1
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Sharma K, Zhang G, Hansen J, Bjornstad P, Lee HJ, Menon R, Hejazi L, Liu JJ, Franzone A, Looker HC, Choi BY, Fernandez R, Venkatachalam MA, Kugathasan L, Sridhar VS, Natarajan L, Zhang J, Sharma VS, Kwan B, Waikar SS, Himmelfarb J, Tuttle KR, Kestenbaum B, Fuhrer T, Feldman HI, de Boer IH, Tucci FC, Sedor J, Heerspink HL, Schaub J, Otto EA, Hodgin JB, Kretzler M, Anderton CR, Alexandrov T, Cherney D, Lim SC, Nelson RG, Gelfond J, Iyengar R. Endogenous adenine mediates kidney injury in diabetic models and predicts diabetic kidney disease in patients. J Clin Invest 2023; 133:e170341. [PMID: 37616058 PMCID: PMC10575723 DOI: 10.1172/jci170341] [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: 03/09/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Diabetic kidney disease (DKD) can lead to end-stage kidney disease (ESKD) and mortality; however, few mechanistic biomarkers are available for high-risk patients, especially those without macroalbuminuria. Urine from participants with diabetes from the Chronic Renal Insufficiency Cohort (CRIC) study, the Singapore Study of Macro-angiopathy and Micro-vascular Reactivity in Type 2 Diabetes (SMART2D), and the American Indian Study determined whether urine adenine/creatinine ratio (UAdCR) could be a mechanistic biomarker for ESKD. ESKD and mortality were associated with the highest UAdCR tertile in the CRIC study and SMART2D. ESKD was associated with the highest UAdCR tertile in patients without macroalbuminuria in the CRIC study, SMART2D, and the American Indian study. Empagliflozin lowered UAdCR in nonmacroalbuminuric participants. Spatial metabolomics localized adenine to kidney pathology, and single-cell transcriptomics identified ribonucleoprotein biogenesis as a top pathway in proximal tubules of patients without macroalbuminuria, implicating mTOR. Adenine stimulated matrix in tubular cells via mTOR and stimulated mTOR in mouse kidneys. A specific inhibitor of adenine production was found to reduce kidney hypertrophy and kidney injury in diabetic mice. We propose that endogenous adenine may be a causative factor in DKD.
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Affiliation(s)
- Kumar Sharma
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Guanshi Zhang
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Jens Hansen
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Petter Bjornstad
- Division of Nephrology, Department of Medicine and Section of Endocrinology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hak Joo Lee
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Rajasree Menon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Leila Hejazi
- Center for Precision Medicine and
- SygnaMap Inc., San Antonio, Texas, USA
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | | | - Helen C. Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Byeong Yeob Choi
- Center for Precision Medicine and
- Department of Population Health Sciences and
| | | | - Manjeri A. Venkatachalam
- Center for Precision Medicine and
- Department of Pathology, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Luxcia Kugathasan
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Vikas S. Sridhar
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Loki Natarajan
- Herbert Wertheim School of Public Health and
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Varun S. Sharma
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Brian Kwan
- Department of Health Science, California State University, Long Beach, Long Beach, California, USA
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University, Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jonathan Himmelfarb
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Katherine R. Tuttle
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Bryan Kestenbaum
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Harold I. Feldman
- Center for Clinical Epidemiology and Biostatistics and Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
- Patient-Centered Outcomes Research Institute, Washington, DC, USA
| | - Ian H. de Boer
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Hiddo Lambers Heerspink
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, Netherlands
- The George Institute for Global Health, Sydney, Australia
| | - Jennifer Schaub
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Edgar A. Otto
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey B. Hodgin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher R. Anderton
- Center for Precision Medicine and
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Cherney
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
- Diabetes Center, Admiralty Medical Center, Khoo Teck Puat Hospital, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Jonathan Gelfond
- Center for Precision Medicine and
- Department of Population Health Sciences and
| | - Ravi Iyengar
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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2
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Grucela PK, Fuhrer T, Sauer U, Chao Y, Zhang YE. Ribose 5-phosphate: the key metabolite bridging the metabolisms of nucleotides and amino acids during stringent response in Escherichia coli? Microb Cell 2023; 10:141-144. [PMID: 37395996 PMCID: PMC10311079 DOI: 10.15698/mic2023.07.799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023]
Abstract
The bacterial stringent response and its effector alarmone guanosine penta- or tetra - phosphates (p)ppGpp are vital for bacterial tolerance and survival of various stresses in environments (including antibiotics) and host cells (virulence). (p)ppGpp does so by binding to its numerous target proteins and reprograming bacterial transcriptome to tune down the synthesis of nucleotides and rRNA/tRNA, and up-regulate amino acid biosynthesis genes. Recent identification of more novel (p)ppGpp direct binding proteins in Escherichia coli and their deep studies have unveiled unprecedented details of how (p)ppGpp coordinates the nucleotide and amino acid metabolic pathways upon stringent response; however, the mechanistic link between nucleotide and amino acid metabolisms remains still incompletely understood. Here we propose the metabolite ribose 5'-phosphate as the key link between nucleotide and amino acid metabolisms and a working model integrating both the transcriptional and metabolic effects of (p)ppGpp on E. coli physiological adaptation during the stringent response.
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Affiliation(s)
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Everett Zhang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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3
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Sharma K, Zhang G, Hansen J, Bjornstad P, Lee HJ, Menon R, Hejazi L, Liu JJ, Franzone A, Looker HC, Choi BY, Fernandez R, Venkatachalam MA, Kugathasan L, Sridhar VS, Natarajan L, Zhang J, Sharma V, Kwan B, Waikar S, Himmelfarb J, Tuttle K, Kestenbaum B, Fuhrer T, Feldman H, de Boer IH, Tucci FC, Sedor J, Heerspink HL, Schaub J, Otto E, Hodgin JB, Kretzler M, Anderton C, Alexandrov T, Cherney D, Lim SC, Nelson RG, Gelfond J, Iyengar R. Role of endogenous adenine in kidney failure and mortality with diabetes. medRxiv 2023:2023.05.31.23290681. [PMID: 37398187 PMCID: PMC10312877 DOI: 10.1101/2023.05.31.23290681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Diabetic kidney disease (DKD) can lead to end-stage kidney disease (ESKD) and mortality, however, few mechanistic biomarkers are available for high risk patients, especially those without macroalbuminuria. Urine from participants with diabetes from Chronic Renal Insufficiency Cohort (CRIC), Singapore Study of Macro-Angiopathy and Reactivity in Type 2 Diabetes (SMART2D), and the Pima Indian Study determined if urine adenine/creatinine ratio (UAdCR) could be a mechanistic biomarker for ESKD. ESKD and mortality were associated with the highest UAdCR tertile in CRIC (HR 1.57, 1.18, 2.10) and SMART2D (HR 1.77, 1.00, 3.12). ESKD was associated with the highest UAdCR tertile in patients without macroalbuminuria in CRIC (HR 2.36, 1.26, 4.39), SMART2D (HR 2.39, 1.08, 5.29), and Pima Indian study (HR 4.57, CI 1.37-13.34). Empagliflozin lowered UAdCR in non-macroalbuminuric participants. Spatial metabolomics localized adenine to kidney pathology and transcriptomics identified ribonucleoprotein biogenesis as a top pathway in proximal tubules of patients without macroalbuminuria, implicating mammalian target of rapamycin (mTOR). Adenine stimulated matrix in tubular cells via mTOR and stimulated mTOR in mouse kidneys. A specific inhibitor of adenine production was found to reduce kidney hypertrophy and kidney injury in diabetic mice. We propose that endogenous adenine may be a causative factor in DKD.
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4
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Meier KHU, Trouillon J, Li H, Lang M, Fuhrer T, Zamboni N, Sunagawa S, Macpherson AJ, Sauer U. Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities. Nat Metab 2023:10.1038/s42255-023-00802-1. [PMID: 37217759 DOI: 10.1038/s42255-023-00802-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/06/2023] [Indexed: 05/24/2023]
Abstract
Distinct niches of the mammalian gut are populated by diverse microbiota, but the contribution of spatial variation to intestinal metabolism remains unclear. Here we present a map of the longitudinal metabolome along the gut of healthy colonized and germ-free male mice. With this map, we reveal a general shift from amino acids in the small intestine to organic acids, vitamins and nucleotides in the large intestine. We compare the metabolic landscapes in colonized versus germ-free mice to disentangle the origin of many metabolites in different niches, which in some cases allows us to infer the underlying processes or identify the producing species. Beyond the known impact of diet on the small intestinal metabolic niche, distinct spatial patterns suggest specific microbial influence on the metabolome in the small intestine. Thus, we present a map of intestinal metabolism and identify metabolite-microbe associations, which provide a basis to connect the spatial occurrence of bioactive compounds to host or microorganism metabolism.
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Affiliation(s)
- Karin H U Meier
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Hai Li
- Department for Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Melanie Lang
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | | | - Andrew J Macpherson
- Department for Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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5
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Duan J, Matute JD, Unger LW, Hanley T, Schnell A, Lin X, Krupka N, Griebel P, Lambden C, Sit B, Grootjans J, Pyzik M, Sommer F, Kaiser S, Falk-Paulsen M, Grasberger H, Kao JY, Fuhrer T, Li H, Paik D, Lee Y, Refetoff S, Glickman JN, Paton AW, Bry L, Paton JC, Sauer U, Macpherson AJ, Rosenstiel P, Kuchroo VK, Waldor MK, Huh JR, Kaser A, Blumberg RS. Endoplasmic reticulum stress in the intestinal epithelium initiates purine metabolite synthesis and promotes Th17 cell differentiation in the gut. Immunity 2023; 56:1115-1131.e9. [PMID: 36917985 PMCID: PMC10175221 DOI: 10.1016/j.immuni.2023.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 09/14/2022] [Revised: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
Intestinal IL-17-producing T helper (Th17) cells are dependent on adherent microbes in the gut for their development. However, how microbial adherence to intestinal epithelial cells (IECs) promotes Th17 cell differentiation remains enigmatic. Here, we found that Th17 cell-inducing gut bacteria generated an unfolded protein response (UPR) in IECs. Furthermore, subtilase cytotoxin expression or genetic removal of X-box binding protein 1 (Xbp1) in IECs caused a UPR and increased Th17 cells, even in antibiotic-treated or germ-free conditions. Mechanistically, UPR activation in IECs enhanced their production of both reactive oxygen species (ROS) and purine metabolites. Treating mice with N-acetyl-cysteine or allopurinol to reduce ROS production and xanthine, respectively, decreased Th17 cells that were associated with an elevated UPR. Th17-related genes also correlated with ER stress and the UPR in humans with inflammatory bowel disease. Overall, we identify a mechanism of intestinal Th17 cell differentiation that emerges from an IEC-associated UPR.
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Affiliation(s)
- Jinzhi Duan
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Juan D Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lukas W Unger
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, and Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK; Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, 10090, Austria
| | - Thomas Hanley
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Xi Lin
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Niklas Krupka
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul Griebel
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Conner Lambden
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Brandon Sit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joep Grootjans
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Location AMC, 1105 AZ Amsterdam, The Netherlands
| | - Michal Pyzik
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Felix Sommer
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Sina Kaiser
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Helmut Grasberger
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John Y Kao
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Hai Li
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Donggi Paik
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yunjin Lee
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel Refetoff
- Department of Medicine, Pediatrics and Committee on Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jonathan N Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, the University of Adelaide, Adelaide, 5005, Australia
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, the University of Adelaide, Adelaide, 5005, Australia
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Andrew J Macpherson
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, and Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Richard S Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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6
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Kwan B, Fuhrer T, Montemayor D, Fink JC, He J, Hsu CY, Messer K, Nelson RG, Pu M, Ricardo AC, Rincon-Choles H, Shah VO, Ye H, Zhang J, Sharma K, Natarajan L. A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study. BMC Bioinformatics 2023; 24:57. [PMID: 36803209 PMCID: PMC9942303 DOI: 10.1186/s12859-023-05171-w] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and disease classification. Yet, many of these methods do not yield biologically interpretable models, despite offering high classification accuracy. An exception, the top-scoring pair (TSP) algorithm derives parameter-free, biologically interpretable single pair decision rules that are accurate and robust in disease classification. However, standard TSP methods do not accommodate covariates that could heavily influence feature selection for the top-scoring pair. Herein, we propose a covariate-adjusted TSP method, which uses residuals from a regression of features on the covariates for identifying top scoring pairs. We conduct simulations and a data application to investigate our method, and compare it to existing classifiers, LASSO and random forests. RESULTS Our simulations found that features that were highly correlated with clinical variables had high likelihood of being selected as top scoring pairs in the standard TSP setting. However, through residualization, our covariate-adjusted TSP was able to identify new top scoring pairs, that were largely uncorrelated with clinical variables. In the data application, using patients with diabetes (n = 977) selected for metabolomic profiling in the Chronic Renal Insufficiency Cohort (CRIC) study, the standard TSP algorithm identified (valine-betaine, dimethyl-arg) as the top-scoring metabolite pair for classifying diabetic kidney disease (DKD) severity, whereas the covariate-adjusted TSP method identified the pair (pipazethate, octaethylene glycol) as top-scoring. Valine-betaine and dimethyl-arg had, respectively, ≥ 0.4 absolute correlation with urine albumin and serum creatinine, known prognosticators of DKD. Thus without covariate-adjustment the top-scoring pair largely reflected known markers of disease severity, whereas covariate-adjusted TSP uncovered features liberated from confounding, and identified independent prognostic markers of DKD severity. Furthermore, TSP-based methods achieved competitive classification accuracy in DKD to LASSO and random forests, while providing more parsimonious models. CONCLUSIONS We extended TSP-based methods to account for covariates, via a simple, easy to implement residualizing process. Our covariate-adjusted TSP method identified metabolite features, uncorrelated from clinical covariates, that discriminate DKD severity stage based on the relative ordering between two features, and thus provide insights into future studies on the order reversals in early vs advanced disease states.
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Grants
- R01 DK110541 NIDDK NIH HHS
- U24 DK060990 NIDDK NIH HHS
- R01DK118736, 1R01DK110541-01A1, U01DK060990, U01DK060984, U01DK061022, U01DK061021, U01DK061028, U01DK060980, U01DK060963, U01DK060902, U24DK060990 NIDDK NIH HHS
- National Science Foundation Graduate Research Fellowship Program
- Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases
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Affiliation(s)
- Brian Kwan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Montemayor
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jeffery C Fink
- Department of Medicine, University of Maryland, Baltimore School of Medicine, Baltimore, MD, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine and Tulane University Translational Science Institute,, New Orleans, LA, USA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Karen Messer
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Minya Pu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Ana C Ricardo
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Hernan Rincon-Choles
- Department of Nephrology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Vallabh O Shah
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Hongping Ye
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Kumar Sharma
- Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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7
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Yilmaz B, Fuhrer T, Morgenthaler D, Krupka N, Wang D, Spari D, Candinas D, Misselwitz B, Beldi G, Sauer U, Macpherson AJ. Plasticity of the adult human small intestinal stoma microbiota. Cell Host Microbe 2022; 30:1773-1787.e6. [PMID: 36318918 DOI: 10.1016/j.chom.2022.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/20/2022] [Revised: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
The human distal small intestine (ileum) has a distinct microbiota, but human studies investigating its composition and function have been limited by the inaccessibility of the ileum without purging and/or deep intubation. We investigated inherent instability, temporal dynamics, and the contribution of fed and fasted states using stoma samples from cured colorectal cancer patients as a non-invasive access route to the otherwise inaccessible small and large intestines. Sequential sampling of the ileum before and after stoma formation indicated that ileostoma microbiotas represented that of the intact small intestine. Ileal and colonic stoma microbiotas were confirmed as distinct, and two types of instability in ileal host-microbial relationships were observed: inter-digestive purging followed by the rapid postprandial blooming of bacterial biomass and sub-strain appearance and disappearance within individual taxa after feeding. In contrast to the relative stability of colonic microbiota, the human small intestinal microbiota biomass and its sub-strain composition can be highly dynamic.
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Affiliation(s)
- Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Deborah Morgenthaler
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Niklas Krupka
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Daniel Spari
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Benjamin Misselwitz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Guido Beldi
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Andrew J Macpherson
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
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8
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Zhang J, Fuhrer T, Ye H, Kwan B, Montemayor D, Tumova J, Darshi M, Afshinnia F, Scialla JJ, Anderson A, Porter AC, Taliercio JJ, Rincon-Choles H, Rao P, Xie D, Feldman H, Sauer U, Sharma K, Natarajan L. High-Throughput Metabolomics and Diabetic Kidney Disease Progression: Evidence from the Chronic Renal Insufficiency (CRIC) Study. Am J Nephrol 2022; 53:215-225. [PMID: 35196658 PMCID: PMC9116599 DOI: 10.1159/000521940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/30/2021] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Metabolomics could offer novel prognostic biomarkers and elucidate mechanisms of diabetic kidney disease (DKD) progression. Via metabolomic analysis of urine samples from 995 CRIC participants with diabetes and state-of-the-art statistical modeling, we aimed to identify metabolites prognostic to DKD progression. METHODS Urine samples (N = 995) were assayed for relative metabolite abundance by untargeted flow-injection mass spectrometry, and stringent statistical criteria were used to eliminate noisy compounds, resulting in 698 annotated metabolite ions. Utilizing the 698 metabolites' ion abundance along with clinical data (demographics, blood pressure, HbA1c, eGFR, and albuminuria), we developed univariate and multivariate models for the eGFR slope using penalized (lasso) and random forest models. Final models were tested on time-to-ESKD (end-stage kidney disease) via cross-validated C-statistics. We also conducted pathway enrichment analysis and a targeted analysis of a subset of metabolites. RESULTS Six eGFR slope models selected 9-30 variables. In the adjusted ESKD model with highest C-statistic, valine (or betaine) and 3-(4-methyl-3-pentenyl)thiophene were associated (p < 0.05) with 44% and 65% higher hazard of ESKD per doubling of metabolite abundance, respectively. Also, 13 (of 15) prognostic amino acids, including valine and betaine, were confirmed in the targeted analysis. Enrichment analysis revealed pathways implicated in kidney and cardiometabolic disease. CONCLUSIONS Using the diverse CRIC sample, a high-throughput untargeted assay, followed by targeted analysis, and rigorous statistical analysis to reduce false discovery, we identified several novel metabolites implicated in DKD progression. If replicated in independent cohorts, our findings could inform risk stratification and treatment strategies for patients with DKD.
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Affiliation(s)
- Jing Zhang
- Moores Cancer Center, University of California, San Diego, California, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hongping Ye
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Brian Kwan
- Moores Cancer Center, University of California, San Diego, California, USA
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, California, USA
| | - Daniel Montemayor
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Jana Tumova
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Manjula Darshi
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Farsad Afshinnia
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan, USA
| | - Julia J. Scialla
- Departments of Medicine and Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Amanda Anderson
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna C. Porter
- Jesse Brown VA Medical Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jonathan J. Taliercio
- Cleveland Clinic Foundation, Glickman Urological & Kidney Institute, Department of Nephrology, Cleveland, Ohio, USA
| | - Hernan Rincon-Choles
- Cleveland Clinic Foundation, Glickman Urological & Kidney Institute, Department of Nephrology, Cleveland, Ohio, USA
| | - Panduranga Rao
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan, USA
| | - Dawei Xie
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kumar Sharma
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Loki Natarajan
- Moores Cancer Center, University of California, San Diego, California, USA
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, California, USA
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Dörner K, Badertscher L, Horváth B, Hollandi R, Molnár C, Fuhrer T, Meier R, Sárazová M, van den Heuvel J, Zamboni N, Horvath P, Kutay U. Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism. Nucleic Acids Res 2022; 50:2872-2888. [PMID: 35150276 PMCID: PMC8934630 DOI: 10.1093/nar/gkac072] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 12/19/2022] Open
Abstract
Ribosome assembly is an essential process that is linked to human congenital diseases and tumorigenesis. While great progress has been made in deciphering mechanisms governing ribosome biogenesis in eukaryotes, an inventory of factors that support ribosome synthesis in human cells is still missing, in particular regarding the maturation of the large 60S subunit. Here, we performed a genome-wide RNAi screen using an imaging-based, single cell assay to unravel the cellular machinery promoting 60S subunit assembly in human cells. Our screen identified a group of 310 high confidence factors. These highlight the conservation of the process across eukaryotes and reveal the intricate connectivity of 60S subunit maturation with other key cellular processes, including splicing, translation, protein degradation, chromatin organization and transcription. Intriguingly, we also identified a cluster of hits comprising metabolic enzymes of the polyamine synthesis pathway. We demonstrate that polyamines, which have long been used as buffer additives to support ribosome assembly in vitro, are required for 60S maturation in living cells. Perturbation of polyamine metabolism results in early defects in 60S but not 40S subunit maturation. Collectively, our data reveal a novel function for polyamines in living cells and provide a rich source for future studies on ribosome synthesis.
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Affiliation(s)
- Kerstin Dörner
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Lukas Badertscher
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Bianka Horváth
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, 8057 Zurich, Switzerland
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary
| | - Csaba Molnár
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Roger Meier
- ScopeM, ETH Zürich, 8093 Zürich, Switzerland
| | - Marie Sárazová
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jasmin van den Heuvel
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Center, 6726 Szeged, Hungary.,Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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10
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Schink SJ, Christodoulou D, Mukherjee A, Athaide E, Brunner V, Fuhrer T, Bradshaw GA, Sauer U, Basan M. Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol Syst Biol 2022; 18:e10704. [PMID: 34994048 PMCID: PMC8738977 DOI: 10.15252/msb.202110704] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022] Open
Abstract
Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse-grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade-offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.
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Affiliation(s)
| | - Dimitris Christodoulou
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Avik Mukherjee
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
- Applied Mathematics DepartmentHarvard CollegeCambridgeMAUSA
| | - Edward Athaide
- Applied Mathematics DepartmentHarvard CollegeCambridgeMAUSA
| | - Viktoria Brunner
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Gary Andrew Bradshaw
- Laboratory of Systems PharmacologyHarvard Program in Therapeutic ScienceHarvard Medical SchoolBostonMAUSA
| | - Uwe Sauer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Markus Basan
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
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11
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Yilmaz B, Mooser C, Keller I, Li H, Zimmermann J, Bosshard L, Fuhrer T, Gomez de Agüero M, Trigo NF, Tschanz-Lischer H, Limenitakis JP, Hardt WD, McCoy KD, Stecher B, Excoffier L, Sauer U, Ganal-Vonarburg SC, Macpherson AJ. Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell Host Microbe 2021; 29:650-663.e9. [PMID: 33662276 DOI: 10.1016/j.chom.2021.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 10/14/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022]
Abstract
Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Catherine Mooser
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Irene Keller
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Hai Li
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Jakob Zimmermann
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Lars Bosshard
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Nerea Fernandez Trigo
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Heidi Tschanz-Lischer
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Julien P Limenitakis
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | | | - Kathy D McCoy
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, 80539 Munich, Germany
| | - Laurent Excoffier
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland.
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12
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Flores-Tinoco CE, Tschan F, Fuhrer T, Margot C, Sauer U, Christen M, Christen B. Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation. Mol Syst Biol 2020; 16:e9419. [PMID: 32490601 PMCID: PMC7268258 DOI: 10.15252/msb.20199419] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.
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Affiliation(s)
| | - Flavia Tschan
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Margot
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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13
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Kwan B, Fuhrer T, Zhang J, Darshi M, Van Espen B, Montemayor D, de Boer IH, Dobre M, Hsu CY, Kelly TN, Raj DS, Rao PS, Saraf SL, Scialla J, Waikar SS, Sharma K, Natarajan L. Metabolomic Markers of Kidney Function Decline in Patients With Diabetes: Evidence From the Chronic Renal Insufficiency Cohort (CRIC) Study. Am J Kidney Dis 2020; 76:511-520. [PMID: 32387023 DOI: 10.1053/j.ajkd.2020.01.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 10/08/2019] [Accepted: 01/17/2020] [Indexed: 02/01/2023]
Abstract
RATIONALE & OBJECTIVE Biomarkers that provide reliable evidence of future diabetic kidney disease (DKD) are needed to improve disease management. In a cross-sectional study, we previously identified 13 urine metabolites that had levels reduced in DKD compared with healthy controls. We evaluated associations of these 13 metabolites with future DKD progression. STUDY DESIGN Prospective cohort. SETTING & PARTICIPANTS 1,001 Chronic Renal Insufficiency Cohort (CRIC) participants with diabetes with estimated glomerular filtration rates (eGFRs) between 20 and 70mL/min/1.73m2 were followed up prospectively for a median of 8 (range, 2-10) years. PREDICTORS 13 urine metabolites, age, race, sex, smoked more than 100 cigarettes in lifetime, body mass index, hemoglobin A1c level, blood pressure, urinary albumin, and eGFR. OUTCOMES Annual eGFR slope and time to incident kidney failure with replacement therapy (KFRT; ie, initiation of dialysis or receipt of transplant). ANALYTICAL APPROACH Several clinical metabolite models were developed for eGFR slope as the outcome using stepwise selection and penalized regression, and further tested on the time-to-KFRT outcome. A best cross-validated (final) prognostic model was selected based on high prediction accuracy for eGFR slope and high concordance statistic for incident KFRT. RESULTS During follow-up, mean eGFR slope was-1.83±1.92 (SD) mL/min/1.73m2 per year; 359 (36%) participants experienced KFRT. Median time to KFRT was 7.45 years from the time of entry to the CRIC Study. In our final model, after adjusting for clinical variables, levels of metabolites 3-hydroxyisobutyrate (3-HIBA) and 3-methylcrotonyglycine had a significant negative association with eGFR slope, whereas citric and aconitic acid were positively associated. Further, 3-HIBA and aconitic acid levels were associated with higher and lower risk for KFRT, respectively (HRs of 2.34 [95% CI, 1.51-3.62] and 0.70 [95% CI, 0.51-0.95]). LIMITATIONS Subgroups for whom metabolite signatures may not be optimal, nontargeted metabolomics by flow-injection analysis, and 2-stage modeling approaches. CONCLUSIONS Urine metabolites may offer insights into DKD progression. If replicated in future studies, aconitic acid and 3-HIBA could identify individuals with diabetes at high risk for GFR decline, potentially leading to improved clinical care and targeted therapies.
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Affiliation(s)
- Brian Kwan
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA; Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - Manjula Darshi
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | | | - Daniel Montemayor
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Ian H de Boer
- Department of Medicine, University of Washington, Seattle, WA
| | - Mirela Dobre
- Division of Nephrology and Hypertension, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Chi-Yuan Hsu
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA
| | - Dominic S Raj
- Division of Kidney Disease and Hypertension, George Washington University, Washington, DC
| | - Panduranga S Rao
- Department of Medicine, University of Michigan, Ann Arbor, Ann Arbor, MI
| | - Santosh L Saraf
- Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Julia Scialla
- Department of Medicine and Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC; Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA; Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Sushrut S Waikar
- Renal Division, Brigham and Women's Hospital, Boston, MA; Renal Section, Boston University Medical Center, Boston, MA
| | - Kumar Sharma
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX.
| | - Loki Natarajan
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA; Moores Cancer Center, University of California, San Diego, La Jolla, CA.
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Wotzka SY, Kreuzer M, Maier L, Arnoldini M, Nguyen BD, Brachmann AO, Berthold DL, Zünd M, Hausmann A, Bakkeren E, Hoces D, Gül E, Beutler M, Dolowschiak T, Zimmermann M, Fuhrer T, Moor K, Sauer U, Typas A, Piel J, Diard M, Macpherson AJ, Stecher B, Sunagawa S, Slack E, Hardt WD. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nat Microbiol 2019; 4:2164-2174. [PMID: 31591555 PMCID: PMC6881180 DOI: 10.1038/s41564-019-0568-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
The microbiota confers colonization resistance, which blocks Salmonella gut colonization1. As diet affects microbiota composition, we studied whether food composition shifts enhance susceptibility to infection. Shifting mice to diets with reduced fibre or elevated fat content for 24 h boosted Salmonella Typhimurium or Escherichia coli gut colonization and plasmid transfer. Here, we studied the effect of dietary fat. Colonization resistance was restored within 48 h of return to maintenance diet. Salmonella gut colonization was also boosted by two oral doses of oleic acid or bile salts. These pathogen blooms required Salmonella's AcrAB/TolC-dependent bile resistance. Our data indicate that fat-elicited bile promoted Salmonella gut colonization. Both E. coli and Salmonella show much higher bile resistance than the microbiota. Correspondingly, competitive E. coli can be protective in the fat-challenged gut. Diet shifts and fat-elicited bile promote S. Typhimurium gut infections in mice lacking E. coli in their microbiota. This mouse model may be useful for studying pathogen-microbiota-host interactions, the protective effect of E. coli, to analyse the spread of resistance plasmids and assess the impact of food components on the infection process.
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Affiliation(s)
- Sandra Y Wotzka
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Markus Kreuzer
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Lisa Maier
- European Molecular Biology Laboratory, Heidelberg, Heidelberg, Germany
| | - Markus Arnoldini
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Bidong D Nguyen
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | | | | | - Mirjam Zünd
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Annika Hausmann
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Erik Bakkeren
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Daniel Hoces
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Ersin Gül
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Markus Beutler
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | | | - Michael Zimmermann
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Kathrin Moor
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Athanasios Typas
- European Molecular Biology Laboratory, Heidelberg, Heidelberg, Germany
| | - Jörn Piel
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Médéric Diard
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Bärbel Stecher
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | | | - Emma Slack
- Institute of Microbiology, D-BIOL, ETH Zürich, Zürich, Switzerland
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15
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Christodoulou D, Kuehne A, Estermann A, Fuhrer T, Lang P, Sauer U. Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms. iScience 2019; 19:1133-1144. [PMID: 31536961 PMCID: PMC6831883 DOI: 10.1016/j.isci.2019.08.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 07/13/2019] [Accepted: 08/24/2019] [Indexed: 02/03/2023] Open
Abstract
All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. Characterization of immediate metabolic response to oxidative stress The metabolic response in glycolysis and PP pathway depends on stress severity Identification of NADPH feedback inhibition on G6PDH as key regulatory interaction The identified oxidative stress regulatory interaction is conserved across kingdoms
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Affiliation(s)
- Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paul Lang
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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16
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Zhang YE, Bærentsen RL, Fuhrer T, Sauer U, Gerdes K, Brodersen DE. (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch. Mol Cell 2019; 74:1239-1249.e4. [PMID: 31023582 DOI: 10.1016/j.molcel.2019.03.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 01/17/2023]
Abstract
The stringent response alarmones pppGpp and ppGpp are essential for rapid adaption of bacterial physiology to changes in the environment. In Escherichia coli, the nucleosidase PpnN (YgdH) regulates purine homeostasis by cleaving nucleoside monophosphates and specifically binds (p)ppGpp. Here, we show that (p)ppGpp stimulates the catalytic activity of PpnN both in vitro and in vivo causing accumulation of several types of nucleobases during stress. The structure of PpnN reveals a tetramer with allosteric (p)ppGpp binding sites located between subunits. pppGpp binding triggers a large conformational change that shifts the two terminal domains to expose the active site, providing a structural rationale for the stimulatory effect. We find that PpnN increases fitness and adjusts cellular tolerance to antibiotics and propose a model in which nucleotide levels can rapidly be adjusted during stress by simultaneous inhibition of biosynthesis and stimulation of degradation, thus achieving a balanced physiological response to constantly changing environments.
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Affiliation(s)
- Yong Everett Zhang
- Department of Biology, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, 2200 Copenhagen, Denmark.
| | - René Lysdal Bærentsen
- Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark
| | - Tobias Fuhrer
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Kenn Gerdes
- Department of Biology, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ditlev Egeskov Brodersen
- Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark.
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17
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Bojar D, Fuhrer T, Fussenegger M. Purity by design: Reducing impurities in bioproduction by stimulus-controlled global translational downregulation of non-product proteins. Metab Eng 2018; 52:110-123. [PMID: 30468874 DOI: 10.1016/j.ymben.2018.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/01/2018] [Accepted: 11/17/2018] [Indexed: 01/22/2023]
Abstract
Capitalizing on the ability of mammalian cells to conduct complex post-translational modifications, most protein therapeutics are currently produced in cell culture systems. Addition of a signal peptide to the product protein enables its accumulation in the cell culture supernatant, but separation of the product from endogenously secreted proteins remains costly and labor-intensive. We considered that global downregulation of translation of non-product proteins would be an efficient strategy to minimize downstream processing requirements. Therefore, taking advantage of the ability of mammalian protein kinase R (PKR) to switch off most cellular translation processes in response to infection by viruses, we fused a caffeine-inducible dimerization domain to the catalytic domain of PKR. Addition of caffeine to this construct results in homodimerization and activation of PKR, effectively rewiring rapid global translational downregulation to the addition of the stimulus in a dose-dependent manner. Then, to protect translation of the target therapeutic, we screened viral and cellular internal ribosomal entry sites (IRESes) known or suspected to be resistant to PKR-induced translational stress. After choosing the best-in-class Seneca valley virus (SVV) IRES, we additionally screened for IRES transactivation factors (ITAFs) as well as for supplementary small molecules to further boost the production titer of the product protein under conditions of global translational downregulation. Importantly, the residual global translation activity of roughly 10% under maximal downregulation is sufficient to maintain cellular viability during a production timeframe of at least five days. Standard industrially used adherent as well as suspension-adapted cell lines transfected with this synthetic biology-inspired Protein Kinase R-Enhanced Protein Production (PREPP) system could produce several medicinally relevant protein therapeutics, such as the blockbuster drug rituximab, in substantial quantities and with significantly higher purity than previous culture technologies. We believe incorporation of such purity-by-design technology in the production process will alleviate downstream processing bottlenecks in future biopharmaceutical manufacturing.
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Affiliation(s)
- Daniel Bojar
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tobias Fuhrer
- ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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18
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Sekar K, Rusconi R, Sauls JT, Fuhrer T, Noor E, Nguyen J, Fernandez VI, Buffing MF, Berney M, Jun S, Stocker R, Sauer U. Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria. Mol Syst Biol 2018; 14:e8623. [PMID: 30397005 PMCID: PMC6217170 DOI: 10.15252/msb.20188623] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
In natural environments, microbes are typically non-dividing and gauge when nutrients permit division. Current models are phenomenological and specific to nutrient-rich, exponentially growing cells, thus cannot predict the first division under limiting nutrient availability. To assess this regime, we supplied starving Escherichia coli with glucose pulses at increasing frequencies. Real-time metabolomics and microfluidic single-cell microscopy revealed unexpected, rapid protein, and nucleic acid synthesis already from minuscule glucose pulses in non-dividing cells. Additionally, the lag time to first division shortened as pulsing frequency increased. We pinpointed division timing and dependence on nutrient frequency to the changing abundance of the division protein FtsZ. A dynamic, mechanistic model quantitatively relates lag time to FtsZ synthesis from nutrient pulses and FtsZ protease-dependent degradation. Lag time changed in model-congruent manners, when we experimentally modulated the synthesis or degradation of FtsZ. Thus, limiting abundance of FtsZ can quantitatively predict timing of the first cell division.
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Affiliation(s)
- Karthik Sekar
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Roberto Rusconi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - John T Sauls
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jen Nguyen
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vicente I Fernandez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Marieke F Buffing
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Suckjoon Jun
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
- Section of Molecular Biology, Division of Biological Science, University of California at San Diego, La Jolla, CA, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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19
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Caldez MJ, Van Hul N, Koh HWL, Teo XQ, Fan JJ, Tan PY, Dewhurst MR, Too PG, Talib SZA, Chiang BE, Stünkel W, Yu H, Lee P, Fuhrer T, Choi H, Björklund M, Kaldis P. Metabolic Remodeling during Liver Regeneration. Dev Cell 2018; 47:425-438.e5. [PMID: 30344111 DOI: 10.1016/j.devcel.2018.09.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [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: 11/03/2017] [Revised: 05/13/2018] [Accepted: 09/21/2018] [Indexed: 12/29/2022]
Abstract
Liver disease is linked to a decreased capacity of hepatocytes to divide. In addition, cellular metabolism is important for tissue homeostasis and regeneration. Since metabolic changes are a hallmark of liver disease, we investigated the connections between metabolism and cell division. We determined global metabolic changes at different stages of liver regeneration using a combination of integrated transcriptomic and metabolomic analyses with advanced functional redox in vivo imaging. Our data indicate that blocking hepatocyte division during regeneration leads to mitochondrial dysfunction and downregulation of oxidative pathways. This resulted in an increased redox ratio and hyperactivity of alanine transaminase allowing the production of alanine and α-ketoglutarate from pyruvate when mitochondrial functions are impaired. Our data suggests that during liver regeneration, cell division leads to hepatic metabolic remodeling. Moreover, we demonstrate that hepatocytes are equipped with a flexible metabolic machinery able to adapt dynamically to changes during tissue regeneration.
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Affiliation(s)
- Matias J Caldez
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore 117597, Republic of Singapore
| | - Noémi Van Hul
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore
| | - Hiromi W L Koh
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, Singapore 117549, Republic of Singapore
| | - Xing Qi Teo
- Singapore Bio-Imaging Consortium, A(∗)STAR, Singapore, Republic of Singapore
| | - Jun Jun Fan
- Institute of Bioengineering and Nanotechnology, A(∗)STAR, The Nanos, #04-01, 31 Biopolis Way, Singapore 138669, Republic of Singapore; Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Republic of Singapore; Department of Orthopaedic Surgery, Xi Jing Hospital, Fourth Military Medical University, #88 Jiefang Road, Xi'an 710032, China
| | - Peck Yean Tan
- Singapore Institute of Clinical Sciences, A(∗)STAR, Singapore, Republic of Singapore
| | - Matthew R Dewhurst
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore; Faculty of Biology, Medicine and Health, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK
| | - Peh Gek Too
- Singapore Institute of Clinical Sciences, A(∗)STAR, Singapore, Republic of Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore
| | - Beatrice E Chiang
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore
| | - Walter Stünkel
- Singapore Institute of Clinical Sciences, A(∗)STAR, Singapore, Republic of Singapore
| | - Hanry Yu
- Institute of Bioengineering and Nanotechnology, A(∗)STAR, The Nanos, #04-01, 31 Biopolis Way, Singapore 138669, Republic of Singapore; Department of Physiology, Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, Singapore 117597, Republic of Singapore; Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Republic of Singapore; Gastroenterology Department, Southern Medical University, Guangzhou 510515, China
| | - Philip Lee
- Singapore Bio-Imaging Consortium, A(∗)STAR, Singapore, Republic of Singapore
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Hyungwon Choi
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore; Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, Singapore 117549, Republic of Singapore
| | - Mikael Björklund
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd, Haining, Zhejiang 314400, China
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A(∗)STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore 117597, Republic of Singapore.
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20
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Uchimura Y, Fuhrer T, Li H, Lawson MA, Zimmermann M, Yilmaz B, Zindel J, Ronchi F, Sorribas M, Hapfelmeier S, Ganal-Vonarburg SC, Gomez de Agüero M, McCoy KD, Sauer U, Macpherson AJ. Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response. Immunity 2018; 49:545-559.e5. [PMID: 30193848 PMCID: PMC6162337 DOI: 10.1016/j.immuni.2018.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 06/12/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023]
Abstract
Although the mammalian microbiota is well contained within the intestine, it profoundly shapes development and metabolism of almost every host organ. We questioned the range and depth of microbial metabolite penetration into the host, and how this is modulated by intestinal immunity. Chemically identical microbial and host metabolites were distinguished by stable isotope tracing from 13C-labeled live non-replicating Escherichia coli, differentiating 12C host isotopes with high-resolution mass spectrometry. Hundreds of endogenous microbial compounds penetrated 23 host tissues and fluids after intestinal exposure: subsequent 12C host metabolome signatures included lipidemia, reduced glycolysis, and inflammation. Penetrant bacterial metabolites from the small intestine were rapidly cleared into the urine, whereas induced antibodies curtailed microbial metabolite exposure by accelerating intestinal bacterial transit into the colon where metabolite transport mechanisms are limiting. Pervasive penetration of microbial molecules can cause extensive host tissue responses: these are limited by immune and non-immune intestinal mucosal adaptations to the microbiota. Metabolites from mutualistic bacteria broadly penetrate host tissues and organs Bacterial metabolites induce widespread host metabolic and immunological responses The small intestine is highly susceptible to host-microbial metabolomic exchange Secretory immunoglobulins accelerate microbial clearance from the small intestine
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Affiliation(s)
- Yasuhiro Uchimura
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland; Department of Anatomy and Cell Biology, Shiga University of Medical Science, 520-2192 Shiga, Japan
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Hai Li
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Melissa A Lawson
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Bahtiyar Yilmaz
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Joel Zindel
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Francesca Ronchi
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Marcel Sorribas
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | | | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Kathy D McCoy
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.
| | - Andrew J Macpherson
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland.
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21
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Piazza I, Kochanowski K, Cappelletti V, Fuhrer T, Noor E, Sauer U, Picotti P. A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication. Cell 2018; 172:358-372.e23. [DOI: 10.1016/j.cell.2017.12.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/27/2017] [Accepted: 12/01/2017] [Indexed: 10/25/2022]
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Abstract
Mammalian body surfaces are inhabited by vast numbers of microbes, the commensal microbiota, which help the host to digest food, provide nutrients, and mature its immune system. For a long time, postnatal colonization was believed to be the main stimulus for microbial-induced immune development. Using a model of reversible colonization of germ-free mice during gestation, we recently showed that the microbial shaping of the neonatal immune system begins even before birth through molecular signals derived from the microbiota of the mother. Maternal microbiota was important to mature intestinal innate immune cells and to alter intestinal gene expression profiles in the offspring. These changes prepare the newborn for postnatal colonization. The majority of the gestational colonization-dependent effects required maternal antibodies. Here, we discuss and provide further evidence how maternal antibodies are important players in transferring a signal originating from the maternal intestinal microbiota to the offspring.
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Affiliation(s)
- Stephanie C. Ganal-Vonarburg
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin, University of Bern, Bern, Switzerland,CONTACT Stephanie C. Ganal-Vonarburg Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Murtenstrasse 35, University of Bern, 3008 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin, University of Bern, Bern, Switzerland
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23
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Abstract
Metabolism is one of the best-understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non-enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single-celled organisms. Here, we systematically mapped the association between > 3,800 single-gene deletions in the bacterium Escherichia coli and relative concentrations of > 7,000 intracellular metabolite ions. Beyond expected metabolic changes in the proximity to abolished enzyme activities, the association map reveals a largely unknown landscape of gene-metabolite interactions that are not represented in metabolic models. Therefore, the map provides a unique resource for assessing the genetic basis of metabolic changes and conversely hypothesizing metabolic consequences of genetic alterations. We illustrate this by predicting metabolism-related functions of 72 so far not annotated genes and by identifying key genes mediating the cellular response to environmental perturbations.
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Affiliation(s)
- Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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Sévin DC, Fuhrer T, Zamboni N, Sauer U. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods 2016; 14:187-194. [DOI: 10.1038/nmeth.4103] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/19/2016] [Indexed: 12/14/2022]
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25
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Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, Amador-Noguez D, Tian L, Sauer U, Lynd LR. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng 2016; 39:169-180. [PMID: 27914869 DOI: 10.1016/j.ymben.2016.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme. First we showed that there is no flux through the ODC pathway by enzyme assay. Flux through the remaining two pathways (PPDK and malate shunt) was determined by dynamic 13C labeling. In the wild-type strain, the malate shunt accounts for about 33±2% of the flux to pyruvate, with the remainder via the PPDK pathway. Deletion of the ppdk gene resulted in a redirection of all pyruvate flux through the malate shunt. This provides the first direct evidence of the in-vivo function of the malate shunt.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jingxuan Cui
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jilai Zhou
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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26
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Geiger R, Rieckmann J, Wolf T, Basso C, Feng Y, Fuhrer T, Kogadeeva M, Picotti P, Meissner F, Mann M, Zamboni N, Sallusto F, Lanzavecchia A. L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity. Cell 2016; 167. [PMID: 27745970 PMCID: PMC5075284 DOI: 10.1016/j.cell.2016.09.031 10.1016/j.cell.2016.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Metabolic activity is intimately linked to T cell fate and function. Using high-resolution mass spectrometry, we generated dynamic metabolome and proteome profiles of human primary naive T cells following activation. We discovered critical changes in the arginine metabolism that led to a drop in intracellular L-arginine concentration. Elevating L-arginine levels induced global metabolic changes including a shift from glycolysis to oxidative phosphorylation in activated T cells and promoted the generation of central memory-like cells endowed with higher survival capacity and, in a mouse model, anti-tumor activity. Proteome-wide probing of structural alterations, validated by the analysis of knockout T cell clones, identified three transcriptional regulators (BAZ1B, PSIP1, and TSN) that sensed L-arginine levels and promoted T cell survival. Thus, intracellular L-arginine concentrations directly impact the metabolic fitness and survival capacity of T cells that are crucial for anti-tumor responses.
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Affiliation(s)
- Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland,Corresponding author
| | - Jan C. Rieckmann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tobias Wolf
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Camilla Basso
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Maria Kogadeeva
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Center of Medical Immunology, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland,Corresponding author
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27
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Gomez de Aguero M, Ganal-Vonarburg SC, Fuhrer T, Rupp S, Uchimura Y, Li H, Steinert A, Heikenwalder M, Hapfelmeier S, Sauer U, McCoy KD, Macpherson AJ. The maternal microbiota drives early postnatal innate immune development. Science 2016; 351:1296-302. [DOI: 10.1126/science.aad2571] [Citation(s) in RCA: 696] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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Zhu L, Amsler M, Fuhrer T, Schaefer B, Faraji S, Rostami S, Ghasemi SA, Sadeghi A, Grauzinyte M, Wolverton C, Goedecker S. A fingerprint based metric for measuring similarities of crystalline structures. J Chem Phys 2016; 144:034203. [DOI: 10.1063/1.4940026] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Li Zhu
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
| | - Maximilian Amsler
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Tobias Fuhrer
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
| | - Bastian Schaefer
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
| | - Somayeh Faraji
- Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran
| | - Samare Rostami
- Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran
| | - S. Alireza Ghasemi
- Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran
| | - Ali Sadeghi
- Physics Department, Shahid Beheshti University, G. C., Evin, 19839 Tehran, Iran
| | - Migle Grauzinyte
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
| | - Chris Wolverton
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Stefan Goedecker
- Department of Physics, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland
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29
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Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, Brugiroux S, Keller I, Macpherson JA, Rupp S, Stolp B, Stein JV, Stecher B, Sauer U, McCoy KD, Macpherson AJ. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun 2015; 6:8292. [PMID: 26392213 PMCID: PMC4595636 DOI: 10.1038/ncomms9292] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [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: 05/01/2015] [Accepted: 08/06/2015] [Indexed: 12/22/2022] Open
Abstract
The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host.
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Affiliation(s)
- Hai Li
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Julien P. Limenitakis
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Markus B. Geuking
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Melissa A. Lawson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Madeleine Wyss
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Sandrine Brugiroux
- Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany
| | - Irene Keller
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Jamie A. Macpherson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Sandra Rupp
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Bettina Stolp
- Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland
| | - Jens V. Stein
- Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Kathy D. McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Andrew J. Macpherson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
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30
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Link H, Fuhrer T, Gerosa L, Zamboni N, Sauer U. Real-time metabolome profiling of the metabolic switch between starvation and growth. Nat Methods 2015; 12:1091-7. [PMID: 26366986 DOI: 10.1038/nmeth.3584] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
Abstract
Metabolic systems are often the first networks to respond to environmental changes, and the ability to monitor metabolite dynamics is key for understanding these cellular responses. Because monitoring metabolome changes is experimentally tedious and demanding, dynamic data on time scales from seconds to hours are scarce. Here we describe real-time metabolome profiling by direct injection of living bacteria, yeast or mammalian cells into a high-resolution mass spectrometer, which enables automated monitoring of about 300 compounds in 15-30-s cycles over several hours. We observed accumulation of energetically costly biomass metabolites in Escherichia coli in carbon starvation-induced stationary phase, as well as the rapid use of these metabolites upon growth resumption. By combining real-time metabolome profiling with modeling and inhibitor experiments, we obtained evidence for switch-like feedback inhibition in amino acid biosynthesis and for control of substrate availability through the preferential use of the metabolically cheaper one-step salvaging pathway over costly ten-step de novo purine biosynthesis during growth resumption.
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Affiliation(s)
- Hannes Link
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Luca Gerosa
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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31
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Nikel PI, Chavarría M, Fuhrer T, Sauer U, de Lorenzo V. Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways. J Biol Chem 2015; 290:25920-32. [PMID: 26350459 DOI: 10.1074/jbc.m115.687749] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [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: 08/24/2015] [Indexed: 01/28/2023] Open
Abstract
The soil bacterium Pseudomonas putida KT2440 lacks a functional Embden-Meyerhof-Parnas (EMP) pathway, and glycolysis is known to proceed almost exclusively through the Entner-Doudoroff (ED) route. To investigate the raison d'être of this metabolic arrangement, the distribution of periplasmic and cytoplasmic carbon fluxes was studied in glucose cultures of this bacterium by using (13)C-labeled substrates, combined with quantitative physiology experiments, metabolite quantification, and in vitro enzymatic assays under both saturating and non-saturating, quasi in vivo conditions. Metabolic flux analysis demonstrated that 90% of the consumed sugar was converted into gluconate, entering central carbon metabolism as 6-phosphogluconate and further channeled into the ED pathway. Remarkably, about 10% of the triose phosphates were found to be recycled back to form hexose phosphates. This set of reactions merges activities belonging to the ED, the EMP (operating in a gluconeogenic fashion), and the pentose phosphate pathways to form an unforeseen metabolic architecture (EDEMP cycle). Determination of the NADPH balance revealed that the default metabolic state of P. putida KT2440 is characterized by a slight catabolic overproduction of reducing power. Cells growing on glucose thus run a biochemical cycle that favors NADPH formation. Because NADPH is required not only for anabolic functions but also for counteracting different types of environmental stress, such a cyclic operation may contribute to the physiological heftiness of this bacterium in its natural habitats.
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Affiliation(s)
- Pablo I Nikel
- From the Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Max Chavarría
- the Escuela de Química, Universidad de Costa Rica, 2060 San José, Costa Rica, and
| | - Tobias Fuhrer
- the Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Uwe Sauer
- the Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Víctor de Lorenzo
- From the Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain,
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32
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Castaño-Cerezo S, Bernal V, Post H, Fuhrer T, Cappadona S, Sánchez-Díaz NC, Sauer U, Heck AJR, Altelaar AFM, Cánovas M. Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. Mol Syst Biol 2014; 10:762. [PMID: 25518064 PMCID: PMC4299603 DOI: 10.15252/msb.20145227] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although protein acetylation is widely observed, it has been associated with few specific
regulatory functions making it poorly understood. To interrogate its functionality, we analyzed the
acetylome in Escherichia coli knockout mutants of cobB, the only
known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase.
For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins,
were identified and differentially quantified. Nearly 65% of these proteins are related to
metabolism. The global activity of CobB contributes to the deacetylation of a large number of
substrates and has a major impact on physiology. Apart from the regulation of acetyl-CoA synthetase,
we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the
glyoxylate shunt. Acetylation of the transcription factor RcsB prevents DNA binding, activating
flagella biosynthesis and motility, and increases acid stress susceptibility. Surprisingly, deletion
of patZ increased acetylation in acetate cultures, which suggests that it regulates
the levels of acetylating agents. The results presented offer new insights into functional roles of
protein acetylation in metabolic fitness and global cell regulation.
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Affiliation(s)
- Sara Castaño-Cerezo
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Vicente Bernal
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Salvatore Cappadona
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Nerea C Sánchez-Díaz
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Manuel Cánovas
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia Campus de Excelencia Mare Nostrum, Murcia, Spain
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Abstract
Non-targeted metabolomics by mass spectrometry has established as the method of choice for investigating metabolic phenotypes in basic and applied research. Compared to other omics, metabolomics provides broad scope and yet direct information on the integrated cellular response with low demand in material and sample preparation. These features render non-targeted metabolomics ideally suited for large scale screens and discovery. Here we review the achievements and potential in high-throughput, non-targeted metabolomics. We found that routine and precise analysis of thousands of small molecular features in thousands of complex samples per day and instrument is already reality, and ongoing developments in microfluidics and integrated interfaces will likely further boost throughput in the next few years.
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Affiliation(s)
- Tobias Fuhrer
- ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Nicola Zamboni
- ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland.
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Miettinen TP, Pessa HKJ, Caldez MJ, Fuhrer T, Diril MK, Sauer U, Kaldis P, Björklund M. Identification of transcriptional and metabolic programs related to mammalian cell size. Curr Biol 2014; 24:598-608. [PMID: 24613310 PMCID: PMC3991852 DOI: 10.1016/j.cub.2014.01.071] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/20/2013] [Accepted: 01/30/2014] [Indexed: 12/16/2022]
Abstract
Background Regulation of cell size requires coordination of growth and proliferation. Conditional loss of cyclin-dependent kinase 1 in mice permits hepatocyte growth without cell division, allowing us to study cell size in vivo using transcriptomics and metabolomics. Results Larger cells displayed increased expression of cytoskeletal genes but unexpectedly repressed expression of many genes involved in mitochondrial functions. This effect appears to be cell autonomous because cultured Drosophila cells induced to increase cell size displayed a similar gene-expression pattern. Larger hepatocytes also displayed a reduction in the expression of lipogenic transcription factors, especially sterol-regulatory element binding proteins. Inhibition of mitochondrial functions and lipid biosynthesis, which is dependent on mitochondrial metabolism, increased the cell size with reciprocal effects on cell proliferation in several cell lines. Conclusions We uncover that large cell-size increase is accompanied by downregulation of mitochondrial gene expression, similar to that observed in diabetic individuals. Mitochondrial metabolism and lipid synthesis are used to couple cell size and cell proliferation. This regulatory mechanism may provide a possible mechanism for sensing metazoan cell size. Gene expression and metabolites levels relative to cell size are analyzed in liver Mitochondrial gene expression is repressed cell-autonomously in larger cells Cell size can be modulated by targeting mitochondria functions and lipid synthesis Lipids are negative regulators of cell size because they promote cell proliferation
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Affiliation(s)
- Teemu P Miettinen
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Heli K J Pessa
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matias J Caldez
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos #03-09, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Wolfgang-Pauli Strasse 16, 8093 Zürich, Switzerland
| | - M Kasim Diril
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos #03-09, Singapore 138673, Singapore
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Wolfgang-Pauli Strasse 16, 8093 Zürich, Switzerland
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos #03-09, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - Mikael Björklund
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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35
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Chavarría M, Fuhrer T, Sauer U, Pflüger-Grau K, de Lorenzo V. Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate : phosphotransferase system of Pseudomonas putida. Environ Microbiol 2012; 15:121-32. [PMID: 22708906 DOI: 10.1111/j.1462-2920.2012.02808.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gene that encodes the catabolite repressor/activator, Cra (FruR), of Pseudomonas putida is divergent from the fruBKA operon for the uptake of fructose via the phosphoenolpyruvate : carbohydrate phosphotransferase system (PTS(Fru)). The expression of the fru cluster has been studied in cells growing on substrates that change the intracellular concentrations of fructose-1-P (F1P), the principal metabolic intermediate that counteracts the DNA-binding ability of Cra on an upstream operator. While the levels of the regulator were not affected by any of the growth conditions tested, the transcription of fruB was stimulated by fructose but not by the gluconeogenic substrate, succinate. The analysis of the P(fruB) promoter activity in a strain lacking the Cra protein and the determination of key metabolites revealed that this regulator represses the expression of PTS(Fru) in a fashion that is dependent on the endogenous concentrations of F1P. Because FruB (i.e. the EI-HPr-EIIA(Fru) polyprotein) can deliver a high-energy phosphate to the EIIA(Ntr) (PtsN) enzyme of the PTS(Ntr) branch, the cross-talk between the two phosphotransferase systems was examined under metabolic regimes that allowed for the high or low transcription of the fruBKA operon. While fructose caused cross-talk, succinate prevented it almost completely. Furthermore, PtsN phosphorylation by FruB occurred in a Δcra mutant regardless of growth conditions. These results traced the occurrence of the cross-talk to intracellular pools of Cra effectors, in particular F1P. The Cra/F1P duo seems to not only control the expression of the PTS(Fru) but also checks the activity of the PTS(Ntr) in vivo.
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Affiliation(s)
- Max Chavarría
- Systems Biology Program, Centro Nacional de Biotecnología, 28049 Cantoblanco-Madrid, Spain
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Renilla S, Bernal V, Fuhrer T, Castaño-Cerezo S, Pastor JM, Iborra JL, Sauer U, Cánovas M. Acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures. Appl Microbiol Biotechnol 2011; 93:2109-24. [PMID: 21881893 DOI: 10.1007/s00253-011-3536-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [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: 04/18/2011] [Revised: 07/27/2011] [Accepted: 08/05/2011] [Indexed: 11/25/2022]
Abstract
Impairment of acetate production in Escherichia coli is crucial for the performance of many biotechnological processes. Aerobic production of acetate (or acetate overflow) results from changes in the expression of central metabolism genes. Acetyl-CoA synthetase scavenges extracellular acetate in glucose-limited cultures. Once converted to acetyl-CoA, it can be catabolized by the tricarboxylic acid cycle or the glyoxylate pathway. In this work, we assessed the significance of these pathways on acetate overflow during glucose excess and limitation. Gene expression, enzyme activities, and metabolic fluxes were studied in E. coli knock-out mutants related to the glyoxylate pathway operon and its regulators. The relevance of post-translational regulation by AceK-mediated phosphorylation of isocitrate dehydrogenase for pathway functionality was underlined. In chemostat cultures performed at increasing dilution rates, acetate overflow occurs when growing over a threshold glucose uptake rate. This threshold was not affected in a glyoxylate-pathway-deficient strain (lacking isocitrate lyase, the first enzyme of the pathway), indicating that it is not relevant for acetate overflow. In carbon-limited chemostat cultures, gluconeogenesis (maeB, sfcA, and pck), the glyoxylate operon and, especially, acetyl-CoA synthetase are upregulated. A mutant in acs (encoding acetyl-CoA synthetase) produced acetate at all dilution rates. This work demonstrates that, in E. coli, acetate production occurs at all dilution rates and that overflow is the result of unbalanced synthesis and scavenging activities. The over-expression of acetyl-CoA synthetase by cAMP-CRP-dependent induction limits this phenomenon in cultures consuming glucose at low rate, ensuring the recycling of the acetyl-CoA and acetyl-phosphate pools, although establishing an energy-dissipating substrate cycle.
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Affiliation(s)
- Sergio Renilla
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Chemistry, University of Murcia, Murcia, Spain
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Fuhrer T, Heer D, Begemann B, Zamboni N. High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry. Anal Chem 2011; 83:7074-80. [DOI: 10.1021/ac201267k] [Citation(s) in RCA: 274] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Dominik Heer
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Boris Begemann
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, ETH Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
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Nunn CEM, Johnsen U, Schönheit P, Fuhrer T, Sauer U, Hough DW, Danson MJ. Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius. J Biol Chem 2010; 285:33701-9. [PMID: 20736170 DOI: 10.1074/jbc.m110.146332] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, D-xylose and L-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of D-xylose and L-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.
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Affiliation(s)
- Charlotte E M Nunn
- Department of Biology and Biochemistry, Centre for Extremophile Research, University of Bath, Bath BA2 7AY, United Kingdom
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Johnsen U, Dambeck M, Zaiss H, Fuhrer T, Soppa J, Sauer U, Schönheit P. D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J Biol Chem 2009; 284:27290-303. [PMID: 19584053 DOI: 10.1074/jbc.m109.003814] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pathway of D-xylose degradation in archaea is unknown. In a previous study we identified in Haloarcula marismortui the first enzyme of xylose degradation, an inducible xylose dehydrogenase (Johnsen, U., and Schönheit, P. (2004) J. Bacteriol. 186, 6198-6207). Here we report a comprehensive study of the complete D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. The analyses include the following: (i) identification of the degradation pathway in vivo following (13)C-labeling patterns of proteinogenic amino acids after growth on [(13)C]xylose; (ii) identification of xylose-induced genes by DNA microarray experiments; (iii) characterization of enzymes; and (iv) construction of in-frame deletion mutants and their functional analyses in growth experiments. Together, the data indicate that D-xylose is oxidized exclusively to the tricarboxylic acid cycle intermediate alpha-ketoglutarate, involving D-xylose dehydrogenase (HVO_B0028), a novel xylonate dehydratase (HVO_B0038A), 2-keto-3-deoxyxylonate dehydratase (HVO_B0027), and alpha-ketoglutarate semialdehyde dehydrogenase (HVO_B0039). The functional involvement of these enzymes in xylose degradation was proven by growth studies of the corresponding in-frame deletion mutants, which all lost the ability to grow on d-xylose, but growth on glucose was not significantly affected. This is the first report of an archaeal D-xylose degradation pathway that differs from the classical D-xylose pathway in most bacteria involving the formation of xylulose 5-phosphate as an intermediate. However, the pathway shows similarities to proposed oxidative pentose degradation pathways to alpha-ketoglutarate in few bacteria, e.g. Azospirillum brasilense and Caulobacter crescentus, and in the archaeon Sulfolobus solfataricus.
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Affiliation(s)
- Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, D-24118 Kiel, Germany
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Frischknecht K, Wälchli C, Fuhrer T, Müller-Aregger C. Frauenmilchbank Schweiz. Z Geburtshilfe Neonatol 2008. [DOI: 10.1055/s-2008-1079101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fuhrer T, Chen L, Sauer U, Vitkup D. Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. J Bacteriol 2007; 189:8073-8. [PMID: 17873044 PMCID: PMC2168661 DOI: 10.1128/jb.01027-07] [Citation(s) in RCA: 50] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although NAD(+)-dependent succinate semialdehyde dehydrogenase activity was first described in Escherichia coli more than 25 years ago, the responsible gene has remained elusive so far. As an experimental proof of concept for a gap-filling algorithm for metabolic networks developed earlier, we demonstrate here that the E. coli gene yneI is responsible for this activity. Our biochemical results demonstrate that the yneI-encoded succinate semialdehyde dehydrogenase can use either NAD(+) or NADP(+) to oxidize succinate semialdehyde to succinate. The gene is induced by succinate semialdehyde, and expression data indicate that yneI plays a unique physiological role in the general nitrogen metabolism of E. coli. In particular, we demonstrate using mutant growth experiments that the yneI gene has an important, but not essential, role during growth on arginine and probably has an essential function during growth on putrescine as the nitrogen source. The NADP(+)-dependent succinate semialdehyde dehydrogenase activity encoded by the functional homolog gabD appears to be important for nitrogen metabolism under N limitation conditions. The yneI-encoded activity, in contrast, functions primarily as a valve to prevent toxic accumulation of succinate semialdehyde. Analysis of available genome sequences demonstrated that orthologs of both yneI and gabD are broadly distributed across phylogenetic space.
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Affiliation(s)
- Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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del Castillo T, Ramos JL, Rodríguez-Herva JJ, Fuhrer T, Sauer U, Duque E. Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J Bacteriol 2007; 189:5142-52. [PMID: 17483213 PMCID: PMC1951859 DOI: 10.1128/jb.00203-07] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we show that glucose catabolism in Pseudomonas putida occurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate, which is metabolized by the Edd and Eda Entner/Doudoroff enzymes to central metabolites. When glucose enters the periplasmic space through specific OprB porins, it can either be internalized into the cytoplasm or be oxidized to gluconate. Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate. Gluconate in the periplasm can be transported into the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate or oxidized to 2-ketogluconate, which is transported to the cytoplasm, and subsequently phosphorylated and reduced to 6-phosphogluconate. In the wild-type strain, glucose was consumed at a rate of around 6 mmol g(-1) h(-1), which allowed a growth rate of 0.58 h(-1) and a biomass yield of 0.44 g/g carbon used. Flux analysis of (13)C-labeled glucose revealed that, in the Krebs cycle, most of the oxalacetate fraction was produced by the pyruvate shunt rather than by the direct oxidation of malate by malate dehydrogenase. Enzymatic and microarray assays revealed that the enzymes, regulators, and transport systems of the three peripheral glucose pathways were induced in response to glucose in the outer medium. We generated a series of isogenic mutants in one or more of the steps of all three pathways and found that, although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate. In physical terms, glucose catabolism genes were organized in a series of clusters scattered along the chromosome. Within each of the clusters, genes encoding porins, transporters, enzymes, and regulators formed operons, suggesting that genes in each cluster coevolved. The glk gene encoding glucokinase was located in an operon with the edd gene, whereas the zwf-1 gene, encoding glucose-6-phosphate dehydrogenase, formed an operon with the eda gene. Therefore, the enzymes of the glucokinase pathway and those of the Entner-Doudoroff pathway are physically linked and induced simultaneously. It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose.
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Affiliation(s)
- Teresa del Castillo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, E-18008 Granada, Spain
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Abstract
Network topology is a necessary fundament to understand function and properties of microbial reaction networks. A valuable method for experimental elucidation of metabolic network topology is metabolic flux ratio analysis, which quantifies the relative contribution of two or more converging pathways to a given metabolite. It is based on 13C-labeling experiments, gas chromatography-mass spectrometry analysis, and probabilistic equations that relate mass distributions in proteinogenic amino acids to pathway activity. Here, we describe the protocol for sample generation and illustrate the principles underlying the calculation of metabolic flux ratios with three examples. These principles are also implemented in the publicly available software FiatFlux, which directly calculates flux ratios from the mass spectra of amino acids.
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Affiliation(s)
- Annik Nanchen
- Institute for Molecular Systems Biology, ETH Zürich, Switzerland
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Revelles O, Espinosa-Urgel M, Fuhrer T, Sauer U, Ramos JL. Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440. J Bacteriol 2005; 187:7500-10. [PMID: 16237033 PMCID: PMC1272968 DOI: 10.1128/jb.187.21.7500-7510.2005] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [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: 04/05/2005] [Accepted: 08/24/2005] [Indexed: 11/20/2022] Open
Abstract
L-lysine catabolism in Pseudomonas putida KT2440 was generally thought to occur via the aminovalerate pathway. In this study we demonstrate the operation of the alternative aminoadipate pathway with the intermediates D-lysine, L-pipecolate, and aminoadipate. The simultaneous operation of both pathways for the use of L-lysine as the sole carbon and nitrogen source was confirmed genetically. Mutants with mutations in either pathway failed to use L-lysine as the sole carbon and nitrogen source, although they still used L-lysine as the nitrogen source, albeit at reduced growth rates. New genes were identified in both pathways, including the davB and davA genes that encode the enzymes involved in the oxidation of L-lysine to delta-aminovaleramide and the hydrolysis of the latter to delta-aminovalerate, respectively. The amaA, dkpA, and amaB genes, in contrast, encode proteins involved in the transformation of Delta1-piperidine-2-carboxylate into aminoadipate. Based on L-[U-13C, U-15N]lysine experiments, we quantified the relative use of pathways in the wild type and its isogenic mutants. The fate of 13C label of L-lysine indicates that in addition to the existing connection between the D- and L-lysine pathways at the early steps of the catabolism of L-lysine mediated by a lysine racemase, there is yet another interconnection at the lower end of the pathways in which aminoadipate is channeled to yield glutarate. This study establishes an unequivocal relationship between gene and pathway enzymes in the metabolism of L-lysine, which is of crucial importance for the successful colonization of the rhizosphere of plants by this microorganism.
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Affiliation(s)
- Olga Revelles
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008 Granada, Spain
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Abstract
The structurally conserved and ubiquitous pathways of central carbon metabolism provide building blocks and cofactors for the biosynthesis of cellular macromolecules. The relative uses of pathways and reactions, however, vary widely among species and depend upon conditions, and some are not used at all. Here we identify the network topology of glucose metabolism and its in vivo operation by quantification of intracellular carbon fluxes from 13C tracer experiments. Specifically, we investigated Agrobacterium tumefaciens, two pseudomonads, Sinorhizobium meliloti, Rhodobacter sphaeroides, Zymomonas mobilis, and Paracoccus versutus, which grow on glucose as the sole carbon source, represent fundamentally different metabolic lifestyles (aerobic, anaerobic, photoheterotrophic, and chemoheterotrophic), and are phylogenetically distinct (firmicutes, gamma-proteobacteria, and alpha-proteobacteria). Compared to those of the model bacteria Escherichia coli and Bacillus subtilis, metabolisms of the investigated species differed significantly in several respects: (i) the Entner-Doudoroff pathway was the almost exclusive catabolic route; (ii) the pentose phosphate pathway exhibited exclusively biosynthetic functions, in many cases also requiring flux through the nonoxidative branch; (iii) all aerobes exhibited fully respiratory metabolism without significant overflow metabolism; and (iv) all aerobes used the pyruvate bypass of the malate dehydrogenase reaction to a significant extent. Exclusively, Pseudomonas fluorescens converted most glucose extracellularly to gluconate and 2-ketogluconate. Overall, the results suggest that metabolic data from model species with extensive industrial and laboratory history are not representative of microbial metabolism, at least not quantitatively.
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Affiliation(s)
- Tobias Fuhrer
- Institute of Biotechnology, ETH Zürich, CH-8093 Zürich, Switzerland
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Rodrigues V, Fuhrer T, Ugarte D. Signature of atomic structure in the quantum conductance of gold nanowires. Phys Rev Lett 2000; 85:4124-4127. [PMID: 11056640 DOI: 10.1103/physrevlett.85.4124] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2000] [Indexed: 05/23/2023]
Abstract
We have used high resolution transmission electron microscopy to determine the structure of gold nanowires generated by mechanical stretching. Just before rupture, the contacts adopt only three possible atomic configurations, whose occurrence probabilities and quantized conductance were subsequently estimated. These predictions have shown a remarkable agreement with conductance measurements from a break junction operating in ultrahigh vacuum, corroborating the derived correlation between nanowire atomic structure and conductance behavior.
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Affiliation(s)
- V Rodrigues
- Laboratório Nacional de Luz Síncrotron, C.P. 6192, 13083-970 Campinas SP, Brazil
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Kreyenschmidt M, Klaerner G, Fuhrer T, Ashenhurst J, Karg S, Chen WD, Lee VY, Scott JC, Miller RD. Thermally Stable Blue-Light-Emitting Copolymers of Poly(alkylfluorene). Macromolecules 1998. [DOI: 10.1021/ma970914e] [Citation(s) in RCA: 356] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Kreyenschmidt
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - G. Klaerner
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - T. Fuhrer
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - J. Ashenhurst
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - S. Karg
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - W. D. Chen
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - V. Y. Lee
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - J. C. Scott
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
| | - R. D. Miller
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120-6099
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