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Xu G, Ma J, Fang Q, Peng Q, Jiao X, Hu W, Zhao Q, Kong Y, Liu F, Shi X, Tang DJ, Tang JL, Ming Z. Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway. Commun Biol 2024; 7:255. [PMID: 38429435 PMCID: PMC10907753 DOI: 10.1038/s42003-024-05921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) plays an important role in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) via the nicotinamide (NAM) salvage pathway. While the structural biochemistry of eukaryote NAMPT has been well studied, the catalysis mechanism of prokaryote NAMPT at the molecular level remains largely unclear. Here, we demonstrated the NAMPT-mediated salvage pathway is functional in the Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) for the synthesis of NAD+, and the enzyme activity of NAMPT in this bacterium is significantly higher than that of human NAMPT in vitro. Our structural analyses of Xcc NAMPT, both in isolation and in complex with either the substrate NAM or the product nicotinamide mononucleotide (NMN), uncovered significant details of substrate recognition. Specifically, we revealed the presence of a NAM binding tunnel that connects the active site, and this tunnel is essential for both catalysis and inhibitor binding. We further demonstrated that NAM binding in the tunnel has a positive cooperative effect with NAM binding in the catalytic site. Additionally, we discovered that phosphorylation of the His residue at position 229 enhances the substrate binding affinity of Xcc NAMPT and is important for its catalytic activity. This work reveals the importance of NAMPT in bacterial NAD+ synthesis and provides insights into the substrate recognition and the catalytic mechanism of bacterial type II phosphoribosyltransferases.
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Affiliation(s)
- Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Jinxue Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiong Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Wei Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiaoqiao Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Yanqiong Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Fenmei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xueqi Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
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Yosief RHS, Lone IM, Nachshon A, Himmelbauer H, Gat‐Viks I, Iraqi FA. Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach. Animal Model Exp Med 2024; 7:36-47. [PMID: 38356021 PMCID: PMC10961901 DOI: 10.1002/ame2.12386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus (Af) using an RNAseq approach in CC lines and hepatic gene expression. METHODS We studied 31 male mice from 25 CC lines at 8 weeks old; the mice were infected with Af. Liver tissues were extracted from these mice 5 days post-infection, and next-generation RNA-sequencing (RNAseq) was performed. The GENE-E analysis platform was used to generate a clustered heat map matrix. RESULTS Significant variation in body weight changes between CC lines was observed. Hepatic gene expression revealed 12 top prioritized candidate genes differentially expressed in resistant versus susceptible mice based on body weight changes. Interestingly, three candidate genes are located within genomic intervals of the previously mapped quantitative trait loci (QTL), including Gm16270 and Stox1 on chromosome 10 and Gm11033 on chromosome 8. CONCLUSIONS Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af. As a next step, eQTL analysis will be performed for our RNA-Seq data. Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.
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Affiliation(s)
- Roa'a H. S. Yosief
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Iqbal M. Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 181190 ViennaAustria
| | - Irit Gat‐Viks
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
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3
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Liu J, Xi K, Zhang L, Han M, Wang Q, Liu X. Tryptophan metabolites and gut microbiota play an important role in pediatric migraine diagnosis. J Headache Pain 2024; 25:2. [PMID: 38177986 PMCID: PMC10768287 DOI: 10.1186/s10194-023-01708-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The pathogenesis of pediatric migraine remains unclear and presents challenges in diagnosis. Recently, growing evidence has indicated that the gut microbiota can exert modulatory functions at the gut-brain axis by directly or indirectly regulating tryptophan metabolism. Consequently, we aimed to elucidate the potential association among gut microbiota, tryptophan metabolism, and pediatric migraine while also identifying diagnostic biomarkers for pediatric migraine. METHODS The gut microbiota composition of 33 migraine children and 42 healthy children, aged less than ten years, from the GMrepo database, was analyzed using the Shannon index, Simpson index, principal coordinates analysis, and Wilcoxon rank-sum test. Microbial diagnostic biomarkers were identified using linear discriminant analysis effect size, ridge regression, and random forest. Plasma concentrations of tryptophan metabolites investigated by enzyme-linked immunosorbent assay were compared between 51 migraine children and 120 healthy children, aged less than eighteen years, using t tests and analysis of variance. The receiver operating characteristic curve was performed to evaluate the diagnostic value of microbial and metabolite biomarkers in pediatric migraine. RESULTS Differences in the composition of gut microbiota, notably the genera that regulate tryptophan metabolism, were observed in pediatric migraine children. Further investigations revealed a significant decrease in plasma kynurenic acid levels (p < 0.001) among migraine children, along with a significant increase in serotonin (p < 0.05) and quinolinic acid (p < 0.001). Subsequently, we established the normal reference intervals for plasma concentrations of tryptophan metabolites in children. More importantly, the ratio of kynurenic acid to quinolinic acid (AUC: 0.871, sensitivity: 86.3%, specificity: 83.3%) exhibited excellent diagnostic efficacy for pediatric migraine. CONCLUSION Our study suggests that the gut microbiota may play an important role in the development of pediatric migraine by regulating tryptophan metabolism. We believe that microbial and metabolite biomarkers are sensitive diagnostic tests for pediatric migraine. TRIAL REGISTRATION The study was registered at ClinicalTrials.gov (NCT05969990).
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Affiliation(s)
- Junhui Liu
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Kaiyan Xi
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Linlin Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Mugu Han
- Shandong First Medical University Affiliated Provincial Hospital, Huaiyin Distinct, Jingwuweiliu Road, Jinan, 250021, Shandong Province, China
| | - Qingran Wang
- Qilu Hospital of Shandong University Dezhou Hospital, 1166 Dongfanghong West Road, Decheng District, Dezhou, 253000, Shandong Province, China
| | - Xinjie Liu
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China.
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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] [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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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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Qiao P, Zhang C, Yu J, Shao S, Zhang J, Fang H, Chen J, Luo Y, Zhi D, Li Q, Ma J, Fu M, Dang E, Yin W, Wang G. Quinolinic acid, a tryptophan metabolite of the skin microbiota, negatively regulates the NLRP3 inflammasome through the aryl hydrocarbon receptor in psoriasis. J Invest Dermatol 2022; 142:2184-2193.e6. [PMID: 35143820 DOI: 10.1016/j.jid.2022.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022]
Abstract
Psoriasis is a chronic inflammatory skin disease whose pathogenesis involves skin microbiota dysbiosis. Multiple studies have revealed changes in microbiota abundances between psoriatic lesions and healthy skin. However, the metabolic pathways of skin microbiota (especially tryptophan metabolism, which is closely related to immunosuppression) are far less understood. In this study, we first detected the major microbial metabolites of tryptophan on skin surfaces, finding that the quinolinic acid (QA) were significantly lower in the lesional skin of patients with psoriasis than in that of healthy subjects and correlated negatively with the severity of psoriasis. In vitro and in vivo, applying QA significantly alleviated skin inflammation in an aryl hydrocarbon receptor (AhR)-dependent manner, resulting in the inhibition of the NLRP3 inflammasome activation. Furthermore, in mice with imiquimod-induced psoriasis-like dermatitis, topical application of AhR small-interfering RNA substantially exacerbated the disease severity with increased NLRP3 inflammasome activation. Collectively, our data suggest that QA, a skin microbiota-derived metabolite, negatively regulates AhR-NLRP3 inflammasome signaling activation in patients with psoriasis, providing an insight into the correlation between microbiota metabolism and the host skin in individuals with psoriasis.
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Affiliation(s)
- Pei Qiao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Department of Microbiology, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Chen Zhang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jinlei Yu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shuai Shao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jieyu Zhang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Hui Fang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiaoling Chen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yixin Luo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Dalong Zhi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qingyang Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingyi Ma
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Meng Fu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Erle Dang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Yin
- Department of Transfusion Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Department of Microbiology, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.
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Basbous H, Volbeda A, Amara P, Rohac R, Martin L, Ollagnier de Choudens S, Fontecilla-Camps JC. Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA. ACS Chem Biol 2021; 16:2423-2433. [PMID: 34609124 DOI: 10.1021/acschembio.1c00541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quinolinate synthase, also called NadA, is a [4Fe-4S]-containing enzyme that uses what is probably the oldest pathway to generate quinolinic acid (QA), the universal precursor of the biologically essential cofactor nicotinamide adenine dinucleotide (NAD). Its synthesis comprises the condensation of dihydroxyacetone phosphate (DHAP) and iminoaspartate (IA), which involves dephosphorylation, isomerization, cyclization, and two dehydration steps. The convergence of the three homologous domains of NadA defines a narrow active site that contains a catalytically essential [4Fe-4S] cluster. A tunnel, which can be opened or closed depending on the nature (or absence) of the bound ligand, connects this cofactor to the protein surface. One outstanding riddle has been the observation that the so far characterized active site is too small to bind IA and DHAP simultaneously. Here, we have used site-directed mutagenesis, X-ray crystallography, functional analyses, and molecular dynamics simulations to propose a condensation mechanism that involves the transient formation of a second active site cavity to which one of the substrates can migrate before this reaction takes place.
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Affiliation(s)
- Hind Basbous
- Univ. Grenoble Alpes, CNRS, CEA, Laboratoire de Chimie et Biologie des Métaux, BioCat, 38000 Grenoble, France
| | - Anne Volbeda
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France
| | - Roman Rohac
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins, F-38000 Grenoble, France
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Wee HN, Liu JJ, Ching J, Kovalik JP, Lim SC. The Kynurenine Pathway in Acute Kidney Injury and Chronic Kidney Disease. Am J Nephrol 2021; 52:771-787. [PMID: 34753140 PMCID: PMC8743908 DOI: 10.1159/000519811] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND The kynurenine pathway (KP) is the major catabolic pathway for tryptophan degradation. The KP plays an important role as the sole de novo nicotinamide adenine dinucleotide (NAD+) biosynthetic pathway in normal human physiology and functions as a counter-regulatory mechanism to mitigate immune responses during inflammation. Although the KP has been implicated in a variety of disorders including Huntington's disease, seizures, cardiovascular disease, and osteoporosis, its role in renal diseases is seldom discussed. SUMMARY This review summarizes the roles of the KP and its metabolites in acute kidney injury (AKI) and chronic kidney disease (CKD) based on current literature evidence. Metabolomics studies demonstrated that the KP metabolites were significantly altered in patients and animal models with AKI or CKD. The diagnostic and prognostic values of the KP metabolites in AKI and CKD were highlighted in cross-sectional and longitudinal human observational studies. The biological impact of the KP on the pathophysiology of AKI and CKD has been studied in experimental models of different etiologies. In particular, the activation of the KP was found to confer protection in animal models of glomerulonephritis, and its immunomodulatory mechanism may involve the regulation of T cell subsets such as Th17 and regulatory T cells. Manipulation of the KP to increase NAD+ production or diversion toward specific KP metabolites was also found to be beneficial in animal models of AKI. Key Messages: KP metabolites are reported to be dysregulated in human observational and animal experimental studies of AKI and CKD. In AKI, the magnitude and direction of changes in the KP depend on the etiology of the damage. In CKD, KP metabolites are altered with the onset and progression of CKD all the way to advanced stages of the disease, including uremia and its related vascular complications. The activation of the KP and diversion to specific sub-branches are currently being explored as therapeutic strategies in these diseases, especially with regards to the immunomodulatory effects of certain KP metabolites. Further elucidation of the KP may hold promise for the development of biomarkers and targeted therapies for these kidney diseases.
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Affiliation(s)
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Jianhong Ching
- Duke-NUS Medical School, Singapore, Singapore
- KK Research Centre, KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Diabetes Centre, Admiralty Medical Centre, Singapore, Singapore
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Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microb Genom 2021; 6. [PMID: 32924924 PMCID: PMC7725326 DOI: 10.1099/mgen.0.000429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny. Elaborate approaches for the reconstruction of ancestral states at the sequence level have been developed, subsequently augmented by methods based on gene content. While these approaches of sequence or gene-content reconstruction have been successfully deployed, there has been less progress on the explicit inference of functional properties of ancestral genomes, in terms of metabolic pathways and other cellular processes. Herein, we describe PathTrace, an efficient algorithm for parsimony-based reconstructions of the evolutionary history of individual metabolic pathways, pivotal representations of key functional modules of cellular function. The algorithm is implemented as a five-step process through which pathways are represented as fuzzy vectors, where each enzyme is associated with a taxonomic conservation value derived from the phylogenetic profile of its protein sequence. The method is evaluated with a selected benchmark set of pathways against collections of genome sequences from key data resources. By deploying a pangenome-driven approach for pathway sets, we demonstrate that the inferred patterns are largely insensitive to noise, as opposed to gene-content reconstruction methods. In addition, the resulting reconstructions are closely correlated with the evolutionary distance of the taxa under study, suggesting that a diligent selection of target pangenomes is essential for maintaining cohesiveness of the method and consistency of the inference, serving as an internal control for an arbitrary selection of queries. The PathTrace method is a first step towards the large-scale analysis of metabolic pathway evolution and our deeper understanding of functional relationships reflected in emerging pangenome collections.
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Affiliation(s)
- Fotis E Psomopoulos
- Institute of Applied Biosciences (INAB), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
| | - Jacques van Helden
- Lab. Technological Advances for Genomics & Clinics (TAGC), Université d'Aix-Marseille (AMU), INSERM Unit U1090, 163, Avenue de Luminy, 13288 Marseille cedex 09, France
| | - Claudine Médigue
- UMR 8030, CNRS, Université Evry-Val-d'Essonne, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry, France
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece
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Bajaj JS, Shamsaddini A, Fagan A, McGeorge S, Gavis E, Sikaroodi M, Brenner LA, Wade JB, Gillevet PM. Distinct gut microbial compositional and functional changes associated with impaired inhibitory control in patients with cirrhosis. Gut Microbes 2021; 13:1953247. [PMID: 34346283 PMCID: PMC8344770 DOI: 10.1080/19490976.2021.1953247] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Most cirrhosis etiologies, such as alcohol, hepatitis C, and obesity, involve behavior that require the loss of inhibitory control. Once cirrhosis develops, patients can also develop cognitive impairment due to minimal hepatic encephalopathy (MHE). Both processes could have distinct imprints on the gut-liver-brain axis. Determine the impact of inhibitory control versus traditional cirrhosis-related cognitive performance on gut microbial composition and function. Outpatients with cirrhosis underwent two tests for MHE: inhibitory control test (MHEICT, computerized associated with response inhibition) and psychometric hepatic encephalopathy score (MHEPHES, paper-pencil HE-specific associated with subcortical impairment) along with stool collection for metagenomics. MHEICT/not, MHEPHES/not, and discordant (positive on one test but negative on the other) were analyzed for demographics, bacterial species, and gut-brain modules (GBM) using multi-variable analyses. Ninety-seven patients [47 (49%) MHEPHES, 76 (78%) MHEICT, 41 discordant] were enrolled. MHEPHES/not: Cirrhosis severity was worse in MHEPHES without differences in alpha/beta diversity on bacterial species or GBMs. Pathobionts (Enterobacteriaceae) and γ-amino-butryic acid (GABA) synthesis GBM were higher in MHEPHES. MHEICT/not: We found similar cirrhosis severity and metagenomic alpha/beta diversity in MHEICT versus not. However, alpha/beta diversity of GBMs were different in MHEICT versus No-MHE patients. Alistipes ihumii, Prevotella copri, and Eubacterium spp. were higher, while Enterococcus spp. were uniquely lower in MHEICT versus no-MHE and discordant comparisons. GBMs belonging to tryptophan, menaquinone, GABA, glutamate, and short-chain fatty acid synthesis were also unique to MHEICT. Gut microbial signature of impaired inhibitory control, which is associated with addictive disorders that can lead to cirrhosis, is distinct from cirrhosis-related cognitive impairment.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | - Lisa A. Brenner
- Departments of Physical Medicine and Rehabilitation, Psychiatry, & Neurology, VA Rocky Mountain Mental Illness Research Education and Clinical Center, Aurora, Colorado, and University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - James B Wade
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
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Karamitros CS, Murray K, Sugiyama Y, Kumada Y, Johnson KA, Georgiou G, D'Arcy S, Stone EM. Conformational Dynamics Contribute to Substrate Selectivity and Catalysis in Human Kynureninase. ACS Chem Biol 2020; 15:3159-3166. [PMID: 33275413 PMCID: PMC11104311 DOI: 10.1021/acschembio.0c00676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Kynureninases (KYNases) are enzymes that play a key role in tryptophan catabolism through the degradation of intermediate kynurenine and 3'-hydroxy-kynurenine metabolites (KYN and OH-KYN, respectively). Bacterial KYNases exhibit high catalytic efficiency toward KYN and moderate activity toward OH-KYN, whereas animal KYNases are highly selective for OH-KYN, exhibiting only minimal activity toward the smaller KYN substrate. These differences reflect divergent pathways for KYN and OH-KYN utilization in the respective kingdoms. We examined the Homo sapiens and Pseudomonas fluorescens KYNases (HsKYNase and PfKYNase respectively) using pre-steady-state and hydrogen-deuterium exchange mass spectrometry (HDX-MS) methodologies. We discovered that the activity of HsKYNase critically depends on formation of hydrogen bonds with the hydroxyl group of OH-KYN to stabilize the entire active site and allow productive substrate turnover. With the preferred OH-KYN substrate, stabilization is observed at the substrate-binding site and the region surrounding the PLP cofactor. With the nonpreferred KYN substrate, less stabilization occurs, revealing a direct correlation with activity. This correlation holds true for PfKYNases; however there is only a modest stabilization at the substrate-binding site, suggesting that substrate discrimination is simply achieved by steric hindrance. We speculate that eukaryotic KYNases use dynamic mobility as a mechanism of substrate specificity to commit OH-KYN to nicotinamide synthesis and avoid futile hydrolysis of KYN. These findings have important ramifications for the engineering of HsKynase with high KYN activity as required for clinical applications in cancer immunotherapy. Our study shows how homologous enzymes with conserved active sites can use dynamics to discriminate between two highly similar substrates.
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Affiliation(s)
- Christos S Karamitros
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Yusuke Sugiyama
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Everett M Stone
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
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12
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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13
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Abstract
An efficient moduling disulfuration was developed for polysulfide construction via a bilateral six-membered thiamine disulfurating reagent. Under the control of energy release of ring strain, diverse unsymmetrical trisulfides and tetrasulfides were generated through the assembly of nucleophiles on both sides of the sulfur-sulfur motif. This strategy exhibits features of high efficiency, mild conditions, and general scope.
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Affiliation(s)
- Jiahui Xue
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, P. R. China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, P. R. China.,State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin 300071, P. R. China
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14
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Kaur H, Bose C, Mande SS. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. Front Neurosci 2019; 13:1365. [PMID: 31920519 PMCID: PMC6930238 DOI: 10.3389/fnins.2019.01365] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022] Open
Abstract
The link between gut microbiome and brain is being slowly acknowledged due to the speculated role of resident gut microbial community in altering the functions of gut-brain axis (GBA). Recently, a number of microbial metabolites (referred to as neuro-active metabolites) produced through tryptophan metabolism have been suggested to influence the GBA. In view of this, the current study focuses on microbial tryptophan metabolism pathways which produce neuro-active metabolites. An in silico analysis was performed on bacterial genomes as well as publicly available gut microbiome data. The results provide a comprehensive catalog of the analyzed pathways across bacteria. The analysis indicates an enrichment of tryptophan metabolism pathways in five gut-associated phyla, namely, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria. Further, five genera, namely, Clostridium, Burkholderia, Streptomyces, Pseudomonas, and Bacillus have been predicted to be enriched in terms of number of the analyzed tryptophan metabolism pathways, suggesting a higher potential of these bacterial groups to metabolize tryptophan in gut. Analysis of available microbiome data corresponding to gut samples from patients of neurological diseases and healthy individuals suggests probable association of different sets of tryptophan metabolizing bacterial pathways with the etiology of different diseases. The insights obtained from the present study are expected to provide directions toward designing of microbiome based diagnostic and therapeutic approaches for neurological diseases/disorders.
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Affiliation(s)
| | | | - Sharmila S. Mande
- Life Sciences R&D, TCS Research, Tata Consultancy Services, Pune, India
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15
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Davis I, Yang Y, Wherritt D, Liu A. Reassignment of the human aldehyde dehydrogenase ALDH8A1 (ALDH12) to the kynurenine pathway in tryptophan catabolism. J Biol Chem 2018; 293:9594-9603. [PMID: 29703752 DOI: 10.1074/jbc.ra118.003320] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
The kynurenine pathway is the primary route for l-tryptophan degradation in mammals. Intermediates and side products of this pathway are involved in immune response and neurodegenerative diseases. This makes the study of enzymes, especially those from mammalian sources, of the kynurenine pathway worthwhile. Recent studies on a bacterial version of an enzyme of this pathway, 2-aminomuconate semialdehyde (2-AMS) dehydrogenase (AMSDH), have provided a detailed understanding of the catalytic mechanism and identified residues conserved for muconate semialdehyde recognition and activation. Findings from the bacterial enzyme have prompted the reconsideration of the function of a previously identified human aldehyde dehydrogenase, ALDH8A1 (or ALDH12), which was annotated as a retinal dehydrogenase based on its ability to preferentially oxidize 9-cis-retinal over trans-retinal. Here, we provide compelling bioinformatics and experimental evidence that human ALDH8A1 should be reassigned to the missing 2-AMS dehydrogenase of the kynurenine metabolic pathway. For the first time, the product of the semialdehyde oxidation by AMSDH is also revealed by NMR and high-resolution MS. We found that ALDH8A1 catalyzes the NAD+-dependent oxidation of 2-AMS with a catalytic efficiency equivalent to that of AMSDH from the bacterium Pseudomonas fluorescens Substitution of active-site residues required for substrate recognition, binding, and isomerization in the bacterial enzyme resulted in human ALDH8A1 variants with 160-fold increased Km or no detectable activity. In conclusion, this molecular study establishes an additional enzymatic step in an important human pathway for tryptophan catabolism.
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Affiliation(s)
- Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Yu Yang
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Daniel Wherritt
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
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16
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Paquola ACM, Asif H, Pereira CADB, Feltes BC, Bonatto D, Lima WC, Menck CFM. Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred. J Mol Evol 2018; 86:190-203. [DOI: 10.1007/s00239-018-9836-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
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17
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Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group. Syst Appl Microbiol 2017; 40:401-410. [PMID: 28890241 DOI: 10.1016/j.syapm.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
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Affiliation(s)
- Eugene Christo-Foroux
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Tatiana Vallaeys
- Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France.
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
| | - Elie Dassa
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Josef Deutscher
- CNRS, UMR 8261 Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Université Paris Diderot, Sorbonne-Paris-Cité, 13 rue Pierre et Marie Curie, Paris, France.
| | - Cécile Wandersman
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Aurélien Livernois
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France
| | - Chloe Hot
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alexis Criscuolo
- Hub, Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Catherine Dauga
- International Group of Data Analysis (IGDA), Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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18
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Gong W, Jia J, Zhang B, Mi S, Zhang L, Xie X, Guo H, Shi J, Tu C. Serum Metabolomic Profiling of Piglets Infected with Virulent Classical Swine Fever Virus. Front Microbiol 2017; 8:731. [PMID: 28496435 PMCID: PMC5406397 DOI: 10.3389/fmicb.2017.00731] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022] Open
Abstract
Classical swine fever (CSF) is a highly contagious swine infectious disease and causes significant economic losses for the pig industry worldwide. The objective of this study was to determine whether small molecule metabolites contribute to the pathogenesis of CSF. Birefly, serum metabolomics of CSFV Shimen strain-infected piglets were analyzed by ultraperformance liquid chromatography/electrospray ionization time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) in combination with multivariate statistical analysis. In CSFV-infected piglets at days 3 and 7 post-infection changes were found in metabolites associated with several key metabolic pathways, including tryptophan catabolism and the kynurenine pathway, phenylalanine metabolism, fatty acid and lipid metabolism, the tricarboxylic acid and urea cycles, branched-chain amino acid metabolism, and nucleotide metabolism. Several pathways involved in energy metabolism including fatty acid biosynthesis and β-oxidation, branched-chain amino acid metabolism, and the tricarboxylic acid cycle were significantly inhibited. Changes were also observed in several metabolites exclusively associated with gut microbiota. The metabolomic profiles indicate that CSFV-host gut microbiome interactions play a role in the development of CSF.
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Affiliation(s)
- Wenjie Gong
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Junjie Jia
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Bikai Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Shijiang Mi
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Li Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Xiaoming Xie
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Huancheng Guo
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Changchun Tu
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
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19
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Ternes CM, Schönknecht G. Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes. Genome Biol Evol 2015; 6:2335-49. [PMID: 25169983 PMCID: PMC4217691 DOI: 10.1093/gbe/evu185] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
NAD+ is an essential molecule for life, present in each living cell. It can function as an electron carrier or cofactor in redox biochemistry and energetics, and serves as substrate to generate the secondary messenger cyclic ADP ribose and nicotinic acid adenine dinucleotide phosphate. Although de novo NAD+ biosynthesis is essential, different metabolic pathways exist in different eukaryotic clades. The kynurenine pathway starting with tryptophan was most likely present in the last common ancestor of all eukaryotes, and is active in fungi and animals. The aspartate pathway, detected in most photosynthetic eukaryotes, was probably acquired from the cyanobacterial endosymbiont that gave rise to chloroplasts. An evolutionary analysis of enzymes catalyzing de novo NAD+ biosynthesis resulted in evolutionary trees incongruent with established organismal phylogeny, indicating numerous gene transfers. Endosymbiotic gene transfers probably introduced the aspartate pathway into eukaryotes and may have distributed it among different photosynthetic clades. In addition, several horizontal gene transfers substituted eukaryotic genes with bacterial orthologs. Although horizontal gene transfer is accepted as a key mechanism in prokaryotic evolution, it is supposed to be rare in eukaryotic evolution. The essential metabolic pathway of de novo NAD+ biosynthesis in eukaryotes was shaped by numerous gene transfers.
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20
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El-Zaatari M, Chang YM, Zhang M, Franz M, Shreiner A, McDermott AJ, van der Sluijs KF, Lutter R, Grasberger H, Kamada N, Young VB, Huffnagle GB, Kao JY. Tryptophan catabolism restricts IFN-γ-expressing neutrophils and Clostridium difficile immunopathology. THE JOURNAL OF IMMUNOLOGY 2014; 193:807-16. [PMID: 24935925 DOI: 10.4049/jimmunol.1302913] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The interplay between Clostridium difficile and the host's metabolome is believed to influence the severity of infection. However, the mechanism for this phenomenon remains unclear. In this study, we model one of these metabolic pathways by focusing on tryptophan metabolism in the host. We found that inhibition of tryptophan catabolism in IDO1-knockout mice led to increased mucosal destruction, cecal hemorrhage, and increased production of IFN-γ in response to C. difficile infection, but no significant change in mucosal effector or regulatory T cell numbers or IL-10 mRNA expression. The increased immunopathology in infected IDO1-knockout mice was associated with a lower C. difficile burden and an increased percentage of IFN-γ-expressing neutrophils. We further demonstrated the ability of kynurenine to induce apoptosis in bone marrow-derived neutrophils, whereas the presence of tryptophan reversed this effect, providing a possible mechanism for the increased neutrophil accumulation in IDO1(-/-) mice. We conclude that C. difficile induces tryptophan catabolism in cecal lamina propria cells, which restricts C. difficile-associated immunopathology and the accumulation of IFN-γ-expressing neutrophils. This might represent a self-regulatory mechanism for neutrophils, via the IFN-γ-IDO1 pathway, to restrict their own accumulation during infection. These findings have important clinical implications because IDO inhibitors are used to treat cancer in clinical trials (in patients particularly susceptible to getting C. difficile infection), and treatment with IDO1 inhibitors may exacerbate the severity of C. difficile colitis.
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Affiliation(s)
- Mohamad El-Zaatari
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109;
| | - Yu-Ming Chang
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Min Zhang
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew Franz
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Andrew Shreiner
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J McDermott
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Koenraad F van der Sluijs
- Laboratory of Experimental Intensive Care and Anesthesiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; Department of Respiratory Medicine, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; and
| | - René Lutter
- Department of Respiratory Medicine, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; and Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Helmut Grasberger
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Nobuhiko Kamada
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Gary B Huffnagle
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - John Y Kao
- Department of Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109;
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Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med 2014; 5:193ra91. [PMID: 23843452 DOI: 10.1126/scitranslmed.3006438] [Citation(s) in RCA: 491] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Progressive HIV infection is characterized by dysregulation of the intestinal immune barrier, translocation of immunostimulatory microbial products, and chronic systemic inflammation that is thought to drive progression of disease to AIDS. Elements of this pathologic process persist despite viral suppression during highly active antiretroviral therapy (HAART), and drivers of these phenomena remain poorly understood. Disrupted intestinal immunity can precipitate dysbiosis that induces chronic inflammation in the mucosa and periphery of mice. However, putative microbial drivers of HIV-associated immunopathology versus recovery have not been identified in humans. Using high-resolution bacterial community profiling, we identified a dysbiotic mucosal-adherent community enriched in Proteobacteria and depleted of Bacteroidia members that was associated with markers of mucosal immune disruption, T cell activation, and chronic inflammation in HIV-infected subjects. Furthermore, this dysbiosis was evident among HIV-infected subjects undergoing HAART, and the extent of dysbiosis correlated with activity of the kynurenine pathway of tryptophan catabolism and plasma concentrations of the inflammatory cytokine interleukin-6 (IL-6), two established markers of disease progression. Gut-resident bacteria with capacity to catabolize tryptophan through the kynurenine pathway were found to be enriched in HIV-infected subjects, strongly correlated with kynurenine levels in HIV-infected subjects, and capable of kynurenine production in vitro. These observations demonstrate a link between mucosal-adherent colonic bacteria and immunopathogenesis during progressive HIV infection that is apparent even in the setting of viral suppression during HAART. This link suggests that gut-resident microbial populations may influence intestinal homeostasis during HIV disease.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco UCSF, San Francisco, CA 94110, USA
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22
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Crnovčić I, Semsary S, Vater J, Keller U. Biosynthetic rivalry of o-aminophenol-carboxylic acids initiates production of hemi-actinomycins in Streptomyces antibioticus. RSC Adv 2014. [DOI: 10.1039/c3ra45661g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Bonitz T, Zubeil F, Grond S, Heide L. Unusual N-prenylation in diazepinomicin biosynthesis: the farnesylation of a benzodiazepine substrate is catalyzed by a new member of the ABBA prenyltransferase superfamily. PLoS One 2013; 8:e85707. [PMID: 24376894 PMCID: PMC3871700 DOI: 10.1371/journal.pone.0085707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/02/2013] [Indexed: 11/29/2022] Open
Abstract
The bacterium Micromonospora sp. RV115, isolated from a marine sponge, produces the unusual metabolite diazepinomicin, a prenylated benzodiazepine derivative. We have cloned the prenyltransferase gene dzmP from this organism, expressed it in Escherichia coli, and the resulting His8-tagged protein was purified and investigated biochemically. It was found to catalyze the farnesylation of the amide nitrogen of dibenzodiazepinone. DzmP belongs to the ABBA prenyltransferases and is the first member of this superfamily which utilizes farnesyl diphosphate as genuine substrate. All previously discovered members utilize either dimethylallyl diphosphate (C5) or geranyl diphosphate (C10). Another putative diazepinomicin biosynthetic gene cluster was identified in the genome of Streptomyces griseoflavus Tü4000, suggesting that the formation of diazepinomicin is not restricted to the genus Micromonospora. The gene cluster contains a gene ssrg_00986 with 61.4% identity (amino acid level) to dzmP. The gene was expressed in E. coli, and the purified protein showed similar catalytic properties as DzmP. Both enzymes also accepted other phenolic or phenazine substrates. ABBA prenyltransferases are useful tools for chemoenzymatic synthesis, due to their nature as soluble, stable biocatalysts. The discovery of DzmP and Ssrg_00986 extends the isoprenoid substrate range of this superfamily. The observed prenylation of an amide nitrogen is an unusual biochemical reaction.
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Affiliation(s)
- Tobias Bonitz
- Pharmaceutical Institute, Eberhard Karls-Universität Tübingen, Tübingen, Germany
| | - Florian Zubeil
- Institute of Organic Chemistry, Eberhard Karls-Universität Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls-Universität Tübingen, Tübingen, Germany
| | - Lutz Heide
- Pharmaceutical Institute, Eberhard Karls-Universität Tübingen, Tübingen, Germany
- * E-mail:
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Seo JS, Keum YS, Li QX. Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates. Biodegradation 2013; 24:795-811. [PMID: 23463356 DOI: 10.1007/s10532-013-9629-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Burkholderia sp. C3, an efficient polycyclic aromatic hydrocarbon degrader, can utilize nine of the ten N-methylcarbamate insecticides including carbaryl as a sole source of carbon. Rapid hydrolysis of carbaryl in C3 is followed by slow catabolism of the resulting 1-naphthol. This study focused on metabolomes and proteomes in C3 cells utilizing carbaryl in comparison to those using glucose or nutrient broth. Sixty of the 867 detected proteins were involved in primary metabolism, adaptive sensing and regulation, transport, stress response, and detoxification. Among the 41 proteins expressed in response to carbaryl were formate dehydrogenase, aldehyde-alcohol dehydrogenase and ethanolamine utilization protein involved in one carbon metabolism. Acetate kinase and phasin were 2 of the 19 proteins that were not detected in carbaryl-supported C3 cells, but detected in glucose-supported C3 cells. Down-production of phasin and polyhydroxyalkanoates in carbaryl-supported C3 cells suggests insufficient carbon sources and lower levels of primary metabolites to maintain an ordinary level of metabolism. Differential metabolomes (~196 identified polar metabolites) showed up-production of metabolites in pentose phosphate pathways and metabolisms of cysteine, cystine and some other amino acids, disaccharides and nicotinate, in contract to down-production of most of the other amino acids and hexoses. The proteomic and metabolomic analyses showed that carbaryl-supported C3 cells experienced strong toxic effects, oxidative stresses, DNA/RNA damages and carbon nutrient deficiency.
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Affiliation(s)
- Jong-Su Seo
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI, 96822, USA
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25
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Crnovčić I, Vater J, Keller U. Occurrence and biosynthesis of C-demethylactinomycins in actinomycin-producing Streptomyces chrysomallus and Streptomyces parvulus. J Antibiot (Tokyo) 2013; 66:211-8. [DOI: 10.1038/ja.2012.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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26
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Naushad HS, Gupta RS. Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales. PLoS One 2013; 8:e55216. [PMID: 23408961 PMCID: PMC3568101 DOI: 10.1371/journal.pone.0055216] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 12/19/2012] [Indexed: 01/31/2023] Open
Abstract
The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets for development of drugs/agents that specifically target these bacteria.
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Affiliation(s)
- Hafiz Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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Liu H, Luo Y, Han J, Wu J, Wu Z, Feng D, Cai S, Li M, Liu J, Zhou J, Xiang H. Proteome Reference Map of Haloarcula hispanica and Comparative Proteomic and Transcriptomic Analysis of Polyhydroxyalkanoate Biosynthesis under Genetic and Environmental Perturbations. J Proteome Res 2013; 12:1300-15. [PMID: 23301558 DOI: 10.1021/pr300969m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hailong Liu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Yuanming Luo
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jing Han
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jinhua Wu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Zhenfang Wu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Deqin Feng
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Shuangfeng Cai
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Ming Li
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jingfang Liu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jian Zhou
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Hua Xiang
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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Liao G, Shi T, Xie J. Regulation mechanisms underlying the biosynthesis of daptomycin and related lipopeptides. J Cell Biochem 2012; 113:735-41. [PMID: 22020738 DOI: 10.1002/jcb.23414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Daptomycin is a lipopeptide antibiotics used to treat Gram-positive pathogens infections, including drug-resistant strains. In-depth exploration of its biosynthesis and regulation is crucial for metabolic engineering improvement of this ever-increasing important antibiotic. The past years have witnessed the significant progresses in the understanding of the molecular mechanisms underlying the biosynthesis and regulation of daptomycin. This information was updated in our review, with special focus on the regulatory network integrating a wide variety of physiological and environmental inputs. This should provide novel insight into the regulatory mechanism of biosynthesis of daptomycin and nodes for strain improvement to increase the yields of daptomycin.
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Affiliation(s)
- Guojian Liao
- Institute of Modern Biopharmaceuticals, School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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29
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Microbial transformation of azaarenes and potential uses in pharmaceutical synthesis. Appl Microbiol Biotechnol 2012; 95:871-89. [PMID: 22740048 DOI: 10.1007/s00253-012-4220-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 10/28/2022]
Abstract
Pyridine, quinoline, acridine, indole, carbazole, and other heterocyclic nitrogen-containing compounds (azaarenes) can be transformed by cultures of bacteria and fungi to produce a variety of new derivatives, many of which have biological activity. In many cases, the microbial biotransformation processes are regio- and stereoselective so that the transformation products may be useful for the synthesis of new candidate drugs.
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30
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Yuasa HJ, Ball HJ. The evolution of three types of indoleamine 2,3 dioxygenases in fungi with distinct molecular and biochemical characteristics. Gene 2012; 504:64-74. [PMID: 22564706 DOI: 10.1016/j.gene.2012.04.082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/07/2012] [Accepted: 04/27/2012] [Indexed: 12/01/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme and known as a mammalian immunosuppressive molecule. In fungi, the primary role of IDO is to supply nicotinamide adenine dinucleotide (NAD(+)) via the kynurenine pathway. We previously reported that the koji-mold, Aspergillus oryzae has two IDO genes, IDOα and IDOβ. In the present study, we found that A. oryzae also has the third IDO, IDOγ. These three-types of IDOs are widely distributed among the Pezizomycotina fungi, although the black truffle, Tuber melanosporum has only one corresponding gene to IDOα/IDOβ. The yeast, Saccharomyces cerevisiae has a single IDO gene. Generally, Pezizomycotina IDOα showed similar enzymatic properties to the yeast IDO, suggesting that the IDOα is a functional homologue of the S. cerevisiae IDO. In contrast to IDOα, the K(m) value of IDOβ is higher. However, the reaction velocity of IDOβ is very fast, resulting in comparable or higher catalytic efficiency than IDOα. Thus IDOβ may functionally substitute for IDOα in fungal L-Trp metabolism. The enzymatic activity of IDOγ was comparatively very low with the values of enzymatic parameters comparable to vertebrate IDO2 enzymes. IDOα and IDOβ have similar gene structures, suggesting that they were generated by gene duplication which occurred rather early in Pezizomycotina evolution, although the timing of the duplication remains debatable. In contrast, the phylogenetic trees suggest that IDOγs form an evolutionarily distinct group of IDO enzymes, with a closer relationship to group I bacterial IDOs than other fungal IDOs. The ancestor of the IDOγ family is likely to have diverged from other eukaryotic IDOs at a very early stage of eukaryotic evolution.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Kochi 780-8520, Japan.
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31
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Tryptophan catabolism via kynurenine production in Streptomyces coelicolor: identification of three genes coding for the enzymes of tryptophan to anthranilate pathway. Appl Microbiol Biotechnol 2012; 94:719-28. [DOI: 10.1007/s00253-011-3833-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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32
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Jiang CS, Müller WEG, Schröder HC, Guo YW. Disulfide- and multisulfide-containing metabolites from marine organisms. Chem Rev 2011; 112:2179-207. [PMID: 22176580 DOI: 10.1021/cr200173z] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheng-Shi Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang High-Tech Park, Shanghai 201203, People's Republic of China
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33
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Yuasa HJ, Ushigoe A, Ball HJ. Molecular evolution of bacterial indoleamine 2,3-dioxygenase. Gene 2011; 485:22-31. [PMID: 21689736 DOI: 10.1016/j.gene.2011.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/30/2011] [Accepted: 06/03/2011] [Indexed: 12/31/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the first step in L-Trp catabolism via the kynurenine pathway. In mammals, TDO is mainly expressed in the liver and primarily supplies nicotinamide adenine dinucleotide (NAD(+)). TDO is widely distributed from mammals to bacteria. Active IDO enzymes have been reported only in vertebrates and fungi. In mammals, IDO activity plays a significant role in the immune system while in fungal species, IDO is constitutively expressed and supplies NAD(+), like mammalian TDO. A search of genomic databases reveals that some bacterial species also have a putative IDO gene. A phylogenetic analysis clustered bacterial IDOs into two groups, group I or group II bacterial IDOs. The catalytic efficiencies of group I bacterial IDOs were very low and they are suspected not to contribute significantly to L-Trp metabolism. The bacterial species bearing the group I bacterial IDO are scattered across a few phyla and no phylogenetically close relationship is observed between them. This suggests that the group I bacterial IDOs might be acquired by horizontal gene transmission that occurred in each lineage independently. In contrast, group II bacterial IDOs showed rather high catalytic efficiency. Particularly, the enzymatic characteristics (K(m), V(max) and inhibitor selectivity) of the Gemmatimonas aurantiaca IDO are comparable to those of mammalian IDO1, although comparison of the IDO sequences does not suggest a close evolutionary relationship. In several bacteria, TDO and the kynureninase gene (kynU) are clustered on their chromosome suggesting that these genes could be transcribed in an operon. Interestingly, G. aurantiaca has no TDO, and the IDO is clustered with kynU on its chromosome. Although the G. aurantiaca also has NadA and NadB to synthesize a quinolinic acid (a precursor of NAD(+)) via the aspartate pathway, the high activity of the G. aurantiaca IDO flanking the kynU gene suggests its IDO has a function similar to eukaryotic enzymes.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, National University Corporation Kochi University, Japan.
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34
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Giessen TW, Kraas FI, Marahiel MA. A Four-Enzyme Pathway for 3,5-Dihydroxy-4-methylanthranilic Acid Formation and Incorporation into the Antitumor Antibiotic Sibiromycin. Biochemistry 2011; 50:5680-92. [DOI: 10.1021/bi2006114] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tobias W. Giessen
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Femke I. Kraas
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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36
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Hirose Y, Watanabe K, Minami A, Nakamura T, Oguri H, Oikawa H. Involvement of common intermediate 3-hydroxy-L-kynurenine in chromophore biosynthesis of quinomycin family antibiotics. J Antibiot (Tokyo) 2010; 64:117-22. [DOI: 10.1038/ja.2010.142] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Crnovcić I, Süssmuth R, Keller U. Aromatic C-methyltransferases with antipodal stereoselectivity for structurally diverse phenolic amino acids catalyze the methylation step in the biosynthesis of the actinomycin chromophore. Biochemistry 2010; 49:9698-705. [PMID: 20945860 DOI: 10.1021/bi101422r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The actinomycin biosynthetic gene cluster of Streptomyces chrysomallus harbors two paralogous genes, acmI and acmL, encoding methyltransferases. To unveil their suspected role in the formation of 3-hydroxy-4-methyl-anthranilic acid (4-MHA), the building block of the actinomycin chromophore, each gene was expressed in Escherichia coli. Testing the resulting ∼40 kDa His(6)-tagged proteins with compounds of biogenetic relevance as substrates and S-adenosyl-l-methionine revealed that each exclusively methylated 3-hydroxykynurenine (3-HK) with formation of 3-hydroxy-4-methylkynurenine (4-MHK) identified by its in vitro conversion to 4-MHA with hydroxykynureninase. AcmI and AcmL methylate also hydroxyphenyl-amino propanoic acids such as p-tyrosine, m-tyrosine, or 3,4-dihydroxy-l-phenylalanine (DOPA) but at a lower rate than 3-HK. The presence of the α-amino group was necessary for substrate recognition. Phenolic acids with shorter chains such as 4-hydoxyphenyl-l-glycine (HPG), 3-hydroxybenzoic acid (3-HB), or 3-hydroxyanthranilic acid (3-HA) gave no product. Both enzymes were stereospecific for the optical configuration at α-C with unprecedented antipodal selectivity for the d-enantiomer of 3-HK and the l-enantiomer of p-tyrosine or m-tyrosine. AcmI and AcmL show sequence similarity to various C- and O-methyltransferases from bacteria. Phylogenetic analysis places them into the clade of C-methyltransferases comprising among others orthologues involved in 4-MHA formation of other biosynthesis systems and methyltransferases putatively involved in the C-methylation of tyrosine. Remarkably, computational remodelling of AcmI and AcmL structures revealed significant similarity with the 3-D structures of type 1 O-methyltransferases from plants such as caffeic acid O-methyltransferase (COMT) and other phenylpropanoid methyltransferases. The relevance of 3-HK or 3-HA methylation in the actinomycin biosynthesis pathways of different actinomycetes is discussed.
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Affiliation(s)
- Ivana Crnovcić
- Technische Universität Berlin, Institut für Chemie, Arbeitsgruppe Biochemie und Molekulare Biologie, Franklinstrasse 29, D-10587 Berlin-Charlottenburg, Germany
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'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it. Biochem J 2009; 425:1-11. [PMID: 20001958 DOI: 10.1042/bj20091328] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Like other forms of engineering, metabolic engineering requires knowledge of the components (the 'parts list') of the target system. Lack of such knowledge impairs both rational engineering design and diagnosis of the reasons for failures; it also poses problems for the related field of metabolic reconstruction, which uses a cell's parts list to recreate its metabolic activities in silico. Despite spectacular progress in genome sequencing, the parts lists for most organisms that we seek to manipulate remain highly incomplete, due to the dual problem of 'unknown' proteins and 'orphan' enzymes. The former are all the proteins deduced from genome sequence that have no known function, and the latter are all the enzymes described in the literature (and often catalogued in the EC database) for which no corresponding gene has been reported. Unknown proteins constitute up to about half of the proteins in prokaryotic genomes, and much more than this in higher plants and animals. Orphan enzymes make up more than a third of the EC database. Attacking the 'missing parts list' problem is accordingly one of the great challenges for post-genomic biology, and a tremendous opportunity to discover new facets of life's machinery. Success will require a co-ordinated community-wide attack, sustained over years. In this attack, comparative genomics is probably the single most effective strategy, for it can reliably predict functions for unknown proteins and genes for orphan enzymes. Furthermore, it is cost-efficient and increasingly straightforward to deploy owing to a proliferation of databases and associated tools.
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Carr G, Tay W, Bottriell H, Andersen SK, Mauk AG, Andersen RJ. Plectosphaeroic acids A, B, and C, indoleamine 2,3-dioxygenase inhibitors produced in culture by a marine isolate of the fungus Plectosphaerella cucumerina. Org Lett 2009; 11:2996-9. [PMID: 19537768 DOI: 10.1021/ol900972j] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Laboratory cultures of the fungus Plectosphaerella cucumerina obtained from marine sediments collected in Barkley Sound, British Columbia, yielded the novel alkaloids plectosphaeroic acids A (1) to C (3). The alkaloids 1-3 are inhibitors of indoleamine 2,3-dioxygenase (IDO).
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Affiliation(s)
- Gavin Carr
- Department of Chemistry, University of British Columbia, Vancouver, B.C., Canada, V6T 1Z1
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40
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Nedelcu AM, Blakney AJC, Logue KD. Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention. J Evol Biol 2009; 22:1882-94. [PMID: 19619164 DOI: 10.1111/j.1420-9101.2009.01797.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.
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Affiliation(s)
- A M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB, Canada.
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