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Filo S, Shaharabani R, Bar Hanin D, Adam M, Ben-David E, Schoffman H, Margalit N, Habib N, Shahar T, Mezer AA. Non-invasive assessment of normal and impaired iron homeostasis in the brain. Nat Commun 2023; 14:5467. [PMID: 37699931 PMCID: PMC10497590 DOI: 10.1038/s41467-023-40999-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Strict iron regulation is essential for normal brain function. The iron homeostasis, determined by the milieu of available iron compounds, is impaired in aging, neurodegenerative diseases and cancer. However, non-invasive assessment of different molecular iron environments implicating brain tissue's iron homeostasis remains a challenge. We present a magnetic resonance imaging (MRI) technology sensitive to the iron homeostasis of the living brain (the r1-r2* relaxivity). In vitro, our MRI approach reveals the distinct paramagnetic properties of ferritin, transferrin and ferrous iron ions. In the in vivo human brain, we validate our approach against ex vivo iron compounds quantification and gene expression. Our approach varies with the iron mobilization capacity across brain regions and in aging. It reveals brain tumors' iron homeostasis, and enhances the distinction between tumor tissue and non-pathological tissue without contrast agents. Therefore, our approach may allow for non-invasive research and diagnosis of iron homeostasis in living human brains.
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Affiliation(s)
- Shir Filo
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Rona Shaharabani
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Bar Hanin
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Adam
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eliel Ben-David
- The Department of Radiology, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanan Schoffman
- The Laboratory of Molecular Neuro-Oncology, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nevo Margalit
- The Department of Neurosurgery, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naomi Habib
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tal Shahar
- The Laboratory of Molecular Neuro-Oncology, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Department of Neurosurgery, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Affiliated with Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviv A Mezer
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Schoffman H, Levin Y, Itzhaki-Alfia A, Tselekovits L, Gonen L, Vainer GW, Hout-Siloni G, Barshack I, Cohen ZR, Margalit N, Shahar T. Comparison of matched formalin-fixed paraffin embedded and fresh frozen meningioma tissue reveals bias in proteomic profiles. Proteomics 2022; 22:e2200085. [PMID: 36098096 DOI: 10.1002/pmic.202200085] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/29/2022]
Abstract
Tissue biopsies are most commonly archived in a paraffin block following tissue fixation with formaldehyde (FFPE) or as fresh frozen tissue (FFT). While both methods preserve biological samples, little is known about how they affect the quantifiable proteome. We performed a 'bottom-up' proteomic analysis (N = 20) of short and long-term archived FFPE surgical samples of human meningiomas and compared them to matched FFT specimens. FFT facilitated a similar number of proteins assigned by MetaMorpheus compared with matched FFPE specimens (5378 vs. 5338 proteins, respectively (p = 0.053), regardless of archival time. However, marked differences in the proteome composition were apparent between FFPE and FFT specimens. Twenty-three percent of FFPE-derived peptides and 8% of FFT-derived peptides contained at least one chemical modification. Methylation and formylation were most prominent in FFPE-derived peptides (36% and 17% of modified FFPE peptides, respectively) while, most of phosphorylation and iron modifications appeared in FFT-derived peptides (p < 0.001). A mean 14% (± 2.9) of peptides identified in FFPE contained at least one modified Lysine residue. Importantly, larger proteins were significantly overrepresented in FFT specimens, while FFPE specimens were enriched with smaller proteins.
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Affiliation(s)
- Hanan Schoffman
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, 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
| | | | - Lea Tselekovits
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Lior Gonen
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Gilad Wolf Vainer
- Department of Pathology, Hadassah Hebrew University Medical School, Jerusalem, Israel
| | - Goni Hout-Siloni
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi R Cohen
- Department of Neurosurgery, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nevo Margalit
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Tal Shahar
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel.,Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
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Zavřel T, Schoffman H, Lukeš M, Fedorko J, Keren N, Červený J. Monitoring fitness and productivity in cyanobacteria batch cultures. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Schoffman H, Brown WM, Paltiel Y, Keren N, Gauger EM. Structure-based Hamiltonian model for IsiA uncovers a highly robust pigment-protein complex. J R Soc Interface 2020; 17:20200399. [PMID: 32842892 PMCID: PMC7482578 DOI: 10.1098/rsif.2020.0399] [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: 05/27/2020] [Accepted: 08/04/2020] [Indexed: 11/12/2022] Open
Abstract
The iron stress-induced protein A (IsiA) is a source of interest and debate in biological research. The IsiA supercomplex, binding over 200 chlorophylls, assembles in multimeric rings around photosystem I (PSI). Recently, the IsiA-PSI structure from Synechocystis sp. PCC 6803 was resolved to 3.48 Å. Based on this structure, we created a model simulating a single excitation event in an IsiA monomer. This model enabled us to calculate the fluorescence and the localization of the excitation in the IsiA structure. To further examine this system, noise was introduced to the model in two forms-thermal and positional. Introducing noise highlights the functional differences in the system between cryogenic temperatures and biologically relevant temperatures. Our results show that the energetics of the IsiA pigment-protein complex are very robust at room temperature. Nevertheless, shifts in the position of specific chlorophylls lead to large changes in their optical and fluorescence properties. Based on these results, we discuss the implication of highly robust structures, with potential for serving different roles in a context-dependent manner, on our understanding of the function and evolution of photosynthetic processes.
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Affiliation(s)
- Hanan Schoffman
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - William M. Brown
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Yossi Paltiel
- Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Erik M. Gauger
- SUPA, Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
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Abstract
The acclimation of cyanobacterial photosynthetic apparatus to iron deficiency is crucial for their performance under limiting conditions. In many cyanobacterial species, one of the major responses to iron deficiency is the induction of isiA. The function of the IsiA pigment-protein complex has been the subject of intensive research. In this study of the model Synechocystis sp. PCC 6803 strain, we probe the accumulation of the pigment-protein complex and its effects on in vivo photosynthetic performance. We provide evidence that in this organism the dominant factor controlling IsiA accumulation is the intracellular iron concentration and not photo-oxidative stress or redox poise. These findings support the use of IsiA as a tool for assessing iron bioavailability in environmental studies. We also present evidence demonstrating that the IsiA pigment-protein complex exerts only small effects on the performance of the reaction centers. We propose that its major function is as a storage depot able to hold up to 50% of the cellular chlorophyll content during transition into iron limitation. During recovery from iron limitation, chlorophyll is released from the complex and used for the reconstruction of photosystems. Therefore, the IsiA pigment-protein complex can play a critical role not only when cells transition into iron limitation, but also in supporting efficient recovery of the photosynthetic apparatus in the transition back out of the iron-limited state.
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Affiliation(s)
- Hanan Schoffman
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.
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Brandenburg F, Schoffman H, Keren N, Eisenhut M. Determination of Mn Concentrations in Synechocystis sp. PCC6803 Using ICP-MS. Bio Protoc 2017; 7:e2623. [PMID: 34595291 DOI: 10.21769/bioprotoc.2623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 10/06/2017] [Accepted: 11/02/2017] [Indexed: 11/02/2022] Open
Abstract
Manganese (Mn) is an essential micronutrient for all photoautotrophic organisms. Two distinct pools of Mn have been identified in the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), with 80% of the Mn residing in the periplasm and 20% in cytoplasm and thylakoid lumen ( Keren et al., 2002 ). In this protocol, we describe a method to quantify the periplasmic and intracellular pools of Mn in Synechocystis accurately, using inductively coupled plasma mass spectrometry (ICP-MS).
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Affiliation(s)
- Fabian Brandenburg
- Institute of Plant Biochemistry, Heinrich Heine University, Duesseldorf, Germany
| | - Hanan Schoffman
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Heinrich Heine University, Duesseldorf, Germany
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Brandenburg F, Schoffman H, Kurz S, Krämer U, Keren N, Weber APM, Eisenhut M. The Synechocystis Manganese Exporter Mnx Is Essential for Manganese Homeostasis in Cyanobacteria. Plant Physiol 2017; 173:1798-1810. [PMID: 28153926 PMCID: PMC5338678 DOI: 10.1104/pp.16.01895] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/26/2017] [Indexed: 05/05/2023]
Abstract
The essential micronutrient manganese (Mn) functions as redox-active cofactor in active sites of enzymes and, thus, is involved in various physiological reactions. Moreover, in oxygenic photosynthetic organisms, Mn is of special importance, since it is central to the oxygen-evolving complex in photosystem II. Although Mn is an essential micronutrient, increased amounts are detrimental to the organism; thus, only a small window exists for beneficial concentrations. Accordingly, Mn homeostasis must be carefully maintained. In contrast to the well-studied uptake mechanisms in cyanobacteria, it is largely unknown how Mn is distributed to the different compartments inside the cell. We identified a protein with so far unknown function as a hypothetical Mn transporter in the cyanobacterial model strain Synechocystis sp. PCC 6803 and named this protein Mnx for Mn exporter. The knockout mutant Δmnx showed increased sensitivity toward externally supplied Mn and Mn toxicity symptoms, which could be linked to intracellular Mn accumulation. 54Mn chase experiments demonstrated that the mutant was not able to release Mn from the internal pool. Microscopic analysis of a Mnx::yellow fluorescent protein fusion showed that the protein resides in the thylakoid membrane. Heterologous expression of mnx suppressed the Mn-sensitive phenotype of the Saccharomyces cerevisiae mutant Δpmr1 Our results indicate that Mnx functions as a thylakoid Mn transporter and is a key player in maintaining Mn homeostasis in Synechocystis sp. PCC 6803. We propose that Mn export from the cytoplasm into the thylakoid lumen is crucial to prevent toxic cytoplasmic Mn accumulation and to ensure Mn provision to photosystem II.
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Affiliation(s)
- Fabian Brandenburg
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Hanan Schoffman
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Samantha Kurz
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Ute Krämer
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Nir Keren
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Duesseldorf, Germany (F.B., S.K., A.P.M.W., M.E.)
- Department of Plant and Environmental Sciences, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel (H.S., N.K.); and
- Department of Plant Physiology, Ruhr University, 44801 Bochum, Germany (U.K.)
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Schoffman H, Lis H, Shaked Y, Keren N. Iron-Nutrient Interactions within Phytoplankton. Front Plant Sci 2016; 7:1223. [PMID: 27588022 PMCID: PMC4989028 DOI: 10.3389/fpls.2016.01223] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/02/2016] [Indexed: 05/04/2023]
Abstract
Iron limits photosynthetic activity in up to one third of the world's oceans and in many fresh water environments. When studying the effects of Fe limitation on phytoplankton or their adaptation to low Fe environments, we must take into account the numerous cellular processes within which this micronutrient plays a central role. Due to its flexible redox chemistry, Fe is indispensable in enzymatic catalysis and electron transfer reactions and is therefore closely linked to the acquisition, assimilation and utilization of essential resources. Iron limitation will therefore influence a wide range of metabolic pathways within phytoplankton, most prominently photosynthesis. In this review, we map out four well-studied interactions between Fe and essential resources: nitrogen, manganese, copper and light. Data was compiled from both field and laboratory studies to shed light on larger scale questions such as the connection between metabolic pathways and ambient iron levels and the biogeographical distribution of phytoplankton species.
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Affiliation(s)
- Hanan Schoffman
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of JerusalemJerusalem, Israel
| | - Hagar Lis
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of JerusalemJerusalem, Israel
| | - Yeala Shaked
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of JerusalemJerusalem, Israel
- Interuniversity Institute for Marine Sciences in EilatEilat, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of JerusalemJerusalem, Israel
- *Correspondence: Nir Keren,
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