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Ramírez Medina CR, Ali I, Baricevic-Jones I, Saleem MA, Whetton AD, Kalra PA, Geifman N. Evaluation of a proteomic signature coupled with the kidney failure risk equation in predicting end stage kidney disease in a chronic kidney disease cohort. Clin Proteomics 2024; 21:34. [PMID: 38762513 PMCID: PMC11102163 DOI: 10.1186/s12014-024-09486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/25/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND The early identification of patients at high-risk for end-stage renal disease (ESRD) is essential for providing optimal care and implementing targeted prevention strategies. While the Kidney Failure Risk Equation (KFRE) offers a more accurate prediction of ESRD risk compared to static eGFR-based thresholds, it does not provide insights into the patient-specific biological mechanisms that drive ESRD. This study focused on evaluating the effectiveness of KFRE in a UK-based advanced chronic kidney disease (CKD) cohort and investigating whether the integration of a proteomic signature could enhance 5-year ESRD prediction. METHODS Using the Salford Kidney Study biobank, a UK-based prospective cohort of over 3000 non-dialysis CKD patients, 433 patients met our inclusion criteria: a minimum of four eGFR measurements over a two-year period and a linear eGFR trajectory. Plasma samples were obtained and analysed for novel proteomic signals using SWATH-Mass-Spectrometry. The 4-variable UK-calibrated KFRE was calculated for each patient based on their baseline clinical characteristics. Boruta machine learning algorithm was used for the selection of proteins most contributing to differentiation between patient groups. Logistic regression was employed for estimation of ESRD prediction by (1) proteomic features; (2) KFRE; and (3) proteomic features alongside KFRE. RESULTS SWATH maps with 943 quantified proteins were generated and investigated in tandem with available clinical data to identify potential progression biomarkers. We identified a set of proteins (SPTA1, MYL6 and C6) that, when used alongside the 4-variable UK-KFRE, improved the prediction of 5-year risk of ESRD (AUC = 0.75 vs AUC = 0.70). Functional enrichment analysis revealed Rho GTPases and regulation of the actin cytoskeleton pathways to be statistically significant, inferring their role in kidney function and the pathogenesis of renal disease. CONCLUSIONS Proteins SPTA1, MYL6 and C6, when used alongside the 4-variable UK-KFRE achieve an improved performance when predicting a 5-year risk of ESRD. Specific pathways implicated in the pathogenesis of podocyte dysfunction were also identified, which could serve as potential therapeutic targets. The findings of our study carry implications for comprehending the involvement of the Rho family GTPases in the pathophysiology of kidney disease, advancing our understanding of the proteomic factors influencing susceptibility to renal damage.
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Affiliation(s)
- Carlos Raúl Ramírez Medina
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
| | - Ibrahim Ali
- Salford Royal Hospital, Northern Care Alliance Foundation NHS Trust, Salford, UK
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, UK
| | - Ivona Baricevic-Jones
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Salford Royal Hospital, Northern Care Alliance Foundation NHS Trust, Salford, UK
| | - Moin A Saleem
- Bristol Renal and Children's Renal Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anthony D Whetton
- Veterinary Health Innovation Engine (vHive), Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Philip A Kalra
- Salford Royal Hospital, Northern Care Alliance Foundation NHS Trust, Salford, UK
| | - Nophar Geifman
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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2
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Vashishtha A, Maina SW, Altman J, Jones G, Lee TJ, Bollinger KE, Ulrich L, Töteberg-Harms M, Estes AJ, Zhi W, Sharma S, Sharma A. Complement System Proteins in the Human Aqueous Humor and Their Association with Primary Open-Angle Glaucoma. J Pers Med 2023; 13:1400. [PMID: 37763167 PMCID: PMC10532607 DOI: 10.3390/jpm13091400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
This study discovers the complement protein profile in the aqueous humor (AH) of human subjects and investigates its association with primary open-angle glaucoma (POAG) pathogenesis. Among the 32 complement proteins identified, 22 were highly abundant and detected in more than 50% of AH samples. The most predominant active complement proteins in the AH are C3, C4B, C4A, CFB, CFD, and C9. Additionally, the most prevalent complement regulators and receptors include CLU, SERPING1, F2, CFH, CFI, and VTN. Significant alterations in complement proteins were observed in individuals with POAG compared to those with cataracts. Specifically, complement protein F2 was upregulated, while C8G, C6, and CFH were downregulated in POAG samples. Stratification of the samples by race and sex revealed distinct alterations of complement proteins in patients with POAG. In the African American cohort, five complement proteins (C4A, C4B, F2, C7, and C3) were upregulated in POAG compared to cataract patients. In the Caucasian cohort, eight complement proteins (C3, SERPING1, CFI, CLU, CFHR1, C8G, C6, and CFH) were downregulated in the POAG samples compared to the cataract samples. Within the male cohort, three complement proteins (CLU, C6, and CFH) were downregulated in POAG patients compared to those with cataracts. Whereas, within the female cohort, two complement proteins (C4B and F2) were upregulated and one (C8G) downregulated in the POAG samples when compared to cataracts. Discerning these changes in the AH complement protein profile will assist in the development of tailored therapies to modulate the complement system for managing ocular disorders. These insights may also lead to novel biomarkers for diagnosing and monitoring disease progression.
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Affiliation(s)
- Ayushi Vashishtha
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Sharon W. Maina
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
| | - Jeremy Altman
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
| | - Garrett Jones
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
| | - Kathryn E. Bollinger
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
| | - Lane Ulrich
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
| | - Marc Töteberg-Harms
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
| | - Amy J. Estes
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
| | - Shruti Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (S.W.M.); (J.A.); (G.J.); (T.J.L.); (W.Z.); (S.S.)
- Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (K.E.B.); (L.U.); (M.T.-H.); (A.J.E.)
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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3
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Crine SL, Acharya KR. Molecular basis of C-mannosylation - a structural perspective. FEBS J 2022; 289:7670-7687. [PMID: 34741587 DOI: 10.1111/febs.16265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 01/14/2023]
Abstract
The structural and functional diversity of proteins can be enhanced by numerous post-translational modifications. C-mannosylation is a rare form of glycosylation consisting of a single alpha or beta D-mannopyranose forming a carbon-carbon bond with the pyrrole ring of a tryptophan residue. Despite first being discovered in 1994, C-mannosylation is still poorly understood and 3D structures are available for only a fraction of the total predicted C-mannosylated proteins. Here, we present the first comprehensive review of C-mannosylated protein structures by analysing the data for all 10 proteins with C-mannosylation/s deposited in the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). We analysed in detail the WXXW/WXXWXXW consensus motif and the highly conserved pair of arginine residues in thrombospondin type 1 repeat C-mannosylation sites or homologous arginine residues in other domains. Furthermore, we identified a conserved PXP sequence C-terminal of the C-mannosylation site. The PXP motif forms a tight turn region in the polypeptide chain and its universal conservation in C-mannosylated protein is worthy of further experimental study. The stabilization of C-mannopyranosyl groups was demonstrated through hydrogen bonding with arginine and other charged or polar amino acids. Where possible, the structural findings were linked to other functional studies demonstrating the role of C-mannosylation in protein stability, secretion or function. With the current technological advances in structural biology, we hope to see more progress in the study of C-mannosylation that may correspond to discoveries of novel C-mannosylation pathways and functions with implications for human health and biotechnology.
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Affiliation(s)
- Samuel L Crine
- Department of Biology and Biochemistry, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
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4
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Kato M, Kudo Y, Hatase M, Tsuchida N, Takeyama S, Sugiyama T, Fujimura M, Yabe I, Tsujimoto H, Fukumori Y, Inoue N, Atsumi T. Moyamoya Disease Associated with a Deficiency of Complement Component 6. J Stroke Cerebrovasc Dis 2022; 31:106601. [PMID: 35717718 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/21/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES Complement component 6 (C6) deficiency is a very rare genetic defect that leads to significantly diminished synthesis, secretion, or function of C6. In the current report, we demonstrate a previously undescribed, homozygous missense mutation in exon 17 of the C6 gene (c.2545A>G p.Arg849Gly) in a 35-year-old Japanese woman with moyamoya disease and extremely low levels of CH50 (<7.0 U/mL). MATERIALS AND METHODS The complement gene analysis using hybridization capture-based next generation sequencing was performed. CH50 was determined in patient's plasma mixed with plasma from a healthy donor or purified human C6 protein. Western blot was performed on patient's plasma using polyclonal antibodies against C6, with healthy donor's plasma and purified human C6 protein as positive controls while C6-depleted human serum as a negative control. The carriage of ring finger protein 213 variant (c.14576G>A p.Arg4859Lys), a susceptibility gene for moyamoya disease, was examined by direct sequencing. RESULTS CH50 mixing test clearly showed a deficiency pattern, being rescued by addition of only 1% healthy donor's plasma or 1 μg/mL purified human C6 protein (1/50-1/100 of physiological concentration). Western blot revealed the absence of C6 protein in the patient's plasma, confirming a quantitative deficiency of C6. The ring finger protein 213 variant was not detected. CONCLUSIONS Our data implies that unrecognized complement deficiencies would be harbored in cerebrovascular diseases with unknown etiologies.
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Affiliation(s)
- Masaru Kato
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N14W5, Kita-Ku, Sapporo 060-8648, Japan.
| | - Yuki Kudo
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N14W5, Kita-Ku, Sapporo 060-8648, Japan
| | - Masanao Hatase
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, N14W5, Kita-Ku, Sapporo 060-8648, Japan
| | - Naohisa Tsuchida
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N14W5, Kita-Ku, Sapporo 060-8648, Japan
| | - Shuhei Takeyama
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N14W5, Kita-Ku, Sapporo 060-8648, Japan
| | - Taku Sugiyama
- Department of Neurosurgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-Ku, Sapporo 060-8648, Japan
| | - Miki Fujimura
- Department of Neurosurgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-Ku, Sapporo 060-8648, Japan
| | - Ichiro Yabe
- The Division of Clinical Genetics, Hokkaido University Hospital, N14W5, Kita-Ku, Sapporo 060-8638, Japan
| | - Hiroshi Tsujimoto
- Department of Molecular Genetics, Wakayama Medical University, Kimiidera 811-1, Wakayama 641-8509, Japan
| | - Yasuo Fukumori
- Department of Molecular Genetics, Wakayama Medical University, Kimiidera 811-1, Wakayama 641-8509, Japan
| | - Norimitsu Inoue
- Department of Molecular Genetics, Wakayama Medical University, Kimiidera 811-1, Wakayama 641-8509, Japan
| | - Tatsuya Atsumi
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N14W5, Kita-Ku, Sapporo 060-8648, Japan
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5
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Cortes C, Desler C, Mazzoli A, Chen JY, Ferreira VP. The role of properdin and Factor H in disease. Adv Immunol 2022; 153:1-90. [PMID: 35469595 DOI: 10.1016/bs.ai.2021.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The complement system consists of three pathways (alternative, classical, and lectin) that play a fundamental role in immunity and homeostasis. The multifunctional role of the complement system includes direct lysis of pathogens, tagging pathogens for phagocytosis, promotion of inflammatory responses to control infection, regulation of adaptive cellular immune responses, and removal of apoptotic/dead cells and immune complexes from circulation. A tight regulation of the complement system is essential to avoid unwanted complement-mediated damage to the host. This regulation is ensured by a set of proteins called complement regulatory proteins. Deficiencies or malfunction of these regulatory proteins may lead to pro-thrombotic hematological diseases, renal and ocular diseases, and autoimmune diseases, among others. This review focuses on the importance of two complement regulatory proteins of the alternative pathway, Factor H and properdin, and their role in human diseases with an emphasis on: (a) characterizing the main mechanism of action of Factor H and properdin in regulating the complement system and protecting the host from complement-mediated attack, (b) describing the dysregulation of the alternative pathway as a result of deficiencies, or mutations, in Factor H and properdin, (c) outlining the clinical findings, management and treatment of diseases associated with mutations and deficiencies in Factor H, and (d) defining the unwanted and inadequate functioning of properdin in disease, through a discussion of various experimental research findings utilizing in vitro, mouse and human models.
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Affiliation(s)
- Claudio Cortes
- Department of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Rochester, MI, United States.
| | - Caroline Desler
- Oakland University William Beaumont School of Medicine, Rochester, MI, United States
| | - Amanda Mazzoli
- Oakland University William Beaumont School of Medicine, Rochester, MI, United States
| | - Jin Y Chen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Viviana P Ferreira
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States.
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6
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Structural basis of soluble membrane attack complex packaging for clearance. Nat Commun 2021; 12:6086. [PMID: 34667172 PMCID: PMC8526713 DOI: 10.1038/s41467-021-26366-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/01/2021] [Indexed: 12/15/2022] Open
Abstract
Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular chaperones (clusterin and vitronectin) capture and clear soluble precursors to the membrane attack complex (sMAC). However, how these chaperones block further polymerization of MAC and prevent the complex from binding target membranes remains unclear. Here, we address that question by combining cryo electron microscopy (cryoEM) and cross-linking mass spectrometry (XL-MS) to solve the structure of sMAC. Together our data reveal how clusterin recognizes and inhibits polymerizing complement proteins by binding a negatively charged surface of sMAC. Furthermore, we show that the pore-forming C9 protein is trapped in an intermediate conformation whereby only one of its two transmembrane β-hairpins has unfurled. This structure provides molecular details for immune pore formation and helps explain a complement control mechanism that has potential implications for how cell clearance pathways mediate immune homeostasis. To prevent unregulated complement activation, extracellular chaperones capture soluble precursors to the membrane attack complex (sMAC). Here, structural analysis of sMAC reveals how clusterin recognizes heterogeneous sMAC complexes and inhibits polymerization of complement protein C9.
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7
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Minakata S, Manabe S, Inai Y, Ikezaki M, Nishitsuji K, Ito Y, Ihara Y. Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine. Molecules 2021; 26:molecules26175258. [PMID: 34500691 PMCID: PMC8433626 DOI: 10.3390/molecules26175258] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
C-Mannosylation is a post-translational modification of proteins in the endoplasmic reticulum. Monomeric α-mannose is attached to specific Trp residues at the first Trp in the Trp-x-x-Trp/Cys (W-x-x-W/C) motif of substrate proteins, by the action of C-mannosyltransferases, DPY19-related gene products. The acceptor substrate proteins are included in the thrombospondin type I repeat (TSR) superfamily, cytokine receptor type I family, and others. Previous studies demonstrated that C-mannosylation plays critical roles in the folding, sorting, and/or secretion of substrate proteins. A C-mannosylation-defective gene mutation was identified in humans as the disease-associated variant affecting a C-mannosylation motif of W-x-x-W of ADAMTSL1, which suggests the involvement of defects in protein C-mannosylation in human diseases such as developmental glaucoma, myopia, and/or retinal defects. On the other hand, monomeric C-mannosyl Trp (C-Man-Trp), a deduced degradation product of C-mannosylated proteins, occurs in cells and extracellular fluids. Several studies showed that the level of C-Man-Trp is upregulated in blood of patients with renal dysfunction, suggesting that the metabolism of C-Man-Trp may be involved in human kidney diseases. Together, protein C-mannosylation is considered to play important roles in the biosynthesis and functions of substrate proteins, and the altered regulation of protein C-manosylation may be involved in the pathophysiology of human diseases. In this review, we consider the biochemical and biomedical knowledge of protein C-mannosylation and C-Man-Trp, and introduce recent studies concerning their significance in biology and medicine.
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Affiliation(s)
- Shiho Minakata
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Shino Manabe
- Pharmaceutical Department, The Institute of Medicinal Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan;
- Research Center for Pharmaceutical Development, Graduate School of Pharmaceutical Science & Faculty of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Inai
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Midori Ikezaki
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
| | - Yukishige Ito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan;
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshito Ihara
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama 641-0012, Japan; (S.M.); (Y.I.); (M.I.); (K.N.)
- Correspondence: ; Tel.: +81-73-441-0628
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8
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Lukassen MV, Franc V, Hevler JF, Heck AJR. Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7. Proteomics 2021; 21:e2000310. [PMID: 34241972 DOI: 10.1002/pmic.202000310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022]
Abstract
The human complement system provides a first line of defence against pathogens. It requires a well-orchestrated sequential assembly of an array of terminal complement components (C5, C6, C7, C8, and C9), ultimately forming the membrane attack complex (MAC). Although much information about MAC assembly is available, the structure of the soluble C7 has remained elusive. The complement proteins C7 and C6 share very high sequence homology and exhibit several conserved domains, disulphide bridges, and C-mannosylation sites. Here, we used an integrative structural MS-based approach combining native MS, glycopeptide-centric MS, in-gel cross-linking MS (IGX-MS) and structural modelling to describe structural features, including glycosylation, of human serum soluble C7. We compare this data with structural and glycosylation data for human serum C6. The new structural model for C7 shows that it adopts a compact conformation in solution. Although C6 and C7 share many similarities, our data reveals distinct O-, and N-linked glycosylation patterns in terms of location and glycan composition. Cumulatively, our data provide valuable new insight into the structure and proteoforms of C7, solving an essential piece of the puzzle in our understanding of MAC assembly.
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Affiliation(s)
- Marie V Lukassen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands.,Netherlands Proteomics Center, The Netherlands
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9
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Tomas NM, Mortensen SA, Wilmanns M, Huber TB. Across scales: novel insights into kidney health and disease by structural biology. Kidney Int 2021; 100:281-288. [PMID: 33940110 DOI: 10.1016/j.kint.2021.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/16/2021] [Accepted: 03/25/2021] [Indexed: 11/25/2022]
Abstract
Over the past decades, structural biology methods such as X-ray crystallography and cryo-electron microscopy have been increasingly used to study protein functions, molecular interactions, physiological processes, and disease mechanisms. This review outlines a selection of structural biology methods, highlights recent examples of how structural analyses have contributed to a more profound understanding of the machinery of life, and gives a perspective on how these methods can be applied to investigate functions of kidney molecules and pathogenic mechanisms of renal diseases.
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Affiliation(s)
- Nicola M Tomas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Mortensen
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; University Hamburg Clinical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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10
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Spicer BA, Dunstone MA. Going full circle: Determining the structures of complement component 9. Methods Enzymol 2021; 649:103-123. [PMID: 33712184 DOI: 10.1016/bs.mie.2021.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pore forming proteins (PFPs) undergo dramatic conformational changes to punch holes in the target membrane. These PFPs have the ability to self-assemble, by way of oligomerization, and have the capacity to transform from a water soluble state (commonly referred to as fluid phase) to a membrane adhered form. Accordingly, PFPs are metastable, that is they are inert until the right conditions cause the release of potential energy stored in the conformational fold leading to a vast structural rearrangement into a membrane-inserted oligomeric form. However, the metastable state of PFPs poses a problem of leading to aggregation and precipitation in conditions typically required for structural biology techniques. Here, we discuss the protein chemistry of the MACPF protein complement component 9 (C9). C9 is part of a larger complex assembly known as the membrane attack complex (MAC) that has been studied extensively for its ability to form pores in bacteria. An unusual artifact of human C9 is the ability to form a soluble oligomeric state of the channel portion of the MAC, called polyC9. PolyC9 formation does not require the presence of membranes or other complement factors. It is only in recent years that structural studies of the MAC have become successful owing to improved recombinant DNA expression systems and the improvement of high-resolution techniques (both X-ray crystallography and single particle cryo-EM). We discuss the expression and purification of recombinant C9, crystallization of the soluble monomeric form of C9 and the preparation of the oligomeric polyC9.
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Affiliation(s)
- Bradley A Spicer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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11
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Hevler JF, Lukassen MV, Cabrera-Orefice A, Arnold S, Pronker MF, Franc V, Heck AJR. Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry. EMBO J 2021; 40:e106174. [PMID: 33459420 PMCID: PMC7883291 DOI: 10.15252/embj.2020106174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protein oligomers, complexes, or conformers. Here we developed a cross-linking workflow combining blue native PAGE with in-gel cross-linking mass spectrometry (IGX-MS). This workflow circumvents steps, such as buffer exchange and cross-linker concentration optimization. Additionally, IGX-MS enables the parallel analysis of co-occurring protein complexes using only small amounts of sample. Another benefit of IGX-MS, demonstrated by experiments on GroEL and purified bovine heart mitochondria, is the substantial reduction of undesired over-length cross-links compared to in-solution cross-linking. We next used IGX-MS to investigate the complement components C5, C6, and their hetero-dimeric C5b6 complex. The obtained cross-links were used to generate a refined structural model of the complement component C6, resembling C6 in its inactivated state. This finding shows that IGX-MS can provide new insights into the initial stages of the terminal complement pathway.
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Affiliation(s)
- Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Marie V Lukassen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
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12
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Miura K, Suzuki T, Sun H, Takada H, Ishizawa Y, Mizuta H, Dohmae N, Simizu S. Requirement for C-mannosylation to be secreted and activated a disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4). Biochim Biophys Acta Gen Subj 2020; 1865:129833. [PMID: 33358865 DOI: 10.1016/j.bbagen.2020.129833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND C-mannosylation is a unique type of glycosylation. A disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4) is a multidomain extracellular metalloproteinase that contains several potential C-mannosylation sites. Although some ADAMTS family proteins have been reported to be C-mannosylated proteins, whether C-mannosylation affects the activation and protease activity of these proteins is unclear. METHODS We established wild-type and mutant ADAMTS4-overexpressing HT1080 cell lines. Recombinant ADAMTS4 was purified from the conditioned medium of the wild-type ADAMTS4-overexpressing cells, and the C-mannosylation sites of ADAMTS4 were identified by LC-MS/MS. The processing, secretion, and intracellular localization of ADAMTS4 were examined by immunoblot and immunofluorescence analyses. ADAMTS4 enzymatic activity was evaluated by assessing the cleavage of recombinant aggrecan. RESULTS We identified that ADAMTS4 is C-mannosylated at Trp404 in the metalloprotease domain and at Trp523, Trp526, and Trp529 in the thrombospondin type 1 repeat (TSR). The replacement of Trp404 with Phe affected ADAMTS4 processing, without affecting secretion and intracellular localization. In contrast, the substitution of Trp523, Trp526, and Trp529 with Phe residues suppressed ADAMTS4 secretion, processing, intracellular trafficking, and enzymatic activity. CONCLUSIONS Our results demonstrated that the C-mannosylation of ADAMTS4 plays important roles in protein processing, intracellular trafficking, secretion, and enzymatic activity. GENERAL SIGNIFICANCE Because C-mannosylation appears to regulate many ADAMTS4 functions, C-mannosylation may also affect other members of the ADAMTS superfamily.
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Affiliation(s)
- Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Wako, 351-0198, Japan
| | - Hongkai Sun
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Haruka Takada
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Yudai Ishizawa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Hayato Mizuta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Wako, 351-0198, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan.
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13
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Krawczyk PA, Laub M, Kozik P. To Kill But Not Be Killed: Controlling the Activity of Mammalian Pore-Forming Proteins. Front Immunol 2020; 11:601405. [PMID: 33281828 PMCID: PMC7691655 DOI: 10.3389/fimmu.2020.601405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/20/2020] [Indexed: 01/01/2023] Open
Abstract
Pore-forming proteins (PFPs) are present in all domains of life, and play an important role in host-pathogen warfare and in the elimination of cancers. They can be employed to deliver specific effectors across membranes, to disrupt membrane integrity interfering with cell homeostasis, and to lyse membranes either destroying intracellular organelles or entire cells. Considering the destructive potential of PFPs, it is perhaps not surprising that mechanisms controlling their activity are remarkably complex, especially in multicellular organisms. Mammalian PFPs discovered to date include the complement membrane attack complex (MAC), perforins, as well as gasdermins. While the primary function of perforin-1 and gasdermins is to eliminate infected or cancerous host cells, perforin-2 and MAC can target pathogens directly. Yet, all mammalian PFPs are in principle capable of generating pores in membranes of healthy host cells which-if uncontrolled-could have dire, and potentially lethal consequences. In this review, we will highlight the strategies employed to protect the host from destruction by endogenous PFPs, while enabling timely and efficient elimination of target cells.
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Affiliation(s)
- Patrycja A Krawczyk
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Marco Laub
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Patrycja Kozik
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, United Kingdom
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14
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Sassmannshausen J, Pradel G, Bennink S. Perforin-Like Proteins of Apicomplexan Parasites. Front Cell Infect Microbiol 2020; 10:578883. [PMID: 33042876 PMCID: PMC7522308 DOI: 10.3389/fcimb.2020.578883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022] Open
Abstract
Perforins are secreted proteins of eukaryotes, which possess a membrane attack complex/perforin (MACPF) domain enabling them to form pores in the membranes of target cells. In higher eukaryotes, they are assigned to immune defense mechanisms required to kill invading microbes or infected cells. Perforin-like proteins (PLPs) are also found in apicomplexan parasites. Here they play diverse roles during lifecycle progression of the intracellularly replicating protozoans. The apicomplexan PLPs are best studied in Plasmodium and Toxoplasma, the causative agents of malaria and toxoplasmosis, respectively. The PLPs are expressed in the different lifecycle stages of the pathogens and can target and lyse a variety of cell membranes of the invertebrate and mammalian hosts. The PLPs thereby either function in host cell destruction during exit or in overcoming epithelial barriers during tissue passage. In this review, we summarize the various PLPs known for apicomplexan parasites and highlight their roles in Plasmodium and Toxoplasma lifecycle progression.
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Affiliation(s)
- Juliane Sassmannshausen
- Division of Cellular and Applied Infection Biology, Institute of Zoology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Sandra Bennink
- Division of Cellular and Applied Infection Biology, Institute of Zoology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
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15
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Frank M, Beccati D, Leeflang BR, Vliegenthart JFG. C-Mannosylation Enhances the Structural Stability of Human RNase 2. iScience 2020; 23:101371. [PMID: 32739833 PMCID: PMC7399192 DOI: 10.1016/j.isci.2020.101371] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/22/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
C-Mannosylation is a relatively rare form of protein glycosylation involving the attachment of an α-mannopyranosyl residue to C-2 of the indole moiety of the amino acid tryptophan. This type of linkage was initially discovered in RNase 2 from human urine but later confirmed to be present in many other important proteins. Based on NMR experiments and extensive molecular dynamics simulations on the hundred microsecond timescale we demonstrate that, for isolated glycopeptides and denatured RNase 2, the C-linked mannopyranosyl residue exists as an ensemble of conformations, among which 1C4 is the most abundant. However, for native RNase 2, molecular dynamics and NMR studies revealed that the mannopyranosyl residue favors a specific conformation, which optimally stabilizes the protein fold through a network of hydrogen bonds and which leads to a significant reduction of the protein dynamics on the microsecond timescale. Our findings contribute to the understanding of the biological role of C-mannosylation. NMR and MD show that C-linked mannose exists as an ensemble of conformations Conformation of mannose is influenced by the protein environment and solvent In RNase 2 mannose favors a conformation that optimally stabilizes the protein fold Efficient methods for analysis of a large number of MD trajectories are presented
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Affiliation(s)
| | - Daniela Beccati
- Bijvoet Center, Division of Bio-Organic Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Bas R Leeflang
- Bijvoet Center, Division of Bio-Organic Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Johannes F G Vliegenthart
- Bijvoet Center, Division of Bio-Organic Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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16
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Krukonis ES, Thomson JJ. Complement evasion mechanisms of the systemic pathogens Yersiniae and Salmonellae. FEBS Lett 2020; 594:2598-2620. [DOI: 10.1002/1873-3468.13771] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Eric S. Krukonis
- Division of Integrated Biomedical Sciences University of Detroit Mercy School of Dentistry Detroit MI USA
| | - Joshua J. Thomson
- Division of Integrated Biomedical Sciences University of Detroit Mercy School of Dentistry Detroit MI USA
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17
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Xu ER, Lafita A, Bateman A, Hyvönen M. The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:124-134. [PMID: 32038043 DOI: 10.1107/s2059798319016747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/14/2019] [Indexed: 05/04/2023]
Abstract
The members of the CCN (Cyr61/CTGF/Nov) family are a group of matricellular regulatory proteins that are essential to a wide range of functional pathways in cell signalling. Through interacting with extracellular matrix components and growth factors via one of their four domains, the CCN proteins are involved in critical biological processes such as angiogenesis, cell proliferation, bone development, fibrogenesis and tumorigenesis. Here, the crystal structure of the thrombospondin module 1 (TSP1) domain of CCN3 (previously known as Nov) is presented, which shares a similar three-stranded fold with the thrombospondin type 1 repeats of thrombospondin-1 and spondin-1, but with variations in the disulfide connectivity. Moreover, the CCN3 TSP1 domain lacks the typical π-stacked ladder of charged and aromatic residues on one side of the domain that is seen in other TSP1 domains. Using conservation analysis among orthologous domains, it is shown that a charged cluster in the centre of the domain is the most conserved site and this cluster is predicted to be a potential functional epitope for heparan sulfate binding. This variant TSP1 domain has also been used to revise the sequence determinants of TSP1 domains and to derive improved Pfam sequence profiles for the identification of novel TSP1 domains in more than 10 000 proteins across diverse phyla.
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Affiliation(s)
- Emma Ruoqi Xu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
| | - Aleix Lafita
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, England
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, England
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
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18
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Shcherbakova A, Preller M, Taft MH, Pujols J, Ventura S, Tiemann B, Buettner FF, Bakker H. C-mannosylation supports folding and enhances stability of thrombospondin repeats. eLife 2019; 8:52978. [PMID: 31868591 PMCID: PMC6954052 DOI: 10.7554/elife.52978] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
Previous studies demonstrated importance of C-mannosylation for efficient protein secretion. To study its impact on protein folding and stability, we analyzed both C-mannosylated and non-C-mannosylated thrombospondin type 1 repeats (TSRs) of netrin receptor UNC-5. In absence of C-mannosylation, UNC-5 TSRs could only be obtained at low temperature and a significant proportion displayed incorrect intermolecular disulfide bridging, which was hardly observed when C-mannosylated. Glycosylated TSRs exhibited higher resistance to thermal and reductive denaturation processes, and the presence of C-mannoses promoted the oxidative folding of a reduced and denatured TSR in vitro. Molecular dynamics simulations supported the experimental studies and showed that C-mannoses can be involved in intramolecular hydrogen bonding and limit the flexibility of the TSR tryptophan-arginine ladder. We propose that in the endoplasmic reticulum folding process, C-mannoses orient the underlying tryptophan residues and facilitate the formation of the tryptophan-arginine ladder, thereby influencing the positioning of cysteines and disulfide bridging.
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Affiliation(s)
| | - Matthias Preller
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Manuel H Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Birgit Tiemann
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk Fr Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
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19
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Johansen W, Grove S, Anonsen JH, Moen A, Agusti-Ridaura C, Azar AS, Strætkvern KO. Complement factor C5 in Atlantic salmon (Salmo salar): Characterization of cDNA, protein and glycosylation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 100:103424. [PMID: 31254563 DOI: 10.1016/j.dci.2019.103424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Complement component 5 (C5) is an essential factor of the defensive complement system in all vertebrates. We report the characterization of C5 cDNA and protein from Atlantic salmon (Salmo salar), a teleost fish species of high importance in aquaculture. The C5 cDNA cloned from liver is 5079 nucleotides long, whose translation product has a molecular weight of 190 kDa, with the classical β-α orientation and motifs/sites for β-α cleavage (678RPKR681) and cleavage by C5 convertases (R758). Mass spectrometric analysis show a single N-linked, biantennary, complex glycan at N1125. Moreover, the N-linked glycan displays an unusual modification in the form of acetylated sialic acid residues. Three anti-C5 antisera produced in mice using purified C5 worked in immunohistochemical analyses of formalin fixed liver tissue. The purification method, whereby inactive and activated (C5b) forms were isolated, opens for interesting studies on the complement function in fish, including possible connection to stress, disease and glycosylation.
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Affiliation(s)
- Wenche Johansen
- Inland Norway University of Applied Sciences, Department of Biotechnology, Campus Hamar, Norway
| | - Søren Grove
- Norwegian Veterinary Institute, Fish Health Research Group, Oslo, Norway; Institute of Marine Research, Diseases and Pathogen Transmission, Bergen, Norway
| | - Jan Haug Anonsen
- University of Oslo, Department of Biosciences IBV, Mass Spectrometry and Proteomics Unit, Oslo, Norway; Norwegian Research Center (NORCE), Mekjarvik 12, Randaberg, Norway
| | - Anders Moen
- University of Oslo, Department of Biosciences IBV, Mass Spectrometry and Proteomics Unit, Oslo, Norway
| | - Celia Agusti-Ridaura
- Norwegian Veterinary Institute, Fish Health Research Group, Oslo, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Oslo, Norway
| | - Amir Sefidmouy Azar
- Inland Norway University of Applied Sciences, Department of Biotechnology, Campus Hamar, Norway
| | - Knut Olav Strætkvern
- Inland Norway University of Applied Sciences, Department of Biotechnology, Campus Hamar, Norway.
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20
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Doorduijn DJ, Rooijakkers SHM, Heesterbeek DAC. How the Membrane Attack Complex Damages the Bacterial Cell Envelope and Kills Gram‐Negative Bacteria. Bioessays 2019; 41:e1900074. [DOI: 10.1002/bies.201900074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/11/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Dennis J. Doorduijn
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
| | - Suzan H. M. Rooijakkers
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
| | - Dani A. C. Heesterbeek
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
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21
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Kiely AP, Murray CE, Foti SC, Benson BC, Courtney R, Strand C, Lashley T, Holton JL. Immunohistochemical and Molecular Investigations Show Alteration in the Inflammatory Profile of Multiple System Atrophy Brain. J Neuropathol Exp Neurol 2019; 77:598-607. [PMID: 29850876 PMCID: PMC6005028 DOI: 10.1093/jnen/nly035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multiple system atrophy (MSA) is an adult-onset neurodegenerative disease characterized by aggregation of α-synuclein in oligodendrocytes to form glial cytoplasmic inclusions. According to the distribution of neurodegeneration, MSA is subtyped as striatonigral degeneration (SND), olivopontocerebellar atrophy (OPCA), or as combination of these 2 (mixed MSA). In the current study, we aimed to investigate regional microglial populations and gene expression in the 3 different MSA subtypes. Microscopy with microglial marker Iba-1 combined with either proinflammatory marker CD68 or anti-inflammatory marker Arginase-1 was analyzed in control, SND, and OPCA cases (n = 5) using paraffin embedded sections. Western immunoblotting and cytokine array were used to determine protein expression in MSA and control brain regions. Gene expression was investigated using the NanoString nCounter Human Inflammation panel v2 mRNA Expression Assay. Analysis of neuropathological subtypes of MSA demonstrated a significant increase in microglia in the substantia nigra of OPCA cases. There was no difference in the microglial activation state in any region. Cytokine expression in MSA was comparable with controls. Decreased expression of CX3CL1 precursor protein and significantly greater CX3CR1 protein was found in MSA. NanoString analysis revealed the >2-fold greater expression of ARG1, MASP1, NOX4, PTGDR2, and C6 in MSA.
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Affiliation(s)
- Aoife P Kiely
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Christina E Murray
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Sandrine C Foti
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Bridget C Benson
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Robert Courtney
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Catherine Strand
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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22
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Zaitseva J, Vaknin D, Krebs C, Doroghazi J, Milam SL, Balasubramanian D, Duck NB, Freigang J. Structure-function characterization of an insecticidal protein GNIP1Aa, a member of an MACPF and β-tripod families. Proc Natl Acad Sci U S A 2019; 116:2897-2906. [PMID: 30728296 PMCID: PMC6386698 DOI: 10.1073/pnas.1815547116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The crystal structure of the Gram-negative insecticidal protein, GNIP1Aa, has been solved at 2.5-Å resolution. The protein consists of two structurally distinct domains, a MACPF (membrane attack complex/PerForin) and a previously uncharacterized type of domain. GNIP1Aa is unique in being a prokaryotic MACPF member to have both its structure and function identified. It was isolated from a Chromobacterium piscinae strain and is specifically toxic to Diabrotica virgifera virgifera larvae upon feeding. In members of the MACPF family, the MACPF domain has been shown to be important for protein oligomerization and formation of transmembrane pores, while accompanying domains define the specificity of the target of the toxicity. In GNIP1Aa the accompanying C-terminal domain has a unique fold composed of three pseudosymmetric subdomains with shared sequence similarity, a feature not obvious from the initial sequence examination. Our analysis places this domain into a protein family, named here β-tripod. Using mutagenesis, we identified functionally important regions in the β-tripod domain, which may be involved in target recognition.
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Affiliation(s)
| | | | | | | | - Sara L Milam
- Agricultural Solutions, BASF, Morrisville, NC 27560
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23
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Hoppe CM, Albuquerque-Wendt A, Bandini G, Leon DR, Shcherbakova A, Buettner FFR, Izquierdo L, Costello CE, Bakker H, Routier FH. Apicomplexan C-Mannosyltransferases Modify Thrombospondin Type I-containing Adhesins of the TRAP Family. Glycobiology 2018; 28:333-343. [PMID: 29432542 DOI: 10.1093/glycob/cwy013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/06/2018] [Indexed: 11/13/2022] Open
Abstract
In many metazoan species, an unusual type of protein glycosylation, called C-mannosylation, occurs on adhesive thrombospondin type 1 repeats (TSRs) and type I cytokine receptors. This modification has been shown to be catalyzed by the Caenorhabditis elegans DPY-19 protein and orthologues of the encoding gene were found in the genome of apicomplexan parasites. Lately, the micronemal adhesin thrombospondin-related anonymous protein (TRAP) was shown to be C-hexosylated in Plasmodium falciparum sporozoites. Here, we demonstrate that also the micronemal protein MIC2 secreted by Toxoplasma gondii tachyzoites is C-hexosylated. When expressed in a mammalian cell line deficient in C-mannosylation, P. falciparum and T. gondii Dpy19 homologs were able to modify TSR domains of the micronemal adhesins TRAP/MIC2 family involved in parasite motility and invasion. In vitro, the apicomplexan enzymes can transfer mannose to a WXXWXXC peptide but, in contrast to C. elegans or mammalian C-mannosyltransferases, are inactive on a short WXXW peptide. Since TSR domains are commonly found in apicomplexan surface proteins, C-mannosylation may be a common modification in this phylum.
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Affiliation(s)
- Carolin M Hoppe
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Andreia Albuquerque-Wendt
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Giulia Bandini
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Deborah R Leon
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Aleksandra Shcherbakova
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Falk F R Buettner
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Luis Izquierdo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), University of Barcelona, Carrer Rosselo 149-153, 08036 Barcelona, Spain
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Hans Bakker
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Françoise H Routier
- Department of Clinical Biochemistry OE4340, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Nat Commun 2018; 9:3266. [PMID: 30111885 PMCID: PMC6093860 DOI: 10.1038/s41467-018-05717-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
Complement component 9 (C9) functions as the pore-forming component of the Membrane Attack Complex (MAC). During MAC assembly, multiple copies of C9 are sequentially recruited to membrane associated C5b8 to form a pore. Here we determined the 2.2 Å crystal structure of monomeric murine C9 and the 3.9 Å resolution cryo EM structure of C9 in a polymeric assembly. Comparison with other MAC proteins reveals that the first transmembrane region (TMH1) in monomeric C9 is uniquely positioned and functions to inhibit its self-assembly in the absence of C5b8. We further show that following C9 recruitment to C5b8, a conformational change in TMH1 permits unidirectional and sequential binding of additional C9 monomers to the growing MAC. This mechanism of pore formation contrasts with related proteins, such as perforin and the cholesterol dependent cytolysins, where it is believed that pre-pore assembly occurs prior to the simultaneous release of the transmembrane regions.
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25
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Seifert L, Hoxha E, Eichhoff AM, Zahner G, Dehde S, Reinhard L, Koch-Nolte F, Stahl RAK, Tomas NM. The Most N-Terminal Region of THSD7A Is the Predominant Target for Autoimmunity in THSD7A-Associated Membranous Nephropathy. J Am Soc Nephrol 2018; 29:1536-1548. [PMID: 29555830 DOI: 10.1681/asn.2017070805] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 02/09/2018] [Indexed: 01/22/2023] Open
Abstract
Background Thrombospondin type 1 domain-containing 7A (THSD7A) has been identified as a pathogenic autoantigen in membranous nephropathy (MN). However, the THSD7A epitopes targeted by patient autoantibodies are unknown.Methods We performed an in silico analysis of the THSD7A multidomain structure, expressed the folded domains in HEK293 cells, and tested for domain reactivity with 31 serum samples from patients with THSD7A-associated MN using Western and native blotting. Immunogenicity of the antigen domains was further investigated by cDNA immunization of rabbits and mice.Results We characterized the extracellular topology of THSD7A as a tandem string of 21 thrombospondin type 1 domains. Overall, 28 serum samples (90%) recognized multiple epitope domains along the molecule. Detailed epitope mapping revealed that the complex consisting of the first and second N-terminal domains (amino acids 48-192) was recognized by 27 of 31 patient serum samples (87%). Serum recognizing one or two epitope domains showed lower anti-THSD7A antibody levels than serum recognizing three or more epitope domains. During follow-up, a loss of epitope recognition was observed in seven of 16 patients, and it was accompanied by decreasing antibody levels and remission of proteinuria. In four of 16 patients, epitope recognition patterns changed during follow-up. Notably, immunization experiments in rabbits and mice revealed that induced antibodies, like patient autoantibodies, preferentially bound to the most N-terminal domains of THSD7A.Conclusions Our data show that the immune response in THSD7A-associated MN is polyreactive and that autoantibodies predominantly target the most N-terminal part of THSD7A.
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Affiliation(s)
| | | | - Anna M Eichhoff
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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26
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Morgan BP, Boyd C, Bubeck D. Molecular cell biology of complement membrane attack. Semin Cell Dev Biol 2017; 72:124-132. [PMID: 28647534 DOI: 10.1016/j.semcdb.2017.06.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 06/10/2017] [Accepted: 06/14/2017] [Indexed: 12/11/2022]
Abstract
The membrane attack complex (MAC) is the pore-forming toxin of the complement system, a relatively early evolutionary acquisition that confers upon complement the capacity to directly kill pathogens. The MAC is more than just a bactericidal missile, having the capacity when formed on self-cells to initiate a host of cell activation events that can have profound consequences for tissue homeostasis in the face of infection or injury. Although the capacity of complement to directly kill pathogens has been recognised for over a century, and the pore-forming killing mechanism for at least 50 years, there remains considerable uncertainty regarding precisely how MAC mediates its killing and cell activation activities. A recent burst of new information on MAC structure provides context and opportunity to re-assess the ways in which MAC kills bacteria and modulates cell functions. In this brief review we will describe key aspects of MAC evolution, function and structure and seek to use the new structural information to better explain how the MAC works.
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Affiliation(s)
- B Paul Morgan
- Systems Immunity University Research Institute, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF144XN, UK.
| | - Courtney Boyd
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, 506 Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Doryen Bubeck
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, 506 Sir Ernst Chain Building, London SW7 2AZ, UK
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27
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Spicer BA, Conroy PJ, Law RH, Voskoboinik I, Whisstock JC. Perforin—A key (shaped) weapon in the immunological arsenal. Semin Cell Dev Biol 2017; 72:117-123. [DOI: 10.1016/j.semcdb.2017.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/05/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
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28
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Iyer A, Xu W, Reid RC, Fairlie DP. Chemical Approaches to Modulating Complement-Mediated Diseases. J Med Chem 2017; 61:3253-3276. [DOI: 10.1021/acs.jmedchem.7b00882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Abishek Iyer
- Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Weijun Xu
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert C. Reid
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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29
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de Jorge EG, Yebenes H, Serna M, Tortajada A, Llorca O, de Córdoba SR. How novel structures inform understanding of complement function. Semin Immunopathol 2017; 40:3-14. [PMID: 28808775 DOI: 10.1007/s00281-017-0643-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/03/2017] [Indexed: 11/30/2022]
Abstract
During the last decade, the complement field has experienced outstanding advancements in the mechanistic understanding of how complement activators are recognized, what C3 activation means, how protein complexes like the C3 convertases and the membrane attack complex are assembled, and how positive and negative complement regulators perform their function. All of this has been made possible mostly because of the contributions of structural biology to the study of the complement components. The wealth of novel structural data has frequently provided support to previously held knowledge, but often has added alternative and unexpected insights into complement function. Here, we will review some of these findings focusing in the alternative and terminal complement pathways.
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Affiliation(s)
- Elena Goicoechea de Jorge
- Department of Microbiology I (Immunology), Complutense University School of Medicine and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Hugo Yebenes
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Marina Serna
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Agustín Tortajada
- Department of Microbiology I (Immunology), Complutense University School of Medicine and 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.,Structural Biology Programme, CNIO, C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Santiago Rodríguez de Córdoba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain. .,Ciber de Enfermedades Raras, Madrid, Spain.
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30
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Bayly-Jones C, Bubeck D, Dunstone MA. The mystery behind membrane insertion: a review of the complement membrane attack complex. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160221. [PMID: 28630159 PMCID: PMC5483522 DOI: 10.1098/rstb.2016.0221] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/14/2022] Open
Abstract
The membrane attack complex (MAC) is an important innate immune effector of the complement terminal pathway that forms cytotoxic pores on the surface of microbes. Despite many years of research, MAC structure and mechanism of action have remained elusive, relying heavily on modelling and inference from biochemical experiments. Recent advances in structural biology, specifically cryo-electron microscopy, have provided new insights into the molecular mechanism of MAC assembly. Its unique 'split-washer' shape, coupled with an irregular giant β-barrel architecture, enable an atypical mechanism of hole punching and represent a novel system for which to study pore formation. This review will introduce the complement terminal pathway that leads to formation of the MAC. Moreover, it will discuss how structures of the pore and component proteins underpin a mechanism for MAC function, modulation and inhibition.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Charles Bayly-Jones
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW2 7AZ, UK
| | - Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
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31
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Schatz-Jakobsen JA, Pedersen DV, Andersen GR. Structural insight into proteolytic activation and regulation of the complement system. Immunol Rev 2017; 274:59-73. [PMID: 27782336 DOI: 10.1111/imr.12465] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complement system is a highly complex and carefully regulated proteolytic cascade activated through three different pathways depending on the activator recognized. The structural knowledge regarding the intricate proteolytic enzymes that activate and control complement has increased dramatically over the last decade. This development has been pivotal for understanding how mutations within complement proteins might contribute to pathogenesis and has spurred new strategies for development of complement therapeutics. Here we describe and discuss the complement system from a structural perspective and integrate the most recent findings obtained by crystallography, small-angle X-ray scattering, and electron microscopy. In particular, we focus on the proteolytic enzymes governing activation and their products carrying the biological effector functions. Additionally, we present the structural basis for some of the best known complement inhibitors. The large number of accumulated molecular structures enables us to visualize the relative size, position, and overall orientation of many of the most interesting complement proteins and assembled complexes on activator surfaces and in membranes.
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Affiliation(s)
| | - Dennis V Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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32
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Yang P, Skiba NP, Tewkesbury GM, Treboschi VM, Baciu P, Jaffe GJ. Complement-Mediated Regulation of Apolipoprotein E in Cultured Human RPE Cells. Invest Ophthalmol Vis Sci 2017. [PMID: 28632844 PMCID: PMC5482245 DOI: 10.1167/iovs.16-20083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose. Complement activation is implicated in the pathogenesis of age-related macular degeneration (AMD). Apolipoprotein E (ApoE) and complement activation products such as membrane attack complex (MAC) are present in eyes of individuals with AMD. Herein, we investigated the effect of complement activation on induction of ApoE accumulation in human retinal pigment epithelial (RPE) cells. Methods. Cultured human RPE cells were primed with a complement-fixing antibody followed by treatment with C1q-depleted (C1q-Dep) human serum to elicit alternative pathway complement activation. Controls included anti-C5 antibody-treated serum and heat-inactivated C1q-Dep. Total protein was determined on RPE cell extracts, conditioned media, and extracellular matrix (ECM) by Western blot. ApoE and MAC colocalization was assessed on cultured RPE cells and human eyes by immunofluorescent stain. ApoE mRNA expression was evaluated by quantitative PCR (qPCR). Results. Complement challenge upregulated cell-associated ApoE, but not apolipoprotein A1. ApoE accumulation was blocked by anti-C5 antibody and enhanced by repetitive complement challenge. ApoE mRNA levels were not affected by complement challenge. ApoE was frequently colocalized with MAC in complement-treated cells and drusen from human eyes. ApoE was released into complement-treated conditioned media after a single complement challenge and accumulated on ECM after repetitive complement challenge. Conclusions. Complement challenge induces time-dependent ApoE accumulation in RPE cells. An understanding of the mechanisms by which complement affects RPE ApoE accumulation may help to better explain drusen composition, and provide insights into potential therapeutic targets.
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Affiliation(s)
- Ping Yang
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Nikolai P Skiba
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Grace M Tewkesbury
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Victoria M Treboschi
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Peter Baciu
- Department of Biology, Allergan, Inc., Irvine, California, United States
| | - Glenn J Jaffe
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
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33
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Leung C, Hodel AW, Brennan AJ, Lukoyanova N, Tran S, House CM, Kondos SC, Whisstock JC, Dunstone MA, Trapani JA, Voskoboinik I, Saibil HR, Hoogenboom BW. Real-time visualization of perforin nanopore assembly. NATURE NANOTECHNOLOGY 2017; 12:467-473. [PMID: 28166206 DOI: 10.1038/nnano.2016.303] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
Perforin is a key protein of the vertebrate immune system. Secreted by cytotoxic lymphocytes as soluble monomers, perforin can self-assemble into oligomeric pores of 10-20 nm inner diameter in the membranes of virus-infected and cancerous cells. These large pores facilitate the entry of pro-apoptotic granzymes, thereby rapidly killing the target cell. To elucidate the pathways of perforin pore assembly, we carried out real-time atomic force microscopy and electron microscopy studies. Our experiments reveal that the pore assembly proceeds via a membrane-bound prepore intermediate state, typically consisting of up to approximately eight loosely but irreversibly assembled monomeric subunits. These short oligomers convert to more closely packed membrane nanopore assemblies, which can subsequently recruit additional prepore oligomers to grow the pore size.
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Affiliation(s)
- Carl Leung
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Adrian W Hodel
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Amelia J Brennan
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia
| | - Natalya Lukoyanova
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Sharon Tran
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia
| | - Colin M House
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia
| | - Stephanie C Kondos
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
| | - Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Joseph A Trapani
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Ilia Voskoboinik
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Helen R Saibil
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
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34
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van Pee K, Neuhaus A, D'Imprima E, Mills DJ, Kühlbrandt W, Yildiz Ö. CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin. eLife 2017; 6. [PMID: 28323617 PMCID: PMC5437283 DOI: 10.7554/elife.23644] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/17/2017] [Indexed: 12/20/2022] Open
Abstract
Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.
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Affiliation(s)
- Katharina van Pee
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alexander Neuhaus
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Özkan Yildiz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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35
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Sampson K, Zaitseva J, Stauffer M, Vande Berg B, Guo R, Tomso D, McNulty B, Desai N, Balasubramanian D. Discovery of a novel insecticidal protein from Chromobacterium piscinae , with activity against Western Corn Rootworm, Diabrotica virgifera virgifera. J Invertebr Pathol 2017; 142:34-43. [DOI: 10.1016/j.jip.2016.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/19/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
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36
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Neely AE, Mandigo KA, Robinson RL, Ness TL, Weiland MH. Chimeric approach for narrowing a membrane-inserting region within human perforin. Protein Eng Des Sel 2016; 30:105-111. [PMID: 27980121 DOI: 10.1093/protein/gzw069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
Perforin is a pore-forming, immune protein that functions to deliver an apoptotic cocktail of proteins into a target pathogen. Recent studies of the bacterial cholesterol-dependent cytolysins (CDCs) have provided a model for perforin's pore-forming mechanism. Both perforin and CDC family members share a conserved β-sheet flanked by two clusters of α-helices. Within the CDCs, these helices refold into two transmembrane β-hairpins, TMH1 and TMH2. Based upon structural conservation and electron microscopy imaging, the analogous helices within perforin are predicted to also be membrane inserting; however, these regions are approximately twice the length of the CDC TMHs. To test the membrane-insertion potential of one of these regions, chimeras were created using a well-characterized CDC, perfringolysin-O (PFO), as the backbone of these constructs. PFO's TMH2 region was replaced with perforin's corresponding helical region. Although hemolytic activity was observed, the chimera was poorly soluble. A second chimera contained the same region truncated to match the length of the PFO TMH2 region. The truncated chimera demonstrated improved solubility, significant hemolytic activity and the ability to form pores characteristic of those created by PFO. These results provide the first evidence that perforin's helices function as TMHs and more importantly narrows the residues responsible for membrane insertion.
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Affiliation(s)
- Amy E Neely
- Department of Chemistry and Physics, Armstrong State University, Savannah, GA 31419, USA
| | - Kimberly A Mandigo
- Department of Chemistry and Physics, Armstrong State University, Savannah, GA 31419, USA
| | - Rebekah L Robinson
- Department of Chemistry and Physics, Armstrong State University, Savannah, GA 31419, USA.,Department of Biology, Armstrong State University, Savannah, GA 31419, USA
| | - Traci L Ness
- Department of Biology, Armstrong State University, Savannah, GA 31419, USA
| | - Mitch H Weiland
- Department of Chemistry and Physics, Armstrong State University, Savannah, GA 31419, USA
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Abstract
The complement system is an important part of the innate and adaptive immune systems. Originally characterized as a single serum component contributing to the killing of bacteria, we now know that there are close to sixty complement proteins, multiple activation pathways and a wide range of effector functions mediated by complement. The system plays a critical role in host defense against bacteria, viruses, fungi and other pathogens. However, inappropriate complement activation contributes to the pathophysiology of autoimmune diseases and many inflammatory syndromes. Over the last several decades, therapeutic approaches to inhibit complement activation at various steps in the pathways have met with initial success, particularly at the level of the terminal pathway. This success, combined with insight from animal model studies, has lead to an unprecedented effort by biotech and pharmaceutical companies to begin developing complement inhibitors. As a result, complement has been brought for the first time to the attention of pharmacologists, toxicologists, project managers and others in the drug development industry, as well as those in the investment world. The purpose of this primer is to provide a broad overview of complement immunobiology to help those new to complement understand the rationale behind the current therapeutic directions and the investment potential of these new therapeutics.
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Affiliation(s)
- Scott R Barnum
- Department of Microbiology, University of Alabama at Birmingham, 845 19th St. S., BBRB/744, Birmingham, AL 35294, United States; Department of Neurology, University of Alabama at Birmingham, 845 19th St. S., BBRB/744, Birmingham, AL 35294, United States.
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38
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Morgan BP, Walters D, Serna M, Bubeck D. Terminal complexes of the complement system: new structural insights and their relevance to function. Immunol Rev 2016; 274:141-151. [PMID: 27782334 DOI: 10.1111/imr.12461] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Complement is a key component of innate immunity in health and a powerful driver of inflammation and tissue injury in disease. The biological and pathological effects of complement activation are mediated by activation products. These come in two flavors: (i) proteolytic fragments of complement proteins (C3, C4, C5) generated during activation that bind specific receptors on target cells to mediate effects; (ii) the multimolecular membrane attack complex generated from the five terminal complement proteins that directly binds to and penetrates target cell membranes. Several recent publications have described structural insights that have changed perceptions of the nature of this membrane attack complex. This review will describe these recent advances in understanding of the structure of the membrane attack complex and its by-product the fluid-phase terminal complement complex and relate these new structural insights to functional consequences and cell responses to complement membrane attack.
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Affiliation(s)
- Bryan Paul Morgan
- Systems Immunity Research Institute, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK.
| | - David Walters
- Systems Immunity Research Institute, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Marina Serna
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London, UK
| | - Doryen Bubeck
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London, UK
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Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism. Biochem J 2016; 473:4473-4491. [PMID: 27738201 DOI: 10.1042/bcj20160744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/06/2023]
Abstract
During the activation of complement C4 to C4b, the exposure of its thioester domain (TED) is crucial for the attachment of C4b to activator surfaces. In the C4b crystal structure, TED forms an Arg104-Glu1032 salt bridge to tether its neighbouring macroglobulin (MG1) domain. Here, we examined the C4b domain structure to test whether this salt bridge affects its conformation. Dual polarisation interferometry of C4b immobilised at a sensor surface showed that the maximum thickness of C4b increased by 0.46 nm with an increase in NaCl concentration from 50 to 175 mM NaCl. Analytical ultracentrifugation showed that the sedimentation coefficient s20,w of monomeric C4b of 8.41 S in 50 mM NaCl buffer decreased to 7.98 S in 137 mM NaCl buffer, indicating that C4b became more extended. Small angle X-ray scattering reported similar RG values of 4.89-4.90 nm for C4b in 137-250 mM NaCl. Atomistic scattering modelling of the C4b conformation showed that TED and the MG1 domain were separated by 4.7 nm in 137-250 mM NaCl and this is greater than that of 4.0 nm in the C4b crystal structure. Our data reveal that in low NaCl concentrations, both at surfaces and in solution, C4b forms compact TED-MG1 structures. In solution, physiologically relevant NaCl concentrations lead to the separation of the TED and MG1 domain, making C4b less capable of binding to its complement regulators. These conformational changes are similar to those seen previously for complement C3b, confirming the importance of this salt bridge for regulating both C4b and C3b.
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40
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An animal model of Miller Fisher syndrome: Mitochondrial hydrogen peroxide is produced by the autoimmune attack of nerve terminals and activates Schwann cells. Neurobiol Dis 2016; 96:95-104. [PMID: 27597525 DOI: 10.1016/j.nbd.2016.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 01/08/2023] Open
Abstract
The neuromuscular junction is a tripartite synapse composed of the presynaptic nerve terminal, the muscle and perisynaptic Schwann cells. Its functionality is essential for the execution of body movements and is compromised in a number of disorders, including Miller Fisher syndrome, a variant of Guillain-Barré syndrome: this autoimmune peripheral neuropathy is triggered by autoantibodies specific for the polysialogangliosides GQ1b and GT1a present in motor axon terminals, including those innervating ocular muscles, and in sensory neurons. Their binding to the presynaptic membrane activates the complement cascade, leading to a nerve degeneration that resembles that caused by some animal presynaptic neurotoxins. Here we have studied the intra- and inter-cellular signaling triggered by the binding and complement activation of a mouse monoclonal anti-GQ1b/GT1a antibody to primary cultures of spinal cord motor neurons and cerebellar granular neurons. We found that a membrane attack complex is rapidly assembled following antibody binding, leading to calcium accumulation, which affects mitochondrial functionality. Consequently, using fluorescent probes specific for mitochondrial hydrogen peroxide, we found that this reactive oxygen species is rapidly produced by mitochondria of damaged neurons, and that it triggers the activation of the MAP kinase pathway in Schwann cells. These results throw light on the molecular and cellular pathogenesis of Miller Fisher syndrome, and may well be relevant to other pathologies of the motor axon terminals, including some subtypes of the Guillain Barré syndrome.
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Zhang J, Yang Y, He W, Sun L. Necrosome core machinery: MLKL. Cell Mol Life Sci 2016; 73:2153-63. [PMID: 27048809 PMCID: PMC11108342 DOI: 10.1007/s00018-016-2190-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 12/22/2022]
Abstract
In the study of regulated cell death, the rapidly expanding field of regulated necrosis, in particular necroptosis, has been drawing much attention. The signaling of necroptosis represents a sophisticated form of a death pathway. Anti-caspase mechanisms (e.g., using inhibitors of caspases, or genetic ablation of caspase-8) switch cell fate from apoptosis to necroptosis. The initial extracellular death signals regulate RIP1 and RIP3 kinase activation. The RIP3-associated death complex assembly is necessary and sufficient to initiate necroptosis. MLKL was initially identified as an essential mediator of RIP1/RIP3 kinase-initiated necroptosis. Recent studies on the signal transduction using chemical tools and biomarkers support the idea that MLKL is able to make more functional sense for the core machinery of the necroptosis death complex, called the necrosome, to connect to the necroptosis execution. The experimental data available now have pointed that the activated MLKL forms membrane-disrupting pores causing membrane leakage, which extends the prototypical concept of morphological and biochemical events following necroptosis happening in vivo. The key role of MLKL in necroptosis signaling thus sheds light on the logic underlying this unique "membrane-explosive" cell death pathway. In this review, we provide the general concepts and strategies that underlie signal transduction of this form of cell death, and then focus specifically on the role of MLKL in necroptosis.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Rd, Shanghai, 200031, China
| | - Yu Yang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Rd, Shanghai, 200031, China
| | - Wenyan He
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Rd, Shanghai, 200031, China
| | - Liming Sun
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Rd, Shanghai, 200031, China.
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Sharp TH, Koster AJ, Gros P. Heterogeneous MAC Initiator and Pore Structures in a Lipid Bilayer by Phase-Plate Cryo-electron Tomography. Cell Rep 2016; 15:1-8. [PMID: 27052168 DOI: 10.1016/j.celrep.2016.03.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/09/2016] [Accepted: 02/24/2016] [Indexed: 02/07/2023] Open
Abstract
Pore formation in membranes is important for mammalian immune defense against invading bacteria. Induced by complement activation, the membrane attack complex (MAC) forms through sequential binding and membrane insertion of C5b6, C7, C8, and C9. Using cryo-electron tomography with a Volta phase plate and subtomogram averaging, we imaged C5b-7, C5b-8, and C5b-9 complexes and determined the C5b-9 pore structure in lipid bilayers. The in situ C5b-9 pore structure at 2.3-nm resolution reveals a 10- to 11.5-nm cone-shaped pore starting with C5b678 and multiple copies of C9 that is poorly closed, yielding a seam between C9 and C6 substituting for the shorter β strands in C6 and C7. However, large variations of composite pore complexes are apparent in subtomograms. Oligomerized initiator complexes C5b-7 and C5b-8 show stages of membrane binding, deformation, and perforation that yield ∼3.5-nm-wide pores. These data indicate a dynamic process of pore formation that likely adapts to biological membranes under attack.
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Affiliation(s)
- Thomas H Sharp
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands.
| | - Abraham J Koster
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, the Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research and Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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43
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Gilbert RJC, Sonnen AFP. Measuring kinetic drivers of pneumolysin pore structure. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:365-76. [PMID: 26906727 PMCID: PMC4823331 DOI: 10.1007/s00249-015-1106-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 11/03/2022]
Abstract
Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - Andreas F-P Sonnen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany
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44
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Dudkina NV, Spicer BA, Reboul CF, Conroy PJ, Lukoyanova N, Elmlund H, Law RHP, Ekkel SM, Kondos SC, Goode RJA, Ramm G, Whisstock JC, Saibil HR, Dunstone MA. Structure of the poly-C9 component of the complement membrane attack complex. Nat Commun 2016; 7:10588. [PMID: 26841934 PMCID: PMC4742998 DOI: 10.1038/ncomms10588] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
The membrane attack complex (MAC)/perforin-like protein complement component 9 (C9) is the major component of the MAC, a multi-protein complex that forms pores in the membrane of target pathogens. In contrast to homologous proteins such as perforin and the cholesterol-dependent cytolysins (CDCs), all of which require the membrane for oligomerisation, C9 assembles directly onto the nascent MAC from solution. However, the molecular mechanism of MAC assembly remains to be understood. Here we present the 8 Å cryo-EM structure of a soluble form of the poly-C9 component of the MAC. These data reveal a 22-fold symmetrical arrangement of C9 molecules that yield an 88-strand pore-forming β-barrel. The N-terminal thrombospondin-1 (TSP1) domain forms an unexpectedly extensive part of the oligomerisation interface, thus likely facilitating solution-based assembly. These TSP1 interactions may also explain how additional C9 subunits can be recruited to the growing MAC subsequent to membrane insertion.
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Affiliation(s)
- Natalya V. Dudkina
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Bradley A. Spicer
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Cyril F. Reboul
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Paul J. Conroy
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Natalya Lukoyanova
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Hans Elmlund
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Susan M. Ekkel
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Stephanie C. Kondos
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Robert J. A. Goode
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Georg Ramm
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - James C. Whisstock
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
| | - Helen R. Saibil
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Michelle A. Dunstone
- ARC Centre of Excellence in Advanced Molecular Imaging, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, Victoria 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton Campus, Monash University, Melbourne, 3800 Victoria, Australia
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45
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Serna M, Giles JL, Morgan BP, Bubeck D. Structural basis of complement membrane attack complex formation. Nat Commun 2016; 7:10587. [PMID: 26841837 PMCID: PMC4743022 DOI: 10.1038/ncomms10587] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/31/2015] [Indexed: 01/26/2023] Open
Abstract
In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a 'multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a 'split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.
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Affiliation(s)
- Marina Serna
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Joanna L. Giles
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - B. Paul Morgan
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
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46
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Xu Y, Guo N, Dou D, Ran X, Ma X, Kuang H. Proteomics Study on Nonallergic Hypersensitivity Induced by Compound 4880 and Ovalbumin. PLoS One 2016; 11:e0148262. [PMID: 26829397 PMCID: PMC4734762 DOI: 10.1371/journal.pone.0148262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/16/2016] [Indexed: 01/25/2023] Open
Abstract
Nonallergic hypersensitivity reaction (NHR) accounts for more than 77% of all immune-mediated immediate hypersensitivity reactions and has become a serious threat to public health. Here, proteomics was used to study the NHR mechanism of two typical substances, the compound 4880 and ovalbumin. Twelve different proteins were suggested as potential biomarkers for examining the NHR mechanism, and our results revealed that the mechanism mainly encompassed 2 processes, i.e., generation and effect processes. The generation process could be classified as direct stimulation, complement (classical and alternative), coagulation, kallikrein-kinin, and integrated pathways. Thus glutathione peroxidase 1, terminal complement complex (complement factor 4d and Bb), coagulation 13, kininogen-1, and IgE could be used as candidate biomarkers for the indication of the corresponding pathways respectively, the proteins were further confirmed by ELISA. And the effect process was mainly composed of histamine as well as proteins such as DCD and MYLPF, which could be used as important indices for the symptoms of NHR. Our study differs from previous studies in that C4880 was found to not only be involved in the direct stimulation pathway, but also in the activated complement and kallikrein-kinin pathways through the coagulation pathway. We also report for the first time that ovalbumin-induced NHR could be a combination of the coagulation, classical complement, and integrated pathways.
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Affiliation(s)
- Yubin Xu
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, China
| | - Na Guo
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Deqiang Dou
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, China
- * E-mail: (DQD); (HXK)
| | - Xiaoku Ran
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, China
| | - Xiande Ma
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, China
| | - Haixue Kuang
- College of pharmacy, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
- * E-mail: (DQD); (HXK)
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47
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Gilbert RJC. Protein-lipid interactions and non-lamellar lipidic structures in membrane pore formation and membrane fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:487-99. [PMID: 26654785 DOI: 10.1016/j.bbamem.2015.11.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/23/2015] [Accepted: 11/30/2015] [Indexed: 12/27/2022]
Abstract
Pore-forming proteins and peptides act on their targeted lipid bilayer membranes to increase permeability. This approach to the modulation of biological function is relevant to a great number of living processes, including; infection, parasitism, immunity, apoptosis, development and neurodegeneration. While some pore-forming proteins/peptides assemble into rings of subunits to generate discrete, well-defined pore-forming structures, an increasing number is recognised to form pores via mechanisms which co-opt membrane lipids themselves. Among these, membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) family proteins, Bax/colicin family proteins and actinoporins are especially prominent and among the mechanisms believed to apply are the formation of non-lamellar (semi-toroidal or toroidal) lipidic structures. In this review I focus on the ways in which lipids contribute to pore formation and contrast this with the ways in which lipids are co-opted also in membrane fusion and fission events. A variety of mechanisms for pore formation that involve lipids exists, but they consistently result in stable hybrid proteolipidic structures. These structures are stabilised by mechanisms in which pore-forming proteins modify the innate capacity of lipid membranes to respond to their environment, changing shape and/or phase and binding individual lipid molecules directly. In contrast, and despite the diversity in fusion protein types, mechanisms for membrane fusion are rather similar to each other, mapping out a pathway from pairs of separated compartments to fully confluent fused membranes. Fusion proteins generate metastable structures along the way which, like long-lived proteolipidic pore-forming complexes, rely on the basic physical properties of lipid bilayers. Membrane fission involves similar intermediates, in the reverse order. I conclude by considering the possibility that at least some pore-forming and fusion proteins are evolutionarily related homologues. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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48
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Reboul CF, Whisstock JC, Dunstone MA. Giant MACPF/CDC pore forming toxins: A class of their own. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:475-86. [PMID: 26607011 DOI: 10.1016/j.bbamem.2015.11.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 01/08/2023]
Abstract
Pore Forming Toxins (PFTs) represent a key mechanism for permitting the passage of proteins and small molecules across the lipid membrane. These proteins are typically produced as soluble monomers that self-assemble into ring-like oligomeric structures on the membrane surface. Following such assembly PFTs undergo a remarkable conformational change to insert into the lipid membrane. While many different protein families have independently evolved such ability, members of the Membrane Attack Complex PerForin/Cholesterol Dependent Cytolysin (MACPF/CDC) superfamily form distinctive giant β-barrel pores comprised of up to 50 monomers and up to 300Å in diameter. In this review we focus on recent advances in understanding the structure of these giant MACPF/CDC pores as well as the underlying molecular mechanisms leading to their formation. Commonalities and evolved variations of the pore forming mechanism across the superfamily are discussed. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Australia
| | - Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
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49
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Hammerschmidt C, Klevenhaus Y, Koenigs A, Hallström T, Fingerle V, Skerka C, Pos KM, Zipfel PF, Wallich R, Kraiczy P. BGA66 and BGA71 facilitate complement resistance of Borrelia bavariensis by inhibiting assembly of the membrane attack complex. Mol Microbiol 2015; 99:407-24. [PMID: 26434356 DOI: 10.1111/mmi.13239] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 01/09/2023]
Abstract
Borrelia (B.) bavariensis exhibits a marked tropism for nervous tissues and frequently causes neurological manifestations in humans. The molecular mechanism by which B. bavariensis overcomes innate immunity, in particular, complement remains elusive. In contrast to other serum-resistant spirochetes, none of the B. bavariensis isolates investigated bound complement regulators of the alternative (AP) and classical pathway (CP) or proteolytically inactivated complement components. Focusing on outer surface proteins BGA66 and BGA71, we demonstrated that both molecules either inhibit AP, CP and terminal pathway (TP) activation, or block activation of the CP and TP respectively. Both molecules bind complement components C7, C8 and C9, and thereby prevent assembly of the terminal complement complex. This inhibitory activity was confirmed by the introduction of the BGA66 and BGA71 encoding genes into a serum-sensitive B. garinii strain. Transformed spirochetes producing either BGA66 or BGA71 overcome complement-mediated killing, thus indicating that both proteins independently facilitate serum resistance of B. bavariensis. The generation of C-terminally truncated proteins as well as a chimeric BGA71 protein lead to the localization of the complement-interacting binding site within the N-terminus. Collectively, our data reveal a novel immune evasion strategy of B. bavariensis that is directed against the activation of the TP.
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Affiliation(s)
- Claudia Hammerschmidt
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Frankfurt, Germany
| | - Yvonne Klevenhaus
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Frankfurt, Germany
| | - Arno Koenigs
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Frankfurt, Germany
| | - Teresia Hallström
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Volker Fingerle
- National Reference Center for Borrelia, Oberschleißheim, Germany
| | - Christine Skerka
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe University of Frankfurt, Frankfurt, Germany
| | - Peter F Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.,Friedrich Schiller University, Jena, Germany
| | - Reinhard Wallich
- Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Frankfurt, Germany
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50
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The Apicomplexan CDC/MACPF-like pore-forming proteins. Curr Opin Microbiol 2015; 26:48-52. [PMID: 26025132 DOI: 10.1016/j.mib.2015.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/01/2015] [Accepted: 05/06/2015] [Indexed: 11/22/2022]
Abstract
Pore-forming proteins (PFPs) encompass a broad family of proteins that are used for virulence or immune defense. Members of the cholesterol-dependent cytolysins (CDCs) and membrane attack complex/perforin (MACPF) family of PFPs form large β-barrel pores in the membrane. The CDC/MACPF proteins contain a characteristic four-stranded β-sheet that is flanked by two α-helical bundles, which unfold to form two transmembrane β-hairpins. Apicomplexan eukaryotic parasites express CDC/MACPFs termed perforin-like proteins (PLPs). Here we review recent studies that provide key insights into the assembly and regulation of the Apicomplexan PLP (ApiMACPF) molecular pore-forming mechanisms, which are necessary for the osmotically driven rupture of the parasitophorous vacuole and host cell membrane, and cell traversal by these parasites.
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