MMP-13, was detected. However, increased expression of these MMPs was not correlated with aggrecan degradation. Analyses using porcine cartilage, cultured with or without catabolic stimulation for 12 h to 20 days, indicated that primary cleavage of the IGD by aggrecanase was responsible for release of aggrecan metabolites at both the early and late time points of culture. Cultures of late-stage OA human articular cartilage samples indicated that aggrecanase activity was upregulated in the absence of catabolic stimulation when compared with normal porcine or bovine cartilage. In addition, even in this late-stage degenerate cartilage, aggrecanase and not MMP activity was responsible for the release of the majority of aggrecan from the cartilage. This study demonstrates that the release of aggrecan from both normal and OA cartilage in response to catabolic stimulation in vitro involves a primary cleavage by aggrecanase and not MMPs.
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Salvachúa, Davinia, Allison Z. Werner, Isabel Pardo, Martyna Michalska, Brenna A. Black, Bryon S. Donohoe, Stefan J. Haugen, et al. "Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440." Proceedings of the National Academy of Sciences 117, no. 17 (April 3, 2020): 9302–10. http://dx.doi.org/10.1073/pnas.1921073117.
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Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic–catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
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Palavecino, Marcos D., Susana R. Correa-García, and Mariana Bermúdez-Moretti. "Genes of Different Catabolic Pathways Are Coordinately Regulated by Dal81 in Saccharomyces cerevisiae." Journal of Amino Acids 2015 (September 17, 2015): 1–8. http://dx.doi.org/10.1155/2015/484702.
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Yeast can use a wide variety of nitrogen compounds. However, the ability to synthesize enzymes and permeases for catabolism of poor nitrogen sources is limited in the presence of a rich one. This general mechanism of transcriptional control is called nitrogen catabolite repression. Poor nitrogen sources, such as leucine, γ-aminobutyric acid (GABA), and allantoin, enable growth after the synthesis of pathway-specific catabolic enzymes and permeases. This synthesis occurs only under conditions of nitrogen limitation and in the presence of a pathway-specific signal. In this work we studied the temporal order in the induction of AGP1, BAP2, UGA4, and DAL7, genes that are involved in the catabolism and use of leucine, GABA, and allantoin, three poor nitrogen sources. We found that when these amino acids are available, cells will express AGP1 and BAP2 in the first place, then DAL7, and at last UGA4. Dal81, a general positive regulator of genes involved in nitrogen utilization related to the metabolisms of GABA, leucine, and allantoin, plays a central role in this coordinated regulation.
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Richardson, Jason S., Michael F. Hynes, and Ivan J. Oresnik. "A Genetic Locus Necessary for Rhamnose Uptake and Catabolism in Rhizobium leguminosarum bv. trifolii." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8433–42. http://dx.doi.org/10.1128/jb.186.24.8433-8442.2004.
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ABSTRACT Rhizobium leguminosarum bv. trifolii mutants unable to catabolize the methyl-pentose rhamnose are unable to compete effectively for nodule occupancy. In this work we show that the locus responsible for the transport and catabolism of rhamnose spans 10,959 bp. Mutations in this region were generated by transposon mutagenesis, and representative mutants were characterized. The locus contains genes coding for an ABC-type transporter, a putative dehydrogenase, a probable isomerase, and a sugar kinase necessary for the transport and subsequent catabolism of rhamnose. The regulation of these genes, which are inducible by rhamnose, is carried out in part by a DeoR-type negative regulator (RhaR) that is encoded within the same transcript as the ABC-type transporter but is separated from the structural genes encoding the transporter by a terminator-like sequence. RNA dot blot analysis demonstrated that this terminator-like sequence is correlated with transcript attenuation only under noninducing conditions. Transport assays utilizing tritiated rhamnose demonstrated that uptake of rhamnose was inducible and dependent upon the presence of the ABC transporter at this locus. Phenotypic analyses of representative mutants from this locus provide genetic evidence that the catabolism of rhamnose differs from previously described methyl-pentose catabolic pathways.
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Yebra, Mar�a Jes�s, Manuel Z��iga, Sophie Beaufils, Gaspar P�rez-Mart�nez, Josef Deutscher, and Vicente Monedero. "Identification of a Gene Cluster Enabling Lactobacillus casei BL23 To Utilize myo-Inositol." Applied and Environmental Microbiology 73, no. 12 (April 20, 2007): 3850–58. http://dx.doi.org/10.1128/aem.00243-07.
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ABSTRACT Genome analysis of Lactobacillus casei BL23 revealed that, compared to L. casei ATCC 334, it carries a 12.8-kb DNA insertion containing genes involved in the catabolism of the cyclic polyol myo-inositol (MI). Indeed, L. casei ATCC 334 does not ferment MI, whereas strain BL23 is able to utilize this carbon source. The inserted DNA consists of an iolR gene encoding a DeoR family transcriptional repressor and a divergently transcribed iolTABCDG1G2EJK operon, encoding a complete MI catabolic pathway, in which the iolK gene probably codes for a malonate semialdehyde decarboxylase. The presence of iolK suggests that L. casei has two alternative pathways for the metabolism of malonic semialdehyde: (i) the classical MI catabolic pathway in which IolA (malonate semialdehyde dehydrogenase) catalyzes the formation of acetyl-coenzyme A from malonic semialdehyde and (ii) the conversion of malonic semialdehyde to acetaldehyde catalyzed by the product of iolK. The function of the iol genes was verified by the disruption of iolA, iolT, and iolD, which provided MI-negative strains. By contrast, the disruption of iolK resulted in a strain with no obvious defect in MI utilization. Transcriptional analyses conducted with different mutant strains showed that the iolTABCDG1G2EJK cluster is regulated by substrate-specific induction mediated by the inactivation of the transcriptional repressor IolR and by carbon catabolite repression mediated by the catabolite control protein A (CcpA). This is the first example of an operon for MI utilization in lactic acid bacteria and illustrates the versatility of carbohydrate utilization in L. casei BL23.
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BÜTTNER, Frank H., Clare E. HUGHES, Daniel MARGERIE, Andrea LICHTE, Harald TSCHESCHE, Bruce CATERSON, and Eckart BARTNIK. "Membrane type 1 matrix metalloproteinase (MT1-MMP) cleaves the recombinant aggrecan substrate rAgg1mut at the ‘aggrecanase’ and the MMP sites." Biochemical Journal 333, no. 1 (July 1, 1998): 159–65. http://dx.doi.org/10.1042/bj3330159.
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The recent detection of membrane type 1 matrix metalloproteinase (MT1-MMP) expression in human articular cartilage [Büttner, Chubinskaya, Margerie, Huch, Flechtenmacher, Cole, Kuettner, and Bartnik (1997) Arthritis Rheum. 40, 704–709] prompted our investigation of MT1-MMP's catabolic activity within the interglobular domain of aggrecan. For these studies we used rAgg1mut, a mutated form of the recombinant fusion protein (rAgg1) that has been used as a substrate to monitor ‘aggrecanase ’ catabolism in vitro [Hughes, Büttner, Eidenmüller, Caterson and Bartnik (1997) J. Biol. Chem. 272, 20269–20274]. The rAgg1 was mutated (G332 to A) to avoid the generation of a splice variant seen with the original genetic construct, which gave rise to heterogeneous glycoprotein products. This mutation yielded a homogeneous recombinant product. Studies in vitro with retinoic acid-stimulated rat chondrosarcoma cells indicated that the rAgg1mut substrate was cleaved at the ‘aggrecanase ’ site equivalent to Glu373-Ala374 (human aggrecan sequence enumeration) in its interglobular domain sequence segment. The differential catabolic activities of the recombinant catalytic domain (cd) of MT1-MMP and matrix metalloproteinases (MMPs) 3 and 8 were then compared by using this rAgg1mut as a substrate. Coomassie staining of rAgg1mut catabolites separated by SDS/PAGE showed similar patterns of degradation with all three recombinant enzymes. However, comparative immunodetection analysis, with neoepitope antibodies BC-3 (anti-ARGS …) and BC-14 (anti-FFGV …) to distinguish between ‘aggrecanase ’ and MMP-generated catabolites, indicated that the catalytic domain of MT1-MMP exhibited strong ‘aggrecanase ’ activity, cdMMP-8 weak activity and cdMMP-3 no activity. In contrast, cdMMP-3 and cdMMP-8 led to strongly BC-14-reactive catabolic fragments, whereas cdMT1-MMP resulted in weak BC-14 reactivity. N-terminal sequence analyses of the catabolites confirmed these results and also identified other potential minor cleavage sites within the interglobular domain of aggrecan. These results indicate that MT1-MMP is yet another candidate for ‘aggrecanase ’ activity in vivo.
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Wargo, Matthew J., and Deborah A. Hogan. "Identification of genes required for Pseudomonas aeruginosa carnitine catabolism." Microbiology 155, no. 7 (July 1, 2009): 2411–19. http://dx.doi.org/10.1099/mic.0.028787-0.
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Carnitine is a quaternary amine compound prevalent in animal tissues, and a potential carbon, nitrogen and energy source for pathogens during infection. Characterization of activities in Pseudomonas aeruginosa cell lysates has previously shown that carnitine is converted to 3-dehydrocarnitine (3-dhc) which is in turn metabolized to glycine betaine (GB), an intermediate metabolite in the catabolism of carnitine to glycine. However, the identities of the enzymes required for carnitine catabolism were not known. We used a genetic screen of the P. aeruginosa PA14 transposon mutant library to identify genes required for growth on carnitine. We identified two genomic regions and their adjacent transcriptional regulators that are required for carnitine catabolism. The PA5388–PA5384 region contains the predicted P. aeruginosa carnitine dehydrogenase homologue along with other genes required for growth on carnitine. The second region identified, PA1999–PA2000, encodes the α and β subunits of a predicted 3-ketoacid CoA-transferase, an enzymic activity hypothesized to be involved in the first step of deacetylation of 3-dhc. Furthermore, we confirmed that an intact GB catabolic pathway is required for growth on carnitine. The PA5389 and PA1998 transcription factors are required for growth on carnitine. PA5389 is required for induction of the PA5388–PA5384 transcripts in response to carnitine, and the PA1999–PA2000 transcripts are induced in a PA1998-dependent manner and induction appears to depend on a carnitine catabolite, possibly 3-dhc. These results provide important insight into elements required for carnitine catabolism in P. aeruginosa and probably in other bacteria.
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Bianco, Riccardo Lo, and Mark Rieger. "Partitioning of Sorbitol and Sucrose Catabolism within Peach Fruit." Journal of the American Society for Horticultural Science 127, no. 1 (January 2002): 115–21. http://dx.doi.org/10.21273/jashs.127.1.115.
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The peach [Prunus persica (L.) Batsch (Peach Group)] fruit is a sink organ comprised of different types of tissue, which undergoes three distinct developmental stages during the growth season. The objective of this study was to characterize the activity and partitioning of sorbitol and sucrose catabolism within `Encore' peach fruit to determine whether the two forms of translocated carbon play different roles in the various fruit tissues and/or stages of development. Sorbitol catabolic activity was defined as the sum of NAD-dependent sorbitol dehydrogenase (SDH) and sorbitol oxidase (SOX) activities, whereas sucrose catabolic activity was defined as the sum of sucrose synthase (SS), soluble acid invertase (AI), and neutral invertase (NI) activities. Partitioning of sorbitol and sucrose catabolism in each tissue was calculated as percentage of total sorbitol or sucrose catabolic activity in the entire fruit. At cell division, sorbitol catabolic activity was similar in the endocarp and mesocarp, but lower in the seed. However, sorbitol catabolism was mostly partitioned into the mesocarp, due to its large size compared to that of other tissues. SDH was more active in the mesocarp, while SOX was more active in the endocarp. Sucrose catabolism was most active and partitioned mainly into the endocarp. At endocarp hardening, both sorbitol and sucrose catabolic activities were highest in the seed, but despite this, sucrose catabolism was partitioned mostly in the mesocarp. At cell expansion, sorbitol and sucrose catabolic activities were still higher in the seed only when expressed on a weight basis and similar in mesocarp and seed when expressed on a protein basis. Both sorbitol and sucrose catabolism were partitioned mostly into the mesocarp. Sorbitol and sucrose contents were generally higher in the tissues that exhibited lower catabolic activities. All carbohydrates were always partitioned mostly into the mesocarp. Our results show that, at the cell division and endocarp hardening stages, sorbitol and sucrose catabolism are partitioned differently in the fruit and that SDH activity may play an important role in mesocarp cell division and final fruit size determination.
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Shevchik, Vladimir E., and Nicole Hugouvieux-Cotte-Pattat. "PaeX, a Second Pectin Acetylesterase of Erwinia chrysanthemi 3937." Journal of Bacteriology 185, no. 10 (May 15, 2003): 3091–100. http://dx.doi.org/10.1128/jb.185.10.3091-3100.2003.
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ABSTRACT Erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. Pectin is a complex polysaccharide. The main chain is constituted of galacturonate residues, and some of them are modified by methyl and/or acetyl esterification. Esterases are necessary to remove these modifications and, thus, to facilitate the further degradation of the polysaccharidic chain. In addition to PaeY, the first pectin acetylesterase identified in the E. chrysanthemi strain 3937, we showed that this bacterium produces a second pectin acetylesterase encoded by the gene paeX. The paeX open reading frame encodes a 322-residue precursor protein of 34,940 Da, including a 21-amino-acid signal peptide. Analysis of paeX transcription, by using gene fusions, revealed that it is induced by pectic catabolic products and affected by catabolite repression. The expression of paeX is regulated by the repressor KdgR, which controls all the steps of pectin catabolism; by the repressor PecS, which controls most of the pectinase genes; and by catabolite regulatory protein, the global activator of sugar catabolism. The paeX gene is situated in a cluster of genes involved in the catabolism and transport of pectic oligomers. In induced conditions, the two contiguous genes kdgM, encoding an oligogalacturonate-specific porin, and paeX are both transcribed as an operon from a promoter proximal to kdgM, but transcription of paeX can also be uncoupled from that of kdgM in noninduced conditions. PaeX is homologous to the C-terminal domain of the Butyrivibrio fibriosolvens xylanase XynB and to a few bacterial esterases. PaeX contains the typical box (GxSxG) corresponding to the active site of the large family of serine hydrolases. Purified PaeX releases acetate from various synthetic substrates and from sugar beet pectin. The PaeX activity increased after previous depolymerization and demethylation of pectin, indicating that its preferred substrates are nonmethylated oligogalacturonides. PaeX is mostly found in the periplasmic space of E. chrysanthemi. These data suggest that PaeX is mainly involved in the deacetylation of esterified oligogalacturonides that enter the periplasm by the KdgM porin.
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Mazzoni, Alessio, Manuela Capone, Matteo Ramazzotti, Anna Vanni, Luca Giovanni Locatello, Oreste Gallo, Raffaele De Palma, et al. "IL4I1 Is Expressed by Head–Neck Cancer-Derived Mesenchymal Stromal Cells and Contributes to Suppress T Cell Proliferation." Journal of Clinical Medicine 10, no. 10 (May 13, 2021): 2111. http://dx.doi.org/10.3390/jcm10102111.
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Amino acids have a primary role in cancer metabolism. Beyond their primary biosynthetic role, they represent also an alternative fuel while their catabolites can influence the epigenetic control of gene expression and suppress anti-tumor immune responses. The accumulation of amino-acid derivatives in the tumor microenvironment depends not only on the activity of tumor cells, but also on stromal cells. In this study, we show that mesenchymal stromal cells derived from head–neck cancer express the amino acid oxidase IL4I1 that has been detected in different types of tumor cells. The catabolic products of IL4I1, H2O2, and kynurenines are known to suppress T cell response. We found that neutralization of IL4I1 activity can restore T cell proliferation. Thus, therapeutical strategies targeting enzymes involved in amino-acid catabolism may be helpful to contemporary block tumor cell migration and restore an efficacious anti-tumor immunity.
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Santos, Pedro Miguel, Janet Martha Blatny, Ilaria Di Bartolo, Svein Valla, and Elisabetta Zennaro. "Physiological Analysis of the Expression of the Styrene Degradation Gene Cluster in Pseudomonas fluorescensST." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1305–10. http://dx.doi.org/10.1128/aem.66.4.1305-1310.2000.
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ABSTRACT The effects of different carbon sources on expression of the styrene catabolism genes in Pseudomonas fluorescens ST were analyzed by using a promoter probe vector, pPR9TT, which contains transcription terminators upstream and downstream of the β-galactosidase reporter system. Expression of the promoter of thestySR operon, which codes for the styrene two-component regulatory system, was found to be constitutive and not subject to catabolite repression. This was confirmed by the results of an analysis of the stySR transcript in P. fluorescensST cells grown on different carbon sources. The promoter of the operon of the upper pathway, designated PstyA, was induced by styrene and repressed to different extents by organic acids or carbohydrates. In particular, cells grown on succinate or lactate in the presence of styrene started to exhibit β-galactosidase activity during the mid-exponential growth phase, before the preferred carbon sources were depleted, indicating that there is a threshold succinate and lactate concentration which allows induction of styrene catabolic genes. In contrast, cells grown on glucose, acetate, or glutamate and styrene exhibited a diauxic growth curve, and β-galactosidase activity was detected only after the end of the exponential growth phase. In each experiment the reliability of the reporter system constructed was verified by comparing the β-galactosidase activity and the activity of the styrene monooxygenase encoded by the first gene of the styrene catabolic operon.
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Xu, Yan-mei, Xian-mei Xiao, Ze-xiang Zeng, Xiao-li Tan, Zong-li Liu, Jian-wen Chen, Xin-guo Su, and Jian-ye Chen. "BrTCP7 Transcription Factor Is Associated with MeJA-Promoted Leaf Senescence by Activating the Expression of BrOPR3 and BrRCCR." International Journal of Molecular Sciences 20, no. 16 (August 14, 2019): 3963. http://dx.doi.org/10.3390/ijms20163963.
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The plant hormone jasmonic acid (JA) has been recognized as an important promoter of leaf senescence in plants. However, upstream transcription factors (TFs) that control JA biosynthesis during JA-promoted leaf senescence remain unknown. In this study, we report the possible involvement of a TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) TF BrTCP7 in methyl jasmonate (MeJA)-promoted leaf senescence in Chinese flowering cabbage. Exogenous MeJA treatment reduced maximum quantum yield (Fv/Fm) and total chlorophyll content, accompanied by the increased expression of senescence marker and chlorophyll catabolic genes, and accelerated leaf senescence. To further understand the transcriptional regulation of MeJA-promoted leaf senescence, a class I member of TCP TFs BrTCP7 was examined. BrTCP7 is a nuclear protein and possesses trans-activation ability through subcellular localization and transcriptional activity assays. A higher level of BrTCP7 transcript was detected in senescing leaves, and its expression was up-regulated by MeJA. The electrophoretic mobility shift assay and transient expression assay showed that BrTCP7 binds to the promoter regions of a JA biosynthetic gene BrOPR3 encoding OPDA reductase3 (OPR3) and a chlorophyll catabolic gene BrRCCR encoding red chlorophyll catabolite reductase (RCCR), activating their transcriptions. Taken together, these findings reveal that BrTCP7 is associated with MeJA-promoted leaf senescence at least partly by activating JA biosynthesis and chlorophyll catabolism, thus expanding our knowledge of the transcriptional mechanism of JA-mediated leaf senescence.
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Curran, Timothy M., Yousheng Ma, Glen C. Rutherford, and Robert E. Marquis. "Turning on and turning off the arginine deiminase system in oral streptococci." Canadian Journal of Microbiology 44, no. 11 (November 1, 1998): 1078–85. http://dx.doi.org/10.1139/w98-106.
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The arginine deiminase system in oral streptococci is highly regulated. It requires induction and is repressed by catabolites such as glucose or by aeration. A comparative study of regulation of the system in Streptococcus gordonii ATCC 10558, Streptococcus rattus FA-1, and Streptococcus sanguis NCTC 10904 showed an increase in activity of the system in S. sanguis of some 1467-fold associated with induction-derepression of cells previously uninduced-repressed. The activity of the system was assayed in terms of levels of arginine deiminase, the signature enzyme of the system, in permeabilized cells. Increases in enzyme levels associated with induction-derepression were less for the other two organisms, mainly because of less severe repression, especially for S. rattus FA-1, which was the least sensitive to catabolite repression or aeration. Regulation of the arginine deiminase system involving induction and catabolite repression was demonstrated also with monoorganism biofilms composed of cells of S. sanguis adherent to glass slides. Fully uninduced-repressed cells from suspension cultures or biofilms were compromised in their abilities to catabolize arginine to protect themselves against acid damage. However, it was found that the system can be rapidly turned on or turned off, although induction-derepression did appear to require cell growth. Still, the system could respond rapidly to the availability of arginine to reestablish high capacity for alkali production.Key words: arginine deiminase, oral streptococci, induction-derepression, acid damage, biofilms.
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Hirooka, Kazutake, Yusuke Kodoi, Takenori Satomura, and Yasutaro Fujita. "Regulation of therhaEWRBMAOperon Involved in l-Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis." Journal of Bacteriology 198, no. 5 (December 28, 2015): 830–45. http://dx.doi.org/10.1128/jb.00856-15.
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ABSTRACTTheBacillus subtilisrhaEWRBMA(formerlyyuxG-yulBCDE) operon consists of four genes encoding enzymes forl-rhamnose catabolism and therhaRgene encoding a DeoR-type transcriptional regulator. DNase I footprinting analysis showed that the RhaR protein specifically binds to the regulatory region upstream of therhaEWgene, in which two imperfect direct repeats are included. Gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of RhaR and that the DNA binding of RhaR was effectively inhibited byl-rhamnulose-1-phosphate, an intermediate ofl-rhamnose catabolism. Moreover, it was demonstrated that the CcpA/P-Ser-HPr complex, primarily governing the carbon catabolite control inB. subtilis, binds to the catabolite-responsive element, which overlaps the RhaR binding site.In vivoanalysis of therhaEWpromoter-lacZfusion in the background ofccpAdeletion showed that thel-rhamnose-responsive induction of therhaEWpromoter was negated by the disruption ofrhaAorrhaBbut notrhaEWorrhaM, whereasrhaRdisruption resulted in constitutiverhaEWpromoter activity. Thesein vitroandin vivoresults clearly indicate that RhaR represses the operon by binding to the operator site, which is detached byl-rhamnulose-1-phosphate formed froml-rhamnose through a sequence of isomerization by RhaA and phosphorylation by RhaB, leading to the derepression of the operon. In addition, thelacZreporter analysis using the strains with or without theccpAdeletion under the background ofrhaRdisruption supported the involvement of CcpA in the carbon catabolite repression of the operon.IMPORTANCESincel-rhamnose is a component of various plant-derived compounds, it is a potential carbon source for plant-associating bacteria. Moreover, it is suggested thatl-rhamnose catabolism plays a significant role in some bacteria-plant interactions, e.g., invasion of plant pathogens and nodulation of rhizobia. Despite the physiological importance ofl-rhamnose catabolism for various bacterial species, the transcriptional regulation of the relevant genes has been poorly understood, except for the regulatory system ofEscherichia coli. In this study, we show that, inBacillus subtilis, one of the plant growth-promoting rhizobacteria, therhaEWRBMAoperon forl-rhamnose catabolism is controlled by RhaR and CcpA. This regulatory system can be another standard model for better understanding the regulatory mechanisms ofl-rhamnose catabolism in other bacterial species.
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Kaysen, G. A., E. Hoye, and H. Jones. "Apolipoprotein AI levels are increased in part as a consequence of reduced catabolism in nephrotic rats." American Journal of Physiology-Renal Physiology 268, no. 3 (March 1, 1995): F532—F540. http://dx.doi.org/10.1152/ajprenal.1995.268.3.f532.
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Apolipoprotein AI (apo AI) synthesis, measured as the turnover of 125I-labeled apo AI-labeled high-density lipoprotein (HDL), was increased significantly in rats with Heymann nephritis (HN) vs. control Sprague-Dawley (SD) rats. However, fractional apo AI catabolic rate was also significantly less in HN vs. SD. We used 125I-apo AI tyramine cellobiose HDL, a marker retained at the catabolic site, to establish where apo AI catabolism decreased in six HN rats, seven rats with adriamycin (Adria)-induced nephrosis, and six control SD. Total renal apo AI catabolism, plus urinary losses, were the same in all three groups, despite significant urinary apo AI in HN and Adria rats. Apo AI catabolism was reduced in skin in both nephrotic groups, accounting for approximately 44% of reduced in apo AI catabolism. Thus a significant fraction of apo AI is catabolized in skin of normal male rats. Reduced apo AI catabolism in skin contributes to increased plasma levels in nephrotic rats.
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Mondanelli, Giada, Elena Orecchini, Claudia Volpi, Eleonora Panfili, Maria Laura Belladonna, Maria Teresa Pallotta, Simone Moretti, Roberta Galarini, Susanna Esposito, and Ciriana Orabona. "Effect of Probiotic Administration on Serum Tryptophan Metabolites in Pediatric Type 1 Diabetes Patients." International Journal of Tryptophan Research 13 (January 2020): 117864692095664. http://dx.doi.org/10.1177/1178646920956646.
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Type 1 diabetes (T1D) is characterized by anomalous functioning of the immuno regulatory, tryptophan-catabolic enzyme indoleamine 2,3 dioxygenase 1 (IDO1). In T1D, the levels of kynurenine—the first byproduct of tryptophan degradation via IDO1—are significantly lower than in nondiabetic controls, such that defective immune regulation by IDO1 has been recognized as potentially contributing to autoimmunity in T1D. Because tryptophan catabolism—and the production of immune regulatory catabolites—also occurs via the gut microbiota, we measured serum levels of tryptophan, and metabolites thereof, in pediatric, diabetic patients after a 3-month oral course of Lactobacillus rhamnosus GG. Daily administration of the probiotic significantly affected circulating levels of tryptophan as well as the qualitative pattern of metabolite formation in the diabetic patients, while it decreased inflammatory cytokine production by the patients. This study suggests for the first time that a probiotic treatment may affect systemic tryptophan metabolism and restrain proinflammatory profile in pediatric T1D.
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Richardson, Jason S., and Ivan J. Oresnik. "l-Rhamnose Transport Is Sugar Kinase (RhaK) Dependent in Rhizobium leguminosarum bv. trifolii." Journal of Bacteriology 189, no. 23 (September 21, 2007): 8437–46. http://dx.doi.org/10.1128/jb.01032-07.
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ABSTRACT Strains of Rhizobium leguminosarum which are unable to catabolize l-rhamnose, a methyl-pentose sugar, are compromised in the ability to compete for nodule occupancy versus wild-type strains. Previous characterization of the 11-kb region necessary for the utilization of rhamnose identified a locus carrying catabolic genes and genes encoding the components of an ABC transporter. Genetic evidence suggested that the putative kinase RhaK carried out the first step in the catabolism of rhamnose. Characterization of this kinase led to the observation that strains carrying rhamnose kinase mutations were unable to transport rhamnose into the cell. The absence of a functional rhamnose kinase did not stop the transcription and translation of the ABC transporter components. By developing an in vitro assay for RhaK activity, we have been able to show that (i) RhaK activity is consistent with RhaK phosphorylating rhamnose and (ii) biochemical activity of RhaK is necessary for rhamnose transport.
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Hirose, Jun, Ryusei Tsukimata, Munetoshi Miyatake, and Haruhiko Yokoi. "Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1." Genes 11, no. 12 (November 27, 2020): 1416. http://dx.doi.org/10.3390/genes11121416.
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Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD+-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain.
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Shimizu, Tetsu, and Akira Nakamura. "Characterization of LgnR, an IclR family transcriptional regulator involved in the regulation of l-gluconate catabolic genes in Paracoccus sp. 43P." Microbiology 160, no. 3 (March 1, 2014): 623–34. http://dx.doi.org/10.1099/mic.0.074286-0.
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Five genes encoding enzymes required for l-gluconate catabolism, together with genes encoding components of putative ABC transporters, are located in a cluster in the genome of Paracoccus sp. 43P. A gene encoding a transcriptional regulator in the IclR family, lgnR, is located in front of the cluster in the opposite direction. Reverse transcription PCR analysis indicated that the cluster was transcribed as an operon, termed the lgn operon. Two promoters, P lgnA and P lgnR , are divergently located in the intergenic region, and transcription from these promoters was induced by addition of l-gluconate or d-idonate, a catabolite of l-gluconate. Deletion of lgnR resulted in constitutive expression of lgnA, lgnH and lgnR, indicating that lgnR encodes a repressor protein for the expression of the lgn operon and lgnR itself. Electrophoretic mobility shift assay and DNase I footprinting analyses revealed that recombinant LgnR binds to both P lgnA and P lgnR , indicating that LgnR represses transcription from these promoters by competing with RNA polymerase for binding to these sequences. d-Idonate was identified as a candidate effector molecule for dissociation of LgnR from these promoters. Phylogenetic analysis revealed that LgnR formed a cluster with putative proteins from other genome sequences, which is distinct from those proteins of known regulatory functions, in the IclR family of transcriptional regulators. Additionally, the phylogeny suggests an evolutionary linkage between the l-gluconate catabolic pathway and d-galactonate catabolic pathways distributed in Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria.
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Xu, Yanyan, Haojie Jiang, Li Li, Fengwu Chen, Yunxia Liu, Meiyi Zhou, Ji Wang, et al. "Branched-Chain Amino Acid Catabolism Promotes Thrombosis Risk by Enhancing Tropomodulin-3 Propionylation in Platelets." Circulation 142, no. 1 (July 7, 2020): 49–64. http://dx.doi.org/10.1161/circulationaha.119.043581.
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Background: Branched-chain amino acids (BCAAs), essential nutrients including leucine, isoleucine, and valine, serve as a resource for energy production and the regulator of important nutrient and metabolic signals. Recent studies have suggested that dysfunction of BCAA catabolism is associated with the risk of cardiovascular disease. Platelets play an important role in cardiovascular disease, but the functions of BCAA catabolism in platelets remain unknown. Methods: The activity of human platelets from healthy subjects before and after ingestion of BCAAs was measured. Protein phosphatase 2Cm specifically dephosphorylates branched-chain α-keto acid dehydrogenase and thereby activates BCAA catabolism. Protein phosphatase 2Cm–deficient mice were used to elucidate the impacts of BCAA catabolism on platelet activation and thrombus formation. Results: We found that ingestion of BCAAs significantly promoted human platelet activity (n=5; P <0.001) and arterial thrombosis formation in mice (n=9; P <0.05). We also found that the valine catabolite α-ketoisovaleric acid and the ultimate oxidation product propionyl-coenzyme A showed the strongest promotion effects on platelet activation, suggesting that the valine/α-ketoisovaleric acid catabolic pathway plays a major role in BCAA-facilitated platelet activation. Protein phosphatase 2Cm deficiency significantly suppresses the activity of platelets in response to agonists (n=5; P <0.05). Our results also suggested that BCAA metabolic pathways may be involved in the integrin αIIbβ3–mediated bidirectional signaling pathway that regulates platelet activation. Mass spectrometry identification and immunoblotting revealed that BCAAs enhanced propionylation of tropomodulin-3 at K255 in platelets or Chinese hamster ovary cells expressing integrin αIIbβ3. The tropomodulin-3 K255A mutation abolished propionylation and attenuated the promotion effects of BCAAs on integrin-mediated cell spreading, suggesting that K255 propionylation of tropomodulin-3 is an important mechanism underlying integrin αIIbβ3–mediated BCAA-facilitated platelet activation and thrombosis formation. In addition, the increased levels of BCAAs and the expression of positive regulators of BCAA catabolism in platelets from patients with type 2 diabetes mellitus are significantly correlated with platelet hyperreactivity. Lowering dietary BCAA intake significantly reduced platelet activity in ob/ob mice (n=4; P <0.05). Conclusions: BCAA catabolism is an important regulator of platelet activation and is associated with arterial thrombosis risk. Targeting the BCAA catabolism pathway or lowering dietary BCAA intake may serve as a novel therapeutic strategy for metabolic syndrome–associated thrombophilia.
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Lewis, Christopher, Raghavan Chinnadurai, and Jacques Galipeau. "Mesenchymal stromal cell immunomodulation and aryl hydrocarbon receptor activation by tryptophan catabolites (IRM9P.462)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 130.7. http://dx.doi.org/10.4049/jimmunol.194.supp.130.7.
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Abstract The catabolism of Trp by indoleamine 2,3-dioxygenase (IDO) is a key correlate of the immunomodulation by human mesenchymal stromal cells (MSCs). AHR is a cytosolic protein expressed by a variety of cells, that upon activation, initiates transcription at aryl hydrocarbon response elements (AHREs). We show MSCs express AHR basally, and hypothesized that the catalytic activity of IDO and signal transduction via AHR are linked, as intracellular signals which deploy MSC suppressive properties. To test this, we treated MSCs with hydrocarbons known to activate AHR: TCDD or FICZ. Upon treatment of resting MSCs with TCDD or FICZ, we observed 100-fold induction of Cyp1a1/1b1 mRNA, reflective of AHRE activation. We next examined the response of MSCs after 48h treatment with 1MT, Trp, kynurenine (Kyn) or kynurenic acid (KynAc), the latter two being IDO-catalyzed Trp metabolites. We observed 1MT and KynAc both induced Cyp1a1/1b1 expression by 60-fold. These data support the theory that IDO-catabolism of Trp generates endogenous ligands (i.e.KynAc) which can directly activate AHR. We performed T cell suppression assays, and observed Trp catabolites augment the immunosuppressive function of MSCs (independently of PDL1 or IDO). Our findings suggest endogenous AHR signals from IDO catalysis may play a role in MSC immunomodulation. This observation supports a novel paradigm for intracellular signaling from catabolic conversion of Trp to AHR ligands and induction of immunomodulatory properties.
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Martinez, Betsy, Jeffrey Tomkins, Lawrence P. Wackett, Rod Wing, and Michael J. Sadowsky. "Complete Nucleotide Sequence and Organization of the Atrazine Catabolic Plasmid pADP-1 from Pseudomonassp. Strain ADP." Journal of Bacteriology 183, no. 19 (October 1, 2001): 5684–97. http://dx.doi.org/10.1128/jb.183.19.5684-5697.2001.
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ABSTRACT The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal ofs-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Regions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncPβ plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were identified and flank each of theatzA, atzB, and atzC genes, forming structures resembling nested catabolic transposons. Functional analyses identified three new catabolic genes, atzD,atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzEand atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how plasmids are structured, and thus evolve, to encode the catabolism of compounds recently added to the biosphere.
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Chow, Virginia, Guang Nong, and James F. Preston. "Structure, Function, and Regulation of the Aldouronate Utilization Gene Cluster from Paenibacillus sp. Strain JDR-2." Journal of Bacteriology 189, no. 24 (October 5, 2007): 8863–70. http://dx.doi.org/10.1128/jb.01141-07.
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ABSTRACT Direct bacterial conversion of the hemicellulose fraction of hardwoods and crop residues to biobased products depends upon extracellular depolymerization of methylglucuronoxylan (MeGAXn), followed by assimilation and intracellular conversion of aldouronates and xylooligosaccharides to fermentable xylose. Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium, secretes a multimodular cell-associated GH10 endoxylanase (XynA1) that catalyzes depolymerization of MeGAXn and rapidly assimilates the principal products, β-1,4-xylobiose, β-1,4-xylotriose, and MeGAX3, the aldotetrauronate 4-O-methylglucuronosyl-α-1,2-xylotriose. Genomic libraries derived from this bacterium have now allowed cloning and sequencing of a unique aldouronate utilization gene cluster comprised of genes encoding signal transduction regulatory proteins, ABC transporter proteins, and the enzymes AguA (GH67 α-glucuronidase), XynA2 (GH10 endoxylanase), and XynB (GH43 β-xylosidase/α-arabinofuranosidase). Expression of these genes, as well as xynA1 encoding the secreted GH10 endoxylanase, is induced by growth on MeGAXn and repressed by glucose. Sequences in the yesN, lplA, and xynA2 genes within the cluster and in the distal xynA1 gene show significant similarity to catabolite responsive element (cre) defined in Bacillus subtilis for recognition of the catabolite control protein (CcpA) and consequential repression of catabolic regulons. The aldouronate utilization gene cluster in Paenibacillus sp. strain JDR-2 operates as a regulon, coregulated with the expression of xynA1, conferring the ability for efficient assimilation and catabolism of the aldouronate product generated by a multimodular cell surface-anchored GH10 endoxylanase. This cluster offers a desirable metabolic potential for bacterial conversion of hemicellulose fractions of hardwood and crop residues to biobased products.
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Horswill, Alexander R., and Jorge C. Escalante-Semerena. "Salmonella typhimurium LT2 Catabolizes Propionate via the 2-Methylcitric Acid Cycle." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5615–23. http://dx.doi.org/10.1128/jb.181.18.5615-5623.1999.
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ABSTRACT We previously identified the prpBCDE operon, which encodes catabolic functions required for propionate catabolism inSalmonella typhimurium. Results from13C-labeling experiments have identified the route of propionate breakdown and determined the biochemical role of each Prp enzyme in this pathway. The identification of catabolites accumulating in wild-type and mutant strains was consistent with propionate breakdown through the 2-methylcitric acid cycle. Our experiments demonstrate that the α-carbon of propionate is oxidized to yield pyruvate. The reactions are catalyzed by propionyl coenzyme A (propionyl-CoA) synthetase (PrpE), 2-methylcitrate synthase (PrpC), 2-methylcitrate dehydratase (probably PrpD), 2-methylisocitrate hydratase (probably PrpD), and 2-methylisocitrate lyase (PrpB). In support of this conclusion, the PrpC enzyme was purified to homogeneity and shown to have 2-methylcitrate synthase activity in vitro.1H nuclear magnetic resonance spectroscopy and negative-ion electrospray ionization mass spectrometry identified 2-methylcitrate as the product of the PrpC reaction. Although PrpC could use acetyl-CoA as a substrate to synthesize citrate, kinetic analysis demonstrated that propionyl-CoA is the preferred substrate.
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Janes, Brian K., and Robert A. Bender. "Alanine Catabolism in Klebsiella aerogenes: Molecular Characterization of the dadAB Operon and Its Regulation by the Nitrogen Assimilation Control Protein." Journal of Bacteriology 180, no. 3 (February 1, 1998): 563–70. http://dx.doi.org/10.1128/jb.180.3.563-570.1998.
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ABSTRACT Klebsiella aerogenes strains with reduced levels ofd-amino acid dehydrogenase not only fail to use alanine as a growth substrate but also become sensitive to alanine in minimal media supplemented with glucose and ammonium. The inability of these mutant strains to catabolize the alanine provided in the medium interferes with both pathways of glutamate production. Alanine derepresses the nitrogen regulatory system (Ntr), which in turn represses glutamate dehydrogenase, one pathway of glutamate production. Alanine also inhibits the enzyme glutamine synthetase, the first enzyme in the other pathway of glutamate production. Therefore, in the presence of alanine, strains with mutations in dadA (the gene that codes for a subunit of the dehydrogenase) exhibit a glutamate auxotrophy when ammonium is the sole source of nitrogen. The alanine catabolic operon of Klebsiella aerogenes,dadAB, was cloned, and its DNA sequence was determined. The clone complemented the alanine defects of dadA strains. The operon has a high similarity to the dadAB operon ofSalmonella typhimurium and the dadAX operon ofEscherichia coli, each of which codes for the smaller subunit of d-amino acid dehydrogenase and the catabolic alanine racemase. Unlike the cases for E. coli and S. typhimurium, the dad operon of K. aerogenes is activated by the Ntr system, mediated in this case by the nitrogen assimilation control protein (NAC). A sequence matching the DNA consensus for NAC-binding sites is located centered at position −44 with respect to the start of transcription. The promoter of this operon also contains consensus binding sites for the catabolite activator protein and the leucine-responsive regulatory protein.
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Junghans, R. P., and T. A. Waldmann. "Metabolism of Tac (IL2Ralpha): physiology of cell surface shedding and renal catabolism, and suppression of catabolism by antibody binding." Journal of Experimental Medicine 183, no. 4 (April 1, 1996): 1587–602. http://dx.doi.org/10.1084/jem.183.4.1587.
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The interleukin 2 receptor alpha (IL2Ralpha; CD25; Tac) is the prototypic model for soluble receptor studies. It exists in vivo as a transmembrane complete molecule (TM-Tac) on cell surfaces and as a truncated soluble form (sTac; sIL2R alpha). sTac has been used as a serum marker of T cell activation in immune disorders and of tumor burden in Tac-expressing malignancies. In vivo, serum levels of all soluble proteins depend on the balance between production and catabolism, but little is known about the metabolic features of this class of molecules. We have developed a model for Tac metabolism that incorporates new insights in its production and catabolism. Tac was shed from the surface of malignant and activated human T cells with a model half-life (t1/2) of 2-6h, but which was prolonged under certain circumstances. The rate of shedding is first order overall and nonsaturable over a two order of magnitude range of substrate (TM-Tac) expression. Once shed from cells Tac is subject to catabolic activities in the host. In vivo studies in mice showed that 90% of Tac was catabolized by the kidney with a t1/2 of 1 h and a filtration fraction of 0.11 relative to creatinine. The remaining 10% of catabolism was mediated by other tissues with a t1/2 of 10 h. Approximately 1-3% of sTac is excreted intact as proteinuria with the remaining 97-99% catabolized to amino acids. Antibody to the receptor induced a marked delay in sTac catabolism by preventing filtration of the smaller protein through the renal glomerulus and additionally suppressing other nonrenal catabolic mechanisms. A discrepancy between the catabolic rats for Tac and anti-Tac in the same complex was interpreted as a previously unrecognized differential catabolic mechanism, suggesting features of the Brambell hypothesis and immunoglobulin G transport and catabolism, in which the antigen-in-complex in intracellular vesicles is relatively less protected from catabolism than the associated antibody. In light of the pivotal role played by the kidney in sTac catabolism and the impact of administered antibody, the serum concentration of Tac in the settings of renal dysfunction or antibody therapy is not a suitable surrogate of activated T cells or of the body burden of tumor. These results provide parameters for assessing soluble receptor-ligand interactions generally.
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Somerville, Greg A., Battouli Saïd-Salim, Jaala M. Wickman, Sandra J. Raffel, Barry N. Kreiswirth, and James M. Musser. "Correlation of Acetate Catabolism and Growth Yield in Staphylococcus aureus: Implications for Host-Pathogen Interactions." Infection and Immunity 71, no. 8 (August 2003): 4724–32. http://dx.doi.org/10.1128/iai.71.8.4724-4732.2003.
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ABSTRACT Recently, we reported that the prototypical Staphylococcus aureus strain RN6390 (a derivative of NCTC 8325) had significantly reduced aconitase activity relative to a diverse group of S. aureus isolates, leading to the hypothesis that strain RN6390 has impaired tricarboxylic acid (TCA) cycle-mediated acetate catabolism. Analysis of the culture supernatant from RN6390 confirmed that acetate was incompletely catabolized, suggesting that the ability to catabolize acetate can be lost by S. aureus. To test this hypothesis, we examined the carbon catabolism of the S. aureus strains whose genome sequences are publicly available. All strains catabolized glucose and excreted acetate into the culture medium. However, strains NCTC 8325 and N315 failed to catabolize acetate during the postexponential growth phase, resulting in significantly lower growth yields relative to strains that catabolized acetate. Strains NCTC 8325 and RN6390 contained an 11-bp deletion in rsbU, the gene encoding a positive regulator of the alternative sigma factor σB encoded by sigB. An isogenic derivative strain of RN6390 containing the wild-type rsbU gene had significantly increased acetate catabolism, demonstrating that σB is required for acetate catabolism. Taken together, the data suggest that naturally occurring mutations can alter the ability of S. aureus to catabolize acetate, a surprising discovery, as TCA cycle function has been demonstrated to be involved in the virulence, survival, and persistence of several pathogenic organisms. Additionally, these mutations decrease the fitness of S. aureus by reducing the number of progeny placed into subsequent generations, suggesting that in certain situations a decreased growth yield is advantageous.
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Shin, Byung-Sik, Soo-Keun Choi, Issar Smith, and Seung-Hwan Park. "Analysis of tnrA Alleles Which Result in a Glucose-Resistant Sporulation Phenotype in Bacillus subtilis." Journal of Bacteriology 182, no. 17 (September 1, 2000): 5009–12. http://dx.doi.org/10.1128/jb.182.17.5009-5012.2000.
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ABSTRACT Bacillus subtilis cells cannot sporulate in the presence of catabolites such as glucose. During the analysis of Tn10-generated mutants, we found that deletion of the C-terminal region of the tnrA gene, which encodes a global regulator that positively regulates a number of genes in response to nitrogen limitation, results in a catabolite-resistant sporulation phenotype. Analyses of nrg-lacZ and nasB-lacZ, which are activated by TnrA under nitrogen limitation, showed that C-terminally truncated TnrA activates nitrogen-regulated genes constitutively. The relief of catabolite repression of sporulation may result from the uncontrolled expression of the TnrA-regulated genes.
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Breiden, Bernadette, and Konrad Sandhoff. "Mechanism of Secondary Ganglioside and Lipid Accumulation in Lysosomal Disease." International Journal of Molecular Sciences 21, no. 7 (April 7, 2020): 2566. http://dx.doi.org/10.3390/ijms21072566.
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Gangliosidoses are caused by monogenic defects of a specific hydrolase or an ancillary sphingolipid activator protein essential for a specific step in the catabolism of gangliosides. Such defects in lysosomal function cause a primary accumulation of multiple undegradable gangliosides and glycosphingolipids. In reality, however, predominantly small gangliosides also accumulate in many lysosomal diseases as secondary storage material without any known defect in their catabolic pathway. In recent reconstitution experiments, we identified primary storage materials like sphingomyelin, cholesterol, lysosphingolipids, and chondroitin sulfate as strong inhibitors of sphingolipid activator proteins (like GM2 activator protein, saposin A and B), essential for the catabolism of many gangliosides and glycosphingolipids, as well as inhibitors of specific catabolic steps in lysosomal ganglioside catabolism and cholesterol turnover. In particular, they trigger a secondary accumulation of ganglioside GM2, glucosylceramide and cholesterol in Niemann–Pick disease type A and B, and of GM2 and glucosylceramide in Niemann–Pick disease type C. Chondroitin sulfate effectively inhibits GM2 catabolism in mucopolysaccharidoses like Hurler, Hunter, Sanfilippo, and Sly syndrome and causes a secondary neuronal ganglioside GM2 accumulation, triggering neurodegeneration. Secondary ganglioside and lipid accumulation is furthermore known in many more lysosomal storage diseases, so far without known molecular basis.
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Tomás-Gallardo, Laura, Eduardo Santero, and Belén Floriano. "Involvement of a Putative Cyclic AMP Receptor Protein (CRP)-Like Binding Sequence and a CRP-Like Protein in Glucose-Mediated Catabolite Repression ofthnGenes in Rhodococcus sp. Strain TFB." Applied and Environmental Microbiology 78, no. 15 (May 25, 2012): 5460–62. http://dx.doi.org/10.1128/aem.00700-12.
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ABSTRACTGlucose catabolite repression of tetralin catabolic genes inRhodococcussp. strain TFB was shown to be exerted by a protein homologous to transcriptional regulators of the cyclic AMP receptor (CRP)-FNR family. The protein was detected bound to putative CRP-like boxes localized at the promoters of thethnA1andthnSgenes.
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Poole, P. S., A. Blyth, C. J. Reid, and K. Walters. "myo-Inositol catabolism and catabolite regulation in Rhizobium leguminosarum bv. viciae." Microbiology 140, no. 10 (October 1, 1994): 2787–95. http://dx.doi.org/10.1099/00221287-140-10-2787.
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Mu, Yang, Qing Chen, Rebecca E. Parales, Zhenmei Lu, Qing Hong, Jian He, Jiguo Qiu, and Jiandong Jiang. "Bacterial catabolism of nicotine: Catabolic strains, pathways and modules." Environmental Research 183 (April 2020): 109258. http://dx.doi.org/10.1016/j.envres.2020.109258.
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Kitagawa, Wataru, Keisuke Miyauchi, Eiji Masai, and Masao Fukuda. "Cloning and Characterization of Benzoate Catabolic Genes in the Gram-Positive Polychlorinated Biphenyl DegraderRhodococcus sp. Strain RHA1." Journal of Bacteriology 183, no. 22 (November 15, 2001): 6598–606. http://dx.doi.org/10.1128/jb.183.22.6598-6606.2001.
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ABSTRACT Benzoate catabolism is thought to play a key role in aerobic bacterial degradation of biphenyl and polychlorinated biphenyls (PCBs). Benzoate catabolic genes were cloned from a PCB degrader,Rhodococcus sp. strain RHA1, by using PCR amplification and temporal temperature gradient electrophoresis separation. A nucleotide sequence determination revealed that the deduced amino acid sequences encoded by the RHA1 benzoate catabolic genes, benABCDK, exhibit 33 to 65% identity with those of Acinetobacter sp. strain ADP1. The gene organization of the RHA1 benABCDKgenes differs from that of ADP1. The RHA1 benABCDK region was localized on the chromosome, in contrast to the biphenyl catabolic genes, which are located on linear plasmids. Escherichia coli cells containing RHA1 benABCD transformed benzoate to catechol via 2-hydro-1,2-dihydroxybenzoate. They transformed neither 2- nor 4-chlorobenzoates but did transform 3-chlorobenzoate. The RHA1 benA gene was inactivated by insertion of a thiostrepton resistance gene. The resultant mutant strain, RBD169, neither grew on benzoate nor transformed benzoate, and it did not transform 3-chlorobenzoate. It did, however, exhibit diminished growth on biphenyl and growth repression in the presence of a high concentration of biphenyl (13 mM). These results indicate that the cloned benABCD genes could play an essential role not only in benzoate catabolism but also in biphenyl catabolism in RHA1. Six rhodococcal benzoate degraders were found to have homologs of RHA1benABC. In contrast, two rhodococcal strains that cannot transform benzoate were found not to have RHA1 benABChomologs, suggesting that many Rhodococcus strains contain benzoate catabolic genes similar to RHA1 benABC.
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Tomlinson, Patricia Tolson, and Carol J. Lovatt. "Nucleotide Metabolism in ‘Washington’ Navel Orange Fruit: I. Pathways of Synthesis and Catabolism." Journal of the American Society for Horticultural Science 112, no. 3 (May 1987): 529–35. http://dx.doi.org/10.21273/jashs.112.3.529.
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Abstract The capacity of ‘Washington’ navel orange fruit [Citrus sinensis (L.) Osbeck] to synthesize and catabolize purines and pyrimidines was assessed. De novo biosynthesis of purine nucleotide was demonstrated by [14C] bicarbonate incorporation into purine nucleotides, blockage of this process by four known inhibitors, and assimilation of radiolabeled carbon from formate, both carbons of glycine, and carbon-3 of serine into the adenine ring. De novo synthesis of pyrimidines via the orotate pathway in young fruit was demonstrated by incorporation of [14C] bicarbonate and [6-14C]orotic acid into uridine nucleotides, release of 14CO2 from [7-14C]orotic acid, and blockage of these processes by 6-azauridine. Synthesis of purine and pyrimidine nucleotides via salvage reactions was demonstrated by incorporation of radiolabeled bases and ribonucleosides into nucleotides and into nucleic acids. Release of 14CO2 from radiolabeled adenine, adenosine, hypoxanthine, and xanthine, uric acid, urea (purines), uracil, and uridine (pyrimidines) provided evidence the pathways for catabolism (degradation) of purines and pyrimidines in navel orange fruit are similar to those found in microorganisms and animal tissues. To the best of our knowledge, this report is the first to assess the capacity of anabolic and catabolic pathways of purine and pyrimidine nucleotide metabolism in fruit of any species. De novo synthetic activities in orange fruit permit increases in the pools of purine and pyrimidine nucleotides using simple precursors. Further, the patterns of salvage and catabolism suggest riboside pools are reused predominantly as nucleotides, while the majority of base pools are degraded to permit recycling of carbon and nitrogen into other metabolites.
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Grantham, Barbara D., and J. Barrett. "Amino acid catabolism in the nematodes Heligmosomoides polygyrus and Panagrellus redivivus 2. Metabolism of the carbon skeleton." Parasitology 93, no. 3 (December 1986): 495–504. http://dx.doi.org/10.1017/s0031182000081208.
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SUMMARYAll of the enzymes of proline catabolism were present in Heligmosomoides polygyrus and Panagrellus redivivus and the activities were, in general, similar to those found in rat liver. Both nematodes were also shown to be able to catabolize the branched-chain amino acids leucine, isoleucine and valine, by pathways similar to those found in mammalian liver. There were no significant differences in amino acid catabolism between the animal-parasitic and free-living species of nematode.
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Gunasekera, Angelo, Francisco J. Alvarez, Lois M. Douglas, Hong X. Wang, Adam P. Rosebrock, and James B. Konopka. "Identification of GIG1, a GlcNAc-Induced Gene in Candida albicans Needed for Normal Sensitivity to the Chitin Synthase Inhibitor Nikkomycin Z." Eukaryotic Cell 9, no. 10 (July 30, 2010): 1476–83. http://dx.doi.org/10.1128/ec.00178-10.
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ABSTRACT The amino sugar N-acetylglucosamine (GlcNAc) is known to be an important structural component of cells from bacteria to humans, but its roles in cell signaling are less well understood. GlcNAc induces two pathways in the human fungal pathogen Candida albicans. One activates cyclic AMP (cAMP) signaling, which stimulates the formation of hyphal cells and the expression of virulence genes, and the other pathway induces genes needed to catabolize GlcNAc. Microarray analysis of gene expression was carried out under four different conditions in order to characterize the transcriptional changes induced by GlcNAc. The most highly induced genes include those that encode a GlcNAc transporter (NGT1) and the GlcNAc catabolic enzymes (HXK1, DAC1, and NAG1). GlcNAc also activated most of the genes whose expression is increased when cells are triggered with other stimuli to form hyphae. Surprisingly, GlcNAc also induced a subset of genes that are regulated by galactose (GAL1, GAL7, and GAL10), which may be due to cross talk between signaling pathways. A novel GlcNAc-induced gene, GIG1, which is not essential for GlcNAc catabolism or the induction of hyphae, was identified. However, a Gig1-green fluorescent protein (GFP) fusion protein was specifically induced by GlcNAc, and not by other sugars. Gig1-GFP localized to the cytoplasm, where GlcNAc metabolism occurs. Significantly, a gig1Δ mutant displayed increased resistance to nikkomycin Z, which inhibits chitin synthase from converting UDP-GlcNAc into cell wall chitin. Gig1 is highly conserved in fungi, especially those that contain GlcNAc catabolic genes. These results implicate Gig1 in GlcNAc metabolism.
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Ewart, H. S., M. Jois, and J. T. Brosnan. "Rapid stimulation of the hepatic glycine-cleavage system in rats fed on a single high-protein meal." Biochemical Journal 283, no. 2 (April 15, 1992): 441–47. http://dx.doi.org/10.1042/bj2830441.
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Glycine catabolism was studied in isolated rat liver mitochondria by measuring the release of 14CO2 from [1-14C]glycine. Mitochondria isolated from rats fed on a high-protein (60% casein) diet for 5 days showed an enhanced ability to catabolize glycine compared with mitochondria from rats fed on a normal-protein (15% casein) diet. Glycine catabolism was also stimulated in normal protein-fed rats if they ingested a single high-protein meal for 2 h before being killed, thus illustrating the rapid response of the glycine-cleavage system to protein intake. The stimulation of glycine catabolism in rats given a high-protein diet or meal was not evident if the mitochondria were incubated in the absence of P(i) (omitting ADP had no effect on the rate). Mitochondria from high-protein- and normal-protein-fed rats did not differ in their ability to accumulate glycine, a process which occurred far too rapidly to impose a limit on the rate of flux through the glycine-cleavage system. The stimulation of glycine catabolism by high-protein feeding was not associated with a change in mitochondrial matrix volume. Furthermore, mitochondria from rats fed on a high-protein meal maintained an enhanced ability to catabolize glycine compared with those from rats fed on a normal-protein meal when incubated in hypo-osmotic solutions of very low osmolarity. When mitochondria from high-protein- or normal-protein-fed rats were maximally activated by incubation in the presence of 0.25 microM-Ca2+, the rates of glycine catabolism were high, but similar, showing that the stimulation of glycine catabolism by high-protein feeding does not involve an increase in the total capacity of the system. These findings show that hepatic glycine catabolism is stimulated rapidly by high-protein feeding, a response that we suggest is involved in the disposal of the excess glycine in the diet.
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Zhang, Meng, Yuting Fu, Yuhao Chen, Yuze Ma, Zhixin Guo, Yanfeng Wang, Huifang Hao, Quan Fu, and Zhigang Wang. "Inhibition of the mTORC1/NF-κB Axis Alters Amino Acid Metabolism in Human Hepatocytes." BioMed Research International 2021 (January 18, 2021): 1–15. http://dx.doi.org/10.1155/2021/8621464.
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In addition to serving as the building blocks for protein synthesis, amino acids can be used as an energy source, through catabolism. The transamination, oxidative deamination, and decarboxylation processes that occur during amino acid catabolism are catalyzed by specific enzymes, including aspartate aminotransferase (AST), glutamate dehydrogenase (GDH), glutamic acid decarboxylase (GAD), and ornithine decarboxylase (ODC); however, the overall molecular mechanisms through which amino acid catabolism occurs remain largely unknown. To examine the role of mechanistic target of rapamycin complex 1 (mTORC1) on amino acid catabolism, mTORC1 was inactivated by rapamycin or shRNA targeting Raptor, versus activated by overexpressing Rheb or amino acids in human hepatocytes. The expression of amino acid catabolic genes and related transcription factor was investigated by RT/real-time PCR and western blot analysis. A few types of amino acid metabolite were examined by ELISA and HPLC analysis. The data showed that inactivated mTORC1 resulted in inhibition of NF-κB and the expression of AST, GDH, GAD, and ODC, whereas activated mTORC1 enhanced NF-κB activation and the expression levels of the catabolism-associated genes. Further, inhibition of NF-κB reduced the expression levels of AST, GDH, GAD, and ODC. mTORC1 upregulated NF-κB activation and the expression of AST and ODC in response to glutamate and ornithine treatments, whereas rapamycin inhibited the utilization of glutamate and ornithine in hepatocytes. Taken together, these results indicated that the mTORC1/NF-κB axis modulates the rate of amino acid catabolism by regulating the expression of key catabolic enzymes in hepatocytes.
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Kramer, Boris W., Machiko Ikegami, and Alan H. Jobe. "Surfactant phospholipid catabolic rate is pool size dependent in mice." American Journal of Physiology-Lung Cellular and Molecular Physiology 279, no. 5 (November 1, 2000): L842—L848. http://dx.doi.org/10.1152/ajplung.2000.279.5.l842.
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We increased surfactant pool size by surfactant treatment in mice to test if the catabolism of the major component of surfactant, saturated phosphatidylcholine (Sat PC), was rate limited. By intratracheal instillation, we gave mice trace doses, doses of 45 or 110 μmol/kg, or three doses of 110 μmol/kg of Sat PC in surfactant that contained radiolabeled dipalmitoylphosphatidylcholine (DPPC) and a radiolabeled phospholipase A-resistant ether analog of DPPC. Two strains of mice with 2-fold differences in alveolar and total Sat PC pool sizes were used; the mice with the higher pool sizes had a 2.3-fold higher steady-state catabolic rate. Acute increases in alveolar surfactant given by intratracheal instillation increased catabolic rates ∼2-fold over the steady-state rates in both strains. There was minimal loss of the ether analog of DPPC from the lungs, and the alveolar macrophages did not accumulate more than 10% of the ether analog. In these two strains of mice, the catabolism of Sat PC was not rate limited because catabolic rate increased when alveolar pool sizes were increased.