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Meril S, Muhlbauer Avni M, Lior C, Bahlsen M, Olender T, Savidor A, Krausz J, Belhanes Peled H, Birisi H, David N, Bialik S, Scherz-Shouval R, Ben David Y, Kimchi A. Loss of EIF4G2 mediates aggressiveness in distinct human endometrial cancer subpopulations with poor survival outcome in patients. Oncogene 2024; 43:1098-1112. [PMID: 38388710 PMCID: PMC10997518 DOI: 10.1038/s41388-024-02981-x] [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: 10/08/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The non-canonical translation initiation factor EIF4G2 plays essential roles in cellular stress responses via translation of selective mRNA cohorts. Currently there is limited and conflicting information regarding its involvement in cancer development and progression. Here we assessed its role in endometrial cancer (EC), in a cohort of 280 EC patients across different types, grades, and stages, and found that low EIF4G2 expression highly correlated with poor overall- and recurrence-free survival in Grade 2 EC patients, monitored over a period of up to 12 years. To establish a causative connection between low EIF4G2 expression and cancer progression, we stably knocked-down EIF4G2 in two human EC cell lines in parallel. EIF4G2 depletion resulted in increased resistance to conventional therapies and increased the prevalence of molecular markers for aggressive cell subsets, altering their transcriptional and proteomic landscapes. Prominent among the proteins with decreased abundance were Kinesin-1 motor proteins, KIF5B and KLC1, 2, 3. Multiplexed imaging of the EC patient tumor cohort showed a correlation between decreased expression of the kinesin proteins, and poor survival in patients with tumors of certain grades and stages. These findings reveal potential novel biomarkers for Grade 2 EC with ramifications for patient stratification and therapeutic interventions.
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Affiliation(s)
- Sara Meril
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Muhlbauer Avni
- Department of Obstetrics and Gynecology, Emek Medical Center, Afula, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Chen Lior
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Marcela Bahlsen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alon Savidor
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Judit Krausz
- Pathology Department, Emek Medical Center, Afula, Israel
| | | | - Hila Birisi
- Pathology Department, Emek Medical Center, Afula, Israel
| | - Nofar David
- Pathology Department, Emek Medical Center, Afula, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yehuda Ben David
- Department of Obstetrics and Gynecology, Emek Medical Center, Afula, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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Meril S, Bahlsen M, Eisenstein M, Savidor A, Levin Y, Bialik S, Pietrokovski S, Kimchi A. Loss-of-function cancer-linked mutations in the EIF4G2 non-canonical translation initiation factor. Life Sci Alliance 2024; 7:e202302338. [PMID: 38129098 PMCID: PMC10746786 DOI: 10.26508/lsa.202302338] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed because of cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site (IRES)- and uORF-dependent initiation mechanisms, which can be used to modulate protein expression in cancer. Here, we explored the contribution of EIF4G2 to cancer by screening the COSMIC database for EIF4G2 somatic mutations in cancer patients. Functional examination of missense mutations revealed deleterious effects on EIF4G2 protein-protein interactions and, importantly, on its ability to mediate non-canonical translation initiation. Specifically, one mutation, R178Q, led to reductions in protein expression and near-complete loss of function. Two other mutations within the MIF4G domain specifically affected EIF4G2's ability to mediate IRES-dependent translation initiation but not that of target mRNAs with uORFs. These results shed light on both the structure-function of EIF4G2 and its potential tumor suppressor effects.
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Affiliation(s)
- Sara Meril
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marcela Bahlsen
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Eisenstein
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- https://ror.org/0316ej306 The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- https://ror.org/0316ej306 The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Shani Bialik
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Kimchi
- https://ror.org/0316ej306 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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3
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Danino YM, Molitor L, Rosenbaum-Cohen T, Kaiser S, Cohen Y, Porat Z, Marmor-Kollet H, Katina C, Savidor A, Rotkopf R, Ben-Isaac E, Golani O, Levin Y, Monchaud D, Hickson I, Hornstein E. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures. Nucleic Acids Res 2023; 51:9369-9384. [PMID: 37503837 PMCID: PMC10516661 DOI: 10.1093/nar/gkad613] [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: 01/18/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.
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Affiliation(s)
- Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lena Molitor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Rosenbaum-Cohen
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Brain science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sebastian Kaiser
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- 1E therapeutics, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Ben-Isaac
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ofra Golani
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, uB Dijon, France
| | - Ian D Hickson
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
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4
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Shakked A, Petrover Z, Aharonov A, Ghiringhelli M, Umansky KB, Kain D, Elkahal J, Divinsky Y, Nguyen PD, Miyara S, Friedlander G, Savidor A, Zhang L, Perez DE, Sarig R, Lendengolts D, Bueno-Levy H, Kastan N, Levin Y, Bakkers J, Gepstein L, Tzahor E. Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury. Nat Cardiovasc Res 2023; 2:383-398. [PMID: 37974970 PMCID: PMC10653068 DOI: 10.1038/s44161-023-00250-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/09/2023] [Indexed: 11/19/2023]
Abstract
Cardiomyocyte proliferation and dedifferentiation have fueled the field of regenerative cardiology in recent years, whereas the reverse process of redifferentiation remains largely unexplored. Redifferentiation is characterized by the restoration of function lost during dedifferentiation. Previously, we showed that ERBB2-mediated heart regeneration has these two distinct phases: transient dedifferentiation and redifferentiation. Here we survey the temporal transcriptomic and proteomic landscape of dedifferentiation-redifferentiation in adult mouse hearts and reveal that well-characterized dedifferentiation features largely return to normal, although elements of residual dedifferentiation remain, even after the contractile function is restored. These hearts appear rejuvenated and show robust resistance to ischemic injury, even 5 months after redifferentiation initiation. Cardiomyocyte redifferentiation is driven by negative feedback signaling and requires LATS1/2 Hippo pathway activity. Our data reveal the importance of cardiomyocyte redifferentiation in functional restoration during regeneration but also protection against future insult, in what could lead to a potential prophylactic treatment against ischemic heart disease for at-risk patients.
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Affiliation(s)
- Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zachary Petrover
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alla Aharonov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Matteo Ghiringhelli
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Kfir-Baruch Umansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Kain
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Elkahal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yalin Divinsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Phong Dang Nguyen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shoval Miyara
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Lingling Zhang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dahlia E. Perez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rachel Sarig
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daria Lendengolts
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hanna Bueno-Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathaniel Kastan
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY, USA
| | - Yishai Levin
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lior Gepstein
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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5
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David M, Olender T, Mizrahi O, Weingarten-Gabbay S, Friedlander G, Meril S, Goldberg N, Savidor A, Levin Y, Salomon V, Stern-Ginossar N, Bialik S, Kimchi A. DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells. RNA 2022; 28:1325-1336. [PMID: 35961752 PMCID: PMC9479741 DOI: 10.1261/rna.079194.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was KMT2D, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or reinitiation at the main coding sequence. Crosslinking protein-RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.
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Affiliation(s)
- Maya David
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Meril
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadav Goldberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vered Salomon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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6
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Goldsmith M, Barad S, Knafo M, Savidor A, Ben-Dor S, Brandis A, Mehlman T, Peleg Y, Albeck S, Dym O, Ben-Zeev E, Barbole RS, Aharoni A, Reich Z. Identification and characterization of the key enzyme in the biosynthesis of the neurotoxin β-ODAP in grass pea. J Biol Chem 2022; 298:101806. [PMID: 35271851 PMCID: PMC9061259 DOI: 10.1016/j.jbc.2022.101806] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
Grass pea (Lathyrus sativus L.) is a grain legume commonly grown in Asia and Africa for food and forage. It is a highly nutritious and robust crop, capable of surviving both droughts and floods. However, it produces a neurotoxic compound, β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a severe neurological disorder when consumed as a primary diet component. While the catalytic activity associated with β-ODAP formation was demonstrated more than 50 years ago, the enzyme responsible for this activity has not been identified. Here, we report on the identity, activity, 3D structure, and phylogenesis of this enzyme—β-ODAP synthase (BOS). We show that BOS belongs to the benzylalcohol O-acetyltransferase, anthocyanin O-hydroxycinnamoyltransferase, anthranilate N-hydroxycinnamoyl/benzoyltransferase, deacetylvindoline 4-O-acetyltransferase superfamily of acyltransferases and is structurally similar to hydroxycinnamoyl transferase. Using molecular docking, we propose a mechanism for its catalytic activity, and using heterologous expression in tobacco leaves (Nicotiana benthamiana), we demonstrate that expression of BOS in the presence of its substrates is sufficient for β-ODAP production in vivo. The identification of BOS may pave the way toward engineering β-ODAP–free grass pea cultivars, which are safe for human and animal consumption.
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Affiliation(s)
- Moshe Goldsmith
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Shiri Barad
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maor Knafo
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alon Savidor
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shifra Ben-Dor
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alexander Brandis
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tevie Mehlman
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yoav Peleg
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shira Albeck
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Orly Dym
- Dept. of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Ben-Zeev
- Medicinal Chemistry Unit, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ranjit S Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel; Plant Molecular Biology Unit, Division of Biochemical Sciences, Council of Scientific and Industrial Research-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Reich
- Dept. of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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7
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Hammer L, Levin‐Salomon V, Yaeli‐Slonim N, Weiss M, Dekel‐Bird NP, Olender T, Porat Z, Winograd‐Katz S, Savidor A, Levin Y, Bialik S, Geiger B, Kimchi A. A new function for the serine protease HtrA2 in controlling radiation‐induced senescence in cancer cells. Mol Oncol 2022; 16:1365-1383. [PMID: 35122388 PMCID: PMC8936513 DOI: 10.1002/1878-0261.13187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/08/2021] [Accepted: 02/03/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Liat Hammer
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Vered Levin‐Salomon
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Naama Yaeli‐Slonim
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Moria Weiss
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Naama P. Dekel‐Bird
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Tsviya Olender
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Ziv Porat
- Dept. Life Sciences Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel
| | | | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G‐INCPM) Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G‐INCPM) Weizmann Institute of Science Rehovot 7610001 Israel
| | - Shani Bialik
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Benjamin Geiger
- Dept. Immunology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Adi Kimchi
- Dept. Molecular Genetics Weizmann Institute of Science Rehovot 7610001 Israel
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8
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Ungar B, Yavzori M, Fudim E, Picard O, Kopylov U, Eliakim R, Shouval D, Levin Y, Savidor A, Ben-Moshe S, Manco R, Dan S, Egozi A, Bahar Halpern K, Mayer C, Barshack I, Ben-Horin S, Itzkovitz S. Host transcriptome signatures in human faecal-washes predict histological remission in patients with IBD. Gut 2022; 71:gutjnl-2021-325516. [PMID: 35046090 DOI: 10.1136/gutjnl-2021-325516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/08/2021] [Indexed: 12/08/2022]
Abstract
BACKGROUND Colonoscopy is the gold standard for evaluation of inflammation in inflammatory bowel diseases (IBDs), yet entails cumbersome preparations and risks of injury. Existing non-invasive prognostic tools are limited in their diagnostic power. Moreover, transcriptomics of colonic biopsies have been inconclusive in their association with clinical features. AIMS To assess the utility of host transcriptomics of faecal wash samples of patients with IBD compared with controls. METHODS In this prospective cohort study, we obtained biopsies and faecal-wash samples from patients with IBD and controls undergoing lower endoscopy. We performed RNAseq of biopsies and matching faecal-washes, and associated them with endoscopic and histological inflammation status. We also performed faecal mass-spectrometry proteomics on a subset of samples. We inferred cell compositions using computational deconvolution and used classification algorithms to identify informative genes. RESULTS We analysed biopsies and faecal washes from 39 patients (20 IBD, 19 controls). Host faecal-transcriptome carried information that was distinct from biopsy RNAseq and faecal proteomics. Transcriptomics of faecal washes, yet not of biopsies, from patients with histological inflammation were significantly correlated to one another (p=5.3×10-12). Faecal-transcriptome had significantly higher statistical power in identifying histological inflammation compared with transctiptome of intestinal biopsies (150 genes with area under the curve >0.9 in faecal samples vs 10 genes in biopsy RNAseq). These results were replicated in a validation cohort of 22 patients (10 IBD, 12 controls). Faecal samples were enriched in inflammatory monocytes, regulatory T cells, natural killer-cells and innate lymphoid cells. CONCLUSIONS Faecal wash host transcriptome is a statistically powerful biomarker reflecting histological inflammation. Furthermore, it opens the way to identifying important correlates and therapeutic targets that may be obscured using biopsy transcriptomics.
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Affiliation(s)
- Bella Ungar
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Ella Fudim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Orit Picard
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Rami Eliakim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, & Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rita Manco
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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9
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Harnik Y, Buchauer L, Ben-Moshe S, Averbukh I, Levin Y, Savidor A, Eilam R, Moor AE, Itzkovitz S. Spatial discordances between mRNAs and proteins in the intestinal epithelium. Nat Metab 2021; 3:1680-1693. [PMID: 34931081 DOI: 10.1038/s42255-021-00504-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
The use of transcriptomes as reliable proxies for cellular proteomes is controversial. In the small intestine, enterocytes operate for 4 days as they migrate along villi, which are highly graded microenvironments. Spatial transcriptomics have demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here we show that enterocyte proteins and messenger RNAs along the villus axis are zonated, yet often spatially discordant. Using spatial sorting with zonated surface markers, together with a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, we find that, while many genes exhibit proteins zonated toward the villus tip, mRNA is zonated toward the villus bottom. Finally, we demonstrate that space-independent protein synthesis delays can explain many of the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium, highlighting the importance of protein measurements for inferring cell states in tissues that operate outside of steady state.
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Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa Buchauer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Averbukh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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10
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Doron S, Lampl N, Savidor A, Katina C, Gabashvili A, Levin Y, Rosenwasser S. SPEAR: A proteomics approach for simultaneous protein expression and redox analysis. Free Radic Biol Med 2021; 176:366-377. [PMID: 34619326 DOI: 10.1016/j.freeradbiomed.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
Oxidation and reduction of protein cysteinyl thiols serve as molecular switches, which is considered the most central mechanism for redox regulation of biological processes, altering protein structure, biochemical activity, subcellular localization, and binding affinity. Redox proteomics allows global identification of redox-modified cysteine (Cys) sites and quantification of their reversible oxidation/reduction responses, serving as a hypothesis-generating platform to stimulate redox biology mechanistic research. Here, we developed Simultaneous Protein Expression and Redox (SPEAR) analysis, a new redox-proteomics approach based on differential labeling of reversibly oxidized and reduced cysteines with light and heavy isotopic forms of commercially available isotopically-labeled N-ethylmaleimide (NEM). The presented method does not require enrichment for labeled peptides, thus enabling simultaneous quantification of Cys reversible oxidation state and protein abundance. Using SPEAR, we were able to quantify the in-vivo reversible oxidation state of thousands of cysteines across the Arabidopsis proteome under steady-state and oxidative stress conditions. Functional assignment of the identified redox-sensitive proteins demonstrated the widespread effect of oxidative conditions on various cellular functions and highlighted the enrichment of chloroplastic proteins. SPEAR provides a simple, straightforward, and cost-effective means of studying redox proteome dynamics. The presented data provide a global quantitative view of the reversible oxidation of well-known redox-regulated active sites and many novel redox-sensitive sites whose role in plant acclimation to stress conditions remains to be further explored.
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Affiliation(s)
- Shani Doron
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Nardy Lampl
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexandra Gabashvili
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.
| | - Shilo Rosenwasser
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel.
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11
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Tamim-Yecheskel BC, Fraiberg M, Kokabi K, Freud S, Shatz O, Marvaldi L, Subic N, Brenner O, Tsoory M, Eilam-Altstadter R, Biton I, Savidor A, Dezorella N, Heimer G, Behrends C, Ben-Zeev B, Elazar Z. A tecpr2 knockout mouse exhibits age-dependent neuroaxonal dystrophy associated with autophagosome accumulation. Autophagy 2020; 17:3082-3095. [PMID: 33218264 DOI: 10.1080/15548627.2020.1852724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mutations in the coding sequence of human TECPR2 were recently linked to spastic paraplegia type 49 (SPG49), a hereditary neurodegenerative disorder involving intellectual disability, autonomic-sensory neuropathy, chronic respiratory disease and decreased pain sensitivity. Here, we report the generation of a novel CRISPR-Cas9 tecpr2 knockout (tecpr2-/-) mouse that exhibits behavioral pathologies observed in SPG49 patients. tecpr2-/- mice develop neurodegenerative patterns in an age-dependent manner, manifested predominantly as neuroaxonal dystrophy in the gracile (GrN) and cuneate nuclei (CuN) of the medulla oblongata in the brainstem and dorsal white matter column of the spinal cord. Age-dependent correlation with accumulation of autophagosomes suggests compromised targeting to lysosome. Taken together, our findings establish the tecpr2 knockout mouse as a potential model for SPG49 and ascribe a new role to TECPR2 in macroautophagy/autophagy-related neurodegenerative disorders.
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Affiliation(s)
| | - Milana Fraiberg
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Kamilya Kokabi
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Saskia Freud
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Oren Shatz
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Letizia Marvaldi
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Nemanja Subic
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Recourses, The Weizmann Institute of Science, Rehovot, Israel
| | - Michael Tsoory
- Veterinary Recourses, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Inbal Biton
- Veterinary Recourses, The Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging, The Weizmann Institute of Science, Rehovot, Israel
| | - Gali Heimer
- Department of Pediatric Neurology Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christian Behrends
- Munich Cluster for Systems Neurology (Synergy), Ludwig-Maximilians-Universität München, München, Germany
| | - Bruria Ben-Zeev
- Department of Pediatric Neurology Unit, Edmond and Lilly Safra Children Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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12
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Kapach G, Nuri R, Schmidt C, Danin A, Ferrera S, Savidor A, Gerlach RG, Shai Y. Loss of the Periplasmic Chaperone Skp and Mutations in the Efflux Pump AcrAB-TolC Play a Role in Acquired Resistance to Antimicrobial Peptides in Salmonella typhimurium. Front Microbiol 2020; 11:189. [PMID: 32210923 PMCID: PMC7075815 DOI: 10.3389/fmicb.2020.00189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/30/2019] [Accepted: 01/27/2020] [Indexed: 01/01/2023] Open
Abstract
Bacterial resistance to antibiotics is a major concern worldwide, leading to an extensive search for alternative drugs. Promising candidates are antimicrobial peptides (AMPs), innate immunity molecules, shown to be highly efficient against multidrug resistant bacteria. Therefore, it is essential to study bacterial resistance mechanisms against them. For that purpose, we used experimental evolution, and isolated a Salmonella enterica serovar typhimurium-resistant line to the AMP 4DK5L7. This AMP displayed promising features including widespread activity against Gram-negative bacteria and protection from proteolytic degradation. However, the resistance that evolved in the isolated strain was particularly high. Whole genome sequencing revealed that five spontaneous mutations had evolved. Of these, three are novel in the context of acquired AMP resistance. Two mutations are related to the AcrAB-TolC multidrug efflux pump. One occurred in AcrB, the substrate-binding domain of the system, and the second in RamR, a transcriptional regulator of the system. Together, the mutations increased the minimal inhibitory concentration (MIC) by twofold toward this AMP. Moreover, the mutation in AcrB induced hypersusceptibility toward ampicillin and colistin. The last mutation occurred in Skp, a periplasmic chaperone that participates in the biogenesis of outer membrane proteins (OMPs). This mutation increased the MIC by twofold to 4DK5L7 and by fourfold to another AMP, seg5D. Proteomic analysis revealed that the mutation abolished Skp expression, reduced OMP abundance, and increased DegP levels. DegP, a protease that was reported to have an additional chaperone activity, escorts OMPs through the periplasm along with Skp, but is also associated with AMP resistance. In conclusion, our data demonstrate that both loss of Skp and manipulation of the AcrAB-TolC system are alternative strategies of AMP acquired resistance in Salmonella typhimurium and might represent a common mechanism in other Gram-negative bacteria.
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Affiliation(s)
- Gal Kapach
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Reut Nuri
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Danin
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Ferrera
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Roman G Gerlach
- Project Group 5, Robert Koch Institute, Wernigerode, Germany
| | - Yechiel Shai
- Departmant of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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13
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Cohen R, Milo S, Sharma S, Savidor A, Covo S. Ribonucleotide reductase from Fusarium oxysporum does not Respond to DNA replication stress. DNA Repair (Amst) 2019; 83:102674. [PMID: 31375409 DOI: 10.1016/j.dnarep.2019.102674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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] [Received: 03/28/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in dNTP biosynthesis and is tightly regulated at the transcription and activity levels. One of the best characterized responses of yeast to DNA damage is up-regulation of RNR transcription and activity and consequently, elevation of the dNTP pools. Hydroxyurea is a universal inhibitor of RNR that causes S phase arrest. It is used in the clinic to treat certain types of cancers. Here we studied the response of the fungal plant pathogen Fusarium oxysporum to hydroxyurea in order to generate hypotheses that can be used in the future in development of a new class of pesticides. F. oxysporum causes severe damage to more than 100 agricultural crops and specifically threatens banana cultivation world-wide. Although the recovery of F. oxysporum from transient hydroxyurea exposure was similar to the one of Saccharomyces cerevisiae, colony formation was strongly inhibited in F. oxysporum in comparison with S. cerevisiae. As expected, genomic and phosphoproteomic analyses of F. oxysporum conidia (spores) exposed to hydroxyurea showed hallmarks of DNA replication perturbation and activation of recombination. Unexpectedly and strikingly, RNR was not induced by either hydroxyurea or the DNA-damaging agent methyl methanesulfonate as determined at the RNA and protein levels. Consequently, dNTP concentrations were significantly reduced, even in response to a low dose of hydroxyurea. Methyl methanesulfonate treatment did not induce dNTP pools in F. oxysporum, in contrast to the response of RNR and dNTP pools to DNA damage and hydroxyurea in several tested organisms. Our results are important because the lack of a feedback mechanism to increase RNR expression in F. oxysporum is expected to sensitize the pathogen to a fungal-specific ribonucleotide inhibitor. The potential impact of our observations on F. oxysporum genome stability and genome evolution is discussed.
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Affiliation(s)
- Rotem Cohen
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Shira Milo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alon Savidor
- de Botton Institute for Protein Profiling, the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel.
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14
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Tamary E, Nevo R, Naveh L, Levin‐Zaidman S, Kiss V, Savidor A, Levin Y, Eyal Y, Reich Z, Adam Z. Chlorophyll catabolism precedes changes in chloroplast structure and proteome during leaf senescence. Plant Direct 2019; 3:e00127. [PMID: 31245770 PMCID: PMC6508775 DOI: 10.1002/pld3.127] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 05/18/2023]
Abstract
The earliest visual changes of leaf senescence occur in the chloroplast as chlorophyll is degraded and photosynthesis declines. Yet, a comprehensive understanding of the sequence of catabolic events occurring in chloroplasts during natural leaf senescence is still missing. Here, we combined confocal and electron microscopy together with proteomics and biochemistry to follow structural and molecular changes during Arabidopsis leaf senescence. We observed that initiation of chlorophyll catabolism precedes other breakdown processes. Chloroplast size, stacking of thylakoids, and efficiency of PSII remain stable until late stages of senescence, whereas the number and size of plastoglobules increase. Unlike catabolic enzymes, whose level increase, the level of most proteins decreases during senescence, and chloroplast proteins are overrepresented among these. However, the rate of their disappearance is variable, mostly uncoordinated and independent of their inherent stability during earlier developmental stages. Unexpectedly, degradation of chlorophyll-binding proteins lags behind chlorophyll catabolism. Autophagy and vacuole proteins are retained at relatively high levels, highlighting the role of extra-plastidic degradation processes especially in late stages of senescence. The observation that chlorophyll catabolism precedes all other catabolic events may suggest that this process enables or signals further catabolic processes in chloroplasts.
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Affiliation(s)
- Eyal Tamary
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
| | - Reinat Nevo
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Leah Naveh
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
| | - Smadar Levin‐Zaidman
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Vladimir Kiss
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Alon Savidor
- de Botton Institute for Protein ProfilingThe Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Yishai Levin
- de Botton Institute for Protein ProfilingThe Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Yoram Eyal
- Institute of Plant SciencesThe Volcani Center ARORishon LeZionIsrael
| | - Ziv Reich
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew UniversityRehovotIsrael
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15
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Dror B, Savidor A, Salam BB, Sela N, Lampert Y, Teper-Bamnolker P, Daus A, Carmeli S, Sela Saldinger S, Eshel D. High Levels of CO 2 Induce Spoilage by Leuconostoc mesenteroides by Upregulating Dextran Synthesis Genes. Appl Environ Microbiol 2019; 85:e00473-18. [PMID: 30367004 PMCID: PMC6293096 DOI: 10.1128/aem.00473-18] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
During nonventilated storage of carrots, CO2 gradually accumulates to high levels and causes modifications in the carrot's microbiome toward dominance of Lactobacillales and Enterobacteriales The lactic acid bacterium Leuconostoc mesenteroides secretes a slimy exudate over the surface of the carrots. The objective of this study was to characterize the slime components and the potential cause for its secretion under high CO2 levels. A proteomic analysis of the exudate revealed bacterial glucosyltransferases as the main proteins, specifically, dextransucrase. A chemical analysis of the exudate revealed high levels of dextran and several simple sugars. The exudate volume and dextran amount were significantly higher when L. mesenteroides was incubated under high CO2 levels than when incubated in an aerated environment. The treatment of carrot medium plates with commercial dextransucrase or exudate protein extract resulted in similar sugar profiles and dextran production. Transcriptome analysis demonstrated that dextran production is related to the upregulation of the L. mesenteroides dextransucrase-encoding genes dsrD and dsrT during the first 4 to 8 h of exposure to high CO2 levels compared to aerated conditions. A phylogenetic analysis of L. mesenteroides YL48 dsrD revealed a high similarity to other dsr genes harbored by different Leuconostoc species. The ecological benefit of dextran production under elevated CO2 requires further investigation. However, this study implies an overlooked role of CO2 in the physiology and fitness of L. mesenteroides in stored carrots, and perhaps in other food items, during storage under nonventilated conditions.IMPORTANCE The bacterium Leuconostoc mesenteroides is known to cause spoilage of different types of foods by secreting a slimy fluid that damages the quality and appearance of the produce. Here, we identified a potential mechanism by which high levels of CO2 affect the spoilage caused by this bacterium by upregulating dextran synthesis genes. These results have broader implications for the study of the physiology, degradation ability, and potential biotechnological applications of Leuconostoc.
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Affiliation(s)
- Barak Dror
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Savidor
- De Button Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Bolaji Babajide Salam
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Yael Lampert
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Paula Teper-Bamnolker
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Avinoam Daus
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Shmuel Carmeli
- Raymond and Beverly Sackler School of Chemistry and Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Sela Saldinger
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Dani Eshel
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
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16
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Adam Z, Aviv-Sharon E, Keren-Paz A, Naveh L, Rozenberg M, Savidor A, Chen J. The Chloroplast Envelope Protease FTSH11 - Interaction With CPN60 and Identification of Potential Substrates. Front Plant Sci 2019; 10:428. [PMID: 31024594 PMCID: PMC6459962 DOI: 10.3389/fpls.2019.00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
FTSH proteases are membrane-bound, ATP-dependent metalloproteases found in bacteria, mitochondria and chloroplasts. The product of one of the 12 genes encoding FTSH proteases in Arabidopsis, FTSH11, has been previously shown to be essential for acquired thermotolerance. However, the substrates of this protease, as well as the mechanism linking it to thermotolerance are largely unknown. To get insight into these, the FTSH11 knockout mutant was complemented with proteolytically active or inactive variants of this protease, tagged with HA-tag, under the control of the native promoter. Using these plants in thermotolerance assay demonstrated that the proteolytic activity, and not only the ATPase one, is essential for conferring thermotolerance. Immunoblot analyses of leaf extracts, isolated organelles and sub-fractionated chloroplast membranes localized FTSH11 mostly to chloroplast envelopes. Affinity purification followed by mass spectrometry analysis revealed interaction between FTSH11 and different components of the CPN60 chaperonin. In affinity enrichment assays, CPN60s as well as a number of envelope, stroma and thylakoid proteins were found associated with proteolytically inactive FTSH11. Comparative proteomic analysis of WT and knockout plants, grown at 20°C or exposed to 30°C for 6 h, revealed a plethora of upregulated chloroplast proteins in the knockout, some of them might be candidate substrates. Among these stood out TIC40, which was stabilized in the knockout line after recovery from heat stress, and three proteins that were found trapped in the affinity enrichment assay: the nucleotide antiporter PAPST2, the fatty acid binding protein FAP1 and the chaperone HSP70. The consistent behavior of these four proteins in different assays suggest that they are potential FTSH11 substrates.
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Affiliation(s)
- Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Zach Adam,
| | - Elinor Aviv-Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alona Keren-Paz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Leah Naveh
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mor Rozenberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, United States
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17
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Myers N, Olender T, Savidor A, Levin Y, Reuven N, Shaul Y. Front Cover: The Disordered Landscape of the 20S Proteasome Substrates Reveals Tight Association with Phase Separated Granules. Proteomics 2018. [DOI: 10.1002/pmic.201870191] [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: 11/07/2022]
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18
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Myers N, Olender T, Savidor A, Levin Y, Reuven N, Shaul Y. The Disordered Landscape of the 20S Proteasome Substrates Reveals Tight Association with Phase Separated Granules. Proteomics 2018; 18:e1800076. [PMID: 30039638 DOI: 10.1002/pmic.201800076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/31/2018] [Revised: 06/28/2018] [Indexed: 12/11/2022]
Abstract
Proteasomal degradation is the main route of regulated proteostasis. The 20S proteasome is the core particle (CP) responsible for the catalytic activity of all proteasome complexes. Structural constraints mean that only unfolded, extended polypeptide chains may enter the catalytic core of the 20S proteasome. It has been previously shown that the 20S CP is active in degradation of certain intrinsically disordered proteins (IDP) lacking structural constrains. Here, a comprehensive analysis of the 20S CP substrates in vitro is conducted. It is revealed that the 20S CP substrates are highly disordered. However, not all the IDPs are 20S CP substrates. The group of the IDPs that are 20S CP substrates, termed 20S-IDPome are characterized by having significantly more protein binding partners, more posttranslational modification sites, and are highly enriched for RNA binding proteins. The vast majority of them are involved in splicing, mRNA processing, and translation. Remarkably, it is found that low complexity proteins with prion-like domain (PrLD), which interact with GR or PR di-peptide repeats, are the most preferential 20S CP substrates. The finding suggests roles of the 20S CP in gene transcription and formation of phase-separated granules.
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Affiliation(s)
- Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science Department of Molecular Genetics, 76100, Rehovot, Israel
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19
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Teper D, Girija AM, Bosis E, Popov G, Savidor A, Sessa G. The Xanthomonas euvesicatoria type III effector XopAU is an active protein kinase that manipulates plant MAP kinase signaling. PLoS Pathog 2018; 14:e1006880. [PMID: 29377937 PMCID: PMC5805367 DOI: 10.1371/journal.ppat.1006880] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 02/03/2017] [Revised: 02/08/2018] [Accepted: 01/15/2018] [Indexed: 11/19/2022] Open
Abstract
The Gram-negative bacterium Xanthomonas euvesicatoria (Xe) is the causal agent of bacterial spot disease of pepper and tomato. Xe delivers effector proteins into host cells through the type III secretion system to promote disease. Here, we show that the Xe effector XopAU, which is conserved in numerous Xanthomonas species, is a catalytically active protein kinase and contributes to the development of disease symptoms in pepper plants. Agrobacterium-mediated expression of XopAU in host and non-host plants activated typical defense responses, including MAP kinase phosphorylation, accumulation of pathogenesis-related (PR) proteins and elicitation of cell death, that were dependent on the kinase activity of the effector. XopAU-mediated cell death was not dependent on early signaling components of effector-triggered immunity and was also observed when the effector was delivered into pepper leaves by Xanthomonas campestris pv. campestris, but not by Xe. Protein-protein interaction studies in yeast and in planta revealed that XopAU physically interacts with components of plant immunity-associated MAP kinase cascades. Remarkably, XopAU directly phosphorylated MKK2 in vitro and enhanced its phosphorylation at multiple sites in planta. Consistent with the notion that MKK2 is a target of XopAU, silencing of the MKK2 homolog or overexpression of the catalytically inactive mutant MKK2K99R in N. benthamiana plants reduced XopAU-mediated cell death and MAPK phosphorylation. Furthermore, yeast co-expressing XopAU and MKK2 displayed reduced growth and this phenotype was dependent on the kinase activity of both proteins. Together, our results support the conclusion that XopAU contributes to Xe disease symptoms in pepper plants and manipulates host MAPK signaling through phosphorylation and activation of MKK2.
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Affiliation(s)
- Doron Teper
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College, Karmiel, Israel
| | - Georgy Popov
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Alon Savidor
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Guido Sessa
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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20
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Zhu W, Ronen M, Gur Y, Minz-Dub A, Masrati G, Ben-Tal N, Savidor A, Sharon I, Eizner E, Valerius O, Braus GH, Bowler K, Bar-Peled M, Sharon A. BcXYG1, a Secreted Xyloglucanase from Botrytis cinerea, Triggers Both Cell Death and Plant Immune Responses. Plant Physiol 2017; 175:438-456. [PMID: 28710128 PMCID: PMC5580746 DOI: 10.1104/pp.17.00375] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
In search of Botrytis cinerea cell death-inducing proteins, we found a xyloglucanase (BcXYG1) that induced strong necrosis and a resistance response in dicot plants. Expression of the BcXYG1 gene was strongly induced during the first 12 h post inoculation, and analysis of disease dynamics using PathTrack showed that a B. cinerea strain overexpressing BcXYG1 produced early local necrosis, supporting a role of BcXYG1 as an early cell death-inducing factor. The xyloglucanase activity of BcXYG1 was not necessary for the induction of necrosis and plant resistance, as a mutant of BcXYG1 lacking the xyloglucanase enzymatic activity retained both functions. Residues in two exposed loops on the surface of BcXYG1 were found to be necessary for the induction of cell death but not to induce plant resistance. Further analyses showed that BcXYG1 is apoplastic and possibly interacts with the proteins of the plant cell membrane and also that the BcXYG1 cell death-promoting signal is mediated by the leucine-rich repeat receptor-like kinases BAK1 and SOBIR1. Our findings support the role of cell death-inducing proteins in establishing the infection of necrotrophic pathogens and highlight the recognition of fungal apoplastic proteins by the plant immune system as an important mechanism of resistance against this class of pathogens.
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Affiliation(s)
- Wenjun Zhu
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Mordechi Ronen
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yonatan Gur
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anna Minz-Dub
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gal Masrati
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alon Savidor
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itai Sharon
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Elad Eizner
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Physical Electronics, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oliver Valerius
- Complex Carbohydrate Research Center, Department of Plant Biology, University of Georgia, Athens, Georgia 30602-4712
| | - Gerhard H Braus
- Complex Carbohydrate Research Center, Department of Plant Biology, University of Georgia, Athens, Georgia 30602-4712
| | - Kyle Bowler
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences, Georg-August-Universität, Goettingen, 37073 Germany
| | - Maor Bar-Peled
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences, Georg-August-Universität, Goettingen, 37073 Germany
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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21
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Despotović D, Brandis A, Savidor A, Levin Y, Fumagalli L, Tawfik DS. Diadenosine tetraphosphate (Ap4A) - an E. coli alarmone or a damage metabolite? FEBS J 2017; 284:2194-2215. [PMID: 28516732 DOI: 10.1111/febs.14113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022]
Abstract
Under stress, metabolism is changing: specific up- or down-regulation of proteins and metabolites occurs as well as side effects. Distinguishing specific stress-signaling metabolites (alarmones) from side products (damage metabolites) is not trivial. One example is diadenosine tetraphosphate (Ap4A) - a side product of aminoacyl-tRNA synthetases found in all domains of life. The earliest observations suggested that Ap4A serves as an alarmone for heat stress in Escherichia coli. However, despite 50 years of research, the signaling mechanisms associated with Ap4A remain unknown. We defined a set of criteria for distinguishing alarmones from damage metabolites to systematically classify Ap4A. In a nutshell, no indications for a signaling cascade that is triggered by Ap4A were found; rather, we found that Ap4A is efficiently removed in a constitutive, nonregulated manner. Several fold perturbations in Ap4A concentrations have no effect, yet accumulation at very high levels is toxic due to disturbance of zinc homeostasis, and also because Ap4A's structural overlap with ATP can result in spurious binding and inactivation of ATP-binding proteins. Overall, Ap4A met all criteria for a damage metabolite. While we do not exclude any role in signaling, our results indicate that the damage metabolite option should be considered as the null hypothesis when examining Ap4A and other metabolites whose levels change upon stress.
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Affiliation(s)
- Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Italy
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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22
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Szymanski J, Levin Y, Savidor A, Breitel D, Chappell-Maor L, Heinig U, Töpfer N, Aharoni A. Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. Plant J 2017; 90:396-417. [PMID: 28112434 DOI: 10.1111/tpj.13490] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 05/18/2023]
Abstract
Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening-related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species, which is presently focused on transcription.
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Affiliation(s)
- Jedrzej Szymanski
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Alon Savidor
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dario Breitel
- Metabolic Biology Department, John Innes Centre, Norwich, NR4 7UH, UK
| | - Louise Chappell-Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nadine Töpfer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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23
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Savidor A, Barzilay R, Elinger D, Yarden Y, Lindzen M, Gabashvili A, Adiv Tal O, Levin Y. Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination. Mol Cell Proteomics 2017; 16:1151-1161. [PMID: 28348172 DOI: 10.1074/mcp.o116.065417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/22/2017] [Indexed: 01/16/2023] Open
Abstract
Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence.
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Affiliation(s)
- Alon Savidor
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot
| | - Rotem Barzilay
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot
| | - Dalia Elinger
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot
| | - Yosef Yarden
- the §Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Moshit Lindzen
- the §Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Alexandra Gabashvili
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot
| | - Ophir Adiv Tal
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot
| | - Yishai Levin
- From ‡The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot;
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24
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Loewenstein S, Lubezky N, Nizri E, Zemel M, Levin Y, Savidor A, Sher O, Klausner JM, Lahat G. Adipose-Induced Retroperitoneal Soft Tissue Sarcoma Tumorigenesis: A Potential Crosstalk between Sarcoma and Fat Cells. Mol Cancer Res 2016; 14:1254-1265. [PMID: 27621268 DOI: 10.1158/1541-7786.mcr-16-0131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/07/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022]
Abstract
Previous data demonstrated that high retroperitoneal visceral fat content increases retroperitoneal soft-tissue sarcoma (RSTS) local recurrence and patients' mortality. Most RSTS tumors initiate and recur within visceral fat. The objective of the current study was to evaluate potential paracrine effects of visceral fat on RSTS. A xenograft model was used to evaluate in vivo effects of human visceral fat on STS growth. Tissue explants were prepared from visceral fat, and their conditioned medium (CM) was utilized for various in vitro experiments designed to evaluate growth, survival, migration, and invasion of STS and endothelial cells. Visceral fat-secreted protumorigenic factors were identified by mass spectrometry. The in vivo experiments demonstrated a significant increase in STS tumor growth rate when SK-LMS-1 leiomyosarcoma cells were colocalized with human visceral fat compared with subcutaneous injection of cancer cells only. The in vitro model demonstrated that visceral fat CM increased STS cellular growth and reduced doxorubicin-induced apoptosis. Visceral fat also enhanced STS cellular migration and invasion. In addition, visceral fat CM significantly increased endothelial cell tube formation, suggesting its role as a proangiogenic factor in the STS tumor microenvironment (TME). Using a robust proteomic approach, liquid chromatography and tandem mass spectrometry resolved various molecules within the visceral fat CM, of which a subset was associated with protumorigenic biologic processes. These results suggest that visceral fat directly interacts with STS cells by secreting specific adipokines into the TME, thus augmenting STS tumor cell proliferation and invasiveness. Fat-induced STS molecular deregulations should be studied to identify new potential prognostic and therapeutic targets. IMPLICATIONS Visceral fat induces protumorigenic effects, in STS, through various secreted factors that should be investigated to improve our understanding of adipose-cancer cell interactions. Mol Cancer Res; 14(12); 1254-65. ©2016 AACR.
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Affiliation(s)
- Shelly Loewenstein
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
| | - Nir Lubezky
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
| | - Eran Nizri
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
| | - Meir Zemel
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel
| | - Osnat Sher
- Department of Pathology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Joseph M Klausner
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
| | - Guy Lahat
- Department of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel. .,Sackler School of Medicine, The Nicholas and Elizabeth Cathedra of Experimental Surgery, Tel Aviv University, Tel Aviv, Israel
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25
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Levy M, Thaiss CA, Zeevi D, Dohnalová L, Zilberman-Schapira G, Mahdi JA, David E, Savidor A, Korem T, Herzig Y, Pevsner-Fischer M, Shapiro H, Christ A, Harmelin A, Halpern Z, Latz E, Flavell RA, Amit I, Segal E, Elinav E. Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling. Cell 2016; 163:1428-43. [PMID: 26638072 DOI: 10.1016/j.cell.2015.10.048] [Citation(s) in RCA: 652] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 10/06/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023]
Abstract
Host-microbiome co-evolution drives homeostasis and disease susceptibility, yet regulatory principles governing the integrated intestinal host-commensal microenvironment remain obscure. While inflammasome signaling participates in these interactions, its activators and microbiome-modulating mechanisms are unknown. Here, we demonstrate that the microbiota-associated metabolites taurine, histamine, and spermine shape the host-microbiome interface by co-modulating NLRP6 inflammasome signaling, epithelial IL-18 secretion, and downstream anti-microbial peptide (AMP) profiles. Distortion of this balanced AMP landscape by inflammasome deficiency drives dysbiosis development. Upon fecal transfer, colitis-inducing microbiota hijacks this microenvironment-orchestrating machinery through metabolite-mediated inflammasome suppression, leading to distorted AMP balance favoring its preferential colonization. Restoration of the metabolite-inflammasome-AMP axis reinstates a normal microbiota and ameliorates colitis. Together, we identify microbial modulators of the NLRP6 inflammasome and highlight mechanisms by which microbiome-host interactions cooperatively drive microbial community stability through metabolite-mediated innate immune modulation. Therefore, targeted "postbiotic" metabolomic intervention may restore a normal microenvironment as treatment or prevention of dysbiosis-driven diseases.
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Affiliation(s)
- Maayan Levy
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Zeevi
- 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
| | - Lenka Dohnalová
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Jemal Ali Mahdi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Savidor
- The Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Korem
- 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
| | - Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Hagit Shapiro
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anette Christ
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany; Department of Medicine, University of Massachusetts, Worcester, MA 01605, USA
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zamir Halpern
- Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Digestive Center, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany; Department of Medicine, University of Massachusetts, Worcester, MA 01605, USA
| | - Richard A Flavell
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ido Amit
- Department of Immunology, 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.
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Bucher T, Oppenheimer-Shaanan Y, Savidor A, Bloom-Ackermann Z, Kolodkin-Gal I. Disturbance of the bacterial cell wall specifically interferes with biofilm formation. Environ Microbiol Rep 2015; 7:990-1004. [PMID: 26472159 DOI: 10.1111/1758-2229.12346] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/08/2015] [Accepted: 10/11/2015] [Indexed: 06/05/2023]
Abstract
In nature, bacteria communicate via chemical cues and establish complex communities referred to as biofilms, wherein cells are held together by an extracellular matrix. Much research is focusing on small molecules that manipulate and prevent biofilm assembly by modifying cellular signalling pathways. However, the bacterial cell envelope, presenting the interface between bacterial cells and their surroundings, is largely overlooked. In our study, we identified specific targets within the biosynthesis pathways of the different cell wall components (peptidoglycan, wall teichoic acids and teichuronic acids) hampering biofilm formation and the anchoring of the extracellular matrix with a minimal effect on planktonic growth. In addition, we provide convincing evidence that biofilm hampering by transglycosylation inhibitors and D-Leucine triggers a highly specific response without changing the overall protein levels within the biofilm cells or the overall levels of the extracellular matrix components. The presented results emphasize the central role of the Gram-positive cell wall in biofilm development, resistance and sustainment.
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Affiliation(s)
- Tabitha Bucher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Centre for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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27
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Emde A, Eitan C, Liou LL, Libby RT, Rivkin N, Magen I, Reichenstein I, Oppenheim H, Eilam R, Silvestroni A, Alajajian B, Ben-Dov IZ, Aebischer J, Savidor A, Levin Y, Sons R, Hammond SM, Ravits JM, Möller T, Hornstein E. Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS. EMBO J 2015; 34:2633-51. [PMID: 26330466 DOI: 10.15252/embj.201490493] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [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: 11/09/2014] [Accepted: 07/20/2015] [Indexed: 12/12/2022] Open
Abstract
Interest in RNA dysfunction in amyotrophic lateral sclerosis (ALS) recently aroused upon discovering causative mutations in RNA-binding protein genes. Here, we show that extensive down-regulation of miRNA levels is a common molecular denominator for multiple forms of human ALS. We further demonstrate that pathogenic ALS-causing mutations are sufficient to inhibit miRNA biogenesis at the Dicing step. Abnormalities of the stress response are involved in the pathogenesis of neurodegeneration, including ALS. Accordingly, we describe a novel mechanism for modulating microRNA biogenesis under stress, involving stress granule formation and re-organization of DICER and AGO2 protein interactions with their partners. In line with this observation, enhancing DICER activity by a small molecule, enoxacin, is beneficial for neuromuscular function in two independent ALS mouse models. Characterizing miRNA biogenesis downstream of the stress response ties seemingly disparate pathways in neurodegeneration and further suggests that DICER and miRNAs affect neuronal integrity and are possible therapeutic targets.
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Affiliation(s)
- Anna Emde
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Lee-Loung Liou
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Ryan T Libby
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Natali Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Iddo Magen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Reichenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hagar Oppenheim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Aurelio Silvestroni
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Betty Alajajian
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Iddo Z Ben-Dov
- Nephrology Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Julianne Aebischer
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Robert Sons
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - John M Ravits
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA Department of Neurosciences, UC San Diego, La Jolla, CA, USA
| | - Thomas Möller
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Abstract
Presented is a data set for benchmarking MS1-based label-free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences in a background of an unchanged complex proteome. The data set provides a unique opportunity to evaluate the proteomic platform (instrumentation and software) in its ability to perform MS1-intensity-based label-free quantification. We show that the presented combination of informatics and instrumentation produces high precision and quantification accuracy. The data were also used to compare different quantitative protein inference methods such as iBAQ and Hi-N. The data can also be used as a resource for development and optimization of proteomics informatics tools, thus the raw data have been deposited to ProteomeXchange with identifier PXD001385.
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Affiliation(s)
- Tali Shalit
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dalia Elinger
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Savidor
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alexandra Gabashvili
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
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Zigdon H, Savidor A, Levin Y, Meshcheriakova A, Schiffmann R, Futerman AH. Identification of a biomarker in cerebrospinal fluid for neuronopathic forms of Gaucher disease. PLoS One 2015; 10:e0120194. [PMID: 25775479 PMCID: PMC4361053 DOI: 10.1371/journal.pone.0120194] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/06/2015] [Indexed: 11/18/2022] Open
Abstract
Gaucher disease, a recessive inherited metabolic disorder caused by defects in the gene encoding glucosylceramidase (GlcCerase), can be divided into three subtypes according to the appearance of symptoms associated with central nervous system involvement. We now identify a protein, glycoprotein non-metastatic B (GPNMB), that acts as an authentic marker of brain pathology in neurological forms of Gaucher disease. Using three independent techniques, including quantitative global proteomic analysis of cerebrospinal fluid (CSF) in samples from Gaucher disease patients that display neurological symptoms, we demonstrate a correlation between the severity of symptoms and GPNMB levels. Moreover, GPNMB levels in the CSF correlate with disease severity in a mouse model of Gaucher disease. GPNMB was also elevated in brain samples from patients with type 2 and 3 Gaucher disease. Our data suggest that GPNMB can be used as a marker to quantify neuropathology in Gaucher disease patients and as a marker of treatment efficacy once suitable treatments towards the neurological symptoms of Gaucher disease become available.
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Affiliation(s)
- Hila Zigdon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Meshcheriakova
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, TX, United States of America
| | - Anthony H. Futerman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Savidor A, Chalupowicz L, Teper D, Gartemann KH, Eichenlaub R, Manulis-Sasson S, Barash I, Sessa G. Clavibacter michiganensis subsp. michiganensis Vatr1 and Vatr2 Transcriptional Regulators Are Required for Virulence in Tomato. Mol Plant Microbe Interact 2015; 2015:1-12. [PMID: 27839071 DOI: 10.1094/mpmi-02-14-0018-r.testissue] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The plant pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) is a Gram-positive bacterium responsible for wilt and canker disease of tomato. While disease development is well characterized and diagnosed, molecular mechanisms of Cmm virulence are poorly understood. Here, we identified and characterized two Cmm transcriptional regulators, Vatr1 and Vatr2, that are involved in pathogenicity of Cmm. Vatr1 and Vatr2 belong to TetR and MocR families of transcriptional regulators, respectively. Mutations in their corresponding genes caused attenuated virulence, with the Δvatr2 mutant showing a more dramatic effect than Δvatr1. While both mutants grew well in vitro and reached a high titer in planta, they caused reduced wilting and canker development in infected plants compared with the wild-type bacterium. They also led to a reduced expression of the ethylene-synthesizing tomato enzyme ACC-oxidase compared with wild-type Cmm and to reduced ethylene production in the plant. Transcriptomic analysis of wild-type Cmm and the two mutants under infection-mimicking conditions revealed that Vatr1 and Vatr2 regulate expression of virulence factors, membrane and secreted proteins, and signal transducing proteins. A 70% overlap between the sets of genes positively regulated by Vatr1 and Vatr2 suggests that these transcriptional regulators are on the same molecular pathway responsible for Cmm virulence.
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Affiliation(s)
- Alon Savidor
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Laura Chalupowicz
- 2 Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan 50250, Israel
| | - Doron Teper
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Karl-Heinz Gartemann
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
- 3 Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Rudolf Eichenlaub
- 3 Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Shulamit Manulis-Sasson
- 2 Department of Plant Pathology and Weed Research, ARO, the Volcani Center, Bet Dagan 50250, Israel
| | - Isaac Barash
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guido Sessa
- 1 Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
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31
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Savidor A, Chalupowicz L, Teper D, Gartemann KH, Eichenlaub R, Manulis-Sasson S, Barash I, Sessa G. Clavibacter michiganensis subsp. michiganensis Vatr1 and Vatr2 transcriptional regulators are required for virulence in tomato. Mol Plant Microbe Interact 2014; 27:1035-1047. [PMID: 24940988 DOI: 10.1094/mpmi-02-14-0061-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The plant pathogen Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterium responsible for wilt and canker disease of tomato. Although disease development is well characterized and diagnosed, molecular mechanisms of C. michiganensis subsp. michiganensis virulence are poorly understood. Here, we identified and characterized two C. michiganensis subsp. michiganensis transcriptional regulators, Vatr1 and Vatr2, that are involved in pathogenicity of C. michiganensis subsp. michiganensis. Vatr1 and Vatr2 belong to TetR and MocR families of transcriptional regulators, respectively. Mutations in their corresponding genes caused attenuated virulence, with the Δvatr2 mutant showing a more dramatic effect than Δvatr1. Although both mutants grew well in vitro and reached a high titer in planta, they caused reduced wilting and canker development in infected plants compared with the wild-type bacterium. They also led to a reduced expression of the ethylene-synthesizing tomato enzyme ACC-oxidase compared with wild-type C. michiganensis subsp. michiganensis and to reduced ethylene production in the plant. Transcriptomic analysis of wild-type C. michiganensis subsp. michiganensis and the two mutants under infection-mimicking conditions revealed that Vatr1 and Vatr2 regulate expression of virulence factors, membrane and secreted proteins, and signal-transducing proteins. A 70% overlap between the sets of genes positively regulated by Vatr1 and Vatr2 suggests that these transcriptional regulators are on the same molecular pathway responsible for C. michiganensis subsp. michiganensis virulence.
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32
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Abstract
Quantitative proteomics by LC-MS/MS is a widely used approach for quantifying a significant portion of any complex proteome. Among the different techniques used for this purpose, one is by use of Data Independent Acquisition (DIA). We present a descriptive protocol for label-free quantitation of proteins by one DIA method termed LC-MS(E), which facilitates large-scale quantification of proteins without the need for isotopic labelling and with no theoretical limit to the number of samples included in an experiment.
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Affiliation(s)
- Alon Savidor
- Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
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33
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Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact 2012; 25:1350-60. [PMID: 22712506 PMCID: PMC3551261 DOI: 10.1094/mpmi-02-12-0028-r] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
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34
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Chalupowicz L, Zellermann EM, Fluegel M, Dror O, Eichenlaub R, Gartemann KH, Savidor A, Sessa G, Iraki N, Barash I, Manulis-Sasson S. Colonization and movement of GFP-labeled Clavibacter michiganensis subsp. michiganensis during tomato infection. Phytopathology 2012; 102:23-31. [PMID: 21879791 DOI: 10.1094/phyto-05-11-0135] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The vascular pathogen Clavibacter michiganensis subsp. michiganensis is responsible for bacterial wilt and canker of tomato. Pathogenicity of this bacterium is dependent on plasmid-borne virulence factors and serine proteases located on the chromosomal chp/tomA pathogenicity island (PAI). In this study, colonization patterns and movement of C. michiganensis subsp. michiganensis during tomato infection was examined using a green fluorescent protein (GFP)-labeled strain. A plasmid expressing GFP in C. michiganensis subsp. michiganensis was constructed and found to be stable in planta for at least 1 month. Confocal laser-scanning microscopy (CLSM) of inoculated stems showed that the pathogen extensively colonizes the lumen of xylem vessels and preferentially attaches to spiral secondary wall thickening of the protoxylem. Acropetal movement of the wild-type strain C. michiganensis subsp. michiganensis NCPPB382 (Cmm382) in tomato resulted in an extensive systemic colonization of the whole plant reaching the apical region after 15 days, whereas Cmm100 (lacking the plasmids pCM1 and pCM2) or Cmm27 (lacking the chp/tomA PAI) remained confined to the area surrounding of the inoculation site. Cmm382 formed biofilm-like structures composed of large bacterial aggregates on the interior of xylem walls as observed by CLSM and scanning electron microscopy. These findings suggest that virulence factors located on the chp/tomA PAI or the plasmids are required for effective movement of the pathogen in tomato and for the formation of cellular aggregates.
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Affiliation(s)
- L Chalupowicz
- Department of Plant Pathology and Weed Research, ARO, Bet Dagan, Israel
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35
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Savidor A, Teper D, Gartemann KH, Eichenlaub R, Chalupowicz L, Manulis-Sasson S, Barash I, Tews H, Mayer K, Giannone RJ, Hettich RL, Sessa G. The Clavibacter michiganensis subsp. michiganensis–Tomato Interactome Reveals the Perception of Pathogen by the Host and Suggests Mechanisms of Infection. J Proteome Res 2011; 11:736-50. [DOI: 10.1021/pr200646a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alon Savidor
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doron Teper
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Karl-Heinz Gartemann
- Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Rudolf Eichenlaub
- Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Laura Chalupowicz
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet Dagan 50250, Israel
| | - Shulamit Manulis-Sasson
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet Dagan 50250, Israel
| | - Isaac Barash
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Helena Tews
- Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Kerstin Mayer
- Department of Genetechnology/Microbiology, Faculty of Biology, University of Bielefeld, 33501 Bielefeld, Germany
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Guido Sessa
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
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Savidor A, Donahoo RS, Hurtado-Gonzales O, Land ML, Shah MB, Lamour KH, McDonald WH. Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum. Mol Cell Proteomics 2008; 7:1501-16. [PMID: 18316789 PMCID: PMC2500229 DOI: 10.1074/mcp.m700431-mcp200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 01/23/2008] [Indexed: 11/06/2022] Open
Abstract
Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narrow host range, whereas P. ramorum has a wide host range. A global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates, and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton, and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the beta-oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth in which energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.
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Affiliation(s)
- Alon Savidor
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory Oak Ridge, Oak Ridge, Tennessee 37830, USA
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37
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Savidor A, Donahoo RS, Hurtado-Gonzales O, Verberkmoes NC, Shah MB, Lamour KH, McDonald WH. Expressed peptide tags: an additional layer of data for genome annotation. J Proteome Res 2007; 5:3048-58. [PMID: 17081056 DOI: 10.1021/pr060134x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [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: 11/28/2022]
Abstract
While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here, we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six-frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well-annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed a high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well-annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller subdatabases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While approximately 76% of Phytophthora EPTs supported the current annotation, a portion of them (7.7% and 12.9% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.
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Affiliation(s)
- Alon Savidor
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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38
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Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CMB, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJG, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JKC, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BWS, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 2006; 313:1261-6. [PMID: 16946064 DOI: 10.1126/science.1128796] [Citation(s) in RCA: 719] [Impact Index Per Article: 39.9] [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: 11/02/2022]
Abstract
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
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Affiliation(s)
- Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Jain NU, Tjioe E, Savidor A, Boulie J. Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings. Biochemistry 2005; 44:9067-78. [PMID: 15966730 DOI: 10.1021/bi050152c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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: 11/29/2022]
Abstract
Structural differences in the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), from the camphor hydroxylation pathway of Pseudomonas putida have been investigated as a function of oxidation state of the iron cluster. Pdx is involved in biological electron transfer to cytochrome P450(cam) (CYP101). Redox-dependent differences have been observed previously for Pdx in terms of binding affinities to CYP101, NMR spectral differences, and dynamic properties. To further characterize these differences, structure refinement of both oxidized and reduced Pdx has been carried out using a hybrid approach utilizing paramagnetic distance restraints and NMR orientational restraints in the form of backbone (15)N residual dipolar couplings. Use of these new restraints has improved the structure of oxidized Pdx considerably over the earlier solution NMR structure without RDC restraints, with the new structure now much closer in overall fold to the recently published X-ray crystal structures. We now observe better defined relative orientations of the major secondary structure elements as also of the conformation of the metal binding loop region. Extension of this approach to structure calculation of reduced Pdx has identified structural differences that are primarily localized for residues in the C-terminal interaction domain consisting of the functionally important residue Trp 106 and regions near the metal binding loop in Pdx. These redox-dependent structural differences in Pdx correlate to dynamic changes observed before and may be linked to differences in binding and electron transfer properties between oxidized and reduced Pdx.
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Affiliation(s)
- Nitin U Jain
- Biochemistry, Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee 37996-0840, USA.
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