1
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Nobs SP, Kolodziejczyk AA, Adler L, Horesh N, Botscharnikow C, Herzog E, Mohapatra G, Hejndorf S, Hodgetts RJ, Spivak I, Schorr L, Fluhr L, Kviatcovsky D, Zacharia A, Njuki S, Barasch D, Stettner N, Dori-Bachash M, Harmelin A, Brandis A, Mehlman T, Erez A, He Y, Ferrini S, Puschhof J, Shapiro H, Kopf M, Moussaieff A, Abdeen SK, Elinav E. Lung dendritic-cell metabolism underlies susceptibility to viral infection in diabetes. Nature 2023; 624:645-652. [PMID: 38093014 PMCID: PMC10733144 DOI: 10.1038/s41586-023-06803-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/31/2023] [Indexed: 12/22/2023]
Abstract
People with diabetes feature a life-risking susceptibility to respiratory viral infection, including influenza and SARS-CoV-2 (ref. 1), whose mechanism remains unknown. In acquired and genetic mouse models of diabetes, induced with an acute pulmonary viral infection, we demonstrate that hyperglycaemia leads to impaired costimulatory molecule expression, antigen transport and T cell priming in distinct lung dendritic cell (DC) subsets, driving a defective antiviral adaptive immune response, delayed viral clearance and enhanced mortality. Mechanistically, hyperglycaemia induces an altered metabolic DC circuitry characterized by increased glucose-to-acetyl-CoA shunting and downstream histone acetylation, leading to global chromatin alterations. These, in turn, drive impaired expression of key DC effectors including central antigen presentation-related genes. Either glucose-lowering treatment or pharmacological modulation of histone acetylation rescues DC function and antiviral immunity. Collectively, we highlight a hyperglycaemia-driven metabolic-immune axis orchestrating DC dysfunction during pulmonary viral infection and identify metabolic checkpoints that may be therapeutically exploited in mitigating exacerbated disease in infected diabetics.
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Affiliation(s)
- Samuel Philip Nobs
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Aleksandra A Kolodziejczyk
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- International Institute of Molecular and Cellular Biology, Warsaw, Poland
| | - Lital Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Horesh
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantations, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ella Herzog
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Gayatree Mohapatra
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sophia Hejndorf
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan-James Hodgetts
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Spivak
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Lena Schorr
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Leviel Fluhr
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Denise Kviatcovsky
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Anish Zacharia
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suzanne Njuki
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dinorah Barasch
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Mally Dori-Bachash
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Ferrini
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Puschhof
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany
| | - Hagit Shapiro
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Arieh Moussaieff
- The Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany.
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2
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Zheng D, Mohapatra G, Kern L, He Y, Shmueli MD, Valdés-Mas R, Kolodziejczyk AA, Próchnicki T, Vasconcelos MB, Schorr L, Hertel F, Lee YS, Rufino MC, Ceddaha E, Shimshy S, Hodgetts RJ, Dori-Bachash M, Kleimeyer C, Goldenberg K, Heinemann M, Stettner N, Harmelin A, Shapiro H, Puschhof J, Chen M, Flavell RA, Latz E, Merbl Y, Abdeen SK, Elinav E. Epithelial Nlrp10 inflammasome mediates protection against intestinal autoinflammation. Nat Immunol 2023; 24:585-594. [PMID: 36941399 DOI: 10.1038/s41590-023-01450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
Unlike other nucleotide oligomerization domain-like receptors, Nlrp10 lacks a canonical leucine-rich repeat domain, suggesting that it is incapable of signal sensing and inflammasome formation. Here we show that mouse Nlrp10 is expressed in distal colonic intestinal epithelial cells (IECs) and modulated by the intestinal microbiome. In vitro, Nlrp10 forms an Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC)-dependent, m-3M3FBS-activated, polyinosinic:polycytidylic acid-modulated inflammasome driving interleukin-1β and interleukin-18 secretion. In vivo, Nlrp10 signaling is dispensable during steady state but becomes functional during autoinflammation in antagonizing mucosal damage. Importantly, whole-body or conditional IEC Nlrp10 depletion leads to reduced IEC caspase-1 activation, coupled with enhanced susceptibility to dextran sodium sulfate-induced colitis, mediated by altered inflammatory and healing programs. Collectively, understanding Nlrp10 inflammasome-dependent and independent activity, regulation and possible human relevance might facilitate the development of new innate immune anti-inflammatory interventions.
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Affiliation(s)
- Danping Zheng
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gayatree Mohapatra
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Lara Kern
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Merav D Shmueli
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tomasz Próchnicki
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Lena Schorr
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Franziska Hertel
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Ye Seul Lee
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | | | - Emmanuelle Ceddaha
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sandy Shimshy
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan James Hodgetts
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mally Dori-Bachash
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Kleimeyer
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Kim Goldenberg
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Melina Heinemann
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Puschhof
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yifat Merbl
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany.
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3
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Suez J, Cohen Y, Valdés-Mas R, Mor U, Dori-Bachash M, Federici S, Zmora N, Leshem A, Heinemann M, Linevsky R, Zur M, Ben-Zeev Brik R, Bukimer A, Eliyahu-Miller S, Metz A, Fischbein R, Sharov O, Malitsky S, Itkin M, Stettner N, Harmelin A, Shapiro H, Stein-Thoeringer CK, Segal E, Elinav E. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell 2022; 185:3307-3328.e19. [PMID: 35987213 DOI: 10.1016/j.cell.2022.07.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023]
Abstract
Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial encompassing 120 healthy adults, administered saccharin, sucralose, aspartame, and stevia sachets for 2 weeks in doses lower than the acceptable daily intake, compared with controls receiving sachet-contained vehicle glucose or no supplement. As groups, each administered NNS distinctly altered stool and oral microbiome and plasma metabolome, whereas saccharin and sucralose significantly impaired glycemic responses. Importantly, gnotobiotic mice conventionalized with microbiomes from multiple top and bottom responders of each of the four NNS-supplemented groups featured glycemic responses largely reflecting those noted in respective human donors, which were preempted by distinct microbial signals, as exemplified by sucralose. Collectively, human NNS consumption may induce person-specific, microbiome-dependent glycemic alterations, necessitating future assessment of clinical implications.
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Affiliation(s)
- Jotham Suez
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yotam Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rafael Valdés-Mas
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uria Mor
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mally Dori-Bachash
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Federici
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Zmora
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel; Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Avner Leshem
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Melina Heinemann
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raquel Linevsky
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Zur
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Ben-Zeev Brik
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aurelie Bukimer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shimrit Eliyahu-Miller
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alona Metz
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruthy Fischbein
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Olga Sharov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagit Shapiro
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Christoph K Stein-Thoeringer
- Microbiome & Cancer Division, DKFZ, Heidelberg, Germany; National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Microbiome & Cancer Division, DKFZ, Heidelberg, Germany.
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4
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Fluhr L, Mor U, Kolodziejczyk AA, Dori-Bachash M, Leshem A, Itav S, Cohen Y, Suez J, Zmora N, Moresi C, Molina S, Ayalon N, Valdés-Mas R, Hornstein S, Karbi H, Kviatcovsky D, Livne A, Bukimer A, Eliyahu-Miller S, Metz A, Brandis A, Mehlman T, Kuperman Y, Tsoory M, Stettner N, Harmelin A, Shapiro H, Elinav E. Gut microbiota modulates weight gain in mice after discontinued smoke exposure. Nature 2021; 600:713-719. [PMID: 34880502 DOI: 10.1038/s41586-021-04194-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/28/2021] [Indexed: 12/20/2022]
Abstract
Cigarette smoking constitutes a leading global cause of morbidity and preventable death1, and most active smokers report a desire or recent attempt to quit2. Smoking-cessation-induced weight gain (SCWG; 4.5 kg reported to be gained on average per 6-12 months, >10 kg year-1 in 13% of those who stopped smoking3) constitutes a major obstacle to smoking abstinence4, even under stable5,6 or restricted7 caloric intake. Here we use a mouse model to demonstrate that smoking and cessation induce a dysbiotic state that is driven by an intestinal influx of cigarette-smoke-related metabolites. Microbiome depletion induced by treatment with antibiotics prevents SCWG. Conversely, fecal microbiome transplantation from mice previously exposed to cigarette smoke into germ-free mice naive to smoke exposure induces excessive weight gain across diets and mouse strains. Metabolically, microbiome-induced SCWG involves a concerted host and microbiome shunting of dietary choline to dimethylglycine driving increased gut energy harvest, coupled with the depletion of a cross-regulated weight-lowering metabolite, N-acetylglycine, and possibly by the effects of other differentially abundant cigarette-smoke-related metabolites. Dimethylglycine and N-acetylglycine may also modulate weight and associated adipose-tissue immunity under non-smoking conditions. Preliminary observations in a small cross-sectional human cohort support these findings, which calls for larger human trials to establish the relevance of this mechanism in active smokers. Collectively, we uncover a microbiome-dependent orchestration of SCWG that may be exploitable to improve smoking-cessation success and to correct metabolic perturbations even in non-smoking settings.
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Affiliation(s)
- Leviel Fluhr
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Mor
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Avner Leshem
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Shlomik Itav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Cohen
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jotham Suez
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Internal Medicine Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Claudia Moresi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Molina
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Ayalon
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Shanni Hornstein
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Hodaya Karbi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Livne
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Aurelie Bukimer
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alona Metz
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel. .,Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany.
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5
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Grosheva I, Zheng D, Levy M, Polansky O, Lichtenstein A, Golani O, Dori-Bachash M, Moresi C, Shapiro H, Del Mare-Roumani S, Valdes-Mas R, He Y, Karbi H, Chen M, Harmelin A, Straussman R, Yissachar N, Elinav E, Geiger B. High-Throughput Screen Identifies Host and Microbiota Regulators of Intestinal Barrier Function. Gastroenterology 2020; 159:1807-1823. [PMID: 32653496 DOI: 10.1053/j.gastro.2020.07.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS The intestinal barrier protects intestinal cells from microbes and antigens in the lumen-breaches can alter the composition of the intestinal microbiota, the enteric immune system, and metabolism. We performed a screen to identify molecules that disrupt and support the intestinal epithelial barrier and tested their effects in mice. METHODS We performed an imaging-based, quantitative, high-throughput screen (using CaCo-2 and T84 cells incubated with lipopolysaccharide; tumor necrosis factor; histamine; receptor antagonists; and libraries of secreted proteins, microbial metabolites, and drugs) to identify molecules that altered epithelial tight junction (TJ) and focal adhesion morphology. We then tested the effects of TJ stabilizers on these changes. Molecules we found to disrupt or stabilize TJs were administered mice with dextran sodium sulfate-induced colitis or Citrobacter rodentium-induced intestinal inflammation. Colon tissues were collected and analyzed by histology, fluorescence microscopy, and RNA sequencing. RESULTS The screen identified numerous compounds that disrupted or stabilized (after disruption) TJs and monolayers of epithelial cells. We associated distinct morphologic alterations with changes in barrier function, and identified a variety of cytokines, metabolites, and drugs (including inhibitors of actomyosin contractility) that prevent disruption of TJs and restore TJ integrity. One of these disruptors (putrescine) disrupted TJ integrity in ex vivo mouse colon tissues; administration to mice exacerbated colon inflammation, increased gut permeability, reduced colon transepithelial electrical resistance, increased pattern recognition receptor ligands in mesenteric lymph nodes, and decreased colon length and survival times. Putrescine also increased intestine levels and fecal shedding of viable C rodentium, increased bacterial attachment to the colonic epithelium, and increased levels of inflammatory cytokines in colon tissues. Colonic epithelial cells from mice given putrescine increased expression of genes that regulate metal binding, oxidative stress, and cytoskeletal organization and contractility. Co-administration of taurine with putrescine blocked disruption of TJs and the exacerbated inflammation. CONCLUSIONS We identified molecules that disrupt and stabilize intestinal epithelial TJs and barrier function and affect development of colon inflammation in mice. These agents might be developed for treatment of barrier intestinal impairment-associated and inflammatory disorders in patients, or avoided to prevent inflammation.
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Affiliation(s)
- Inna Grosheva
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Danping Zheng
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Maayan Levy
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Omer Polansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | | | - Claudia Moresi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Del Mare-Roumani
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Rafael Valdes-Mas
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hodaya Karbi
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nissan Yissachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Cancer-Microbiome Research Division, DKFZ, Heidelberg, Germany.
| | - Benjamin Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
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6
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Tuganbaev T, Mor U, Bashiardes S, Liwinski T, Nobs SP, Leshem A, Dori-Bachash M, Thaiss CA, Pinker EY, Ratiner K, Adlung L, Federici S, Kleimeyer C, Moresi C, Yamada T, Cohen Y, Zhang X, Massalha H, Massasa E, Kuperman Y, Koni PA, Harmelin A, Gao N, Itzkovitz S, Honda K, Shapiro H, Elinav E. Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. Cell 2020; 182:1441-1459.e21. [DOI: 10.1016/j.cell.2020.08.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/27/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023]
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7
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Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell 2019; 174:1406-1423.e16. [PMID: 30193113 DOI: 10.1016/j.cell.2018.08.047] [Citation(s) in RCA: 623] [Impact Index Per Article: 124.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 06/05/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.
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Affiliation(s)
- Jotham Suez
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Niv Zmora
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel; Internal Medicine Department, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel
| | | | - Uria Mor
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Mally Dori-Bachash
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Stavros Bashiardes
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maya Zur
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dana Regev-Lehavi
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Rotem Ben-Zeev Brik
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sara Federici
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Max Horn
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yotam Cohen
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas E Moor
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Zeevi
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tal Korem
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eran Kotler
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nitsan Maharshak
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Oren Shibolet
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | | | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, 11016 Kiryat Shmona, Israel; Tel Hai College, Upper Galilee, 1220800, Israel
| | - Zamir Halpern
- Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Research Center for Digestive tract and Liver Diseases, Tel Aviv Sourasky Medical Center, 6423906 Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel.
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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8
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Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, Tuganbaev T, Federici S, Zmora N, Zeevi D, Dori-Bachash M, Pevsner-Fischer M, Kartvelishvily E, Brandis A, Harmelin A, Shibolet O, Halpern Z, Honda K, Amit I, Segal E, Elinav E. Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. Cell 2016; 167:1495-1510.e12. [DOI: 10.1016/j.cell.2016.11.003] [Citation(s) in RCA: 470] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 09/27/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
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9
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Thaiss CA, Itav S, Rothschild D, Meijer MT, Levy M, Moresi C, Dohnalová L, Braverman S, Rozin S, Malitsky S, Dori-Bachash M, Kuperman Y, Biton I, Gertler A, Harmelin A, Shapiro H, Halpern Z, Aharoni A, Segal E, Elinav E. Persistent microbiome alterations modulate the rate of post-dieting weight regain. Nature 2016; 540:544-551. [PMID: 27906159 DOI: 10.1038/nature20796] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 11/18/2016] [Indexed: 12/18/2022]
Abstract
In tackling the obesity pandemic, considerable efforts are devoted to the development of effective weight reduction strategies, yet many dieting individuals fail to maintain a long-term weight reduction, and instead undergo excessive weight regain cycles. The mechanisms driving recurrent post-dieting obesity remain largely elusive. Here we identify an intestinal microbiome signature that persists after successful dieting of obese mice and contributes to faster weight regain and metabolic aberrations upon re-exposure to obesity-promoting conditions. Faecal transfer experiments show that the accelerated weight regain phenotype can be transmitted to germ-free mice. We develop a machine-learning algorithm that enables personalized microbiome-based prediction of the extent of post-dieting weight regain. Additionally, we find that the microbiome contributes to diminished post-dieting flavonoid levels and reduced energy expenditure, and demonstrate that flavonoid-based 'post-biotic' intervention ameliorates excessive secondary weight gain. Together, our data highlight a possible microbiome contribution to accelerated post-dieting weight regain, and suggest that microbiome-targeting approaches may help to diagnose and treat this common disorder.
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Affiliation(s)
- Christoph A Thaiss
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shlomik Itav
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Daphna Rothschild
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 76100 Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Mariska T Meijer
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Maayan Levy
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Claudia Moresi
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lenka Dohnalová
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sofia Braverman
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shachar Rozin
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Mally Dori-Bachash
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Inbal Biton
- Department of Veterinary Resources, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Arieh Gertler
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zamir Halpern
- Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.,Digestive Center, Tel Aviv Sourasky Medical Center, 64239 Tel Aviv, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 76100 Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
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10
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Gury-BenAri M, Thaiss CA, Serafini N, Winter DR, Giladi A, Lara-Astiaso D, Levy M, Salame TM, Weiner A, David E, Shapiro H, Dori-Bachash M, Pevsner-Fischer M, Lorenzo-Vivas E, Keren-Shaul H, Paul F, Harmelin A, Eberl G, Itzkovitz S, Tanay A, Di Santo JP, Elinav E, Amit I. The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. Cell 2016; 166:1231-1246.e13. [PMID: 27545347 DOI: 10.1016/j.cell.2016.07.043] [Citation(s) in RCA: 399] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/18/2016] [Accepted: 07/27/2016] [Indexed: 12/22/2022]
Abstract
Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remains elusive. Here, we combine genome-wide RNA-seq, ChIP-seq, and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq and flow and mass cytometry analyses reveal compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes and highlight transcriptional states beyond the current canonical classification. In addition, using antibiotic intervention and germ-free mice, we characterize the effect of the microbiome on the ILC regulatory landscape and determine the response of ILCs to microbial colonization at the single-cell level. Together, our work characterizes the spectrum of transcriptional identities of small intestinal ILCs and describes how ILCs differentially integrate signals from the microbial microenvironment to generate phenotypic and functional plasticity.
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Affiliation(s)
- Meital Gury-BenAri
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nicolas Serafini
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1223 Paris, France
| | - Deborah R Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maayan Levy
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tomer Meir Salame
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hagit Shapiro
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mally Dori-Bachash
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Erika Lorenzo-Vivas
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gérard Eberl
- Institut Pasteur, Microenvironment & Immunity Unit, 75724 Paris, France; INSERM U1224, 75724 Paris, France
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1223 Paris, France
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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11
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Freeman S, Sharon M, Dori-Bachash M, Maymon M, Belausov E, Maoz Y, Margalit O, Protasov A, Mendel Z. Symbiotic association of three fungal species throughout the life cycle of the ambrosia beetle Euwallacea nr. fornicatus. Symbiosis 2015. [DOI: 10.1007/s13199-015-0356-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Karunker I, Rotem O, Dori-Bachash M, Jurkevitch E, Sorek R. A global transcriptional switch between the attack and growth forms of Bdellovibrio bacteriovorus. PLoS One 2013; 8:e61850. [PMID: 23613952 PMCID: PMC3627812 DOI: 10.1371/journal.pone.0061850] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/14/2013] [Indexed: 11/18/2022] Open
Abstract
Bdellovibrio bacteriovorus is an obligate predator of bacteria ubiquitously found in the environment. Its life cycle is composed of two essential phases: a free-living, non-replicative, fast swimming attack phase (AP) wherein the predator searches for prey; and a non-motile, actively dividing growth phase (GP) in which it consumes the prey. The molecular regulatory mechanisms governing the switch between AP and GP are largely unknown. We used RNA-seq to generate a single-base-resolution map of the Bdellovibrio transcriptome in AP and GP, revealing a specific "AP" transcriptional program, which is largely mutually exclusive of the GP program. Based on the expression map, most genes in the Bdellovibrio genome are classified as "AP only" or "GP only". We experimentally generated a genome-wide map of 140 AP promoters, controlling the majority of AP-specific genes. This revealed a common sigma-like DNA binding site highly similar to the E. coli flagellar genes regulator sigma28 (FliA). Further analyses suggest that FliA has evolved to become a global AP regulator in Bdellovibrio. Our results also reveal a non-coding RNA that is massively expressed in AP. This ncRNA contains a c-di-GMP riboswitch. We suggest it functions as an intracellular reservoir for c-di-GMP, playing a role in the rapid switch from AP to GP.
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Affiliation(s)
- Iris Karunker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Or Rotem
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mally Dori-Bachash
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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13
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Dori-Bachash M, Shalem O, Manor YS, Pilpel Y, Tirosh I. Widespread promoter-mediated coordination of transcription and mRNA degradation. Genome Biol 2012; 13:R114. [PMID: 23237624 PMCID: PMC4056365 DOI: 10.1186/gb-2012-13-12-r114] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 12/13/2012] [Indexed: 12/16/2022] Open
Abstract
Background Previous work showed that mRNA degradation is coordinated with transcription in yeast, and in several genes the control of mRNA degradation was linked to promoter elements through two different mechanisms. Here we show at the genomic scale that the coordination of transcription and mRNA degradation is promoter-dependent in yeast and is also observed in humans. Results We first demonstrate that swapping upstream cis-regulatory sequences between two yeast species affects both transcription and mRNA degradation and suggest that while some cis-regulatory elements control either transcription or degradation, multiple other elements enhance both processes. Second, we show that adjacent yeast genes that share a promoter (through divergent orientation) have increased similarity in their patterns of mRNA degradation, providing independent evidence for the promoter-mediated coupling of transcription to mRNA degradation. Finally, analysis of the differences in mRNA degradation rates between mammalian cell types or mammalian species suggests a similar coordination between transcription and mRNA degradation in humans. Conclusions Our results extend previous studies and suggest a pervasive promoter-mediated coordination between transcription and mRNA degradation in yeast. The diverse genes and regulatory elements associated with this coordination suggest that it is generated by a global mechanism of gene regulation and modulated by gene-specific mechanisms. The observation of a similar coupling in mammals raises the possibility that coupling of transcription and mRNA degradation may reflect an evolutionarily conserved phenomenon in gene regulation.
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Abstract
mRNA levels are determined by the balance between transcription and mRNA degradation, and while transcription has been extensively studied, very little is known regarding the regulation of mRNA degradation and its coordination with transcription. Here we examine the evolution of mRNA degradation rates between two closely related yeast species. Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels. Analysis of mRNA degradation rates in an interspecific hybrid further suggests that opposite evolutionary changes in transcription and in mRNA degradation are mechanistically coupled and were generated by the same individual mutations. Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs. These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast.
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Affiliation(s)
- Mally Dori-Bachash
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Efrat Shema
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Itay Tirosh
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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15
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Wurtzel O, Dori-Bachash M, Pietrokovski S, Jurkevitch E, Sorek R. Mutation detection with next-generation resequencing through a mediator genome. PLoS One 2010; 5:e15628. [PMID: 21209874 PMCID: PMC3013116 DOI: 10.1371/journal.pone.0015628] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 11/17/2010] [Indexed: 11/18/2022] Open
Abstract
The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes.
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Affiliation(s)
- Omri Wurtzel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Mally Dori-Bachash
- Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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16
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Dori-Bachash M, Dassa B, Peleg O, Pineiro SA, Jurkevitch E, Pietrokovski S. Bacterial intein-like domains of predatory bacteria: a new domain type characterized in Bdellovibrio bacteriovorus. Funct Integr Genomics 2009; 9:153-66. [PMID: 19153786 DOI: 10.1007/s10142-008-0106-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2008] [Revised: 12/08/2008] [Accepted: 12/20/2008] [Indexed: 10/21/2022]
Abstract
We report a new family of bacterial intein-like domains (BILs) identified in ten proteins of four diverse predatory bacteria. BILs belong to the HINT (Hedgehog/Intein) superfamily of domains that post-translationally self-process their protein molecules by protein splicing and self-cleavage. The new, C-type, BILs appear with other domains, including putative predator-specific domain 1 (PPS-1), a new domain typically appearing immediately upstream of C-type BILs. The Bd2400 protein of the obligate predator Bdellovibrio bacteriovorus includes a C-type BIL and a PPS-1 domains at its C-terminal part, and a signal peptide and two polycystic kidney disease domains at its N-terminal part. We demonstrate the in vivo transcription, translation, secretion, and processing of the B. bacteriovorus protein, and the in vitro autocatalytic N-terminal cleavage activity of its C-type BIL. Interestingly, whereas the Bd2400 gene is constitutively expressed, its protein product is differentially processed throughout the dimorphic life cycle of the B. bacteriovorus predator. The modular structure of the protein, its localization, and complex processing suggest that it may be involved in the interaction between the predator and its prey.
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Affiliation(s)
- Mally Dori-Bachash
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel
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Dori-Bachash M, Dassa B, Pietrokovski S, Jurkevitch E. Proteome-based comparative analyses of growth stages reveal new cell cycle-dependent functions in the predatory bacterium Bdellovibrio bacteriovorus. Appl Environ Microbiol 2008; 74:7152-62. [PMID: 18836011 PMCID: PMC2592910 DOI: 10.1128/aem.01736-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 09/25/2008] [Indexed: 11/20/2022] Open
Abstract
Bdellovibrio and like organisms are obligate predators of bacteria that are ubiquitously found in the environment. Most exhibit a peculiar dimorphic life cycle during which free-swimming attack-phase (AP) cells search for and invade bacterial prey cells. The invader develops in the prey as a filamentous polynucleoid-containing cell that finally splits into progeny cells. Therapeutic and biocontrol applications of Bdellovibrio in human and animal health and plant health, respectively, have been proposed, but more knowledge of this peculiar cell cycle is needed to develop such applications. A proteomic approach was applied to study cell cycle-dependent expression of the Bdellovibrio bacteriovorus proteome in synchronous cultures of a facultative host-independent (HI) strain able to grow in the absence of prey. Results from two-dimensional gel electrophoresis, mass spectrometry, and temporal expression of selected genes in predicted operons were analyzed. In total, about 21% of the in silico predicted proteome was covered. One hundred ninety-six proteins were identified, including 63 hitherto unknown proteins and 140 life stage-dependent spots. Of those, 47 were differentially expressed, including chemotaxis, attachment, growth- and replication-related, cell wall, and regulatory proteins. Novel cell cycle-dependent adhesion, gliding, mechanosensing, signaling, and hydrolytic functions were assigned. The HI model was further studied by comparing HI and wild-type AP cells, revealing that proteins involved in DNA replication and signaling were deregulated in the former. A complementary analysis of the secreted proteome identified 59 polypeptides, including cell contact proteins and hydrolytic enzymes specific to predatory bacteria.
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Affiliation(s)
- Mally Dori-Bachash
- Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Tuvia S, Taglicht D, Erez O, Alroy I, Alchanati I, Bicoviski V, Dori-Bachash M, Ben-Avraham D, Reiss Y. The ubiquitin E3 ligase POSH regulates calcium homeostasis through spatial control of Herp. ACTA ACUST UNITED AC 2007; 177:51-61. [PMID: 17420289 PMCID: PMC2064109 DOI: 10.1083/jcb.200611036] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ubiquitin (Ub) domain protein Herp plays a crucial role in the maintenance of calcium homeostasis during endoplasmic reticulum (ER) stress. We now show that Herp is a substrate as well as an activator of the E3 Ub ligase POSH. Herp-mediated POSH activation requires the Ubl domain and exclusively promotes lysine-63-linked polyubiquitination. Confocal microscopy demonstrates that Herp resides mostly in the trans-Golgi network, but, shortly after calcium perturbation by thapsigargin (Tpg), it appears mainly in the ER. Substitution of all lysine residues within the Ubl domain abolishes lysine-63-linked polyubiquitination of Herp in vitro and calcium-induced Herp relocalization that is also abrogated by the overexpression of a dominant-negative POSHV14A. A correlation exists between the kinetics of Tpg-induced Herp relocalization and POSH-dependent polyubiquitination. Finally, the overexpression of POSH attenuates, whereas the inhibition of POSH by the expression of POSHV14A or by RNA interference enhances Tpg-induced calcium burst. Altogether, these results establish a critical role for POSH-mediated ubiquitination in the maintenance of calcium homeostasis through the spatial control of Herp.
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Affiliation(s)
- Shmuel Tuvia
- Proteologics Ltd., Kiryat Weizmann, Rehovot 76124, Israel
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