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Wilson Alphonse CR, Rajesh Kannan R, Nagarajan N. PITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer's disease. J Biomol Struct Dyn 2022:1-12. [PMID: 35751131 DOI: 10.1080/07391102.2022.2092554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Amyloid β-protein (ABP) is found to be the major cause for the development of neurodegeneration which leads to Alzheimer's. The Aβ nonapeptide segment, QKLVFFAED (amino acids 15-23) is the highly amyloidogenic central region of Aβ. Familial mutation in Aβ increases the aggregation property of the peptide compared to the Native (Wild) amyloid-beta (Aβ) and these mutations fall on the Aβ nonapeptide segment. The catalytic activity of pitrilysin metallopeptidase 1(PITRM1) with familial mutant Aβ (Flemish, Arctic, Dutch, Italian and Iowa) during interaction is examined using molecular dynamic simulation. The molecular dynamics simulation of PITRM1 and the Aβ nonapeptide segment showed similar RMSD with respect to stability. The active site amino acid (AA) H108, hydrophobic pocket AA residues L111, F123, F124, and L127 and the basic pocket AA residues R888 and H896 showed similar interactions with both wild and familial Aβ. The molecular level interaction between amyloid beta and PITRM1 were similar in the wild and familial mutants except for the Arctic mutant. The hydrophobic interaction was commonly observed between the S1 hydrophobic pocket and the LVFF region, the Arctic mutant showed less hydrogen bond formation consistently when compared to other complexes. This molecular information on catalytic activity suggests that modulating inactive PITRM1 or an increase in expression of PITRM1 can help in eliminating different kinds of familial mutant Aβ in neurodegenerative cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlton Ranjith Wilson Alphonse
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Nagasundaram Nagarajan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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2
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Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Nat Commun 2022; 13:1833. [PMID: 35383169 PMCID: PMC8983764 DOI: 10.1038/s41467-022-29322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption. Thereby, we elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3–4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives a rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations. Presequence protease (PreP) is essential to mitochondrial proteostasis. This study leverages advanced vitrification techniques to solve cryoEM structures of apo- and substrate-bound PreP and integrates these data with other analysis to reveal key stages and mechanistic insights of the PreP catalytic cycle.
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3
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Expression of IDE and PITRM1 genes in ERN1 knockdown U87 glioma cells: effect of hypoxia and glucose deprivation. Endocr Regul 2021; 54:183-195. [PMID: 32857715 DOI: 10.2478/enr-2020-0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE The aim of the present investigation was to study the expression of genes encoding polyfunctional proteins insulinase (insulin degrading enzyme, IDE) and pitrilysin metallopeptidase 1 (PITRM1) in U87 glioma cells in response to inhibition of endoplasmic reticulum stress signaling mediated by ERN1/IRE1 (endoplasmic reticulum to nucleus signaling 1) for evaluation of their possible significance in the control of metabolism through ERN1 signaling as well as hypoxia, glucose and glutamine deprivations. METHODS The expression level of IDE and PITRM1 genes was studied in control and ERN1 knockdown U87 glioma cells under glucose and glutamine deprivations as well as hypoxia by quantitative polymerase chain reaction. RESULTS It was found that the expression level of IDE and PITRM1 genes was down-regulated in ERN1 knockdown (without ERN1 protein kinase and endoribonuclease activity) glioma cells in comparison with the control glioma cells, being more significant for PITRM1 gene. We also found up-regulation of microRNA MIR7-2 and MIRLET7A2, which have specific binding sites in 3'-untranslated region of IDE and PITRM1 mRNAs, correspondingly, and can participate in posttranscriptional regulation of these mRNA expressions. Only inhibition of ERN1 endoribonuclease did not change significantly the expression of IDE and PITRM1 genes in glioma cells. The expression of IDE and PITRM1 genes is preferentially regulated by ERN1 protein kinase. We also showed that hypoxia down-regulated the expression of IDE and PITRM1 genes and that knockdown of ERN1 signaling enzyme function modified the response of these gene expressions to hypoxia. Glucose deprivation increased the expression level of IDE and PITRM1 genes, but ERN1 knockdown enhanced only the effect of glucose deprivation on PITRM1 gene expression. Glutamine deprivation did not affect the expression of IDE gene in both types of glioma cells, but up-regulated PITRM1 gene and this up-regulation was stronger in ERN1 knockdown cells. CONCLUSIONS Results of this investigation demonstrate that ERN1 knockdown significantly decreases the expression of IDE and PITRM1 genes by ERN1 protein kinase mediated mechanism. The expression of both studied genes was sensitive to hypoxia as well as glucose deprivation and dependent on ERN1 signaling in gene-specific manner. It is possible that the level of these genes expression under hypoxia and glucose deprivation is a result of complex interaction of variable endoplasmic reticulum stress related and unrelated regulatory factors and contributed to the control of the cell metabolism.
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Lebeau J, Rainbolt TK, Wiseman RL. Coordinating Mitochondrial Biology Through the Stress-Responsive Regulation of Mitochondrial Proteases. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 340:79-128. [PMID: 30072094 PMCID: PMC6402875 DOI: 10.1016/bs.ircmb.2018.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteases are localized throughout mitochondria and function as critical regulators of all aspects of mitochondrial biology. As such, the activities of these proteases are sensitively regulated through transcriptional and post-translational mechanisms to adapt mitochondrial function to specific cellular demands. Here, we discuss the stress-responsive mechanisms responsible for regulating mitochondrial protease activity and the implications of this regulation on mitochondrial function. Furthermore, we describe how imbalances in the activity or regulation of mitochondrial proteases induced by genetic, environmental, or aging-related factors influence mitochondria in the context of disease. Understanding the molecular mechanisms by which cells regulate mitochondrial function through alterations in protease activity provide insights into the contributions of these proteases in pathologic mitochondrial dysfunction and reveals new therapeutic opportunities to ameliorate this dysfunction in the context of diverse classes of human disease.
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Affiliation(s)
- Justine Lebeau
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - T Kelly Rainbolt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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5
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Smith‐Carpenter JE, Alper BJ. Functional requirement for human pitrilysin metallopeptidase 1 arginine 183, mutated in amyloidogenic neuropathy. Protein Sci 2018; 27:861-873. [PMID: 29383861 PMCID: PMC5866943 DOI: 10.1002/pro.3380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 01/01/2023]
Abstract
Here we report the enzymologic characterization of recombinant human pitrilysin metallopeptidase 1 (Pitrm1) and derivative mutants including the arginine-to-glutamine substitution mutant Pitrm1 R183Q, which has been implicated in inherited amyloidogenic neuropathy. Recombinant Pitrm1 R183Q was readily expressed in and purified from Escherichia coli, but was less active than the recombinant wild-type enzyme against recombinant amyloid beta-peptide (Aβ 1-40). A novel fluorogenic substrate derived from the reported Aβ 1-40 core peptide cleavage sequence, Mca-KLVFFAEDK-(Dnp)-OH, was synthesized and applied to real-time kinetic study of Pitrm1 and derivative mutants including Pitrm1 R183Q. The Pitrm1 R183Q mutant exhibited significantly decreased rate of fluorogenic peptide hydrolysis, yet retained similar binding affinity by comparison with the wild-type enzyme. Targeted mutagenic analysis revealed a functional requirement for uncharged or electropositive residues in place of Pitrm1 R183. Residue R183 is positioned within an N-terminal strand-loop-strand motif that is conserved among M16C, but not M16A or M16B family metallopeptidases. Truncation analysis revealed that this strand-loop-strand motif inclusive of residue R183 is essential Pitrm1 function. A requirement for charged residues within 4.5 Å of residue R183 was demonstrated, and Pitrm1 R183Q was found to exhibit increased sensitivity to heat inactivation. Our findings indicate that charge sharing in the vicinity of Pitrm1 R183 is critical to enzyme activity, providing potential insight into a molecular basis of Pitrm1 dysfunction.
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Affiliation(s)
| | - Benjamin J. Alper
- Department of ChemistrySacred Heart UniversityFairfieldConnecticut06825
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6
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Teixeira PF, Masuyer G, Pinho CM, Branca RMM, Kmiec B, Wallin C, Wärmländer SKTS, Berntsson RPA, Ankarcrona M, Gräslund A, Lehtiö J, Stenmark P, Glaser E. Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin. J Mol Biol 2017; 430:348-362. [PMID: 29183787 DOI: 10.1016/j.jmb.2017.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/21/2017] [Indexed: 11/29/2022]
Abstract
Proteolysis plays an important role in mitochondrial biogenesis, from the processing of newly imported precursor proteins to the degradation of mitochondrial targeting peptides. Disruption of peptide degradation activity in yeast, plant and mammalian mitochondria is known to have deleterious consequences for organism physiology, highlighting the important role of mitochondrial peptidases. In the present work, we show that the human mitochondrial peptidase neurolysin (hNLN) can degrade mitochondrial presequence peptides as well as other fragments up to 19 amino acids long. The crystal structure of hNLNE475Q in complex with the products of neurotensin cleavage at 2.7Å revealed a closed conformation with an internal cavity that restricts substrate length and highlighted the mechanism of enzyme opening/closing that is necessary for substrate binding and catalytic activity. Analysis of peptide degradation in vitro showed that hNLN cooperates with presequence protease (PreP or PITRM1) in the degradation of long targeting peptides and amyloid-β peptide, Aβ1-40, associated with Alzheimer disease, particularly cleaving the hydrophobic fragment Aβ35-40. These findings suggest that a network of proteases may be required for complete degradation of peptides localized in mitochondria.
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Affiliation(s)
- Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Catarina M Pinho
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Science and Society, Karolinska Institutet, Stockholm, Sweden
| | - Rui M M Branca
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Cecilia Wallin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | | | - Maria Ankarcrona
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Science and Society, Karolinska Institutet, Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
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7
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Guan H, Chow KM, Song E, Verma N, Despa F, Hersh LB. The Mitochondrial Peptidase Pitrilysin Degrades Islet Amyloid Polypeptide in Beta-Cells. PLoS One 2015; 10:e0133263. [PMID: 26191799 PMCID: PMC4507941 DOI: 10.1371/journal.pone.0133263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 06/25/2015] [Indexed: 01/09/2023] Open
Abstract
Amyloid formation and mitochondrial dysfunction are characteristics of type 2 diabetes. The major peptide constituent of the amyloid deposits in type 2 diabetes is islet amyloid polypeptide (IAPP). In this study, we found that pitrilysin, a zinc metallopeptidase of the inverzincin family, degrades monomeric, but not oligomeric, islet amyloid polypeptide in vitro. In insulinoma cells when pitrilysin expression was decreased to 5% of normal levels, there was a 60% increase in islet amyloid polypeptide-induced apoptosis. In contrast, overexpression of pitrilysin protects insulinoma cells from human islet amyloid polypeptide-induced apoptosis. Since pitrilysin is a mitochondrial protein, we used immunofluorescence staining of pancreases from human IAPP transgenic mice and Western blot analysis of IAPP in isolated mitochondria from insulinoma cells to provide evidence for a putative intramitochondrial pool of IAPP. These results suggest that pitrilysin regulates islet amyloid polypeptide in beta cells and suggest the presence of an intramitochondrial pool of islet amyloid polypeptide involved in beta-cell apoptosis.
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Affiliation(s)
- Hanjun Guan
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Biomedical Biological Sciences Research Building, 741 South Limestone St., Lexington, KY, 40536–0509, United States of America
- * E-mail:
| | - K. Martin Chow
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Biomedical Biological Sciences Research Building, 741 South Limestone St., Lexington, KY, 40536–0509, United States of America
| | - Eunsuk Song
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Biomedical Biological Sciences Research Building, 741 South Limestone St., Lexington, KY, 40536–0509, United States of America
| | - Nirmal Verma
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, 459 Wethington Bldg., 800 Rose St., Lexington, KY, 40536–0200, United States of America
| | - Florin Despa
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, 459 Wethington Bldg., 800 Rose St., Lexington, KY, 40536–0200, United States of America
| | - Louis B. Hersh
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Biomedical Biological Sciences Research Building, 741 South Limestone St., Lexington, KY, 40536–0509, United States of America
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8
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Wilson BA, Cruz-Diaz N, Marshall AC, Pirro NT, Su Y, Gwathmey TM, Rose JC, Chappell MC. An angiotensin-(1-7) peptidase in the kidney cortex, proximal tubules, and human HK-2 epithelial cells that is distinct from insulin-degrading enzyme. Am J Physiol Renal Physiol 2015; 308:F594-601. [PMID: 25568136 DOI: 10.1152/ajprenal.00609.2014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Angiotensin 1-7 [ANG-(1-7)] is expressed within the kidney and exhibits renoprotective actions that antagonize the inflammatory, fibrotic, and pro-oxidant effects of ANG II. We previously identified an peptidase that preferentially metabolized ANG-(1-7) to ANG-(1-4) in the brain medulla and cerebrospinal fluid (CSF) of sheep (Marshall AC, Pirro NT, Rose JC, Diz DI, Chappell MC. J Neurochem 130: 313-323, 2014); thus the present study established the expression of the peptidase in the kidney. Utilizing a sensitive HPLC-based approach, we demonstrate a peptidase activity that hydrolyzed ANG-(1-7) to ANG-(1-4) in the sheep cortex, isolated tubules, and human HK-2 renal epithelial cells. The peptidase was markedly sensitive to the metallopeptidase inhibitor JMV-390; human HK-2 cells expressed subnanomolar sensitivity (IC50 = 0.5 nM) and the highest specific activity (123 ± 5 fmol·min(-1)·mg(-1)) compared with the tubules (96 ± 12 fmol·min(-1)·mg(-1)) and cortex (107 ± 9 fmol·min(-1)·mg(-1)). The peptidase was purified 41-fold from HK-2 cells; the activity was sensitive to JMV-390, the chelator o-phenanthroline, and the mercury-containing compound p-chloromercuribenzoic acid (PCMB), but not to selective inhibitors against neprilysin, neurolysin and thimet oligopeptidase. Both ANG-(1-7) and its endogenous analog [Ala(1)]-ANG-(1-7) (alamandine) were preferentially hydrolyzed by the peptidase compared with ANG II, [Asp(1)]-ANG II, ANG I, and ANG-(1-12). Although the ANG-(1-7) peptidase and insulin-degrading enzyme (IDE) share similar inhibitor characteristics of a metallothiolendopeptidase, we demonstrate marked differences in substrate specificity, which suggest these peptidases are distinct. We conclude that an ANG-(1-7) peptidase is expressed within the renal proximal tubule and may play a potential role in the renal renin-angiotensin system to regulate ANG-(1-7) tone.
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Affiliation(s)
- Bryan A Wilson
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
| | - Nildris Cruz-Diaz
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
| | - Allyson C Marshall
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
| | - Nancy T Pirro
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
| | - Yixin Su
- Department of Obstetrics and Gynecology, Wake Forest University School of Medicine, Winston-Salem, North Cartolina
| | - TanYa M Gwathmey
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
| | - James C Rose
- Department of Obstetrics and Gynecology, Wake Forest University School of Medicine, Winston-Salem, North Cartolina
| | - Mark C Chappell
- Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Cartolina; and
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9
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Sekar S, McDonald J, Cuyugan L, Aldrich J, Kurdoglu A, Adkins J, Serrano G, Beach TG, Craig DW, Valla J, Reiman EM, Liang WS. Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes. Neurobiol Aging 2014; 36:583-91. [PMID: 25448601 DOI: 10.1016/j.neurobiolaging.2014.09.027] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/26/2014] [Accepted: 09/27/2014] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is characterized by deficits in cerebral metabolic rates of glucose in the posterior cingulate (PC) and precuneus in AD subjects, and in APOEε4 carriers, decades before the onset of measureable cognitive deficits. However, the cellular and molecular basis of this phenotype remains to be clarified. Given the roles of astrocytes in energy storage and brain immunity, we sought to characterize the transcriptome of AD PC astrocytes. Cells were laser capture microdissected from AD (n = 10) and healthy elderly control (n = 10) subjects for RNA sequencing. We generated >5.22 billion reads and compared sequencing data between controls and AD patients. We identified differentially expressed mitochondria-related genes including TRMT61B, FASTKD2, and NDUFA4L2, and using pathway and weighted gene coexpression analyses, we identified differentially expressed immune response genes. A number of these genes, including CLU, C3, and CD74, have been implicated in beta amyloid generation or clearance. These data provide key insights into astrocyte-specific contributions to AD, and we present this data set as a publicly available resource.
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Affiliation(s)
- Shobana Sekar
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Jacquelyn McDonald
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Lori Cuyugan
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Jessica Aldrich
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ahmet Kurdoglu
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Adkins
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Geidy Serrano
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA; Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA; Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - David W Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Valla
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA; Department of Biochemistry, Midwestern University, Glendale, AZ, USA
| | - Eric M Reiman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA; Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA; Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Winnie S Liang
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA.
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10
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Markadieu N, Rios K, Spiller BW, McDonald WH, Welling PA, Delpire E. Short forms of Ste20-related proline/alanine-rich kinase (SPAK) in the kidney are created by aspartyl aminopeptidase (Dnpep)-mediated proteolytic cleavage. J Biol Chem 2014; 289:29273-84. [PMID: 25164821 DOI: 10.1074/jbc.m114.604009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ste20-related kinase SPAK regulates sodium, potassium, and chloride transport in a variety of tissues. Recently, SPAK fragments, which lack the catalytic domain and are inhibitory to Na(+) transporters, have been detected in kidney. It has been hypothesized that the fragments originate from alternative translation start sites, but their precise origin is unknown. Here, we demonstrate that kidney lysate possesses proteolytic cleavage activity toward SPAK. Ion exchange and size exclusion chromatography combined with mass spectrometry identified the protease as aspartyl aminopeptidase. The presence of the protease was verified in the active fractions, and recombinant aspartyl aminopeptidase recapitulated the cleavage pattern observed with kidney lysate. Identification of the sites of cleavage by mass spectrometry allowed us to test the function of the smaller fragments and demonstrate their inhibitory action toward the Na(+)-K(+)-2Cl(-) cotransporter, NKCC2.
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Affiliation(s)
| | | | | | - W Hayes McDonald
- Biochemistry and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 and
| | - Paul A Welling
- the Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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11
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King JV, Liang WG, Scherpelz KP, Schilling AB, Meredith SC, Tang WJ. Molecular basis of substrate recognition and degradation by human presequence protease. Structure 2014; 22:996-1007. [PMID: 24931469 DOI: 10.1016/j.str.2014.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/12/2014] [Accepted: 05/01/2014] [Indexed: 01/17/2023]
Abstract
Human presequence protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing an ∼13,300-Å(3) catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and β-amyloid (Aβ), the latter of which contributes to Alzheimer disease pathogenesis. Here, we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and have their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP.
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Affiliation(s)
- John V King
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA
| | - Wenguang G Liang
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA
| | - Kathryn P Scherpelz
- Department of Biochemistry and Molecular Biophysics, The University of Chicago, Chicago, IL 60637, USA
| | - Alexander B Schilling
- Mass Spectrometry, Metabolomics, and Proteomics Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stephen C Meredith
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Wei-Jen Tang
- Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA.
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12
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Mitchell AJ, Lone AM, Tinoco AD, Saghatelian A. Proteolysis controls endogenous substance P levels. PLoS One 2013; 8:e68638. [PMID: 23894327 PMCID: PMC3716696 DOI: 10.1371/journal.pone.0068638] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/05/2013] [Indexed: 01/28/2023] Open
Abstract
Substance P (SP) is a prototypical neuropeptide with roles in pain and inflammation. Numerous mechanisms regulate endogenous SP levels, including the differential expression of SP mRNA and the controlled secretion of SP from neurons. Proteolysis has long been suspected to regulate extracellular SP concentrations but data in support of this hypothesis is scarce. Here, we provide evidence that proteolysis controls SP levels in the spinal cord. Using peptidomics to detect and quantify endogenous SP fragments, we identify the primary SP cleavage site as the C-terminal side of the ninth residue of SP. If blocking this pathway increases SP levels, then proteolysis controls SP concentration. We performed a targeted chemical screen using spinal cord lysates as a proxy for the endogenous metabolic environment and identified GM6001 (galardin, ilomastat) as a potent inhibitor of the SP 1–9-producing activity present in the tissue. Administration of GM6001 to mice results in a greater-than-three-fold increase in the spinal cord levels of SP, which validates the hypothesis that proteolysis controls physiological SP levels.
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Affiliation(s)
- Andrew J. Mitchell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Anna Mari Lone
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Arthur D. Tinoco
- Department of Chemistry, University of Puerto Rico, San Juan, Puerto Rico
- * E-mail: (ADT); (AS)
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (ADT); (AS)
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de Tullio MB, Castelletto V, Hamley IW, Martino Adami PV, Morelli L, Castaño EM. Proteolytically inactive insulin-degrading enzyme inhibits amyloid formation yielding non-neurotoxic aβ peptide aggregates. PLoS One 2013; 8:e59113. [PMID: 23593132 PMCID: PMC3623905 DOI: 10.1371/journal.pone.0059113] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/11/2013] [Indexed: 01/18/2023] Open
Abstract
Insulin-degrading enzyme (IDE) is a neutral Zn2+ peptidase that degrades short peptides based on substrate conformation, size and charge. Some of these substrates, including amyloid β (Aβ) are capable of self-assembling into cytotoxic oligomers. Based on IDE recognition mechanism and our previous report of the formation of a stable complex between IDE and intact Aβ in vitro and in vivo, we analyzed the possibility of a chaperone-like function of IDE. A proteolytically inactive recombinant IDE with Glu111 replaced by Gln (IDEQ) was used. IDEQ blocked the amyloidogenic pathway of Aβ yielding non-fibrillar structures as assessed by electron microscopy. Measurements of the kinetics of Aβ aggregation by light scattering showed that 1) IDEQ effect was promoted by ATP independent of its hydrolysis, 2) end products of Aβ-IDEQ co-incubation were incapable of “seeding” the assembly of monomeric Aβ and 3) IDEQ was ineffective in reversing Aβ aggregation. Moreover, Aβ aggregates formed in the presence of IDEQ were non-neurotoxic. IDEQ had no conformational effects upon insulin (a non-amyloidogenic protein under physiological conditions) and did not disturb insulin receptor activation in cultured cells. Our results suggest that IDE has a chaperone-like activity upon amyloid-forming peptides. It remains to be explored whether other highly conserved metallopeptidases have a dual protease-chaperone function to prevent the formation of toxic peptide oligomers from bacteria to mammals.
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Affiliation(s)
- Matias B. de Tullio
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading, United Kingdom
| | - Ian W. Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading, United Kingdom
| | - Pamela V. Martino Adami
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Morelli
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eduardo M. Castaño
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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Guan H, Chow KM, Shah R, Rhodes CJ, Hersh LB. Degradation of islet amyloid polypeptide by neprilysin. Diabetologia 2012; 55:2989-98. [PMID: 22898766 PMCID: PMC3660010 DOI: 10.1007/s00125-012-2678-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 07/16/2012] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS A progressive loss of pancreatic beta cell function, a decrease in beta cell mass and accumulation of islet amyloid is characteristic of type 2 diabetes mellitus. The main constituent of islet amyloid is islet amyloid polypeptide (IAPP). In this study, we examined the ability of the peptidase neprilysin to cleave IAPP and prevent human IAPP-induced pancreatic beta cell toxicity. METHODS Neprilysin and a catalytically compromised neprilysin mutant were tested for their ability to inhibit human IAPP fibrillisation and human IAPP-induced pancreatic beta cell cytotoxicity. Degradation of human IAPP by neprilysin was followed by HPLC, and the degradation products were identified by MS. RESULTS Neprilysin prevented IAPP fibrillisation by cleaving IAPP at Arg(11)-Leu(12), Leu(12)-Ala(13), Asn(14)-Phe(15), Phe(15)-Leu(16), Asn(22)-Phe(23) and Ala(25)-Ile(26). It also appears to prevent human IAPP fibrillisation through a non-catalytic interaction. Neprilysin protected against beta cell cytotoxicity induced by exogenously added or endogenously produced human IAPP. CONCLUSIONS/INTERPRETATION The data presented support a potential therapeutic role for neprilysin in preventing type 2 diabetes mellitus. This study supports the hypothesis that extracellular human IAPP contributes to human IAPP-induced beta cell cytotoxicity. Whether human IAPP exerts its cytotoxic effect through a totally extracellular mechanism or through a cellular reuptake mechanism is unclear at this time.
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Affiliation(s)
- H Guan
- Department of Molecular and Cellular Biochemistry, University of Kentucky, B236 Biomedical Biological Sciences Research Building, 741 South Limestone Street, Lexington, KY 40536-0509, USA.
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Abstract
A novel mitochondrial and chloroplast peptidasome, the Presequence Protease (PreP) degrades organellar targeting peptides as well as other unstructured peptides up to 65 amino acid residues in length. PreP belongs to the pitrilysin oligopeptidase family (M16C) containing an inverted zinc-binding motif. The crystal structure of Arabidopsis thaliana PreP, AtPreP, refined at 2.1 Å, revealed a novel mechanism of proteolysis in which two halves of the enzyme connected by a hinge region enclose a large catalytic chamber opening and closing in response to peptide binding. Double knock-out mutant of AtPreP1 and AtPreP2 results in a severe phenotype, including decreased size and growth rate, chlorosis and organellar abnormalities, such as altered chloroplast starch content, partial loss of the integrity of the inner mitochondrial membrane and reduced mitochondrial respiration. PreP homologues are also present in yeast and humans. Interestingly, human PreP has been associated with Alzheimer's disease as it is responsible for degradation of amyloid-β peptide in brain mitochondria.
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Affiliation(s)
- Beata Kmiec
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, SE-10691 Stockholm, Sweden
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Alikhani N, Berglund AK, Engmann T, Spånning E, Vögtle FN, Pavlov P, Meisinger C, Langer T, Glaser E. Targeting capacity and conservation of PreP homologues localization in mitochondria of different species. J Mol Biol 2011; 410:400-10. [PMID: 21621546 DOI: 10.1016/j.jmb.2011.05.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/02/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Mitochondrial presequences and other unstructured peptides are degraded inside mitochondria by presequence proteases (PrePs) identified in Arabidopsis thaliana (AtPreP), humans (hPreP), and yeast (Cym1/Mop112). The presequences of A. thaliana and human PreP are predicted to consist of 85 and 29 amino acids, respectively, whereas the Saccharomyces cerevisiae Cym1/Mop112 presequence contains only 7 residues. These differences may explain the reported targeting of homologous proteins to different mitochondrial subcompartments. Here we have investigated the targeting capacity of the PreP homologues' presequences. We have produced fusion constructs containing N-terminal portions of AtPreP(1-125), hPreP(1-69), and Cym1(1-40) coupled to green fluorescent protein (GFP) and studied their import into isolated plant, mammalian, and yeast mitochondria, followed by mitochondrial subfractionation. Whereas the AtPreP presequence has the capacity to target GFP into the mitochondrial matrix of all three species, the hPreP presequence only targets GFP to the matrix of mammalian and yeast mitochondria. The Cym1/Mop112 presequence has an overall much weaker targeting capacity and only ensures mitochondrial sorting in its host species yeast. Revisiting the submitochondrial localization of Cym1 revealed that endogenous Cym1/Mop112 is localized to the matrix space, as has been previously reported for the plant and human homologues. Moreover, complementation studies in yeast show that native AtPreP restores the growth phenotype of yeast cells lacking Cym1, demonstrating functional conservation.
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Affiliation(s)
- Nyosha Alikhani
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, SE-10691 Stockholm, Sweden
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Chow KM, Guan H, Hersh LB. Aminopeptidases do not directly degrade tau protein. Mol Neurodegener 2010; 5:48. [PMID: 21054848 PMCID: PMC2988785 DOI: 10.1186/1750-1326-5-48] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/05/2010] [Indexed: 11/10/2022] Open
Abstract
Background Tau hyperphosphorylation and aggregation to form intracellular neurofibrillar tangles is prevalent in a number of tauopathies. Thus there is current interest in the mechanisms involved in Tau clearance. It was recently reported that Tau can be degraded by an aminopeptidase known as the puromycin sensitive aminopeptidase (PSA). Until now PSA has been reported to only cleave peptides, with the largest reported substrates having 30-50 amino acids. We have studied this unique PSA cleavage reaction using a number of different PSA preparations. Results An N-terminally His tagged-PSA was expressed and purified from Sf9 insect cells. Although this PSA preparation cleaved Tau, product analysis with N and C terminal Tau antibodies coupled with mass spectrometry showed an endoproteolytic cleavage atypical for an aminopeptidase. Furthermore, the reaction was not blocked by the general aminopeptidase inhibitor bestatin or the specific PSA inhibitor puromycin. In order to test whether Tau hydrolysis might be caused by a protease contaminant the enzyme was expressed in E. coli as glutathione S-transferase and maltose binding protein fusion proteins or in Sf9 cells as a C-terminally His-tagged protein. After purification to near homogeneity none of these other recombinant forms of PSA cleaved Tau. Further, Tau-cleaving activity and aminopeptidase activities derived from the Sf9 cell expression system were separable by molecular sieve chromatography. When tested in a cellular context we again failed to see a PSA dependent cleavage of Tau. A commercial preparation of a related aminopeptidase, aminopeptidase N, also exhibited Tau cleaving activity, but this activity could also be separated from aminopeptidase activity. Conclusion It is concluded that PSA does not directly cleave Tau.
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Affiliation(s)
- K Martin Chow
- From the Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA.
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Short JR, Knox C, Dorrington RA. Subcellular localization and live-cell imaging of the Helicoverpa armigera stunt virus replicase in mammalian and Spodoptera frugiperda cells. J Gen Virol 2010; 91:1514-23. [PMID: 20107015 DOI: 10.1099/vir.0.020156-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Whilst their structure has been well studied, there is little information on the replication biology of tetraviruses because of the lack of suitable tissue-culture cell lines that support virus replication. In this study, the potential site of Helicoverpa armigera stunt virus replication was investigated by transient expression of the replicase protein fused to enhanced green fluorescent protein (EGFP) in mammalian and insect cells. When EGFP was present at the C terminus of the protein, fluorescence was located in punctate cytoplasmic structures that were distinct from the peripheral Golgi, endoplasmic reticulum, early endosomes, lysosomes and mitochondria, but overlapped partially with late endosomes. In experiments where targeting to endosomal compartments was examined further by using Cascade Blue-dextran in live cells, no overlap between the replicase and active endocytic organelles was apparent. Analysis of the punctate structures using time-lapse imaging in live cells revealed that they undergo fusion, fission and 'kiss-and-run' events. Whilst the source of the membranes used to form the punctate structures remains unclear, we propose that the replicase sequesters membranes from the late endosomes and actively excludes host proteins, either by normal recycling processes or by a replicase-dependent mechanism that may result in the destabilization of the associated membranes and a release of luminal contents into the cytosol. This is the first study describing the localization of a tetravirus.
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Affiliation(s)
- James Roswell Short
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, 6140 Grahamstown, South Africa
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