1
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Jia N, Ganesan D, Guan H, Jeong YY, Han S, Rajapaksha G, Nissenbaum M, Kusnecov AW, Cai Q. Mitochondrial bioenergetics stimulates autophagy for pathological MAPT/Tau clearance in tauopathy neurons. Autophagy 2024:1-26. [PMID: 39171695 DOI: 10.1080/15548627.2024.2392408] [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: 01/26/2024] [Revised: 08/04/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
Hyperphosphorylation and aggregation of MAPT (microtubule-associated protein tau) is a pathogenic hallmark of tauopathies and a defining feature of Alzheimer disease (AD). Pathological MAPT/tau is targeted by macroautophagy/autophagy for clearance after being sequestered within autophagosomes, but autophagy dysfunction is indicated in tauopathy. While mitochondrial bioenergetic deficits have been shown to precede MAPT/tau pathology in tauopathy brains, it is unclear whether energy metabolism deficiency is involved in the pathogenesis of autophagy defects. Here, we reveal that stimulation of anaplerotic metabolism restores defective oxidative phosphorylation (OXPHOS) in tauopathy neurons which, strikingly, leads to pronounced MAPT/tau clearance by boosting autophagy functionality through enhancements of mitochondrial biosynthesis and supply of phosphatidylethanolamine for autophagosome biogenesis. Furthermore, early anaplerotic stimulation of OXPHOS elevates autophagy activity and attenuates MAPT/tau pathology, thereby counteracting memory impairment in tauopathy mice. Taken together, our study sheds light on a pivotal role of mitochondrial bioenergetic deficiency in tauopathy-related autophagy defects and suggests a new therapeutic strategy to prevent the buildup of pathological MAPT/tau in AD and other tauopathy diseases.Abbreviation: AA: antimycin A; AD, Alzheimer disease; ATP, adenosine triphosphate; AV, autophagosome/autophagic vacuole; AZ, active zone; Baf-A1: bafilomycin A1; CHX, cycloheximide; COX, cytochrome c oxidase; DIV, days in vitro; DRG, dorsal root ganglion; ETN, ethanolamine; FRET, Förster/fluorescence resonance energy transfer; FTD, frontotemporal dementia; Gln, glutamine; HA: hydroxylamine; HsMAPT/Tau, human MAPT; IMM, inner mitochondrial membrane; LAMP1, lysosomal-associated membrane protein 1; LIs, lysosomal inhibitors; MDAV, mitochondria-derived autophagic vacuole; MmMAPT/Tau, murine MAPT; NFT, neurofibrillary tangle; OCR, oxygen consumption rate; Omy: oligomycin; OXPHOS, oxidative phosphorylation; PPARGC1A/PGC-1alpha: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; PE, phosphatidylethanolamine; phospho-MAPT/tau, hyperphosphorylated MAPT; PS, phosphatidylserine; PISD, phosphatidylserine decarboxylase;SQSTM1/p62, sequestosome 1; STX1, syntaxin 1; SYP, synaptophysin; Tg, transgenic; TCA, tricarboxylic acid; TEM, transmission electron microscopy.
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Affiliation(s)
- Nuo Jia
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Dhasarathan Ganesan
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Hongyuan Guan
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Yu Young Jeong
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Sinsuk Han
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Gavesh Rajapaksha
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marialaina Nissenbaum
- Department of Psychology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Alexander W Kusnecov
- Department of Psychology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Qian Cai
- Department of Cell Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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2
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Veera S, Tang F, Mourad Y, Kim S, Liu T, Li H, Wang Y, Warren JS, Park J, Van C, Sadoshima J, Oka SI. A transcriptional regulatory mechanism of genes in the tricarboxylic acid cycle in the heart. J Biol Chem 2024; 300:107677. [PMID: 39151728 PMCID: PMC11415578 DOI: 10.1016/j.jbc.2024.107677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/05/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
The tricarboxylic acid (TCA) cycle plays a crucial role in mitochondrial ATP production in the healthy heart. However, in heart failure, the TCA cycle becomes dysregulated. Understanding the mechanism by which TCA cycle genes are transcribed in the healthy heart is an important prerequisite to understanding how these genes become dysregulated in the failing heart. PPARγ coactivator 1α (PGC-1α) is a transcriptional coactivator that broadly induces genes involved in mitochondrial ATP production. PGC-1α potentiates its effects through the coactivation of coupled transcription factors, such as estrogen-related receptor (ERR), nuclear respiratory factor 1 (Nrf1), GA-binding protein-a (Gabpa), and Yin Yang 1 (YY1). We hypothesized that PGC-1α plays an essential role in the transcription of TCA cycle genes. Thus, utilizing localization peaks of PGC-1α to TCA cycle gene promoters would allow the identification of coupled transcription factors. PGC-1α potentiated the transcription of 13 out of 14 TCA cycle genes, partly through ERR, Nrf1, Gabpa, and YY1. ChIP-sequencing showed PGC-1α localization peaks in TCA cycle gene promoters. Transcription factors with binding elements that were found proximal to PGC-1α peak localization were generally essential for the transcription of the gene. These transcription factor binding elements were well conserved between mice and humans. Among the four transcription factors, ERR and Gabpa played a major role in potentiating transcription when compared to Nrf1 and YY1. These transcription factor-dependent PGC-1α recruitment was verified with Idh3a, Idh3g, and Sdha promoters with DNA binding assay. Taken together, this study clarifies the mechanism by which TCA cycle genes are transcribed, which could be useful in understanding how those genes are dysregulated in pathological conditions.
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Affiliation(s)
- Samta Veera
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Fan Tang
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Youssef Mourad
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Samuel Kim
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School and Cancer Institute of New Jersey, Newark, New Jersey, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School and Cancer Institute of New Jersey, Newark, New Jersey, USA
| | - Yunjue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Junco S Warren
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, Virginia, USA
| | - Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Carter Van
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Shin-Ichi Oka
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA.
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3
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Lange KR, Rasheed N, Su X, Diaz-Rubio ME, Firestein BL. Valacyclovir and Acyclovir Are Substrates of the Guanine Deaminase Cytosolic PSD-95 Interactor (Cypin). Proteins 2024. [PMID: 39210666 DOI: 10.1002/prot.26740] [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: 04/30/2024] [Revised: 07/27/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Valacyclovir, enzymatically hydrolyzed in the body to acyclovir, is a guanine-based nucleoside analog commonly prescribed as an antiviral therapy. Previous reports suggest that guanosine analogs bind to guanine deaminase; however, it is unclear whether they act as inhibitors or substrates. Data from our laboratory suggest that inhibition of guanine deaminase by small molecules attenuates spinal cord injury-induced neuropathic pain. Here, we examine whether the guanosine analogs valacyclovir and acyclovir are deaminated by cypin (cytosolic PSD-95 interactor), the major guanine deaminase in the body, or if they act as cypin inhibitors. Using purified Rattus norvegicus cypin, we use NADH-coupled assay to confirm deamination of valacyclovir and determined Michaelis-Menten constants. Subsequently, we use tryptophan fluorescence quenching assay to calculate dissociation constants for valacyclovir and acyclovir and find that inclusion of the valine motif in valacyclovir increases affinity for cypin compared to acyclovir. To our knowledge, neither Km nor KD values for cypin has been previously reported for either compound. We use Amplex Red assay and demonstrate that both valacyclovir and acyclovir are cypin substrates and that their metabolites are further processed by xanthine oxidase and uricase. Using molecular dynamics simulations, we demonstrate that an alpha helix near the active site is displaced when valacyclovir binds to cypin. Furthermore, we used LC-MS-based assay to directly confirm deamination of valacyclovir by cypin. Taken together, our results demonstrate a novel role for cypin in deamination of valacyclovir and acyclovir and suggest that therapeutics based on purine structures may be inactivated by cypin, decreasing inhibitory efficacy.
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Affiliation(s)
- Keith R Lange
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Graduate Program in Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Noor Rasheed
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Xiaoyang Su
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Rutgers Metabolomics Shared Resource, Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - M Elena Diaz-Rubio
- Rutgers Metabolomics Shared Resource, Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Bonnie L Firestein
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Lopes EC, Shi F, Sawant A, Ibrahim M, Gomez-Jenkins M, Hu Z, Manchiraju P, Bhatt V, Wang W, Hinrichs CS, Wallace DC, Su X, Rabinowitz JD, Chan CS, Guo JY, Ganesan S, Lattime EC, White E. RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596339. [PMID: 38853873 PMCID: PMC11160605 DOI: 10.1101/2024.05.28.596339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mitochondrial function is important for both energetic and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations directly impact these functions, resulting in the detrimental consequences seen in human mitochondrial diseases. The role of pathogenic mtDNA mutations in human cancers is less clear; while pathogenic mtDNA mutations are observed in some cancer types, they are almost absent in others. We report here that the proofreading mutant DNA polymerase gamma ( PolG D256A ) induced a high mtDNA mutation burden in non-small-cell lung cancer (NSCLC), and promoted the accumulation of defective mitochondria, which is responsible for decreased tumor cell proliferation and viability and increased cancer survival. In NSCLC cells, pathogenic mtDNA mutations increased glycolysis and caused dependence on glucose. The glucose dependency sustained mitochondrial energetics but at the cost of a decreased NAD+/NADH ratio that inhibited de novo serine synthesis. Insufficient serine synthesis, in turn, impaired the downstream synthesis of GSH and nucleotides, leading to impaired tumor growth that increased cancer survival. Unlike tumors with intact mitochondrial function, NSCLC with pathogenic mtDNA mutations were sensitive to dietary serine and glycine deprivation. Thus, mitochondrial function in NSCLC is required specifically to sustain sufficient serine synthesis for nucleotide production and redox homeostasis to support tumor growth, explaining why these cancers preserve functional mtDNA. In brief High mtDNA mutation burden in non-small-cell lung cancer (NSCLC) leads to the accumulation of respiration-defective mitochondria and dependency on glucose and glycolytic metabolism. Defective respiratory metabolism causes a massive accumulation of cytosolic nicotinamide adenine dinucleotide + hydrogen (NADH), which impedes serine synthesis and, thereby, glutathione (GSH) and nucleotide synthesis, leading to impaired tumor growth and increased survival. Highlights Proofreading mutations in Polymerase gamma led to a high burden of mitochondrial DNA mutations, promoting the accumulation of mitochondria with respiratory defects in NSCLC.Defective respiration led to reduced proliferation and viability of NSCLC cells increasing survival to cancer.Defective respiration caused glucose dependency to fuel elevated glycolysis.Altered glucose metabolism is associated with high NADH that limits serine synthesis, leading to impaired GSH and nucleotide production.Mitochondrial respiration defects sensitize NSCLC to dietary serine/glycine starvation, further increasing survival. Abstract Figure
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5
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Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics. eLife 2023; 12:RP87039. [PMID: 37991493 PMCID: PMC10665018 DOI: 10.7554/elife.87039] [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] [Indexed: 11/23/2023] Open
Abstract
Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.
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Affiliation(s)
- John S Favate
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New JerseyPiscatawayUnited States
| | - Kyle S Skalenko
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Eric Chiles
- Cancer Institute of New JerseyNew BrunswickUnited States
| | - Xiaoyang Su
- Cancer Institute of New JerseyNew BrunswickUnited States
| | - Srujana Samhita Yadavalli
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Premal Shah
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New JerseyPiscatawayUnited States
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6
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Das A, Liu T, Li H, Husain S. The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei. mSphere 2023; 8:e0027323. [PMID: 37581443 PMCID: PMC10654194 DOI: 10.1128/msphere.00273-23] [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: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players in coordinated post-transcriptional regulation of functionally related genes, defined as RNA regulons. RNA regulons play particularly critical roles in parasitic trypanosomes, which exhibit unregulated co-transcription of long unrelated gene arrays. In this report, we present a systematic analysis of an essential RBP, RBP42, in the mammalian-infective bloodstream form of African trypanosome and show that RBP42 is a key regulator of parasite's central carbon and energy metabolism. Using individual-nucleotide resolution UV cross-linking and immunoprecipitation to identify genome-wide RBP42-RNA interactions, we show that RBP42 preferentially binds within the coding region of mRNAs encoding core metabolic enzymes. Global quantitative transcriptomic and proteomic analyses reveal that loss of RBP42 reduces the abundance of target mRNA-encoded proteins, but not target mRNA, suggesting a positive translational regulatory role of RBP42. Significant changes in central carbon metabolic intermediates, following loss of RBP42, further support its critical role in cellular energy metabolism. Trypanosoma brucei infection, transmitted through the bite of blood-feeding tsetse flies, causes deadly diseases in humans and livestock. This disease, if left untreated, is almost always fatal. Existing therapies are toxic and difficult to administer. During T. brucei's lifecycle in two different host environments, the parasite progresses through distinctive life stages with major morphological and metabolic changes, requiring precise alteration of parasite gene expression program. In the absence of regulated transcription, post-transcriptional processes mediated by RNA-binding proteins play critical roles in T. brucei gene regulation. In this study, we show that the RNA-binding protein RBP42 plays crucial roles in cellular energy metabolic regulation of this important human pathogen. Metabolic dysregulation observed in RBP42 knockdown cells offers a breadth of potential interest to researchers studying parasite biology and can also impact research in general eukaryotic biology.
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Affiliation(s)
- Anish Das
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Seema Husain
- Genomics Center, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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7
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Khanna P, Mehta R, Mehta GA, Bhatt V, Guo JY, Gatza ML. SOX4-SMARCA4 complex promotes glycolysis-dependent TNBC cell growth through transcriptional regulation of Hexokinase 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.557071. [PMID: 37745600 PMCID: PMC10515838 DOI: 10.1101/2023.09.10.557071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Tumor cells rely on increased glycolytic capacity to promote cell growth and progression. While glycolysis is known to be upregulated in the majority of triple negative (TNBC) or basal-like subtype breast cancers, the mechanism remains unclear. Here, we used integrative genomic analyses to identify a subset of basal-like tumors characterized by increased expression of the oncogenic transcription factor SOX4 and its co-factor the SWI/SNF ATPase SMARCA4. These tumors are defined by unique gene expression programs that correspond with increased tumor proliferation and activation of key metabolic pathways, including glycolysis. Mechanistically, we demonstrate that the SOX4-SMARCA4 complex mediates glycolysis through direct transcriptional regulation of Hexokinase 2 (HK2) and that aberrant HK2 expression and altered glycolytic capacity are required to mediate SOX4-SMARCA4-dependent cell growth. Collectively, we have defined the SOX4-SMARCA4-HK2 signaling axis in basal-like breast tumors and established that this axis promotes metabolic reprogramming which is required to maintain tumor cell growth.
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Affiliation(s)
- Pooja Khanna
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Rushabh Mehta
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Gaurav A. Mehta
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Vrushank Bhatt
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901
- Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - Jessie Y. Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901
- Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - Michael L. Gatza
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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8
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Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the E. coli Long-Term Evolution Experiment using metabolomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528756. [PMID: 36874203 PMCID: PMC9985142 DOI: 10.1101/2023.02.15.528756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long-Term Evolution Experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass-spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.
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Affiliation(s)
- John S. Favate
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Kyle S. Skalenko
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Eric Chiles
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Xiaoyang Su
- Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Srujana S. Yadavalli
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
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9
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Shah A, Wang Y, Wondisford FE. Differential Metabolism of Glycerol Based on Oral versus Intravenous Administration in Humans. Metabolites 2022; 12:metabo12100890. [PMID: 36295792 PMCID: PMC9611849 DOI: 10.3390/metabo12100890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Glycerol can be metabolized to glucose via gluconeogenesis or lactate via glycolysis. It is unknown if glycerol is metabolized similarly in the portal and systemic circulations in humans. Eight metabolically healthy overnight-fasted individuals received equimolar amounts of 13C3-glycerol orally and intravenously on two separate occasions with serial blood draws over four hours. Serum samples underwent liquid chromatography–mass spectrometry analysis. Oral 13C3-glycerol administration led to higher average serum glucose enrichment than intravenous administration (5.02 ± 1.43 versus 4.07 ± 0.79%, p = 0.009). In contrast, intravenous 13C3-glycerol administration yielded higher average serum lactate enrichment than oral administration (5.67 ± 0.80 versus 4.85 ± 1.30%, p = 0.032). Peak serum glucose enrichment was also higher with oral administration (9.37 ± 2.93 versus 7.12 ± 1.28%, p = 0.010). Glycerol metabolism across the portal and systemic circulations is not congruent. Orally administered labeled glycerol led to greater labeled glucose production, while intravenously administration yielded greater lactate production. These data support direct glycerol to lactate conversion in humans.
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Affiliation(s)
- Ankit Shah
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Yujue Wang
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Fredric E. Wondisford
- Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
- Correspondence:
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Wu Y, Wong CW, Chiles EN, Mellinger AL, Bae H, Jung S, Peterson T, Wang J, Negrete M, Huang Q, Wang L, Jang C, Muddiman DC, Su X, Williamson I, Shen X. Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance. Cell Metab 2022; 34:1042-1053.e6. [PMID: 35688154 PMCID: PMC9897509 DOI: 10.1016/j.cmet.2022.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 12/21/2021] [Accepted: 05/18/2022] [Indexed: 02/06/2023]
Abstract
Dietary fructose, especially in the context of a high-fat western diet, has been linked to type 2 diabetes. Although the effect of fructose on liver metabolism has been extensively studied, a significant portion of the fructose is first metabolized in the small intestine. Here, we report that dietary fat enhances intestinal fructose metabolism, which releases glycerate into the blood. Chronic high systemic glycerate levels induce glucose intolerance by slowly damaging pancreatic islet cells and reducing islet sizes. Our findings provide a link between dietary fructose and diabetes that is modulated by dietary fat.
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Affiliation(s)
- Yanru Wu
- Department of Prosthodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Chi Wut Wong
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Eric N Chiles
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA
| | - Allyson L Mellinger
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hosung Bae
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Sunhee Jung
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Ted Peterson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Jamie Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Marcos Negrete
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Qiang Huang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pediatric Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, China
| | - Lihua Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA; Molecular Education, Technology and Research Innovation Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ian Williamson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Gastroenterology Division, Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
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11
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Shah A, Wang Y, Su X, Wondisford FE. Glycerol's contribution to lactate production outside of a glucose intermediate in fasting humans. Metabolism 2022; 132:155214. [PMID: 35562085 DOI: 10.1016/j.metabol.2022.155214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Glycerol is a well-recognized substrate for new glucose production via gluconeogenesis in the liver. However, its carbon contribution to the glycolytic intermediate lactate is not known in humans. METHODS Here we infused stable isotope tracers 13C3-glycerol and 6,6-D2-glucose into six metabolically healthy individuals after an overnight fast to study glycerol metabolism and measure glucose rate of appearance. Serum samples underwent liquid chromatography-mass spectrometry analysis. RESULTS Glycerol and glucose rates of appearance were 2.21 ± 1.42 μmol/kg/min and 7.81 ± 1.15 μmol/kg/min, respectively. Under steady-state conditions, the 13C enrichment for lactate was significantly higher than that of glucose (2.90 ± 0.52% versus 1.53 ± 0.78%, p = 0.017), suggesting direct glycerol to lactate metabolism. The percentage of lactate derived from glycerol was also significantly higher than the percentage of glucose (13.88 ± 2.69% versus 6.50 ± 2.59%, p = 0.005). CONCLUSION Given that lactate itself is a carbon source for gluconeogenesis and tricycarboxylic cycle intermediates, glycerol's ability to donate carbons to lactate may make it quantitatively more important to intermediary metabolism than currently appreciated.
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Affiliation(s)
- Ankit Shah
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Yujue Wang
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Xiaoyang Su
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Fredric E Wondisford
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA.
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12
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Li S, Dina Kuo HC, Wang L, Wu R, Sargsyan D, Kong AN. UVB Drives Metabolic Rewiring and Epigenetic Reprograming and Protection by Sulforaphane in Human Skin Keratinocytes. Chem Res Toxicol 2022; 35:1220-1233. [PMID: 35700067 DOI: 10.1021/acs.chemrestox.1c00432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sulforaphane (SFN) is a potent anticancer agent which could protect the skin from ultraviolet (UV) radiation-induced insults. Currently, the metabolic rewiring and epigenetic reprograming induced by UVB and the role of SFN in UVB-mediated skin cell transformation remain largely unknown. Herein, we study the metabolome, epigenome, and transcriptome of human keratinocytes (HaCaT cells) exposed to UVB with or without SFN using liquid chromatography-mass spectroscopy, DNA methylation sequencing, and RNA sequencing. UVB increases intracellular reactive oxygen species (ROS) and SFN enhances ROS acutely in post-UVB-exposed HaCaT cells. UVB and SFN alter multiple metabolites and metabolism-related signaling pathways. Pathway analysis shows that UVB impacts numerous signaling pathways including STAT3, inhibition of matrix metalloproteases, and TGF-β, among others. DNA/CpG methylation analysis shows that SFN could partially reverse some of the alterations of UVB-induced CpG methylome. Integrating RNA-seq and Methyl-seq data, starburst plots show the correlation of mRNA expression and CpG methylation status. The potential linkages between the metabolome, CpG methylome, and transcriptome suggest that metabolites produced during metabolism act as cofactors or substrates for catalytic epigenetic modification and transcriptional regulation. These results indicate that UVB drives metabolic rewiring, epigenetic reprograming, and phenotypic transcriptomic alterations and SFN would block or attenuate many of these aberrations, potentially contributing to the overall protective effect of SFN against UVB-induced skin damage.
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Affiliation(s)
- Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States.,International Center for Aging and Cancer, Hainan Medical University, Haikou, Hainan 571199, China
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States.,Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States.,Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States.,Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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13
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Zhu Y, Zang Q, Luo Z, He J, Zhang R, Abliz Z. An Organ-Specific Metabolite Annotation Approach for Ambient Mass Spectrometry Imaging Reveals Spatial Metabolic Alterations of a Whole Mouse Body. Anal Chem 2022; 94:7286-7294. [PMID: 35548855 DOI: 10.1021/acs.analchem.2c00557] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Rapid and accurate metabolite annotation in mass spectrometry imaging (MSI) can improve the efficiency of spatially resolved metabolomics studies and accelerate the discovery of reliable in situ disease biomarkers. To date, metabolite annotation tools in MSI generally utilize isotopic patterns, but high-throughput fragmentation-based identification and biological and technical factors that influence structure elucidation are active challenges. Here, we proposed an organ-specific, metabolite-database-driven approach to facilitate efficient and accurate MSI metabolite annotation. Using data-dependent acquisition (DDA) in liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to generate high-coverage product ions, we identified 1620 unique metabolites from eight mouse organs (brain, liver, kidney, heart, spleen, lung, muscle, and pancreas) and serum. Following the evaluation of the adduct form difference of metabolite ions between LC-MS and airflow-assisted desorption electrospray ionization (AFADESI)-MSI and deciphering organ-specific metabolites, we constructed a metabolite database for MSI consisting of 27,407 adduct ions. An automated annotation tool, MSIannotator, was then created to conduct metabolite annotation in the MSI dataset with high efficiency and confidence. We applied this approach to profile the spatially resolved landscape of the whole mouse body and discovered that metabolites were distributed across the body in an organ-specific manner, which even spanned different mouse strains. Furthermore, the spatial metabolic alteration in diabetic mice was delineated across different organs, exhibiting that differentially expressed metabolites were mainly located in the liver, brain, and kidney, and the alanine, aspartate, and glutamate metabolism pathway was simultaneously altered in these three organs. This approach not only enables robust metabolite annotation and visualization on a body-wide level but also provides a valuable database resource for underlying organ-specific metabolic mechanisms.
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Affiliation(s)
- Ying Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhigang Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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14
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Li S, Wu R, Wang L, Dina Kuo HC, Sargsyan D, Zheng X, Wang Y, Su X, Kong AN. Triterpenoid ursolic acid drives metabolic rewiring and epigenetic reprogramming in treatment/prevention of human prostate cancer. Mol Carcinog 2022; 61:111-121. [PMID: 34727410 PMCID: PMC8665082 DOI: 10.1002/mc.23365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023]
Abstract
Ursolic acid (UA) is a triterpenoid phytochemical with a strong anticancer effect. The metabolic rewiring, epigenetic reprogramming, and chemopreventive effect of UA in prostate cancer (PCa) remain unknown. Herein, we investigated the efficacy of UA in PCa xenograft, and its biological effects on cellular metabolism, DNA methylation, and transcriptomic using multi-omics approaches. The metabolomics was quantified by liquid-chromatography-mass spectrometry (LC-MS) while epigenomic CpG methylation in parallel with transcriptomic gene expression was studied by next-generation sequencing technologies. UA administration attenuated the growth of transplanted human VCaP-Luc cells in immunodeficient mice. UA regulated several cellular metabolites and metabolism-related signaling pathways including S-adenosylmethionine (SAM), methionine, glucose 6-phosphate, CDP-choline, phosphatidylcholine biosynthesis, glycolysis, and nucleotide sugars metabolism. RNA-seq analyses revealed UA regulated several signaling pathways, including CXCR4 signaling, cancer metastasis signaling, and NRF2-mediated oxidative stress response. Epigenetic reprogramming study with DNA Methyl-seq uncovered a list of differentially methylated regions (DMRs) associated with UA treatment. Transcriptome-DNA methylome correlative analysis uncovered a list of genes, of which changes in gene expression correlated with the promoter CpG methylation status. Altogether, our results suggest that UA regulates metabolic rewiring of metabolism including SAM potentially driving epigenetic CpG methylation reprogramming, and transcriptomic signaling resulting in the overall anticancer chemopreventive effect.
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Affiliation(s)
- Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- International Center for Aging and Cancer, Hainan Medical University, Haikou, Hainan, China
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Xi Zheng
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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15
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Cerrato A, Aita SE, Capriotti AL, Cavaliere C, Montone CM, Piovesana S, Laganà A. Fully Automatized Detection of Phosphocholine-Containing Lipids through an Isotopically Labeled Buffer Modification Workflow. Anal Chem 2021; 93:15042-15048. [PMID: 34726396 DOI: 10.1021/acs.analchem.1c02944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution mass spectrometry is the foremost technique for qualitative and quantitative lipidomics analyses. Glycerophospholipids and sphingolipids, collectively termed polar lipids, are commonly investigated by hyphenated liquid chromatography-mass spectrometry (LC-MS) techniques that reduce aggregation effects and provide a greater dynamic range of detection sensitivity compared to shotgun lipidomics. However, automatic polar lipid identification is hindered by several isobaric and isomer mass overlaps, which cause software programs to often fail to correctly annotate the lipid species. In the present paper, a buffer modification workflow based on the use of labeled and unlabeled acetate ions in the chromatographic buffers was optimized by Box-Behnken design of the experiments and applied to the characterization of phosphocholine-containing lipids in human plasma samples. The contemporary generation of [M + CH3COO]-, [M + CD3COO]-, and [M - CH3]- coupled with a dedicated data processing workflow, which was specifically set up on Compound Discoverer software, allowed us to correctly determine adduct composition, molecular formulas, and grouping, as well as granting a lower false-positive rate and streamlining the manual validation step compared to commonly employed lipidomics platforms. The proposed workflow represents a robust yet easier alternative to the existing approaches for improving lipid annotation, as it does not require extensive sample pretreatment or prior isotopic enrichment or derivatization.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sara Elsa Aita
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.,CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
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16
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Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella AD, Shen Y, Cowan A, McReynolds MR, Kennedy BJ, Lato AM, Campagna SR, Singh M, Rabinowitz JD. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods 2021; 18:1377-1385. [PMID: 34711973 PMCID: PMC8733904 DOI: 10.1038/s41592-021-01303-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/16/2021] [Indexed: 11/08/2022]
Abstract
Liquid chromatography-high-resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantify all metabolites, but most LC-MS peaks remain unidentified. Here we present a global network optimization approach, NetID, to annotate untargeted LC-MS metabolomics data. The approach aims to generate, for all experimentally observed ion peaks, annotations that match the measured masses, retention times and (when available) tandem mass spectrometry fragmentation patterns. Peaks are connected based on mass differences reflecting adduction, fragmentation, isotopes, or feasible biochemical transformations. Global optimization generates a single network linking most observed ion peaks, enhances peak assignment accuracy, and produces chemically informative peak-peak relationships, including for peaks lacking tandem mass spectrometry spectra. Applying this approach to yeast and mouse data, we identified five previously unrecognized metabolites (thiamine derivatives and N-glucosyl-taurine). Isotope tracer studies indicate active flux through these metabolites. Thus, NetID applies existing metabolomic knowledge and global optimization to substantially improve annotation coverage and accuracy in untargeted metabolomics datasets, facilitating metabolite discovery.
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Affiliation(s)
- Li Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Lin Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Xi Xing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ziyang Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xin Teng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xianfeng Zeng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Antonio D Muscarella
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yihui Shen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexis Cowan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Melanie R McReynolds
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Brandon J Kennedy
- Lotus Separations, LLC, Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ashley M Lato
- Department of Chemistry, The University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA.
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17
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Wang Y, Parsons LR, Su X. AccuCor2: isotope natural abundance correction for dual-isotope tracer experiments. J Transl Med 2021; 101:1403-1410. [PMID: 34193963 PMCID: PMC9645465 DOI: 10.1038/s41374-021-00631-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 11/09/2022] Open
Abstract
Stable isotope labeling techniques have been widely applied in the field of metabolomics and proteomics. Before the measured mass spectral data can be used for quantitative analysis, it must be accurately corrected for isotope natural abundance and tracer isotopic impurity. Despite the increasing popularity of dual-isotope tracing strategy such as 13C-15N or 13C-2H, there are no accurate tools for correcting isotope natural abundance for such experiments in a resolution-dependent manner. Here, we present AccuCor2 as an R-based tool to perform the correction for 13C-15N or 13C-2H labeling experiments. Our method uses a newly designed algorithm to construct the correction matrices that link labeling pattern and measured mass fractions, then use non-negative least-squares to solve the labeling patterns. Our results show that the dual-isotope experiments often require a mass resolution that is high enough to resolve 13C and 15N or 13C and 2H. Otherwise, the labeling pattern is not solvable. However, this mass resolution may not be sufficiently high to resolve other non-tracer elements such as oxygen or sulfur from the tracer elements. Therefore, we design AccuCor2 to perform the correction based on the actual mass resolution of the measurements. Using both simulated and experimental data, we show that AccuCor2 performs accurate and resolution-dependent correction for dual-isotope tracer data.
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Affiliation(s)
- Yujue Wang
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Lance R Parsons
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Xiaoyang Su
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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18
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Mycobacterium tuberculosis VapC4 toxin engages small ORFs to initiate an integrated oxidative and copper stress response. Proc Natl Acad Sci U S A 2021; 118:2022136118. [PMID: 34362841 DOI: 10.1073/pnas.2022136118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Mycobacterium tuberculosis (Mtb) VapBC4 toxin-antitoxin system is essential for the establishment of Mtb infection. Using a multitier, systems-level approach, we uncovered the sequential molecular events triggered by the VapC4 toxin that activate a circumscribed set of critical stress survival pathways which undoubtedly underlie Mtb virulence. VapC4 exclusively inactivated the sole transfer RNACys (tRNACys) through cleavage at a single site within the anticodon sequence. Depletion of the pool of tRNACys led to ribosome stalling at Cys codons within actively translating messenger RNAs. Genome mapping of these Cys-stalled ribosomes unexpectedly uncovered several unannotated Cys-containing open reading frames (ORFs). Four of these are small ORFs (sORFs) encoding Cys-rich proteins of fewer than 50 amino acids that function as Cys-responsive attenuators that engage ribosome stalling at tracts of Cys codons to control translation of downstream genes. Thus, VapC4 mimics a state of Cys starvation, which then activates Cys attenuation at sORFs to globally redirect metabolism toward the synthesis of free Cys. The resulting newly enriched pool of Cys feeds into the synthesis of mycothiol, the glutathione counterpart in this pathogen that is responsible for maintaining cellular redox homeostasis during oxidative stress, as well as into a circumscribed subset of cellular pathways that enable cells to defend against oxidative and copper stresses characteristically endured by Mtb within macrophages. Our ability to pinpoint activation or down-regulation of pathways that collectively align with Mtb virulence-associated stress responses and the nonreplicating persistent state brings to light a direct and vital role for the VapC4 toxin in mediating these critical pathways.
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19
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Kim J, Balasubramanian I, Bandyopadhyay S, Nadler I, Singh R, Harlan D, Bumber A, He Y, Kerkhof LJ, Gao N, Su X, Ferraris RP. Lactobacillus rhamnosus GG modifies the metabolome of pathobionts in gnotobiotic mice. BMC Microbiol 2021; 21:165. [PMID: 34082713 PMCID: PMC8176599 DOI: 10.1186/s12866-021-02178-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Background Lactobacillus rhamnosus GG (LGG) is the most widely used probiotic, but the mechanisms underlying its beneficial effects remain unresolved. Previous studies typically inoculated LGG in hosts with established gut microbiota, limiting the understanding of specific impacts of LGG on host due to numerous interactions among LGG, commensal microbes, and the host. There has been a scarcity of studies that used gnotobiotic animals to elucidate LGG-host interaction, in particular for gaining specific insights about how it modifies the metabolome. To evaluate whether LGG affects the metabolite output of pathobionts, we inoculated with LGG gnotobiotic mice containing Propionibacterium acnes, Turicibacter sanguinis, and Staphylococcus aureus (PTS). Results 16S rRNA sequencing of fecal samples by Ion Torrent and MinION platforms showed colonization of germ-free mice by PTS or by PTS plus LGG (LTS). Although the body weights and feeding rates of mice remained similar between PTS and LTS groups, co-associating LGG with PTS led to a pronounced reduction in abundance of P. acnes in the gut. Addition of LGG or its secretome inhibited P. acnes growth in culture. After optimizing procedures for fecal metabolite extraction and metabolomic liquid chromatography-mass spectrometry analysis, unsupervised and supervised multivariate analyses revealed a distinct separation among fecal metabolites of PTS, LTS, and germ-free groups. Variables-important-in-projection scores showed that LGG colonization robustly diminished guanine, ornitihine, and sorbitol while significantly elevating acetylated amino acids, ribitol, indolelactic acid, and histamine. In addition, carnitine, betaine, and glutamate increased while thymidine, quinic acid and biotin were reduced in both PTS and LTS groups. Furthermore, LGG association reduced intestinal mucosal expression levels of inflammatory cytokines, such as IL-1α, IL-1β and TNF-α. Conclusions LGG co-association had a negative impact on colonization of P. acnes, and markedly altered the metabolic output and inflammatory response elicited by pathobionts. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02178-2.
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Affiliation(s)
- Jinhee Kim
- Department of Pharmacology, Physiology and Neurosciences, Medical Science Building, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | | | - Sheila Bandyopadhyay
- Department of Biological Sciences, Life Science Center, Rutgers University, Newark, NJ, 07102, USA
| | - Ian Nadler
- Department of Pharmacology, Physiology and Neurosciences, Medical Science Building, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Rajbir Singh
- Department of Biological Sciences, Life Science Center, Rutgers University, Newark, NJ, 07102, USA
| | - Danielle Harlan
- Department of Pharmacology, Physiology and Neurosciences, Medical Science Building, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Amanda Bumber
- Comparative Medicine Resources, Rutgers University, Newark, NJ, 07103, USA
| | - Yuling He
- Department of Medicine, Clinical Academic Building, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA.,Present address: Geriatric Endocrinology Division, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ, 08901, USA
| | - Nan Gao
- Department of Biological Sciences, Life Science Center, Rutgers University, Newark, NJ, 07102, USA
| | - Xiaoyang Su
- Department of Medicine, Clinical Academic Building, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology and Neurosciences, Medical Science Building, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
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Barton B, Grinnell A, Morgenstein RM. Disruption of the MreB Elongasome Is Overcome by Mutations in the Tricarboxylic Acid Cycle. Front Microbiol 2021; 12:664281. [PMID: 33968001 PMCID: PMC8102728 DOI: 10.3389/fmicb.2021.664281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 01/20/2023] Open
Abstract
The bacterial actin homolog, MreB, is highly conserved among rod-shaped bacteria and essential for growth under normal growth conditions. MreB directs the localization of cell wall synthesis and loss of MreB results in round cells and death. Using the MreB depolymerizing drug, A22, we show that changes to central metabolism through deletion of malate dehydrogenase from the tricarboxylic acid (TCA) cycle results in cells with an increased tolerance to A22. We hypothesize that deletion of malate dehydrogenase leads to the upregulation of gluconeogenesis resulting in an increase in cell wall precursors. Consistent with this idea, metabolite analysis revealed that malate dehydrogenase (mdh) deletion cells possess elevated levels of several glycolysis/gluconeogenesis compounds and the cell wall precursor, uridine diphosphate N-acetylglucosamine (UDP-NAG). In agreement with these results, the increased A22 resistance phenotype can be recapitulated through the addition of glucose to the media. Finally, we show that this increase in antibiotic tolerance is not specific to A22 but also applies to the cell wall-targeting antibiotic, mecillinam.
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Affiliation(s)
- Brody Barton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Addison Grinnell
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Randy M Morgenstein
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
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21
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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22
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Williams A, Chiles EN, Conetta D, Pathmanathan JS, Cleves PA, Putnam HM, Su X, Bhattacharya D. Metabolomic shifts associated with heat stress in coral holobionts. SCIENCE ADVANCES 2021; 7:eabd4210. [PMID: 33523848 PMCID: PMC7775768 DOI: 10.1126/sciadv.abd4210] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/06/2020] [Indexed: 05/26/2023]
Abstract
Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is "coral bleaching," usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric N Chiles
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
| | - Dennis Conetta
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Jananan S Pathmanathan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Phillip A Cleves
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA.
- Division of Endocrinology, Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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