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Newton A, McCann L, Huo L, Liu A. Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan. Metabolites 2023; 13:metabo13040500. [PMID: 37110158 PMCID: PMC10143591 DOI: 10.3390/metabo13040500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD+. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.
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Affiliation(s)
- Ashley Newton
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Luree McCann
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lu Huo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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2
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He J, Zhang K, Wang L, Du Y, Yang Y, Yuan C. Highly efficient degradation of cypermethrin by a co-culture of Rhodococcus sp. JQ-L and Comamonas sp. A-3. Front Microbiol 2022; 13:1003820. [PMID: 36188009 PMCID: PMC9522905 DOI: 10.3389/fmicb.2022.1003820] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Cypermethrin is an important synthetic pyrethroid pesticide that widely used to control pests in agriculture. However, extensive use has caused its residue and the metabolite 3-phenoxybenzoic acid (3-PBA) to seriously pollute the environments and agricultural products. In this study, a highly efficient cypermethrin-degrading bacterial consortium was acclimated from long-term pyrethroid-contaminated soil. Two strains, designated JQ-L and A-3, were screened from the consortium, and identified as Rhodococcus sp. and Comamonas sp., respectively. Strain JQ-L transformed 100 mg/L of cypermethrin to 3-PBA within 60 h of incubation; however, 3-PBA could not be further degraded by the strain. Strain A-3 utilized 3-PBA as sole carbon for growth, and completely degraded 100 mg/L of 3-PBA within 15 h of incubation. Co-culture of JQ-L and A-3 completely degraded 100 mg/L of cypermethrin within 24 h of incubation. Furthermore, a complete catabolic pathway of cypermethrin and the metabolite 3-PBA by the co-culture was proposed. This study provided a promising strategy for efficient elimination of cypermethrin residue-contaminated environments and agricultural products.
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Affiliation(s)
- Jian He
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kaiyun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lin Wang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Yingchun Du
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
| | - Cansheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing, China
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Weber M, Fuchs TM. Metabolism in the Niche: a Large-Scale Genome-Based Survey Reveals Inositol Utilization To Be Widespread among Soil, Commensal, and Pathogenic Bacteria. Microbiol Spectr 2022; 10:e0201322. [PMID: 35924911 PMCID: PMC9430895 DOI: 10.1128/spectrum.02013-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Phytate is the main phosphorus storage molecule of plants and is therefore present in large amounts in the environment and in the diet of humans and animals. Its dephosphorylated form, the polyol myo-inositol (MI), can be used by bacteria as a sole carbon and energy source. The biochemistry and regulation of MI degradation were deciphered in Bacillus subtilis and Salmonella enterica, but a systematic survey of this catabolic pathway has been missing until now. For a comprehensive overview of the distribution of MI utilization, we analyzed 193,757 bacterial genomes, representing a total of 24,812 species, for the presence, organization, and taxonomic prevalence of inositol catabolic gene clusters (IolCatGCs). The genetic capacity for MI degradation was detected in 7,384 (29.8%) of all species for which genome sequences were available. IolCatGC-positive species were particularly found among Actinobacteria and Proteobacteria and to a much lesser extent in Bacteroidetes. IolCatGCs are very diverse in terms of gene number and functions, whereas the order of core genes is highly conserved on the phylum level. We predict that 111 animal pathogens, more than 200 commensals, and 430 plant pathogens or rhizosphere bacteria utilize MI, underscoring that IolCatGCs provide a growth benefit within distinct ecological niches. IMPORTANCE This study reveals that the capacity to utilize inositol is unexpectedly widespread among soil, commensal, and pathogenic bacteria. We assume that this yet-neglected metabolism plays a pivotal role in the microbial turnover of phytate and inositols. The bioinformatic tool established here enables predicting to which extent and genetic variance a bacterial determinant is present in all genomes sequenced so far.
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Affiliation(s)
- Michael Weber
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Thilo M. Fuchs
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
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4
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Zhao L, Jiang Y, Zhao Z, Wang K, Zhang X, Hong Q, Qiu J, He J. Biodegradation of Quinolinic acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ191. FEMS Microbiol Lett 2022; 369:6567840. [PMID: 35416242 DOI: 10.1093/femsle/fnac040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Quinolinic acid (QA) is a pyridine derivative that can be found in many organisms and is widely used in the chemical industry. However, QA possesses excitotoxic properties. To date, the catabolism of QA mediated by microorganisms has rarely been reported. In this study, a QA-degrading strain (JQ191) was isolated from sewage sludge. Based on phenotypic and 16S rRNA gene phylogenetic analysis, the strain was identified as Alcaligenes faecalis. Strain JQ191 was able to utilize QA as the sole source of carbon and nitrogen for growth. QA-cultured cells of JQ191 completely degrade 200 mg/L QA within 2 days in a mineral salt medium, whereas the LB-cultured cells experienced a 2-day lag period before degrading QA, indicating that the catabolic enzymes involved in QA degradation were induced by QA. 6-Hydroxypicolinic acid (6HPA) was identified as an intermediate of QA degradation by strain JQ191. A 6HPA monooxygenase gene picB was cloned, genetically disrupted, and heterologously expressed, and the results show that picB was responsible for catalyzing 6HPA to 3,6DHPA in JQ191. A new QA mineralization pathway was proposed. This study identifies a new bacterium candidate that has a potential application prospect in the bioremediation of QA-polluted environment, as well as provides new insights into the bacterial catabolism of QA.
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Affiliation(s)
- Lingling Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinhu Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenyang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kexin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Ordoñez-Díaz JL, Moreno-Ortega A, Roldán-Guerra FJ, Ortíz-Somovilla V, Moreno-Rojas JM, Pereira-Caro G. In Vitro Gastrointestinal Digestion and Colonic Catabolism of Mango ( Mangifera indica L.) Pulp Polyphenols. Foods 2020; 9:foods9121836. [PMID: 33321767 PMCID: PMC7764420 DOI: 10.3390/foods9121836] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mango (Mangifera indica L.), a fruit with sensorial attractiveness and extraordinary nutritional and phytochemical composition, is one of the most consumed tropical varieties in the world. A growing body of evidence suggests that their bioactive composition differentiates them from other fruits, with mango pulp being an especially rich and diverse source of polyphenols. In this study, mango pulp polyphenols were submitted to in vitro gastrointestinal digestion and colonic fermentation, and aliquots were analyzed by HPLC-HRMS. The main phenolic compounds identified in the mango pulp were hydroxybenzoic acid-hexoside, two mono-galloyl-glucoside isomers and vanillic acid. The release of total polyphenols increased after the in vitro digestion, with an overall bioaccessibility of 206.3%. Specifically, the most bioaccessible mango polyphenols were gallic acid, 3-O-methylgallic acid, two hydroxybenzoic acid hexosides, methyl gallate, 3,4-dihydroxybenzoic acid and benzoic acid, which potentially cross the small intestine reaching the colon for fermentation by the resident microbiota. After 48 h of fecal fermentation, the main resultant mango catabolites were pyrogallol, gallic and 3,4-dihydroxybenzoic acids. This highlighted the extensive transformation of mango pulp polyphenols through the gastrointestinal tract and by the resident gut microbiota, with the resultant formation of mainly simple phenolics, which can be considered as biomarkers of the colonic metabolism of mango.
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Affiliation(s)
- José Luis Ordoñez-Díaz
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
| | - Alicia Moreno-Ortega
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
- Department of Food Science and Technology, University of Córdoba, Campus Rabanales, Ed. Darwin-anexo, 14071 Córdoba, Spain
| | - Francisco Javier Roldán-Guerra
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
| | - Victor Ortíz-Somovilla
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
| | - José Manuel Moreno-Rojas
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
| | - Gema Pereira-Caro
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, s/n, 14004 Córdoba, Spain; (J.L.O.-D.); (A.M.-O.); (F.J.R.-G.); (V.O.-S.); (J.M.M.-R.)
- Correspondence: ; Tel.: +34-671-532-734
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6
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Lyratzakis A, Valsamidis G, Kanavaki I, Nikolaki A, Rupprecht F, Langer JD, Tsiotis G. Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds. Proteomics 2020; 21:e2000003. [PMID: 33108051 DOI: 10.1002/pmic.202000003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 10/13/2020] [Indexed: 11/06/2022]
Abstract
The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here, Pseudomonas sp. strain phDV1, a gram-negative bacterium that is selected for its ability to degrade aromatic compounds is studied. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain is analyzed in the presence of succinate, phenol, and o-, m-, and p-cresol as the sole carbon source. As a reference proteome, the bacteria are grown in succinate and then compared with the respective proteomes of bacteria grown on phenol and different cresols. In total, 2295 proteins are identified; 1908 proteins are used for quantification between different growth conditions. The carbon source affects the synthesis of enzymes related to aromatic compound degradation and in particular the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, show higher abundance in the presence of monocyclic aromatic compounds. The results provide, for the first time, comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.
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Affiliation(s)
- Alexandros Lyratzakis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Giannis Valsamidis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Iliana Kanavaki
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Antigoni Nikolaki
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
| | - Fiona Rupprecht
- Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, Frankfurt am Main, D-60438, Germany.,Max Planck Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, D-60438, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, Frankfurt am Main, D-60438, Germany.,Max Planck Institute for Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, D-60438, Germany
| | - Georgios Tsiotis
- Division of Biochemistry, Department of Chemistry, University of Crete, Voutes, Heraklion, GR-71003, Greece
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Abstract
Many different biodegradation pathways, both aerobic and anaerobic, have already been characterised, and the phylogenetic relationships among catabolic genes within the different types of pathways have been studied. However, new biodegradation activities and their coding genes are continuously being reported, including those involved in the catabolism of emerging contaminants or those generally regarded as non-biodegradable. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to the bacterial physiological needs. New biodegradation pathways can be assembled in a particular strain or in a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, constitute valuable indicators of the biodegradation potential of a particular environmental niche. This knowledge paves the way to systems metabolic engineering approaches to valorise biowaste for the production of value-added products.
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8
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Younis SA, El-Gendy NS, Nassar HN. Biokinetic aspects for biocatalytic remediation of xenobiotics polluted seawater. J Appl Microbiol 2020; 129:319-334. [PMID: 32118335 DOI: 10.1111/jam.14626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/22/2020] [Accepted: 02/26/2020] [Indexed: 02/03/2023]
Abstract
AIMS This research was conducted to investigate the biocatalytic remediation of xenobiotics polluted seawater using two biocatalysts; whole bacterial cells of facultative aerobic halotolerant Corynebacterium variabilis Sh42 and its extracted crude enzymes. METHODS AND RESULTS One-Factor-at-A-Time technique and statistical analysis were applied to study the effect of initial substrate concentrations, pH, temperature, and initial biocatalyst concentrations on the batch biocatalytic degradation of three xenobiotic pollutants (2-hydroxybiphenyl (2-HBP), catechol and benzoic acid) in artificial seawater (salinity 3·1%). HPLC and gas-chromatography mass spectroscopy analyses were utilized to illustrate the quantitative removal of the studied aromatic xenobiotic pollutants and their catabolic pathway. The results revealed that the microbial and enzymatic cultures followed substrate inhibition kinetics. Yano and Koga's equation showed the best fit for the biokinetic degradation rates of 2-HBP and benzoic acid, whereas Haldane biokinetic model adequately expressed the specific biodegradation rate of catechol. The biokinetic results indicated the good efficiency and tolerance of crude enzyme for biocatalytic degradation of extremely high concentrations of aromatic pollutants than whole C. variabilis Sh42 cells. The monitored by-products indicated that the catabolic degradation pathway followed an oxidation mechanism via a site-specific monooxygenase enzyme. Benzoic acid and catechol were identified as major intermediates in the biodegradation pathway of 2-HBP, which were then biodegraded through meta-cleavage to 2-hydroxymuconic semialdehyde. With time elapsed, the semialdehyde product was further biodegraded to acetaldehyde and pyruvic acid, which would be further metabolized via the bacterial TCA cycle. CONCLUSION The batch enzymatic bioreactors performed superior-specific biocatalytic degradation rates for all the studied xenobiotic pollutants. SIGNIFICANCE AND IMPACT OF THE STUDY The enzymatic system of C. variabilis Sh42 is tolerable for toxic xenobiotics and different physicochemical environmental parameters. Thus, it can be recommended as an effective biocatalyst for biocatalytic remediation of xenobiotics polluted seawater.
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Affiliation(s)
- S A Younis
- Egyptian Petroleum Research Institute, Nasr City, Cairo, Egypt.,Department of Civil and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - N Sh El-Gendy
- Egyptian Petroleum Research Institute, Nasr City, Cairo, Egypt.,Center of Excellence, October University for Modern Sciences and Arts (MSA), 6th of October City, Egypt
| | - H N Nassar
- Egyptian Petroleum Research Institute, Nasr City, Cairo, Egypt.,Department of Microbiology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October City, Egypt
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9
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Abe A, Hiraoka M, Ohguro H, Tesmer JJ, Shayman JA. Preferential hydrolysis of truncated oxidized glycerophospholipids by lysosomal phospholipase A2. J Lipid Res 2016; 58:339-349. [PMID: 27993948 DOI: 10.1194/jlr.m070730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/08/2016] [Indexed: 01/18/2023] Open
Abstract
Truncated oxidized glycerophospholipids (ox-PLs) are bioactive lipids resulting from oxidative stress. The catabolic pathways for truncated ox-PLs are not fully understood. Lysosomal phospholipase A2 (LPLA2) with phospholipase A and transacylase activities is a key enzyme in phospholipid homeostasis. The present study assessed whether LPLA2 could hydrolyze truncated ox-PLs. Incubation of LPLA2 with liposomes consisting of 1,2-O-octadecenyl-sn-glycero-3-phosphocholine (DODPC)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or truncated oxidized phosphatidylcholine (ox-PC)/N-acetylsphingosine (NAS) under acidic conditions resulted in the preferential deacylation at the sn-1 position of the truncated ox-PCs. Additionally, the release of free fatty acid from the truncated ox-PCs preferentially occurred compared with the NAS-acylation. Incubation of LPLA2 with the liposomes consisting of DODPC/DOPC/truncated ox-PC/NAS resulted in the same preferential fatty acid release from the truncated ox-PC. The cationic amphiphilic drug, amiodarone, did not inhibit such fatty acid release, indicating that truncated ox-PCs partition from the lipid membrane into the aqueous phase and react with free LPLA2. Consistent with this mechanism, the hydrolysis of some truncated ox-PCs, but not DOPC, by LPLA2 was detected at neutral pH. Additionally, LPLA2-overexpressed Chinese hamster ovary cells efficiently catabolized truncated ox-PC and were protected from growth inhibition. These findings support the existence of a novel catabolic pathway for truncated ox-PLs via LPLA2.
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Affiliation(s)
- Akira Abe
- Department of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Miki Hiraoka
- Department of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hiroshi Ohguro
- Department of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - John J Tesmer
- Life Sciences Institute and Departments of Pharmacology, Biological Chemistry, University of Michigan, Ann Arbor, MI
| | - James A Shayman
- Internal Medicine, University of Michigan Medical School, University of Michigan, Ann Arbor, MI
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10
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Grishin AM, Cygler M. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway. Biology (Basel) 2015; 4:424-42. [PMID: 26075354 DOI: 10.3390/biology4020424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.
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11
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Zrenner R, Riegler H, Marquard CR, Lange PR, Geserick C, Bartosz CE, Chen CT, Slocum RD. A functional analysis of the pyrimidine catabolic pathway in Arabidopsis. New Phytol 2009; 183:117-132. [PMID: 19413687 PMCID: PMC2713857 DOI: 10.1111/j.1469-8137.2009.02843.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/19/2009] [Indexed: 05/04/2023]
Abstract
* Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.
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Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops14979 Großbeeren, Germany
| | - Heike Riegler
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Cathleen R Marquard
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Peter R Lange
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Claudia Geserick
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Caren E Bartosz
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Celine T Chen
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Robert D Slocum
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
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Van der Geize R, Yam K, Heuser T, Wilbrink MH, Hara H, Anderton MC, Sim E, Dijkhuizen L, Davies JE, Mohn WW, Eltis LD. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci U S A 2007; 104:1947-52. [PMID: 17264217 PMCID: PMC1794314 DOI: 10.1073/pnas.0605728104] [Citation(s) in RCA: 392] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Indexed: 01/21/2023] Open
Abstract
Rhodococcus sp. strain RHA1, a soil bacterium related to Mycobacterium tuberculosis, degrades an exceptionally broad range of organic compounds. Transcriptomic analysis of cholesterol-grown RHA1 revealed a catabolic pathway predicted to proceed via 4-androstene-3,17-dione and 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (3,4-DHSA). Inactivation of each of the hsaC, supAB, and mce4 genes in RHA1 substantiated their roles in cholesterol catabolism. Moreover, the hsaC(-) mutant accumulated 3,4-DHSA, indicating that HsaC(RHA1), formerly annotated as a biphenyl-degrading dioxygenase, catalyzes the oxygenolytic cleavage of steroid ring A. Bioinformatic analyses revealed that 51 rhodococcal genes specifically expressed during growth on cholesterol, including all predicted to specify the catabolism of rings A and B, are conserved within an 82-gene cluster in M. tuberculosis H37Rv and Mycobacterium bovis bacillus Calmette-Guérin. M. bovis bacillus Calmette-Guérin grew on cholesterol, and hsaC and kshA were up-regulated under these conditions. Heterologously produced HsaC(H37Rv) and HsaD(H37Rv) transformed 3,4-DHSA and its ring-cleaved product, respectively, with apparent specificities approximately 40-fold higher than for the corresponding biphenyl metabolites. Overall, we annotated 28 RHA1 genes and proposed physiological roles for a similar number of mycobacterial genes. During survival of M. tuberculosis in the macrophage, these genes are specifically expressed, and many appear to be essential. We have delineated a complete suite of genes necessary for microbial steroid degradation, and pathogenic mycobacteria have been shown to catabolize cholesterol. The results suggest that cholesterol metabolism is central to M. tuberculosis's unusual ability to survive in macrophages and provide insights into potential targets for novel therapeutics.
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Affiliation(s)
- Robert Van der Geize
- *Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN, Groningen, The Netherlands
| | - Katherine Yam
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Thomas Heuser
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Maarten H. Wilbrink
- *Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN, Groningen, The Netherlands
| | - Hirofumi Hara
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Matthew C. Anderton
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Edith Sim
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Lubbert Dijkhuizen
- *Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN, Groningen, The Netherlands
| | - Julian E. Davies
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Lindsay D. Eltis
- *Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN, Groningen, The Netherlands
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