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De Vos WM, Nguyen Trung M, Davids M, Liu G, Rios-Morales M, Jessen H, Fiedler D, Nieuwdorp M, Bui TPN. Phytate metabolism is mediated by microbial cross-feeding in the gut microbiota. Nat Microbiol 2024; 9:1812-1827. [PMID: 38858593 DOI: 10.1038/s41564-024-01698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/04/2024] [Indexed: 06/12/2024]
Abstract
Dietary intake of phytate has various reported health benefits. Previous work showed that the gut microbiota can convert phytate to short-chain fatty acids (SCFAs), but the microbial species and metabolic pathway are unclear. Here we identified Mitsuokella jalaludinii as an efficient phytate degrader, which works synergistically with Anaerostipes rhamnosivorans to produce the SCFA propionate. Analysis of published human gut taxonomic profiles revealed that Mitsuokella spp., in particular M. jalaludinii, are prevalent in human gut microbiomes. NMR spectroscopy using 13C-isotope labelling, metabolomic and transcriptomic analyses identified a complete phytate degradation pathway in M. jalaludinii, including production of the intermediate Ins(2)P/myo-inositol. The major end product, 3-hydroxypropionate, was converted into propionate via a synergistic interaction with Anaerostipes rhamnosivorans both in vitro and in mice. Upon [13C6]phytate administration, various 13C-labelled components were detected in mouse caecum in contrast with the absence of [13C6] InsPs or [13C6]myo-inositol in plasma. Caco-2 cells incubated with co-culture supernatants exhibited improved intestinal barrier integrity. These results suggest that the microbiome plays a major role in the metabolism of this phytochemical and that its fermentation to propionate by M. jalaludinii and A. rhamnosivorans may contribute to phytate-driven health benefits.
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Affiliation(s)
- Willem M De Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institute of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mark Davids
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
| | - Guizhen Liu
- Institute of Organic Chemistry & Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Melany Rios-Morales
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
| | - Henning Jessen
- Institute of Organic Chemistry & Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institute of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Center, Location AMC, Amsterdam, the Netherlands.
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2
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Ghasemi MR, Tehrani Fateh S, Moeinafshar A, Sadeghi H, Karimzadeh P, Mirfakhraie R, Rezaei M, Hashemi-Gorji F, Rezvani Kashani M, Fazeli Bavandpour F, Bagheri S, Moghimi P, Rostami M, Madannejad R, Roudgari H, Miryounesi M. Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review. BMC Med Genomics 2024; 17:51. [PMID: 38347586 PMCID: PMC10863249 DOI: 10.1186/s12920-024-01810-0] [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: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features of these disorders. The aim of this study is to provide an in-depth review of PCH and to identify disease genes and their inheritance patterns in 12 distinct Iranian families with clinically confirmed PCH. METHODS Cases included in this study were selected based on their phenotypic and genetic information available at the Center for Comprehensive Genetic Services. Whole-exome sequencing (WES) was used to discover the underlying genetic etiology of participants' problems, and Sanger sequencing was utilized to confirm any suspected alterations. We also conducted a comprehensive molecular literature review to outline the genetic features of the various subtypes of PCH. RESULTS This study classified and described the underlying etiology of PCH into three categories based on the genes involved. Twelve patients also were included, eleven of whom were from consanguineous parents. Ten different variations in 8 genes were found, all of which related to different types of PCH. Six novel variations were reported, including SEPSECS, TSEN2, TSEN54, AMPD2, TOE1, and CLP1. Almost all patients presented with developmental delay, hypotonia, seizure, and microcephaly being common features. Strabismus and elevation in lactate levels in MR spectroscopy were novel phenotypes for the first time in PCH types 7 and 9. CONCLUSIONS This study merges previously documented phenotypes and genotypes with unique novel ones. Due to the diversity in PCH, we provided guidance for detecting and diagnosing these heterogeneous groups of disorders. Moreover, since certain critical conditions, such as spinal muscular atrophy, can be a differential diagnosis, providing cases with novel variations and clinical findings could further expand the genetic and clinical spectrum of these diseases and help in better diagnosis. Therefore, six novel genetic variants and novel clinical and paraclinical findings have been reported for the first time. Further studies are needed to elucidate the underlying mechanisms and potential therapeutic targets for PCH.
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Affiliation(s)
- Mohammad-Reza Ghasemi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Aysan Moeinafshar
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Mitra Rezaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morteza Rezvani Kashani
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Saman Bagheri
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Masoumeh Rostami
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Madannejad
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Roudgari
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran.
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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Chabert V, Kim GD, Qiu D, Liu G, Michaillat Mayer L, Jamsheer K M, Jessen HJ, Mayer A. Inositol pyrophosphate dynamics reveals control of the yeast phosphate starvation program through 1,5-IP 8 and the SPX domain of Pho81. eLife 2023; 12:RP87956. [PMID: 37728314 PMCID: PMC10511240 DOI: 10.7554/elife.87956] [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: 09/21/2023] Open
Abstract
Eukaryotic cells control inorganic phosphate to balance its role as essential macronutrient with its negative bioenergetic impact on reactions liberating phosphate. Phosphate homeostasis depends on the conserved INPHORS signaling pathway that utilizes inositol pyrophosphates and SPX receptor domains. Since cells synthesize various inositol pyrophosphates and SPX domains bind them promiscuously, it is unclear whether a specific inositol pyrophosphate regulates SPX domains in vivo, or whether multiple inositol pyrophosphates act as a pool. In contrast to previous models, which postulated that phosphate starvation is signaled by increased production of the inositol pyrophosphate 1-IP7, we now show that the levels of all detectable inositol pyrophosphates of yeast, 1-IP7, 5-IP7, and 1,5-IP8, strongly decline upon phosphate starvation. Among these, specifically the decline of 1,5-IP8 triggers the transcriptional phosphate starvation response, the PHO pathway. 1,5-IP8 inactivates the cyclin-dependent kinase inhibitor Pho81 through its SPX domain. This stimulates the cyclin-dependent kinase Pho85-Pho80 to phosphorylate the transcription factor Pho4 and repress the PHO pathway. Combining our results with observations from other systems, we propose a unified model where 1,5-IP8 signals cytosolic phosphate abundance to SPX proteins in fungi, plants, and mammals. Its absence triggers starvation responses.
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Affiliation(s)
- Valentin Chabert
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Geun-Don Kim
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Danye Qiu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Guizhen Liu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | | | | | - Henning J Jessen
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Andreas Mayer
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
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Ritter K, Jork N, Unmüßig AS, Köhn M, Jessen HJ. Assigning the Absolute Configuration of Inositol Poly- and Pyrophosphates by NMR Using a Single Chiral Solvating Agent. Biomolecules 2023; 13:1150. [PMID: 37509185 PMCID: PMC10377360 DOI: 10.3390/biom13071150] [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: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Inositol phosphates constitute a family of highly charged messenger molecules that play diverse roles in cellular processes. The various phosphorylation patterns they exhibit give rise to a vast array of different compounds. To fully comprehend the biological interconnections, the precise molecular identification of each compound is crucial. Since the myo-inositol scaffold possesses an internal mirror plane, enantiomeric pairs can be formed. Most commonly employed methods for analyzing InsPs have been geared towards resolving regioisomers, but they have not been capable of resolving enantiomers. In this study, we present a general approach for enantiomer assignment using NMR measurements. To achieve this goal, we used 31P-NMR in the presence of L-arginine amide as a chiral solvating agent, which enables the differentiation of enantiomers. Using chemically synthesized standard compounds allows for an unambiguous assignment of the enantiomers. This method was applied to highly phosphorylated inositol pyrophosphates, as well as to lowly phosphorylated inositol phosphates and bisphosphonate analogs. Our method will facilitate the assignment of biologically relevant isomers when isolating naturally occurring compounds from biological specimens.
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Affiliation(s)
- Kevin Ritter
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Anne-Sophie Unmüßig
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Maja Köhn
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Institute of Biology 3, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS-Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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Yu J, Leibiger B, Yang SN, Shears SB, Leibiger IB, Berggren PO, Barker CJ. Multiple Inositol Polyphosphate Phosphatase Compartmentalization Separates Inositol Phosphate Metabolism from Inositol Lipid Signaling. Biomolecules 2023; 13:885. [PMID: 37371464 DOI: 10.3390/biom13060885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Multiple inositol polyphosphate phosphatase (MINPP1) is an enigmatic enzyme that is responsible for the metabolism of inositol hexakisphosphate (InsP6) and inositol 1,3,4,5,6 pentakisphosphate (Ins(1,3,4,5,6)P5 in mammalian cells, despite being restricted to the confines of the ER. The reason for this compartmentalization is unclear. In our previous studies in the insulin-secreting HIT cell line, we expressed MINPP1 in the cytosol to artificially reduce the concentration of these higher inositol phosphates. Undocumented at the time, we noted cytosolic MINPP1 expression reduced cell growth. We were struck by the similarities in substrate preference between a number of different enzymes that are able to metabolize both inositol phosphates and lipids, notably IPMK and PTEN. MINPP1 was first characterized as a phosphatase that could remove the 3-phosphate from inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4). This molecule shares strong structural homology with the major product of the growth-promoting Phosphatidyl 3-kinase (PI3K), phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and PTEN can degrade both this lipid and Ins(1,3,4,5)P4. Because of this similar substrate preference, we postulated that the cytosolic version of MINPP1 (cyt-MINPP1) may not only attack inositol polyphosphates but also PtdIns(3,4,5)P3, a key signal in mitogenesis. Our experiments show that expression of cyt-MINPP1 in HIT cells lowers the concentration of PtdIns(3,4,5)P3. We conclude this reflects a direct effect of MINPP1 upon the lipid because cyt-MINPP1 actively dephosphorylates synthetic, di(C4:0)PtdIns(3,4,5)P3 in vitro. These data illustrate the importance of MINPP1's confinement to the ER whereby important aspects of inositol phosphate metabolism and inositol lipid signaling can be separately regulated and give one important clarification for MINPP1's ER seclusion.
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Affiliation(s)
- Jia Yu
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Barbara Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Shao-Nian Yang
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Stephen B Shears
- Inositol Signaling Section, NIEHS, 111, Alexander Drive, Research Triangle Park, Durham, NC 27709, USA
| | - Ingo B Leibiger
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Christopher J Barker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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Dürr EM, Köhn M. Exploring Uncharted Territory: Toward Metabolite Network Maps. ACS CENTRAL SCIENCE 2022; 8:1576-1578. [PMID: 36589883 PMCID: PMC9801499 DOI: 10.1021/acscentsci.2c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Eva-Maria Dürr
- Signalling Research
Centres BIOSS and CIBSS, University of Freiburg, Freiburg 79104, Germany
- Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Maja Köhn
- Signalling Research
Centres BIOSS and CIBSS, University of Freiburg, Freiburg 79104, Germany
- Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
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