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Hirsch N, Dahan I, D'haene E, Avni M, Vergult S, Vidal-García M, Magini P, Graziano C, Bonora E, Nardone AM, Brancati F, Fernández-Jaén A, Rory OJ, Hallgrimsson B, Birnbaum RY. HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations. Genome Res 2022; 32:1242-1253. [PMID: 35710300 PMCID: PMC9341515 DOI: 10.1101/gr.276196.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the Histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or Ctcf site (CtcfΔ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior\posterior limb expression patterns of Shh pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a Ctcf site and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9INV/+) in mice that does not disrupt HDAC9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidated essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence It suggests that SVs, encompassing protein-coding sequence could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
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Affiliation(s)
| | | | | | | | | | | | - Pamela Magini
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
| | - Claudio Graziano
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
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2
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Hirsch N, Eshel R, Bar Yaacov R, Shahar T, Shmulevich F, Dahan I, Levaot N, Kaplan T, Lupiáñez DG, Birnbaum RY. Unraveling the transcriptional regulation of TWIST1 in limb development. PLoS Genet 2018; 14:e1007738. [PMID: 30372441 PMCID: PMC6233932 DOI: 10.1371/journal.pgen.1007738] [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: 03/06/2018] [Revised: 11/13/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
The transcription factor TWIST1 plays a vital role in mesoderm development, particularly in limb and craniofacial formation. Accordingly, haploinsufficiency of TWIST1 can cause limb and craniofacial malformations as part of Saethre-Chotzen syndrome. However, the molecular basis of TWIST1 transcriptional regulation during development has yet to be elucidated. Here, we characterized active enhancers in the TWIST1-HDAC9 locus that drive transcription in the developing limb and branchial arches. Using available p300 and H3K27ac ChIP-seq data, we identified 12 enhancer candidates, located both within and outside the coding sequences of the neighboring gene, Histone deacetyase 9 (HDAC9). Using zebrafish and mouse enhancer assays, we showed that eight of these candidates have limb/fin and branchial arch enhancer activity that resemble Twist1 expression. Using 4C-seq, we showed that the Twist1 promoter region interacts with three enhancers (eTw-5, 6, 7) in the limb bud and branchial arch of mouse embryos at day 11.5. Furthermore, we found that two transcription factors, LMX1B and TFAP2, bind these enhancers and modulate their enhancer activity. Finally, using CRISPR/Cas9 genome editing, we showed that homozygous deletion of eTw5-7 enhancers reduced Twist1 expression in the limb bud and caused pre-axial polydactyly, a phenotype observed in Twist1+/- mice. Taken together, our findings reveal that each enhancer has a discrete activity pattern, and together comprise a spatiotemporal regulatory network of Twist1 transcription in the developing limbs/fins and branchial arches. Our study suggests that mutations in TWIST1 enhancers could lead to reduced TWIST1 expression, resulting in phenotypic outcome as seen with TWIST1 coding mutations.
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Affiliation(s)
- Naama Hirsch
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reut Eshel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reut Bar Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Shahar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fania Shmulevich
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idit Dahan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Levaot
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Darío G. Lupiáñez
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ramon Y. Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Center for Evolutionary Genomics and Medicine, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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Dahan I, Sorrentino S, Boujemaa-Paterski R, Medalia O. Tiopronin-Protected Gold Nanoparticles as a Potential Marker for Cryo-EM and Tomography. Structure 2018; 26:1408-1413.e3. [PMID: 30078643 DOI: 10.1016/j.str.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 03/16/2018] [Revised: 06/03/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Gold nanoparticles (AuNPs) and their conjugation to biological samples have numerous potential applications. When combined with cryo-electron microscopy and tomography analysis, AuNPs may provide a versatile and powerful tool to identify and precisely localize proteins even when attached to cellular components. Here, we describe a general and facile approach for the synthesis of homogeneous and stable AuNPs, which can readily be conjugated to a molecule of interest and imaged by cryo-electron tomography (cryo-ET). We demonstrate the synthesis of 2.2 ± 0.45-nm tiopronin-protected AuNPs, followed by their conjugation with recombinant proteins and peptides. Visualization of the ∼2.2-nm gold-tagged peptides by cryo-ET reveals the potential use of this strategy to label and localize accessible proteins in a cellular environment with nanometric resolution.
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Affiliation(s)
- Idit Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Simona Sorrentino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Université Grenoble Alpes, 38400 Grenoble, France
| | - Ohad Medalia
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel; Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Tamir A, Sorrentino S, Motahedeh S, Shai E, Dubrovsky A, Dahan I, Eibauer M, Studt JD, Sapra KT, Varon D, Medalia O. The macromolecular architecture of platelet-derived microparticles. J Struct Biol 2016; 193:181-187. [PMID: 26767592 DOI: 10.1016/j.jsb.2015.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/16/2015] [Accepted: 12/23/2015] [Indexed: 12/22/2022]
Abstract
Platelets are essential for hemostasis and wound healing. They are involved in fundamental processes of vascular biology such as angiogenesis, tissue regeneration, and tumor metastasis. Upon activation, platelets shed small plasma membrane vesicles termed platelet-derived microparticles (PMPs). PMPs include functional cell adhesion machinery that comprises transmembrane receptors (most abundant are the αIIbβ3 integrins), cytoskeletal systems and a large variety of adapter and signaling molecules. Glanzmann thrombasthenia (GT) is a condition characterized by platelets that are deficient of the integrin αIIbβ3 heterodimer. Here, we use cryo-electron tomography (cryo-ET) to study the structural organization of PMPs (in both healthy and GT patients), especially the cytoskeleton organization and receptor architecture. PMPs purified from GT patients show a significantly altered cytoskeletal organization, characterized by a reduced number of filaments present, compared to the healthy control. Furthermore, our results show that incubating healthy PMPs with manganese ions (Mn(2+)), in the presence of fibrinogen, induces a major conformational change of integrin receptors, whereas thrombin activation yields a moderate response. These results provide the first insights into the native molecular organization of PMPs.
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Affiliation(s)
- Adi Tamir
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Simona Sorrentino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sarah Motahedeh
- Coagulation Unit, Department of Hematology, Hadassah University Hospital, Jerusalem, Israel
| | - Ela Shai
- Coagulation Unit, Department of Hematology, Hadassah University Hospital, Jerusalem, Israel
| | - Anna Dubrovsky
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Idit Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jan-Dirk Studt
- Division of Hematology, University Hospital Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
| | - K Tanuj Sapra
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - David Varon
- Coagulation Unit, Department of Hematology, Hadassah University Hospital, Jerusalem, Israel
| | - Ohad Medalia
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel; Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Dahan I, Smith SME, Pick E. A Cys-Gly-Cys triad in the dehydrogenase region of Nox2 plays a key role in the interaction with p67phox. J Leukoc Biol 2015; 98:859-74. [DOI: 10.1189/jlb.4a0315-107r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022] Open
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Rosenberg L, Maeir A, Yochman A, Dahan I, Hirsch I. Effectiveness of a Cognitive–Functional Group Intervention Among Preschoolers With Attention Deficit Hyperactivity Disorder: A Pilot Study. Am J Occup Ther 2015; 69:6903220040p1-8. [DOI: 10.5014/ajot.2015.014795] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Abstract
OBJECTIVE. To test functional improvement after a group cognitive–functional occupational therapy intervention for preschoolers with attention deficit hyperactivity disorder (ADHD).
METHOD. Seventeen preschooler–parent dyads attended 11 weekly group sessions focused on acquiring executive strategies through occupational performance. Functional improvement was measured using the Canadian Occupational Performance Measure (COPM) and Goal Attainment Scaling (GAS); executive function, using the Behavior Rating Inventory of Executive Function–Pediatric; ADHD symptomatology, using Conners’ Parent Rating Scale–Revised and Conners’ Teacher Rating Scale–Revised; and social functioning, using the Social Participation scale of the Sensory Processing Measure.
RESULTS. Significant improvement was found on the COPM and GAS measures, whereas mixed results were found on the other measures, with improvements found in children whose scores indicated impairment at baseline.
CONCLUSIONS. Cognitive–functional group intervention appears to significantly improve daily functioning, executive function, and social functioning for children who demonstrate clinical impairment. Further research with a larger sample, a control group, and follow-up is required.
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Affiliation(s)
- Lori Rosenberg
- Lori Rosenberg, MSc, OT, is Head of Occupational Therapy, Ilanot School, Jerusalem, Israel, and Lecturer, School of Occupational Therapy, Faculty of Medicine, Hadassah and the Hebrew University of Jerusalem, Mount Scopus, Jerusalem, Israel;
| | - Adina Maeir
- Adina Maeir, PhD, OT, is Head, School of Occupational Therapy, Faculty of Medicine, Hadassah and the Hebrew University of Jerusalem, Mount Scopus, Jerusalem, Israel
| | - Aviva Yochman
- Aviva Yochman, PhD, OT, is Lecturer and Researcher, School of Occupational Therapy, Faculty of Medicine, Hadassah and the Hebrew University of Jerusalem, Mount Scopus, Jerusalem, Israel
| | - Idit Dahan
- Idit Dahan, MSc, OT, is Head, Pediatric Occupational Therapy, Maccabi Health Service, Jerusalem, Israel
| | - Idit Hirsch
- Idit Hirsch, MSc, OT, is Occupational Therapist, Maccabi Health Service, Jerusalem, Israel
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7
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Chan JSD, Abdo S, Ghosh A, Alquier T, Chenier I, Filep JG, Ingelfinger JR, Zhang SL, Ross EA, Willenberg BJ, Oca-Cossio J, Clapp WL, Terada N, Abrahamson DR, Ellison GW, Matthews CE, Batich CD, Ihoriya C, Satoh M, Sasaki T, Kashihara N, Piwkowska A, Rogacka D, Angielski S, Jankowski M, Pontrelli P, Conserva F, Papale M, Accetturo M, Gigante M, Vocino G, Dipalma AM, Grandaliano G, Di Paolo S, Gesualdo L, Franzen S, Pihl L, Khan N, Gustafsson H, Palm F, Koszegi S, Hodrea J, Lenart L, Hosszu A, Wagner L, Vannay A, Tulassay T, Szabo A, Fekete A, Aoki R, Sekine F, Kikuchi K, Miyazaki S, Yamashita Y, Itoh Y, Kolling M, Park JK, Haller H, Thum T, Lorenzen J, Hirayama A, Yoh K, Ueda A, Itoh H, Owada S, Kokeny G, Szabo L, Fazekas K, Rosivall L, Mozes MM, Kim Y, Koh ES, Lim JH, Kim MY, Chang YS, Park CW, Kim Y, Kim HW, Kim MY, Lim JH, Chang YS, Park CW, Shin BC, Kim HL, Chung JH, Chan JS, Wu TC, Chen JW, Rogacka D, Piwkowska A, Angielski S, Jankowski M, Clotet S, Soler MJ, Rebull M, Pascual J, Riera M, Patinha D, Afonso J, Sousa T, Morato M, Albino-Teixeira A, Kim H, Min HS, Kang MJ, Kim JE, Lee JE, Kang YS, Cha DR, Jo YI, Seo EH, Kim JD, Lee SH, Jorge L, Silva KAS, Luiz RS, Rampaso RR, Lima W, Cunha TS, Schor N, Lee HJ, Park JY, Kim SK, Moon JY, Lee SH, Ihm CG, Lee TW, Jeong KH, Moon JY, Kim S, Park JY, Kim SY, Kim YG, Jeong KH, Lee SH, Ihm CG, Marques C, Mega C, Goncalves A, Rodrigues-Santos P, Teixeira-Lemos E, Teixeira F, Fontes Ribeiro C, Reis F, Fernandes R, Sutariya BK, Badgujar LB, Kshtriya AA, Saraf MN, Chiu CH, Lee WC, Chau YY, Lee LC, Lee CT, Chen JB, Dahan I, Nakhoul F, Thawho N, Ben-Itzhaq O, Levy AP, Conserva F, Pontrelli P, Accetturo M, Cordisco G, Fiorentino L, Federici M, Grandaliano G, Di Paolo S, Gesualdo L, Wystrychowski G, Havel PJ, Graham JL, Zukowska-Szczechowska E, Obuchowicz E, Psurek A, Grzeszczak W, Wystrychowski A, Clotet S, Soler MJ, Rebull M, Gimeno J, Pascual J, Riera M, Almeida BZD, Seraphim DCC, Punaro G, Nascimento M, Mouro M, Lanzoni VP, Lopes GS, Higa EMS, Roca-Ho H, Riera M, Marquez E, Pascual J, Soler MJ. DIABETES EXPERIMENTAL. Nephrol Dial Transplant 2014. [DOI: 10.1093/ndt/gfu149] [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: 11/13/2022] Open
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Shochat M, Shotan A, Kazatsker M, Asif A, Shochat I, Dahan I, Vasilenko L, Levy Y, Sigalov T, Meisel S. Short and long-term outcome of impedance-guided preemptive therapy provided to prevent pulmonary congestion-edema in the course of acute myocardial infarction. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht310.p5083] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Shochat M, Shotan A, Kazatsker M, Asif A, Shochat I, Dahan I, Frimerman A, Levy Y, Blondheim D, Meisel S. Evaluation of the effectiveness of in-hospital treatment of chronic heart failure patients during exacerbation by non-invasive net lung impedance monitoring during during admission. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht308.p1506] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Maimon T, Elad N, Dahan I, Medalia O. The human nuclear pore complex as revealed by cryo-electron tomography. Structure 2012; 20:998-1006. [PMID: 22632834 DOI: 10.1016/j.str.2012.03.025] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 03/27/2012] [Accepted: 03/27/2012] [Indexed: 12/25/2022]
Abstract
Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, allow free diffusion of small molecules and ions while mediating selective energy-dependent nucleocytoplasmic transport of large macromolecules. Here, we applied cryo-electron tomography to human fibroblast cells, reconstructing their nuclear envelopes without applying any purification steps. From these reconstructions, we extracted subtomograms containing individual NPCs and utilized in silico subtomogram averaging procedures to determine the structure of the mammalian pore complex at a resolution of ∼6.6 nm. Beyond revealing the canonical features of the human NPC, our analysis identified inner lateral channels and fusing bridge-like structures, suggesting alternative routes of peripheral nuclear passage. Finally, we concluded from our structural analysis that the human NPC is structurally distinct from that of lower eukaryotes in terms of dimension and organization but resembles its amphibian (frog) counterpart.
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Affiliation(s)
- Tal Maimon
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, 84105, Israel
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11
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Grossman E, Dahan I, Stick R, Goldberg MW, Gruenbaum Y, Medalia O. Filaments assembly of ectopically expressed Caenorhabditis elegans lamin within Xenopus oocytes. J Struct Biol 2012; 177:113-8. [DOI: 10.1016/j.jsb.2011.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/21/2011] [Accepted: 11/01/2011] [Indexed: 12/23/2022]
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Bokstad M, Sabanay H, Dahan I, Geiger B, Medalia O. Reconstructing adhesion structures in tissues by cryo-electron tomography of vitrified frozen sections. J Struct Biol 2011; 178:76-83. [PMID: 22085747 DOI: 10.1016/j.jsb.2011.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 10/27/2011] [Accepted: 10/30/2011] [Indexed: 01/15/2023]
Abstract
Cryo-electron tomography enables three-dimensional insights into the macromolecular architecture of cells in a close-to-life state. However, it is limited to thin specimens, <1.0 μm in thickness, typically restricted to the peripheral areas of intact eukaryotic cells. Analysis of tissue ultrastructure, on the other hand, requires physical sectioning approaches, preferably cryo-sectioning, following which electron tomography (ET) may be performed. Nevertheless, cryo-electron microscopy of vitrified sections is a demanding technique and typically cannot be used to examine thick sections, >80-100 nm, due to surface crevasses. Here, we explore the potential use of cryo-ET of vitrified frozen sections (VFSs) for imaging cell adhesions in chicken smooth muscle and mouse epithelial tissues. By investigating 300-400 nm thick sections, which are collected on the EM grid and re-vitrified, we resolved fine 3D structural details of the membrane-associated dense plaques and flanking caveoli in smooth muscle tissue, and desmosomal adhesions in stratified epithelium. Technically, this method offers a simple approach for reconstructing thick volumes of hydrated frozen sections.
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Affiliation(s)
- Melanie Bokstad
- Department of Life Sciences, Ben-Gurion University of the Negev, BeerSheva 84105, Israel
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Yahav T, Maimon T, Grossman E, Dahan I, Medalia O. Cryo-electron tomography: gaining insight into cellular processes by structural approaches. Curr Opin Struct Biol 2011; 21:670-7. [PMID: 21813274 DOI: 10.1016/j.sbi.2011.07.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [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: 05/13/2011] [Revised: 06/23/2011] [Accepted: 07/11/2011] [Indexed: 11/18/2022]
Abstract
Visualization of cellular processes at a resolution of the individual protein should involve integrative and complementary approaches that can eventually draw realistic functional and cellular landscapes. Electron tomography of vitrified but otherwise unaltered cells emerges as a central method for three-dimensional reconstruction of cellular architecture at a resolution of 2-6 nm. While a combination of correlative light-based microscopy with cryo-electron tomography (cryo-ET) provides medium-resolution insight into pivotal cellular processes, fitting high-resolution structural approaches, for example, X-ray crystallography, into reconstructed macromolecular assemblies provides unprecedented information on native protein assemblies. Thus, cryo-ET bridges the resolution gap between cellular and structural biology. In this article, we focus on the study of eukaryotic cells and macromolecular complexes in a close-to-life-state. We discuss recent developments and structural findings enabling major strides to be made in understanding complex physiological functions.
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Affiliation(s)
- Tal Yahav
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Abstract
In vitro, archaeal SRP54 binds SRP RNA in the absence of SRP19, suggesting the latter to be expendable in Archaea. Accordingly, the Haloferax volcanii SRP19 gene was deleted. Although normally transcribed at a level comparable to that of the essential SRP54 gene, SRP19 deletion had no effect on cell growth, membrane protein insertion, protein secretion, or ribosome levels. The absence of SRP19 did, however, increase membrane bacterioruberin levels.
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Affiliation(s)
- Sophie Yurist
- Department of Life Sciences, Ben Gurion University, P.O. Box 653, Beersheva 84105, Israel
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15
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Fine A, Irihimovitch V, Dahan I, Konrad Z, Eichler J. Cloning, expression, and purification of functional Sec11a and Sec11b, type I signal peptidases of the archaeon Haloferax volcanii. J Bacteriol 2006; 188:1911-9. [PMID: 16484202 PMCID: PMC1426568 DOI: 10.1128/jb.188.5.1911-1919.2006] [Citation(s) in RCA: 28] [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: 11/20/2022] Open
Abstract
Across evolution, type I signal peptidases are responsible for the cleavage of secretory signal peptides from proteins following their translocation across membranes. In Archaea, type I signal peptidases combine domain-specific features with traits found in either their eukaryal or bacterial counterparts. Eukaryal and bacterial type I signal peptidases differ in terms of catalytic mechanism, pharmacological profile, and oligomeric status. In this study, genes encoding Sec11a and Sec11b, two type I signal peptidases of the halophilic archaeon Haloferax volcanii, were cloned. Although both genes are expressed in cells grown in rich medium, gene deletion approaches suggest that Sec11b, but not Sec11a, is essential. For purification purposes, tagged versions of the protein products of both genes were expressed in transformed Haloferax volcanii, with Sec11a and Sec11b being fused to a cellulose-binding domain capable of interaction with cellulose in hypersaline surroundings. By employing an in vitro signal peptidase assay designed for use with high salt concentrations such as those encountered by halophilic archaea such as Haloferax volcanii, the signal peptide-cleaving activities of both isolated membranes and purified Sec11a and Sec11b were addressed. The results show that the two enzymes differentially cleave the assay substrate, raising the possibility that the Sec11a and Sec11b serve distinct physiological functions.
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Affiliation(s)
- Amir Fine
- Dept. of Life Sciences, Ben Gurion University, P.O. Box 653, Beersheva 84105, Israel
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Shmuely H, Dinitz E, Dahan I, Eichler J, Fischer D, Shaanan B. Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics 2004; 20:1248-53. [PMID: 14871864 DOI: 10.1093/bioinformatics/bth075] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 11/12/2022] Open
Abstract
MOTIVATION A large fraction of open reading frames (ORFs) identified as 'hypothetical' proteins correspond to either 'conserved hypothetical' proteins, representing sequences homologous to ORFs of unknown function from other organisms, or to hypothetical proteins lacking any significant sequence similarity to other ORFs in the databases. Elucidating the functions and three-dimensional structures of such orphan ORFs, termed ORFans or poorly conserved ORFs (PCOs), is essential for understanding biodiversity. However, it has been claimed that many ORFans may not encode for expressed proteins. RESULTS A genome-wide experimental study of 'paralogous PCOs' in the halophilic archaea Halobacterium sp. NRC-1 was conducted. Paralogous PCOs are ORFs with at least one homolog in the same organism, but with no clear homologs in other organisms. The results reveal that mRNA is synthesized for a majority of the Halobacterium sp. NRC-1 paralogous PCO families, including those comprising relatively short proteins, strongly suggesting that these Halobacterium sp. NRC-1 paralogous PCOs correspond to true, expressed proteins. Hence, further computational and experimental studies aimed at characterizing PCOs in this and other organisms are merited. Such efforts could shed light on PCOs' functions and origins, thereby serving to elucidate the vast diversity observed in the genetic material.
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Affiliation(s)
- H Shmuely
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
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Abstract
Leishmania parasites are ancient eukaryotes, characterized by unusual molecular mechanisms. We have used the gene encoding for Hsp83 as a model system for studying regulatory mechanisms that control developmental gene regulation. We previously showed that protein coding genes are regulated exclusively by post-transcriptional mechanisms, while no transcriptional activation could be observed even for the conserved Hsp83 gene. We now show that processing and maturation of the Hsp83 polycistronic primary transcripts is more efficient at elevated temperatures. The mature transcripts are more stable during heat shock, with regulation conferred by 3' UTRs. Poly(A) tails of Hsp83 are approximately 30 nucleotides long, as common for other low eukaryotes. The mechanism that signals differential degradation is still unclear, since it was not possible to detect differences in deadenylation of Hsp83 transcripts at varying temperatures. Heat shock transcripts are preferentially translated at 33-37 degrees C, but unlike Drosophila, translational regulation is controlled by a region within the 3' UTR. Using this traditionally conserved system emphasizes that regulatory mechanisms in Leishmania differ from those prevailing in other eukaryotes.
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Affiliation(s)
- M Shapira
- Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel.
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Abstract
Flavocytochrome b558 (Cyt b) is important in generating superoxide and other toxic oxygen species involved in inflammation and host defense. Monoclonal antibodies (mAbs) 48 and 449 bind the gp91Phox and p22phox subunits of Cyt b, respectively, and have been used to characterize this enzyme complex. Until now, data were unavailable to predict which regions of the protein were bound by each antibody. Random sequence phage-display peptide library analysis of each antibody was used to select peptides that mimic the sequence of each protein epitope. Phage sequences selected by mAb 48 presented the consensus peptide sequence, DRDVXTGL, which closely resembles 498EKDVITGL505 of gp91Phox. Phage selected by mAb 449 contributed the consensus WRWPGPQVL, resembling in part 182GPQV185 of p22phox. Confirmation for this second epitope was provided by peptide walking analysis. Identifying the protein residues bound by these antibodies makes each a more informative probe for Cyt b analysis.
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Affiliation(s)
- J B Burritt
- Department of Microbiology, Montana State University, Bozeman 59717, USA.
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