1
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Sekeresova Kralova J, Donic C, Dassa B, Livyatan I, Jansen PM, Ben-Dor S, Fidel L, Trzebanski S, Narunsky-Haziza L, Asraf O, Brenner O, Dafni H, Jona G, Boura-Halfon S, Stettner N, Segal E, Brunke S, Pilpel Y, Straussman R, Zeevi D, Bacher P, Hube B, Shlezinger N, Jung S. Competitive fungal commensalism mitigates candidiasis pathology. J Exp Med 2024; 221:e20231686. [PMID: 38497819 PMCID: PMC10949073 DOI: 10.1084/jem.20231686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 09/14/2023] [Revised: 01/17/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. heterogenica or K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.
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Affiliation(s)
| | - Catalina Donic
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Livyatan
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Paul Mathias Jansen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Lena Fidel
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Trzebanski
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Omer Asraf
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Dafni
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ghil Jona
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Yitzhak Pilpel
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ravid Straussman
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Zeevi
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Petra Bacher
- Institute of Immunology, Christian-Albrecht-University of Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Kiel, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Neta Shlezinger
- The Robert H. Smith Faculty of Agriculture, Food and Environment The Hebrew University of Jerusalem, Rehovot, Israel
| | - Steffen Jung
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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2
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Ben Nissan R, Milshtein E, Pahl V, de Pins B, Jona G, Levi D, Yung H, Nir N, Ezra D, Gleizer S, Link H, Noor E, Milo R. Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes. eLife 2024; 12:RP88793. [PMID: 38381041 PMCID: PMC10942610 DOI: 10.7554/elife.88793] [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] [Indexed: 02/22/2024] Open
Abstract
Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme's activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle's electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.
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Affiliation(s)
- Roee Ben Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Eliya Milshtein
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Vanessa Pahl
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of TübingenTübingenGermany
| | - Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Dikla Levi
- Department of Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Hadas Yung
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Noga Nir
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Dolev Ezra
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of TübingenTübingenGermany
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
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3
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Rezenman S, Knafo M, Tsigalnitski I, Barad S, Jona G, Levi D, Dym O, Reich Z, Kapon R. gUMI-BEAR, a modular, unsupervised population barcoding method to track variants and evolution at high resolution. PLoS One 2023; 18:e0286696. [PMID: 37285353 DOI: 10.1371/journal.pone.0286696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
Cellular lineage tracking provides a means to observe population makeup at the clonal level, allowing exploration of heterogeneity, evolutionary and developmental processes and individual clones' relative fitness. It has thus contributed significantly to understanding microbial evolution, organ differentiation and cancer heterogeneity, among others. Its use, however, is limited because existing methods are highly specific, expensive, labour-intensive, and, critically, do not allow the repetition of experiments. To address these issues, we developed gUMI-BEAR (genomic Unique Molecular Identifier Barcoded Enriched Associated Regions), a modular, cost-effective method for tracking populations at high resolution. We first demonstrate the system's application and resolution by applying it to track tens of thousands of Saccharomyces cerevisiae lineages growing together under varying environmental conditions applied across multiple generations, revealing fitness differences and lineage-specific adaptations. Then, we demonstrate how gUMI-BEAR can be used to perform parallel screening of a huge number of randomly generated variants of the Hsp82 gene. We further show how our method allows isolation of variants, even if their frequency in the population is low, thus enabling unsupervised identification of modifications that lead to a behaviour of interest.
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Affiliation(s)
- Shahar Rezenman
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Maor Knafo
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Ivgeni Tsigalnitski
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Shiri Barad
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Ghil Jona
- Life Sciences Core Facilities, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Dikla Levi
- Life Sciences Core Facilities, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Orly Dym
- The Dana and Yossie Hollander Center for Structural Proteomics, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
| | - Ruti Kapon
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, Israel
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4
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Jona G, Furman‐Haran E, Schmidt R. Realistic head-shaped phantom with brain-mimicking metabolites for 7 T spectroscopy and spectroscopic imaging. NMR Biomed 2021; 34:e4421. [PMID: 33015864 PMCID: PMC7757235 DOI: 10.1002/nbm.4421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/30/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
PURPOSE Moving to ultra-high fields (≥7 T), the inhomogeneity of both RF (B1 ) and static (B0 ) magnetic fields increases, which further motivates us to design a realistic head-shaped phantom, especially for spectroscopic imaging. Such phantoms provide images similar to the human brain and serve as a reliable tool for developing and examining methods in MRI. This study aims to develop and characterize a realistic head-shaped phantom filled with brain-mimicking metabolites for MRS and magnetic resonance spectroscopic imaging in a 7 T MRI scanner. METHODS A 3D head-shaped container with three sections-mimicking brain, muscle and precranial lipid-was constructed. The phantom was designed to provide robustness to heating, mechanical damage and leakage, with easy refilling. The head's shape and the agarose mixture were optimized to provide B0 and B1 distributions and T1 /T2 relaxation values similar to those of human brain. Eight brain-tissue-mimicking metabolites were included for spectroscopy. The phantom was evaluated for localized spectroscopy, fast spectroscopic imaging and fat suppression. RESULTS The B0 and B1 maps showed distribution similar to that of human brain, with increased B0 inhomogeneity near the nasal and ear areas and reduced B1 in the temporal lobe and brain stem regions, as expected in vivo. The metabolites' concentrations were verified by single-voxel spectroscopy, showing an average deviation of 11%. Fast spectroscopic imaging and imaging with fat suppression were demonstrated. CONCLUSION A 3D head-shaped phantom for human brain imaging and spectroscopic imaging in 7 T MRI was demonstrated, making it a realistic phantom for methodology development at 7 T.
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Affiliation(s)
- Ghil Jona
- Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Edna Furman‐Haran
- Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
- The Azrieli National Institute for Human Brain Imaging and ResearchWeizmann Institute of ScienceRehovotIsrael
| | - Rita Schmidt
- The Azrieli National Institute for Human Brain Imaging and ResearchWeizmann Institute of ScienceRehovotIsrael
- Neurobiology DepartmentWeizmann Institute of ScienceRehovotIsrael
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5
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Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, Jona G, Krieger E, Shamshoum M, Bar-Even A, Milo R. Conversion of Escherichia coli to Generate All Biomass Carbon from CO 2. Cell 2020; 179:1255-1263.e12. [PMID: 31778652 PMCID: PMC6904909 DOI: 10.1016/j.cell.2019.11.009] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/17/2019] [Accepted: 11/04/2019] [Indexed: 01/11/2023]
Abstract
The living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds. In spite of widespread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge. Here, we report the achievement of this transformation on laboratory timescales. We constructed and evolved Escherichia coli to produce all its biomass carbon from CO2. Reducing power and energy, but not carbon, are supplied via the one-carbon molecule formate, which can be produced electrochemically. Rubisco and phosphoribulokinase were co-expressed with formate dehydrogenase to enable CO2 fixation and reduction via the Calvin-Benson-Bassham cycle. Autotrophic growth was achieved following several months of continuous laboratory evolution in a chemostat under intensifying organic carbon limitation and confirmed via isotopic labeling.
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Affiliation(s)
- Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Krieger
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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6
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Korem Kohanim Y, Levi D, Jona G, Towbin BD, Bren A, Alon U. A Bacterial Growth Law out of Steady State. Cell Rep 2019; 23:2891-2900. [PMID: 29874577 DOI: 10.1016/j.celrep.2018.05.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 10/02/2017] [Revised: 02/21/2018] [Accepted: 05/01/2018] [Indexed: 11/28/2022] Open
Abstract
Bacterial growth follows simple laws in constant conditions. However, bacteria in nature often face fluctuating environments. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for upshifts using an optimal resource-allocation model: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and batch culture experiments, as well as previous data from several species. The increase in growth rate after an upshift indicates that ribosomes have spare capacity (SC). We demonstrate theoretically that SC has the cost of slow steady-state growth but is beneficial after an upshift because it prevents large overshoots in intracellular metabolites and allows rapid response to change. We also provide predictions for downshifts. The present study quantifies the optimal degree of SC, which rises the slower the growth rate, and suggests that SC can be precisely regulated.
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Affiliation(s)
- Yael Korem Kohanim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dikla Levi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Benjamin D Towbin
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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7
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Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y. Evolthon: A community endeavor to evolve lab evolution. PLoS Biol 2019; 17:e3000182. [PMID: 30925180 PMCID: PMC6440615 DOI: 10.1371/journal.pbio.3000182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Indexed: 11/29/2022] Open
Abstract
In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress—low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation. This Community Page article describes Evolthon; a first-of-its-kind community-based effort, involving about 30 participant labs around the world, aiming to explore the best strategy for evolving microorganisms to cope with an environmental challenge.
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Affiliation(s)
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Aaron N. Brooks
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Aditya M. Kunjapur
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alex N. Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Alice Flint
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Andras Solt
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Mershin
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
| | - Atray Dixit
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States of America
| | - Avihu H. Yona
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bálint Csörgő
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bede Phillip Busby
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Bianca P. Hennig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Csaba Pál
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - David G. Wernick
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Deepa Agashe
- National Centre for Biological Sciences, Bangalore, India
| | - Dikla Levi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dmitry Zabezhinsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dor Russ
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Ehud Sass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Tamar
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D. Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Idan Yelin
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Iftach Nachman
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jeffrey E. Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph M. Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lars M. Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marc Rübsam
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- The Molecular Biology of Metabolism laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Charitè University Medicine, Berlin, Germany
| | - Michael Klutstein
- Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael M. Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Ning Yin
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Noa Aharon Hefetz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Noah Jakimo
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
| | - Olga Snitser
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Omri Adini
- Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prashant Kumar
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Soo Hoo Smith
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
| | - Razi Zeidan
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Hazan
- Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roni Rak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roy Kishony
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
- Faculty of Computer Science, Technion–Israel Institute of Technology, Haifa, Israel
| | - Shannon Johnson
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
- Harvard University Extension School, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shira Nouriel
- Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sibylle C. Vonesch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Simmie Foster
- Harvard Medical School, Boston, Massachusetts, United States of America
- Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Tanita Wein
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Thrasyvoulos Karydis
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
| | - Timothy M. Wannier
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy Stiles
- Massachusetts Institute of Technology, Center for Bits and Atoms, Cambridge, Massachusetts, United States of America
- BosLab, Somerville, Massachusetts, United States of America
| | - Viridiana Olin-Sandoval
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Nutrition Physiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - William F. Mueller
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Yinon M. Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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8
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Goldshmit Y, Jona G, Schmukler E, Solomon S, Pinkas-Kramarski R, Ruban A. Blood Glutamate Scavenger as a Novel Neuroprotective Treatment in Spinal Cord Injury. J Neurotrauma 2018; 35:2581-2590. [DOI: 10.1089/neu.2017.5524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yona Goldshmit
- Steyer School of Health Professions, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Australian Regenerative Medicine Institute, Monash Biotechnology, Clayton, Victoria, Australia
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Schmukler
- Department of Neurobiology, Tel-Aviv University, Tel Aviv, Israel
| | - Shira Solomon
- Department of Neurobiology, Tel-Aviv University, Tel Aviv, Israel
| | | | - Angela Ruban
- Steyer School of Health Professions, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
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9
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Herbst RH, Bar-Zvi D, Reikhav S, Soifer I, Breker M, Jona G, Shimoni E, Schuldiner M, Levy AA, Barkai N. Heterosis as a consequence of regulatory incompatibility. BMC Biol 2017; 15:38. [PMID: 28494792 PMCID: PMC5426048 DOI: 10.1186/s12915-017-0373-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposite of hybrid incompatibility. In this view, the superior performance of the hybrid is attributed to heterozygote combinations that compensate for deleterious mutations accumulating in each individual genome, or lead to new, over-dominating interactions with improved performance. Still, only fragmented knowledge is available on genes and processes contributing to heterosis. RESULTS We describe a budding yeast hybrid that grows faster than both its parents under different environments. Phenotypically, the hybrid progresses more rapidly through cell cycle checkpoints, relieves the repression of respiration in fast growing conditions, does not slow down its growth when presented with ethanol stress, and shows increased signs of DNA damage. A systematic genetic screen identified hundreds of S. cerevisiae alleles whose deletion reduced growth of the hybrid. These growth-affecting alleles were condition-dependent, and differed greatly from alleles that reduced the growth of the S. cerevisiae parent. CONCLUSIONS Our results define a budding yeast hybrid that is perturbed in multiple regulatory processes but still shows a clear growth heterosis. We propose that heterosis results from incompatibilities that perturb regulatory mechanisms, which evolved to protect cells against damage or prepare them for future challenges by limiting cell growth.
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Affiliation(s)
- Rebecca H Herbst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02114, USA
| | - Dana Bar-Zvi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sharon Reikhav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilya Soifer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Current affiliation: Calico Labs, South San Francisco, CA, 94080, USA
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Avraham A Levy
- Plant and Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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10
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Abstract
Dissolution dynamic nuclear polarization (dDNP) is used to enhance the sensitivity of nuclear magnetic resonance (NMR), enabling monitoring of metabolism and specific enzymatic reactions in vivo. dDNP involves rapid sample dissolution and transfer to a spectrometer/scanner for subsequent signal detection. So far, most biologically oriented dDNP studies have relied on hyperpolarizing long-lived nuclear spin species such as (13)C in small molecules. While advantages could also arise from observing hyperpolarized (1)H, short relaxation times limit the utility of prepolarizing this sensitive but fast relaxing nucleus. Recently, it has been reported that (1)H NMR peaks in solution-phase experiments could be hyperpolarized by spontaneous magnetization transfers from bound (13)C nuclei following dDNP. This work demonstrates the potential of this sensitivity-enhancing approach to probe the enzymatic process that could not be suitably resolved by (13)C dDNP MR. Here we measured, in microorganisms, the action of pyruvate decarboxylase (PDC) and pyruvate formate lyase (PFL)-enzymes that catalyze the decarboxylation of pyruvate to form acetaldehyde and formate, respectively. While (13)C NMR did not possess the resolution to distinguish the starting pyruvate precursor from the carbonyl resonances in the resulting products, these processes could be monitored by (1)H NMR at 500 MHz. These observations were possible in both yeast and bacteria in minute-long kinetic measurements where the hyperpolarized (13)C enhanced, via (13)C → (1)H cross-relaxation, the signals of protons binding to the (13)C over the course of enzymatic reactions. In addition to these spontaneous heteronuclear enhancement experiments, single-shot acquisitions based on J-driven (13)C → (1)H polarization transfers were also carried out. These resulted in higher signal enhancements of the (1)H resonances but were not suitable for multishot kinetic studies. The potential of these (1)H-based approaches for measurements in vivo is briefly discussed.
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Affiliation(s)
- Piotr Dzien
- Klinik und Poliklinik für Nuklearmedizin, Technische Universität München , München 81675, Germany
- Cancer Research UK Cancer Institute , Cambridge CB2 0RE, United Kingdom
| | | | | | - Kevin M Brindle
- Cancer Research UK Cancer Institute , Cambridge CB2 0RE, United Kingdom
| | - Markus Schwaiger
- Klinik und Poliklinik für Nuklearmedizin, Technische Universität München , München 81675, Germany
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11
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Antonovsky N, Gleizer S, Noor E, Zohar Y, Herz E, Barenholz U, Zelcbuch L, Amram S, Wides A, Tepper N, Davidi D, Bar-On Y, Bareia T, Wernick DG, Shani I, Malitsky S, Jona G, Bar-Even A, Milo R. Sugar Synthesis from CO2 in Escherichia coli. Cell 2016; 166:115-25. [PMID: 27345370 PMCID: PMC4930481 DOI: 10.1016/j.cell.2016.05.064] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 11/29/2022]
Abstract
Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology. PaperClip
Non-native Calvin-Benson cycle allows for sugar synthesis from CO2 in E. coli Metabolic cutoff allows for the decoupling of energy harvesting from biomass synthesis Chemostat-based directed evolution led to the emergence of sugar synthesis from CO2 Mutations in flux branchpoints are essential for the CBB cycle stable operation
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Affiliation(s)
- Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Barenholz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aryeh Wides
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Tepper
- Department of Computer Science, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tasneem Bareia
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David G Wernick
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Shani
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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12
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Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PLoS One 2016; 11:e0153782. [PMID: 27100792 PMCID: PMC4839710 DOI: 10.1371/journal.pone.0153782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 08/31/2015] [Accepted: 04/04/2016] [Indexed: 11/25/2022] Open
Abstract
One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was to assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differentiating mouse embryonic bodies, and their expression patterns were measured. This novel approach was used to assess the accuracy of the tools, as established by comparing the observed results versus the results expected of the mouse controlled spiked-in transcripts. We found that detection of differential expression at the gene level is adequate, yet on the transcript-isoform level, all tools tested lacked accuracy and precision.
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Affiliation(s)
- Dena Leshkowitz
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- * E-mail:
| | - Ester Feldmesser
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gilgi Friedlander
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ghil Jona
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Elena Ainbinder
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yisrael Parmet
- Industrial Engineering and Management Department, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Shirley Horn-Saban
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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13
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Keren L, van Dijk D, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R, Segal E. Noise in gene expression is coupled to growth rate. Genome Res 2015; 25:1893-902. [PMID: 26355006 PMCID: PMC4665010 DOI: 10.1101/gr.191635.115] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [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: 02/27/2015] [Accepted: 09/09/2015] [Indexed: 11/24/2022]
Abstract
Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle–regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications.
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Affiliation(s)
- Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David van Dijk
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York 10027, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ghil Jona
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Segal E. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science 2015; 349:1101-1106. [PMID: 26229116 DOI: 10.1126/science.aac4812] [Citation(s) in RCA: 285] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/16/2015] [Indexed: 12/22/2022]
Abstract
Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.
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Affiliation(s)
- Tal Korem
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Jotham Suez
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Avnit-Sagi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Pompan-Lotan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Matot
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ghil Jona
- Department of Biological services, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Cohen
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Alexandra Sirota-Madi
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute
| | | | | | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ramnik Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
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15
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Ruban A, Malina KCK, Cooper I, Graubardt N, Babakin L, Jona G, Teichberg VI. Combined Treatment of an Amyotrophic Lateral Sclerosis Rat Model with Recombinant GOT1 and Oxaloacetic Acid: A Novel Neuroprotective Treatment. NEURODEGENER DIS 2015; 15:233-42. [PMID: 26113413 DOI: 10.1159/000382034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIM The sporadic form of the disease affects the majority of amyotrophic lateral sclerosis (ALS) patients. The role of glutamate (Glu) excitotoxicity in ALS has been extensively documented and remains one of the prominent hypotheses of ALS pathogenesis. In light of this evidence, the availability of a method to remove excess Glu from brain and spinal cord extracellular fluids without the need to deliver drugs across the blood-brain barrier and with minimal or no adverse effects may provide a major therapeutic asset, which is the primary aim of this study. METHODS The therapeutic efficacy of the combined treatment with recombinant Glu-oxaloacetate-transaminase (rGOT) and its co-factor oxaloacetic acid (OxAc) has been tested in an animal model of sporadic ALS. RESULTS We found that OxAc/rGOT treatment provides significant neuroprotection to spinal cord motor neurons. It also slows down the development of motor weakness and prolongs survival. CONCLUSION In this study we bring evidence that the administration of Glu scavengers to rats with sporadic ALS inhibited the massive death of spinal cord motor neurons, slowed the onset of motor weakness and prolonged survival. This treatment may be of high clinical significance for the future treatment of chronic neurodegenerative diseases.
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Affiliation(s)
- Angela Ruban
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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16
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Beck A, Vinik Y, Shatz-Azoulay H, Isaac R, Streim S, Jona G, Boura-Halfon S, Zick Y. Otubain 2 is a novel promoter of beta cell survival as revealed by siRNA high-throughput screens of human pancreatic islets. Diabetologia 2013; 56:1317-26. [PMID: 23515685 DOI: 10.1007/s00125-013-2889-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/28/2013] [Indexed: 12/19/2022]
Abstract
AIMS/HYPOTHESIS Pro-inflammatory cytokines induce death of beta cells and hamper engraftment of transplanted islet mass. Our aim was to reveal novel genes involved in this process, as a platform for innovative therapeutic approaches. METHODS Small interfering RNA (siRNA) high-throughput screening (HTS) of primary human islets was employed to identify novel genes involved in cytokine-induced beta cell apoptosis. Dispersed human islets from nine human donors, treated with a combination of TNF-α, IL-1β and IFN-γ were transfected with ∼730 different siRNAs. Caspase-3/7 activity was measured, results were analysed and potential anti- and pro-apoptotic genes were identified. RESULTS Dispersed human pancreatic islets appeared to be suitable targets for performance of siRNA HTS. Using this methodology we found a number of potential pro- and anti-apoptotic target hits that have not been previously associated with pancreatic beta cell death. One such hit was the de-ubiquitinating enzyme otubain 2 (OTUB2). OTUB2 knockdown increased caspase-3/7 activity in MIN6 cells and primary human islets and inhibited insulin secretion and increased nuclear factor-κB (NF-κB) activity both under basal conditions and following cytokine treatment. CONCLUSIONS Use of dispersed human islets provides a new platform for functional HTS in a highly physiological system. Employing this technique enabled the identification of OTUB2 as a novel promoter of viability and insulin secretion in human beta cells. OTUB2 acts through the inhibition of NF-κB signalling, which is deleterious to beta cell survival. siRNA screens of human islets may therefore identify new targets, such as OTUB2, for therapeutic intervention in type 1 diabetes and islet transplantation.
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Affiliation(s)
- A Beck
- Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl Street, Rehovot 76100, Israel
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17
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Meliopoulos VA, Andersen LE, Birrer KF, Simpson KJ, Lowenthal JW, Bean AGD, Stambas J, Stewart CR, Tompkins SM, van Beusechem VW, Fraser I, Mhlanga M, Barichievy S, Smith Q, Leake D, Karpilow J, Buck A, Jona G, Tripp RA. Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. FASEB J 2012; 26:1372-86. [PMID: 22247330 PMCID: PMC3316894 DOI: 10.1096/fj.11-193466] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [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] [Indexed: 01/23/2023]
Abstract
Influenza virus encodes only 11 viral proteins but replicates in a broad range of avian and mammalian species by exploiting host cell functions. Genome-wide RNA interference (RNAi) has proven to be a powerful tool for identifying the host molecules that participate in each step of virus replication. Meta-analysis of findings from genome-wide RNAi screens has shown influenza virus to be dependent on functional nodes in host cell pathways, requiring a wide variety of molecules and cellular proteins for replication. Because rapid evolution of the influenza A viruses persistently complicates the effectiveness of vaccines and therapeutics, a further understanding of the complex host cell pathways coopted by influenza virus for replication may provide new targets and strategies for antiviral therapy. RNAi genome screening technologies together with bioinformatics can provide the ability to rapidly identify specific host factors involved in resistance and susceptibility to influenza virus, allowing for novel disease intervention strategies.
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Affiliation(s)
- Victoria A Meliopoulos
- Department of Infectious Diseases, University of Georgia, 111 Carlton St., Athens, GA 30602, USA
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18
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Ho SW, Jona G, Chen CTL, Johnston M, Snyder M. Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A 2006; 103:9940-5. [PMID: 16785442 PMCID: PMC1502558 DOI: 10.1073/pnas.0509185103] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [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: 11/18/2022] Open
Abstract
Analyses of whole-genome sequences and experimental data sets have revealed a large number of DNA sequence motifs that are conserved in many species and may be functional. However, methods of sufficient scale to explore the roles of these elements are lacking. We describe the use of protein arrays to identify proteins that bind to DNA sequences of interest. A microarray of 282 known and potential yeast transcription factors was produced and probed with oligonucleotides of evolutionarily conserved sequences that are potentially functional. Transcription factors that bound to specific DNA sequences were identified. One previously uncharacterized DNA-binding protein, Yjl103, was characterized in detail. We defined the binding site for this protein and identified a number of its target genes, many of which are involved in stress response and oxidative phosphorylation. Protein microarrays offer a high-throughput method for determining DNA-protein interactions.
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Affiliation(s)
- Su-Wen Ho
- *Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108; and
| | - Ghil Jona
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8103
| | - Christina T. L. Chen
- *Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108; and
| | - Mark Johnston
- *Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108; and
- To whom correspondence may be addressed. E-mail:
or
| | - Michael Snyder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8103
- To whom correspondence may be addressed. E-mail:
or
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19
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Zhu H, Hu S, Jona G, Zhu X, Kreiswirth N, Willey BM, Mazzulli T, Liu G, Song Q, Chen P, Cameron M, Tyler A, Wang J, Wen J, Chen W, Compton S, Snyder M. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc Natl Acad Sci U S A 2006; 103:4011-6. [PMID: 16537477 PMCID: PMC1449637 DOI: 10.1073/pnas.0510921103] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [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: 02/04/2023] Open
Abstract
To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was constructed. These microarrays were used to screen approximately 400 Canadian sera from the SARS outbreak, including samples from confirmed SARS-CoV cases, respiratory illness patients, and healthcare professionals. A computer algorithm that uses multiple classifiers to predict samples from SARS patients was developed and used to predict 206 sera from Chinese fever patients. The test assigned patients into two distinct groups: those with antibodies to SARS-CoV and those without. The microarray also identified patients with sera reactive against other coronavirus proteins. Our results correlated well with an indirect immunofluorescence test and demonstrated that viral infection can be monitored for many months after infection. We show that protein microarrays can serve as a rapid, sensitive, and simple tool for large-scale identification of viral-specific antibodies in sera.
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Affiliation(s)
- Heng Zhu
- Departments of *Molecular, Cellular, and Developmental Biology and
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Shaohui Hu
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Ghil Jona
- Departments of *Molecular, Cellular, and Developmental Biology and
| | - Xiaowei Zhu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
| | - Nate Kreiswirth
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; and
| | - Barbara M. Willey
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; and
| | - Tony Mazzulli
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; and
| | - Guozhen Liu
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- **College of Life Sciences, Agricultural University of Hebei, Hebei, Baoding 071001, China
| | - Qifeng Song
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Peng Chen
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Mark Cameron
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; and
| | - Andrea Tyler
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; and
| | - Jian Wang
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jie Wen
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Weijun Chen
- Biochip Platform Division, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | | | - Michael Snyder
- Departments of *Molecular, Cellular, and Developmental Biology and
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
- To whom correspondence should be addressed. E-mail:
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20
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Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJR, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. Global analysis of protein phosphorylation in yeast. Nature 2005; 438:679-84. [PMID: 16319894 DOI: 10.1038/nature04187] [Citation(s) in RCA: 750] [Impact Index Per Article: 39.5] [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] [Received: 06/21/2005] [Accepted: 09/01/2005] [Indexed: 11/08/2022]
Abstract
Protein phosphorylation is estimated to affect 30% of the proteome and is a major regulatory mechanism that controls many basic cellular processes. Until recently, our biochemical understanding of protein phosphorylation on a global scale has been extremely limited; only one half of the yeast kinases have known in vivo substrates and the phosphorylating kinase is known for less than 160 phosphoproteins. Here we describe, with the use of proteome chip technology, the in vitro substrates recognized by most yeast protein kinases: we identified over 4,000 phosphorylation events involving 1,325 different proteins. These substrates represent a broad spectrum of different biochemical functions and cellular roles. Distinct sets of substrates were recognized by each protein kinase, including closely related kinases of the protein kinase A family and four cyclin-dependent kinases that vary only in their cyclin subunits. Although many substrates reside in the same cellular compartment or belong to the same functional category as their phosphorylating kinase, many others do not, indicating possible new roles for several kinases. Furthermore, integration of the phosphorylation results with protein-protein interaction and transcription factor binding data revealed novel regulatory modules. Our phosphorylation results have been assembled into a first-generation phosphorylation map for yeast. Because many yeast proteins and pathways are conserved, these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes.
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Affiliation(s)
- Jason Ptacek
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
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21
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Abstract
Protein microarrays containing thousands of proteins arrayed at high density can be prepared and probed for a wide variety of activities, thereby allowing the large scale analysis of many proteins simultaneously. In addition to identifying the activities of many previously uncharacterized proteins, protein microarrays can reveal new activities of well-characterized proteins, thus providing new insights about the functions of these proteins. Below, we describe the construction and use of protein microarrays and their applications using yeast as a model system.
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Affiliation(s)
- Michael G Smith
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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22
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Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 2004; 36:1331-9. [PMID: 15543148 PMCID: PMC2692596 DOI: 10.1038/ng1473] [Citation(s) in RCA: 291] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Accepted: 10/18/2004] [Indexed: 11/10/2022]
Abstract
We developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding-site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.
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Affiliation(s)
- Sonali Mukherjee
- Division of Genetics, Department of Medicine, Harvard Medical School; Boston; Massachusetts 02115, USA.
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23
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Jona G, Snyder M. Recent developments in analytical and functional protein microarrays. Curr Opin Mol Ther 2003; 5:271-7. [PMID: 12870437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In recent years, the genomes of many different organisms have been fully sequenced and annotated. As a consequence of this information, a number of methods have emerged to study the function of many genes and proteins in parallel. One recent approach for the large-scale analysis of proteins is the use of protein microarrays in which hundreds to thousands of proteins are arrayed and assayed simultaneously. Protein arrays can be used for assessing protein levels and following disease markers, identifying biochemical activities, analyzing post-translational modifications, building interaction networks, and for drug discovery and development. In this review, we discuss the construction of different types of protein arrays, and their numerous and diverse applications.
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Affiliation(s)
- Ghil Jona
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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24
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Jona G, Livi LL, Gileadi O. Mutations in the RING domain of TFB3, a subunit of yeast transcription factor IIH, reveal a role in cell cycle progression. J Biol Chem 2002; 277:39409-16. [PMID: 12176978 DOI: 10.1074/jbc.m202733200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase II general transcription factor TFIIH is composed of 9 known subunits and possesses DNA helicase and protein kinase activities. The kinase subunits of TFIIH in animal cells, Cdk7, cyclin H, and MAT1, were independently isolated as an activity termed CAK (Cdk-activating kinase), which phosphorylates and activates cell cycle kinases. However, CAK activity of TFIIH subunits could not be demonstrated in budding yeast. TFB3, the 38-kDa subunit of yeast TFIIH, is the homolog of mammalian MAT1. By random mutagenesis we have isolated a temperature-sensitive mutation in the conserved RING domain. The mutant Tfb3 protein associates less efficiently with the kinase moiety of TFIIH than the wild type protein. In contrast to lethal mutants in other subunits of TFIIH, this mutation does not impair general transcription. Transcription of CLB2, and possibly other genes, is reduced in the mutant. At the restrictive temperature, the cells display a defect in cell cycle progression, which is manifest at more than one phase of the cycle. To conclude, in the present study we bring another demonstration of the multifunctional nature of TFIIH.
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Affiliation(s)
- Ghil Jona
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Abstract
Yeast cells lacking transcription elongation factor genes such as PPR2 (TFIIS) and ELP (Elongator) are viable and show deleterious phenotypes only when transcription is rendered less effective by RNA polymerase mutations or by decreasing nucleotide pools. Here we demonstrate that deletion of the CTK1 gene, encoding the kinase subunit of RNA polymerase II carboxy-terminal domain kinase I (CTDK-I), is synthetically lethal when combined with deletion of PPR2 or ELP genes. The inviability of ctk1 elp3 double mutants can be rescued by expression of an Elp3 mutant that has retained its ability to form the Elongator complex but has severely diminished histone acetyltransferase activity, suggesting that the functional overlap between CTDK-I and Elongator is in assembly of RNA polymerase II elongation complexes. Our results suggest that CTDK-I plays an important role in transcriptional elongation in vivo, possibly by creating a form of RNA polymerase that is less prone to transcriptional arrest.
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Affiliation(s)
- G Jona
- Department of Molecular Genetics, The Weizmann Institute of Science, 76100, Rehovot, Israel
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26
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Shani G, Henis-Korenblit S, Jona G, Gileadi O, Eisenstein M, Ziv T, Admon A, Kimchi A. Autophosphorylation restrains the apoptotic activity of DRP-1 kinase by controlling dimerization and calmodulin binding. EMBO J 2001; 20:1099-113. [PMID: 11230133 PMCID: PMC145456 DOI: 10.1093/emboj/20.5.1099] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [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] [Indexed: 11/13/2022] Open
Abstract
DRP-1 is a pro-apoptotic Ca2+/calmodulin (CaM)-regulated serine/threonine kinase, recently isolated as a novel member of the DAP-kinase family of proteins. It contains a short extra-catalytic tail required for homodimerization. Here we identify a novel regulatory mechanism that controls its pro-apoptotic functions. It comprises a single autophosphorylation event mapped to Ser308 within the CaM regulatory domain. A negative charge at this site reduces both the binding to CaM and the formation of DRP-1 homodimers. Conversely, the dephosphorylation of Ser308, which takes place in response to activated Fas or tumour necrosis factor-alpha death receptors, increases the formation of DRP-1 dimers, facilitates the binding to CaM and activates the pro-apoptotic effects of the protein. Thus, the process of enzyme activation is controlled by two unlocking steps that must work in concert, i.e. dephosphorylation, which probably weakens the electrostatic interactions between the CaM regulatory domain and the catalytic cleft, and homodimerization. This mechanism of negative autophosphorylation provides a safety barrier that restrains the killing effects of DRP-1, and a target for efficient activation of the kinase by various apoptotic stimuli.
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Affiliation(s)
| | | | | | | | - Miriam Eisenstein
- Departments of Molecular Genetics and
Chemical Services, Weizmann Institute of Science, Rehovot 76100 and The Smoler Protein Research Center, Department of Biology, Technion Haifa 32000, Israel Corresponding author e-mail:
| | - Tamar Ziv
- Departments of Molecular Genetics and
Chemical Services, Weizmann Institute of Science, Rehovot 76100 and The Smoler Protein Research Center, Department of Biology, Technion Haifa 32000, Israel Corresponding author e-mail:
| | - Arie Admon
- Departments of Molecular Genetics and
Chemical Services, Weizmann Institute of Science, Rehovot 76100 and The Smoler Protein Research Center, Department of Biology, Technion Haifa 32000, Israel Corresponding author e-mail:
| | - Adi Kimchi
- Departments of Molecular Genetics and
Chemical Services, Weizmann Institute of Science, Rehovot 76100 and The Smoler Protein Research Center, Department of Biology, Technion Haifa 32000, Israel Corresponding author e-mail:
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27
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Jona G, Choder M, Gileadi O. Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochim Biophys Acta 2000; 1491:37-48. [PMID: 10760568 DOI: 10.1016/s0167-4781(00)00016-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gradual depletion of essential nutrients in yeast cultures induces a complex physiological response, leading initially to induction of pathways required for the utilization of alternative nutrients and, when such sources are depleted, to entry into stationary phase. Abrupt removal of sugar does not allow the proper establishment of stationary phase. Here we report that abrupt removal of glucose from the growth medium elicits a coordinated response in yeast cells that resembles, in some aspects, the gradual passage to stationary phase. Phosphorylation of RNA polymerase II at a subset of sites in the COOH-terminal domain (CTD) is decreased. Transcription by RNA polymerases I and II is shut down almost completely, whereas transcription by RNA polymerase III continues. In parallel, the rate of mRNA degradation is drastically reduced, at a stage preceding poly(A) shortening. This response is suited for conservation of scarce resources while preserving the ability of cells to recover when nutrients become available.
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Affiliation(s)
- G Jona
- Department of Molecular Genetics, The Weizmann Institute, Rehovot, Israel
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28
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Ringo J, Jona G, Rockwell R, Segal D, Cohen E. Genetic variation for resistance to chlorpyrifos in Drosophila melanogaster (Diptera: Drosophilidae) infesting grapes in Israel. J Econ Entomol 1995; 88:1158-1163. [PMID: 7593893 DOI: 10.1093/jee/88.5.1158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Five species of drosophilid flies were observed breeding in grapes growing in Israel; of these, 2 species, Drosophila melanogaster (Meigen) and D. simulans Sturtevant, are major pests. Natural populations of both species were sampled and tested for resistance to chlorpyrifos; the 2 more intensively sampled populations were D. melanogaster in commercial vineyards. One vineyard had been treated repeatedly with chlorpyrifos to control this secondary pest species; the other had never been treated with an organophosphorus compound. The LC50 to chlorpyrifos of a genetically heterogeneous line of D. melanogaster from the exposed population (Be'er Tuvia) was 99 ng/cm2, and the LC50 of a corresponding line from the unexposed population (Sde Eliahu) was 52 ng/cm2; the wild-caught lines were much more resistant than a laboratory strain, Canton-S, whose LC50 was 0.25 ng/cm2. Genetic variance for resistance existed in both natural populations but realized heritability did not differ significantly between the populations. In crosses between a highly resistant strain and several sensitive laboratory strains of D. melanogaster, resistance was dominant. A resistance factor was mapped to a locus on chromosome 2 (approximately 2-72).
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Affiliation(s)
- J Ringo
- Department of Entomology, Faculty of Agriculture, Hebrew University, Rehovot, Israel
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29
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Bernard E, Jona G. [Measurement of anxiety in a population of prisoners]. Quad Criminol Clin 1978; 20:293-9. [PMID: 756569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Cattle's IPAT anxiety scale test has been used in a population of prisoners during a three years period. The specific features of these subjects suggest great caution in the interpretation of this tests, that was originally validated on different populations. For psychodiagnostic and therapeutic purposes each score should be specifically checked. Other observations are made and some suggestions are also given.
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30
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Krompecher T, Krompecher-Kiss E, Jona G. [Cytochrome oxidase activity in various rat organs following 200 Rad whole-body 60Co-irradiation]. Strahlentherapie 1974; 147:432-6. [PMID: 4369527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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31
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Jona G, Ricci V. [Psychic examination of a long hospitalized patient. Semeiotic notes]. Osp Psichiatr 1971; 39:188-208. [PMID: 5151142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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32
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Jona G, Sacerdote G, Rossi G. [Aphasia as a disorder of communication. Preliminary notes on symptomatology]. Minerva Med 1968; 59:2564-9. [PMID: 5691457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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33
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Sacerdote G, Jona G, Rossi G. [Aphasia as a disturbance of communication]. Minerva Med 1967; 58:1248-52. [PMID: 4860809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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