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Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy GJ, Drew K, Emili A, Taylor DW, Marcotte EM. The protein organization of a red blood cell. Cell Rep 2022; 40:111103. [PMID: 35858567 PMCID: PMC9764456 DOI: 10.1016/j.celrep.2022.111103] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism. We validate protein complexes through electron microscopy and chemical crosslinking and, with these data, build 3D structural models of the ankyrin/Band 3/Band 4.2 complex that bridges the spectrin cytoskeleton to the RBC membrane. The model suggests spring-like compression of ankyrin may contribute to the characteristic RBC cell shape and flexibility. Taken together, our study provides an in-depth view of the global protein organization of human RBCs and serves as a comprehensive resource for future research.
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Affiliation(s)
- Wisath Sae-Lee
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Eric J Verbeke
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Pierre C Havugimana
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Claire D McWhite
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - John R Houser
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Kim Vanuytsel
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA.
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2
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Tomkinson B. Tripeptidyl-peptidase II: Update on an oldie that still counts. Biochimie 2019; 166:27-37. [DOI: 10.1016/j.biochi.2019.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
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3
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Dutoit R, Van Gompel T, Brandt N, Van Elder D, Van Dyck J, Sobott F, Droogmans L. How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima. J Biol Chem 2019; 294:17777-17789. [PMID: 31611236 DOI: 10.1074/jbc.ra119.009281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/24/2019] [Indexed: 11/06/2022] Open
Abstract
The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedron-shaped structure with 12 subunits. Their quaternary structure results from the self-assembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric-state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures has allowed us to describe how the metal ion cofactors modulate the active-site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.
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Affiliation(s)
- Raphaël Dutoit
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium .,Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Tom Van Gompel
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Nathalie Brandt
- Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Dany Van Elder
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
| | - Jeroen Van Dyck
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium.,Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Louis Droogmans
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
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4
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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5
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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6
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John-Herpin A, Tittl A, Altug H. Quantifying the Limits of Detection of Surface-Enhanced Infrared Spectroscopy with Grating Order-Coupled Nanogap Antennas. ACS PHOTONICS 2018; 5:4117-4124. [PMID: 30828588 PMCID: PMC6390698 DOI: 10.1021/acsphotonics.8b00847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Indexed: 05/08/2023]
Abstract
Infrared spectroscopy is widely used for biomolecular studies, but struggles when investigating minute quantities of analytes due to the mismatch between vibrational cross sections and IR wavelengths. It is therefore beneficial to enhance absorption signals by confining the infrared light to deeply subwavelength volumes comparable in size to the biomolecules of interest. This can be achieved with surface-enhanced infrared absorption spectroscopy, for which plasmonic nanorod antennas represent the predominant implementation. However, unifying design guidelines for such systems are still lacking. Here, we introduce an experimentally verified framework for designing antenna-based molecular IR spectroscopy sensors. Specifically, we find that in order to maximize the sensing performance, it is essential to combine the signal enhancement originating from nanoscale gaps between the antenna elements with the enhancement obtained from coupling to the grating order modes of the unit cell. Using an optimized grating order-coupled nanogap design, our experiments and numerical simulations show a hotspot limit of detection of two proteins per nanogap. Furthermore, we introduce and analyze additional limit of detection parameters, specifically for deposited surface mass, in-solution concentration, and secondary structure determination. These limits of detection provide valuable reference points for performance metrics of surface-enhanced infrared absorption spectroscopy in practical applications, such as the characterization of biological samples in aqueous solution.
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7
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In situ structural studies of tripeptidyl peptidase II (TPPII) reveal spatial association with proteasomes. Proc Natl Acad Sci U S A 2017; 114:4412-4417. [PMID: 28396430 DOI: 10.1073/pnas.1701367114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tripeptidyl peptidase II (TPPII) is a eukaryotic protease acting downstream of the 26S proteasome; it removes tripeptides from the degradation products released by the proteasome. Structural studies in vitro have revealed the basic architecture of TPPII, a two-stranded linear polymer that assembles to form a spindle-shaped complex of ∼6 MDa. Dependent on protein concentration, TPPII has a distinct tendency for polymorphism. Therefore, its structure in vivo has remained unclear. To resolve this issue, we have scrutinized cryo-electron tomograms of rat hippocampal neurons for the occurrence and spatial distribution of TPPII by template matching. The quality of the tomograms recorded with the Volta phase plate enabled a detailed structural analysis of TPPII despite its low abundance. Two different assembly states (36-mers and 32-mers) coexist as well as occasional extended forms with longer strands. A distance analysis of the relative locations of TPPII and 26S proteasomes confirmed the visual impression that these two complexes spatially associate in agreement with TPPII's role in postproteasomal degradation.
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8
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Substrate recognition in selective autophagy and the ubiquitin-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:163-81. [PMID: 23545414 DOI: 10.1016/j.bbamcr.2013.03.019] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/15/2013] [Accepted: 03/20/2013] [Indexed: 12/21/2022]
Abstract
Dynamic protein turnover through regulated protein synthesis and degradation ensures cellular growth, proliferation, differentiation and adaptation. Eukaryotic cells utilize two mechanistically distinct but largely complementary systems - the 26S proteasome and the lysosome (or vacuole in yeast and plants) - to effectively target a wide range of proteins for degradation. The concerted action of the ubiquitination machinery and the 26S proteasome ensures the targeted and tightly regulated degradation of a subset of commonly short-lived cellular proteins. Autophagy is a distinct degradation pathway, which transports a highly heterogeneous set of cargos in dedicated vesicles, called autophagosomes, to the lysosome. There the cargo becomes degraded and its molecular building blocks are recycled. While general autophagy randomly engulfs portions of the cytosol, selective autophagy employs dedicated cargo adaptors to specifically enrich the forming autophagosomes for a certain type of cargo as a response to various intra- or extracellular signals. Selective autophagy targets a wide range of cargos including long-lived proteins and protein complexes, organelles, protein aggregates and even intracellular microbes. In this review we summarize available data on cargo recognition mechanisms operating in selective autophagy and the ubiquitin-proteasome system (UPS), and emphasize their differences and common themes. Moreover, we derive general regulatory principles underlying cargo recognition in selective autophagy, and describe the system-wide crosstalk between these two cellular protein degradation systems. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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9
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Eklund S, Dogan J, Jemth P, Kalbacher H, Tomkinson B. Characterization of the endopeptidase activity of tripeptidyl-peptidase II. Biochem Biophys Res Commun 2012; 424:503-7. [PMID: 22771804 DOI: 10.1016/j.bbrc.2012.06.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Tripeptidyl-peptidase II (TPP II) is a giant cytosolic peptidase with a proposed role in cellular protein degradation and protection against apoptosis. Beside its well-characterised exopeptidase activity, TPP II also has an endopeptidase activity. Little is known about this activity, and since it could be important for the physiological role of TPP II, we have investigated it in more detail. Two peptides, Nef(69-87) and LL37, were incubated with wild-type murine TPP II and variants thereof as well as TPP II from human and Drosophila melanogaster. Two intrinsically disordered proteins were also included in the study. We conclude that the endopeptidase activity is more promiscuous than previously reported. It is also clear that TPP II can attack longer disordered peptides up to 75 amino acid residues. Using a novel FRET substrate, the catalytic efficiency of the endopeptidase activity could be determined to be 5 orders of magnitude lower than for the exopeptidase activity.
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Affiliation(s)
- Sandra Eklund
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 751 23 Uppsala, Sweden.
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10
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Ruttekolk IR, Witsenburg JJ, Glauner H, Bovee-Geurts PHM, Ferro ES, Verdurmen WPR, Brock R. The intracellular pharmacokinetics of terminally capped peptides. Mol Pharm 2012; 9:1077-86. [PMID: 22497602 DOI: 10.1021/mp200331g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With significant progress in delivery technologies, peptides and peptidomimetics are receiving increasing attention as potential therapeutics also for intracellular applications. However, analyses of the intracellular behavior of peptides are a challenge; therefore, knowledge on the intracellular pharmacokinetics of peptides is limited. So far, most research has focused on peptide degradation in the context of antigen processing, rather than on peptide stability. Here, we studied the structure-activity relationship of peptides with respect to intracellular residence time and proteolytic breakdown. The peptides comprised a collection of interaction motifs of SH2 and SH3 domains with different charge but that were of similar size and carried an N-terminal fluorescein moiety. First, we show that electroporation is a highly powerful technique to introduce peptides with different charge and hydrophobicity in uniform yields. Remarkably, the peptides differed strongly in retention of intracellular fluorescence with half-lives ranging from only 1 to more than 10 h. Residence times were greatly increased for retro-inverso peptides, demonstrating that rapid loss of fluorescence is a function of peptide degradation rather than the physicochemical characteristics of the peptide. Differences in proteolytic sensitivity were further confirmed using fluorescence correlation spectroscopy as a separation-free analytical technique to follow degradation in crude cell lysates and also in intact cells. The results provide a straightforward analytical access to a better understanding of the principles of peptide stability inside cells and will therefore greatly assist the development of bioactive peptides.
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Affiliation(s)
- Ivo R Ruttekolk
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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11
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Abstract
Molecular structures can serve to either validate or rule out existing hypotheses, and they can also spawn new, deeper proposals about biochemical mechanism. In this issue of Structure, Schönegge et al. use single-particle cryo-electron microscopy and flexible docking to examine the function of human tripeptidyl peptidase II, including the role of conformational changes in enzyme activation.
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Affiliation(s)
- Robert M Glaeser
- Donner Laboratory, Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
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12
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Schönegge AM, Villa E, Förster F, Hegerl R, Peters J, Baumeister W, Rockel B. The structure of human tripeptidyl peptidase II as determined by a hybrid approach. Structure 2012; 20:593-603. [PMID: 22483107 DOI: 10.1016/j.str.2012.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 10/28/2022]
Abstract
Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation.
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Affiliation(s)
- Anne-Marie Schönegge
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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13
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Eklund S, Lindås AC, Hamnevik E, Widersten M, Tomkinson B. Exploring the active site of tripeptidyl-peptidase II through studies of pH dependence of reaction kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:561-70. [DOI: 10.1016/j.bbapap.2012.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/03/2012] [Accepted: 01/03/2012] [Indexed: 11/16/2022]
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14
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Peters J, Schönegge AM, Rockel B, Baumeister W. Molecular ruler of tripeptidylpeptidase II: mechanistic principle of exopeptidase selectivity. Biochem Biophys Res Commun 2011; 414:209-14. [PMID: 21946061 DOI: 10.1016/j.bbrc.2011.09.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 09/11/2011] [Indexed: 11/28/2022]
Abstract
The structure of tripeptidylpeptidase II (TPPII) has shown that it belongs to the group of exopeptidases which use a double-Glu motif to convey aminopeptidase activity. TPPII has been implicated in vital biological processes. At least one of these, antigen processing, requires the involvement of its endopeptidase activity. In order to understand the extent and molecular basis of this unusual functional promiscuity we have performed a systematic kinetic analysis of wild type Drosophila melanogaster TPPII and five point mutants of the double-Glu-motif (E312/E343) involving natural substrates. Unlike the known double-Glu motives of other exopeptidases, the double-Glu motif of TPPII is distinctly asymmetrical: E312 is the crucial determinant of the aminotripeptidolytic ruler mechanism. It both blocks the active-site cleft at substrate position P4 and forms a salt bridge with the N-terminus of the substrate. In contrast, E343 forms a much weaker salt bridge than E312 and it does not have a blocking role. An endopeptidase substrate can bind at relatively high affinity if the length of the substrate permits binding to several S' sites. However, the lacking alignment of the substrate by the double-Glu motif causes the endopeptidolytic K(cat)/K(M) of TPPII to be very low.
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Affiliation(s)
- Jürgen Peters
- Max-Planck-Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
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15
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Malik A, Korol A, Hübner S, Hernandez AG, Thimmapuram J, Ali S, Glaser F, Paz A, Avivi A, Band M. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns. PLoS One 2011; 6:e21227. [PMID: 21857902 PMCID: PMC3155515 DOI: 10.1371/journal.pone.0021227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 05/23/2011] [Indexed: 12/21/2022] Open
Abstract
The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.
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Affiliation(s)
- Assaf Malik
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sariel Hübner
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Alvaro G. Hernandez
- W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, Illinois, United States of America
| | - Jyothi Thimmapuram
- W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, Illinois, United States of America
| | - Shahjahan Ali
- W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, Illinois, United States of America
| | - Fabian Glaser
- Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Arnon Paz
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aaron Avivi
- Institute of Evolution, University of Haifa, Haifa, Israel
- * E-mail: (MB); (AA)
| | - Mark Band
- W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, Illinois, United States of America
- * E-mail: (MB); (AA)
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16
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Duensing S, Darr S, Cuevas R, Melquiot N, Brickner AG, Duensing A, Münger K. Tripeptidyl Peptidase II Is Required for c-MYC-Induced Centriole Overduplication and a Novel Therapeutic Target in c-MYC-Associated Neoplasms. Genes Cancer 2011; 1:883-92. [PMID: 21647238 DOI: 10.1177/1947601910389605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 10/12/2010] [Accepted: 10/12/2010] [Indexed: 12/20/2022] Open
Abstract
Centrosome aberrations are frequently detected in c-MYC-associated human malignancies. Here, we show that c-MYC-induced centrosome and centriole overduplication critically depend on the protease tripeptidyl peptidase II (TPPII). We found that TPPII localizes to centrosomes and that overexpression of TPPII, similar to c-MYC, can disrupt centriole duplication control and cause centriole multiplication, a process during which maternal centrioles nucleate the formation of more than a single daughter centriole. We report that inactivation of TPPII using chemical inhibitors or siRNA-mediated protein knockdown effectively reduced c-MYC-induced centriole overduplication. Remarkably, the potent and selective TPPII inhibitor butabindide not only potently suppressed centriole aberrations but also caused significant cell death and growth suppression in aggressive human Burkitt lymphoma cells with c-MYC overexpression. Taken together, these results highlight the role of TPPII in c-MYC-induced centriole overduplication and encourage further studies to explore TPPII as a novel antineoplastic drug target.
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Affiliation(s)
- Stefan Duensing
- Cancer Virology Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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17
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Rockel B, Kopec KO, Lupas AN, Baumeister W. Structure and function of tripeptidyl peptidase II, a giant cytosolic protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:237-45. [PMID: 21771670 DOI: 10.1016/j.bbapap.2011.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 01/25/2023]
Abstract
Tripeptidyl peptidase II is the largest known eukaryotic peptidase. It has been described as a multi-purpose peptidase, which, in addition to its house-keeping function in intracellular protein degradation, plays a role in several vital cellular processes such as antigen processing, apoptosis, or cell division, and is involved in diseases like muscle wasting, obesity, and in cancer. Biochemical studies and bioinformatics have identified TPPII as a subtilase, but its structure is very unusual: it forms a large homooligomeric complex (6 MDa) with a spindle-like shape. Recently, the high-resolution structure of TPPII homodimers (300 kDa) was solved and a hybrid structure of the holocomplex built of 20 dimers was obtained by docking it into the EM-density. Here, we summarize our current knowledge about TPPII with a focus on structural aspects. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Beate Rockel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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18
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van Endert P. Post-proteasomal and proteasome-independent generation of MHC class I ligands. Cell Mol Life Sci 2011; 68:1553-67. [PMID: 21390545 PMCID: PMC11115176 DOI: 10.1007/s00018-011-0662-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 12/18/2022]
Abstract
Peptide ligands presented by MHC class I molecules are produced by intracellular proteolysis, which often involves multiple steps. Initial antigen degradation seems to rely almost invariably on the proteasome, although tripeptidyl peptidase II (TPP II) and insulin-degrading enzyme (IDE) may be able to substitute for the proteasome in rare cases. Recent evidence suggests that the net effect of cytosolic aminopeptidases is destruction of potential class I ligands, although a positive role in selected cases has been documented. This may apply particularly to the trimming of long precursors by TPP II. In contrast, trimming of ligand precursors in the endoplasmic reticulum is essential for the generation of suitable peptides and has a substantial impact on the repertoire of ligands presented. Trimming by the ER aminopeptidase (ERAP) enzymes most likely acts on free precursors and is adapted to the needs of class I molecules by way of a molecular ruler mechanism. Trimming by ERAP enzymes also occurs for cross-presented ligands, which can alternatively be processed in a special endosomal compartment by insulin-regulated aminopeptidase.
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Affiliation(s)
- Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris 75015, France.
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Mulenga A, Erikson K. A snapshot of the Ixodes scapularis degradome. Gene 2011; 482:78-93. [PMID: 21596113 DOI: 10.1016/j.gene.2011.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/04/2011] [Accepted: 04/15/2011] [Indexed: 01/19/2023]
Abstract
Parasitic encoded proteases are essential to regulating interactions between parasites and their hosts and thus they represent attractive anti-parasitic druggable and/or vaccine target. We have utilized annotations of Ixodes scapularis proteases in gene bank and version 9.3 MEROPS database to compile an index of at least 233 putatively active and 150 putatively inactive protease enzymes that are encoded by the I. scapularis genome. The 233 putatively active protease homologs hereafter referred to as the degradome (the full repertoire of proteases encoded by the I. scapularis genome) represent ~1.14% of the 20485 putative I. scapularis protein content. Consistent with observations in other animals, the content of the I. scapularis degradome is ~6.0% (14/233) aspartic, ~19% (44/233) cysteine, ~40% (93/233) metallo, ~28.3% (66/233) serine and ~6.4% (15/233) threonine proteases. When scanned against other tick sequences, ~11% (25/233) of I. scapularis putatively active proteases are conserved in other tick species with ≥ 60% amino acid identity levels. The I. scapularis genome does not apparently encode for putatively inactive aspartic proteases. Of the 150 putative inactive protease homologs none are from the aspartic protease class, ~8% (12/150) are cysteine, ~58.7% (88/150) metallo, 30% (45/150) serine and ~3.3% (5/150) are threonine proteases. The I. scapularis tick genome appears to have evolutionarily lost proteolytic activity of at least 6 protease families, C56 and C64 (cysteine), M20 and M23 (metallo), S24 and S28 (serine) as revealed by a lack of the putatively active proteases in these families. The overall protease content is comparable to other organisms. However, the paucity of the S1 chymotrypsin/trypsin-like serine protease family in the I. scapularis genome where it is ~12.7% (28/233) of the degradome as opposed to ~22-48% content in other blood feeding arthropods, Pediculus humanus humanus, Anopheles gambiae, Aedes Aegypti and Culex pipiens quinquefasciatus is notable. The data is presented as a one-stop index of proteases encoded by the I. scapularis genome.
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Affiliation(s)
- Albert Mulenga
- Texas A & M University AgriLife Research, Department of Entomology, College Station, TX 77843, USA.
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Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 2010; 39:D456-64. [PMID: 20935055 PMCID: PMC3013769 DOI: 10.1093/nar/gkq880] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
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Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA.
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