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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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2
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Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Colin C. Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA,Chan Zuckerberg Biohub, San Francisco, California, USA
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3
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Bhandari S, Bisht KS, Merkler DJ. The Biosynthesis and Metabolism of the N-Acylated Aromatic Amino Acids: N-Acylphenylalanine, N-Acyltyrosine, N-Acyltryptophan, and N-Acylhistidine. Front Mol Biosci 2022; 8:801749. [PMID: 35047560 PMCID: PMC8762209 DOI: 10.3389/fmolb.2021.801749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
The fatty acid amides are a family of lipids composed of two chemical moieties, a fatty acid and a biogenic amine linked together in an amide bond. This lipid family is structurally related to the endocannabinoid anandamide (N-arachidonoylethanolamine) and, thus, is frequently referred to as a family of endocannabinoid-related lipids. The fatty acid amide family is divided into different classes based on the conjugate amine; anandamide being a member of the N-acylethanolamine class (NAE). Another class within the fatty acid amide family is the N-acyl amino acids (NA-AAs). The focus of this review is a sub-class of the NA-AAs, the N-acyl aromatic amino acids (NA-ArAAs). The NA-ArAAs are not broadly recognized, even by those interested in the endocannabinoids and endocannabinoid-related lipids. Herein, the NA-ArAAs that have been identified from a biological source will be highlighted and pathways for their biosynthesis, degradation, enzymatic modification, and transport will be presented. Also, information about the cellular functions of the NA-ArAAs will be placed in context with the data regarding the identification and metabolism of these N-acylated amino acids. A review of the current state-of-knowledge about the NA-ArAAs is to stimulate future research about this underappreciated sub-class of the fatty acid amide family.
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Affiliation(s)
- Suzeeta Bhandari
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Kirpal S Bisht
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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4
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Abstract
Covering: Up to 2020.It is widely accepted that small molecule natural products (NPs) evolved to carry out a particular ecological function and that these finely-tuned molecules can sometimes be appropriated for the treatment of disease in humans. Unfortunately, for the natural products chemist, NPs did not evolve to possess favorable physicochemical properties needed for HPLC-MS analysis. The process known as derivatization, whereby an NP in a complex mixture is decorated with a nonnatural moiety using a derivatizing agent (DA), arose from this sad state of affairs. Here, NPs are freed from the limitations of natural functionality and endowed, usually with some degree of chemoselectivity, with additional structural features that make HPLC-MS analysis more informative. DAs that selectively label amines, carboxylic acids, alcohols, phenols, thiols, ketones, and aldehydes, terminal alkynes, electrophiles, conjugated alkenes, and isocyanides have been developed and will be discussed here in detail. Although usually employed for targeted metabolomics, chemical labeling strategies have been effectively applied to uncharacterized NP extracts and may play an increasing role in the detection and isolation of certain classes of NPs in the future.
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Affiliation(s)
- Chambers C Hughes
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany 72076.
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5
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Huang YB, Cai W, Del Rio Flores A, Twigg FF, Zhang W. Facile Discovery and Quantification of Isonitrile Natural Products via Tetrazine-Based Click Reactions. Anal Chem 2019; 92:599-602. [PMID: 31815449 DOI: 10.1021/acs.analchem.9b05147] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A facile method for the quick discovery and quantification of isonitrile compounds from microbial cultures was established based on the isonitrile-tetrazine click reaction. This method was successfully applied to the rediscovery of diisonitrile antibotic SF2768 from an unknown strain Streptomyces tsukubensis. Finally, an in situ reduction further enabled bioorthogonal ligation of primary and secondary isonitriles for the first time.
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Affiliation(s)
- Yao-Bing Huang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources , Nanjing Forestry University , Nanjing 210037 , China.,Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Frederick F Twigg
- Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
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6
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Abstract
Isocyanide functional groups can be found in a variety of natural products. Rhabduscin is one such isocyanide-functionalized immunosuppressant produced in Xenorhabdus and Photorhabdus gammaproteobacterial pathogens, and deletion of its biosynthetic gene cluster inhibits virulence in an invertebrate animal infection model. Here, we characterized the first "opine-glycopeptide" class of natural products termed rhabdoplanins, and strikingly, these molecules are spontaneously produced from rhabduscin via an unprecedented multicomponent "Ugi-like" reaction sequence in nature. The rhabdoplanins also represent new lead G protein-coupled receptor (GPCR) agonists, stimulating the bombesin receptor subtype-3 (BB3) GPCR.
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Affiliation(s)
- Joonseok Oh
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Nam Y Kim
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Haiwei Chen
- Department of Immunobiology , Yale School of Medicine , New Haven , Connecticut 06520 , United States
| | - Noah W Palm
- Department of Immunobiology , Yale School of Medicine , New Haven , Connecticut 06520 , United States
| | - Jason M Crawford
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Microbial Pathogenesis , Yale School of Medicine , New Haven , Connecticut 06536 , United States
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Marchetti PM, Richardson SM, Kariem NM, Campopiano DJ. Synthesis of N-acyl amide natural products using a versatile adenylating biocatalyst. Medchemcomm 2019; 10:1192-1196. [PMID: 31741729 PMCID: PMC6677021 DOI: 10.1039/c9md00063a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/22/2019] [Indexed: 11/30/2022]
Abstract
TamA is the enzyme that controls the acyl chain length of the tambjamine natural products. Here we show that the catalytic ANL domain of TamA can be used to prepare a range of N-acyl amides.
Natural products are secondary metabolites produced by many different organisms such as bacteria, fungi and plants. These biologically active molecules have been widely exploited for clinical application. Here we investigate TamA, a key enzyme from the biosynthetic pathway of tambjamine YP1, an acylated bipyrrole that is produced by the marine microorganism Pseudoalteromonas tunicata. TamA is a didomain enzyme composed of a catalytic adenylation (ANL) and an acyl carrier protein (ACP) domain that together control the fatty acid chain length of the YP1. Here we show that the TamA ANL domain alone can be used to generate a range of acyl adenylates that can be captured by a number of amines thus leading to the production of a series of fatty N-acyl amides. We exploit this biocatalytic promiscuity to produce the recently discovered class of N-acyl histidine amide natural products from Legionella pneumophila.
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Affiliation(s)
- Piera M Marchetti
- EastCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh , EH9 3FJ , UK .
| | - Shona M Richardson
- EastCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh , EH9 3FJ , UK .
| | - Noor M Kariem
- EastCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh , EH9 3FJ , UK .
| | - Dominic J Campopiano
- EastCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh , EH9 3FJ , UK .
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Hai Y, Tang Y. Biosynthesis of Long-Chain N-Acyl Amide by a Truncated Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthase in Fungi. J Am Chem Soc 2018; 140:1271-1274. [PMID: 29343058 DOI: 10.1021/jacs.7b13350] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Truncated iterative polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) megasynthases in which only the C domain is present are widespread in fungi, yet nearly all members have unknown functions. Bioinformatics analysis showed that the C domains of such PKS-C enzymes are noncanonical due to substitution at the second histidine in the active site HHxxxDG motif. Here, we used genome mining strategy to characterize a cryptic PKS-C hybrid from Talaromyces wortmanii and discovered the products are reduced long-chain polyketides amidated with a specific ω-amino acid 5-aminopentanoic acid (5PA). The wortmanamides resemble long-chain N-acyl-amide signaling lipids that target diverse receptors including GPCRs. The noncanonical C domain of this PKS-C hybrid was also demonstrated to be a bona fide condensation domain that specifically selects 5PA and catalyzes amidation to release polyketide chain.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
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9
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Evangelatos N, Bauer P, Reumann M, Satyamoorthy K, Lehrach H, Brand A. Metabolomics in Sepsis and Its Impact on Public Health. Public Health Genomics 2018; 20:274-285. [PMID: 29353273 DOI: 10.1159/000486362] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/16/2017] [Indexed: 12/11/2022] Open
Abstract
Sepsis, with its often devastating consequences for patients and their families, remains a major public health concern that poses an increasing financial burden. Early resuscitation together with the elucidation of the biological pathways and pathophysiological mechanisms with the use of "-omics" technologies have started changing the clinical and research landscape in sepsis. Metabolomics (i.e., the study of the metabolome), an "-omics" technology further down in the "-omics" cascade between the genome and the phenome, could be particularly fruitful in sepsis research with the potential to alter the clinical practice. Apart from its benefit for the individual patient, metabolomics has an impact on public health that extends beyond its applications in medicine. In this review, we present recent developments in metabolomics research in sepsis, with a focus on pneumonia, and we discuss the impact of metabolomics on public health, with a focus on free/libre open source software.
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Affiliation(s)
- Nikolaos Evangelatos
- Intensive Care Medicine Unit, Department of Respiratory Medicine, Allergology and Sleep Medicine, Paracelsus Medical University, Nuremberg, Germany.,UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands
| | - Pia Bauer
- Intensive Care Medicine Unit, Department of Respiratory Medicine, Allergology and Sleep Medicine, Paracelsus Medical University, Nuremberg, Germany
| | - Matthias Reumann
- UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands.,IBM Research - Zurich, Rueschlikon, Switzerland
| | | | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Angela Brand
- UNU-MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Maastricht, the Netherlands.,Public Health Genomics, Department of International Health, Maastricht University, Maastricht, the Netherlands.,Manipal University, Madhav Nagar, Manipal, India
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