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Major G, Simcock J, Kumar A, Kleffmann T, Woodfield TBF, Lim KS. Comprehensive Matrisome Profiling of Human Adipose Tissue for Soft Tissue Reconstruction. Adv Biol (Weinh) 2024; 8:e2300448. [PMID: 37953659 DOI: 10.1002/adbi.202300448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/14/2023] [Indexed: 11/14/2023]
Abstract
For effective translation of research from tissue engineering and regenerative medicine domains, the cell-instructive extracellular matrix (ECM) of specific tissues must be accurately realized. As adipose tissue is gaining traction as a biomaterial for soft tissue reconstruction, with highly variable clinical outcomes obtained, a quantitative investigation of the adipose tissue matrisome is overdue. In this study, the human adipose tissue matrisome is profiled using quantitative sequential windowed acquisition of all theoretical fragment ion spectra - mass spectrometry (SWATH-MS) proteomics across a cohort of 13 fat-grafting patients, to provide characterization of ECM proteins within the tissue, and to understand human population variation. There are considerable differences in the expression of matrisome proteins across the patient cohort, with age and lipoaspirate collection technique contributing to the greatest variation across the core matrisome. A high abundance of basement membrane proteins (collagen IV and heparan sulfate proteoglycan) is detected, as well as fibrillar collagens I and II, reflecting the hierarchical structure of the tissue. This study provides a comprehensive proteomic evaluation of the adipose tissue matrisome and contributes to an enhanced understanding of the influence of the matrisome in adipose-related pathologies by providing a healthy reference cohort and details an experimental pipeline that can be further exploited for future biomaterial development.
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Affiliation(s)
- Gretel Major
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
| | - Jeremy Simcock
- Department of Surgery, University of Otago, Christchurch, 8011, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, Research Infrastructure Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Research Infrastructure Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Tim B F Woodfield
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
| | - Khoon S Lim
- Department of Orthopaedic Surgery and Musculoskeletal Medicine, Centre for Bioengineering & Nanomedicine, University of Otago, Christchurch, 8011, New Zealand
- Light-Activated Biomaterials Group, School of Medical Science, University of Sydney, Sydney, NSW, 2006, Australia
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2
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Hawkins S, Zetika GA, Kinaston R, Firmando YR, Sari DM, Suniarti Y, Lucas M, Roberts P, Reepmeyer C, Maloney T, Kealy S, Stirling C, Reid M, Barr D, Kleffmann T, Kumar A, Yuwono P, Litster M, Husni M, Ririmasse M, Mahirta, Mujabuddawat M, Harriyadi, O'Connor S. Earliest known funerary rites in Wallacea after the last glacial maximum. Sci Rep 2024; 14:282. [PMID: 38168501 PMCID: PMC10762057 DOI: 10.1038/s41598-023-50294-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The insular region of Wallacea has become a focal point for studying Pleistocene human ecological and cultural adaptations in island environments, however, little is understood about early burial traditions during the Pleistocene. Here we investigate maritime interactions and burial practices at Ratu Mali 2, an elevated coastal cave site on the small island of Kisar in the Lesser Sunda Islands of eastern Indonesia dated to 15,500-3700 cal. BP. This multidisciplinary study demonstrates extreme marine dietary adaptations, engagement with an extensive exchange network across open seas, and early mortuary practices. A flexed male and a female, interred in a single grave with abundant shellfish and obsidian at Ratu Mali 2 by 14.7 ka are the oldest known human burials in Wallacea with established funerary rites. These findings highlight the impressive flexibility of our species in marginal environments and provide insight into the earliest known ritualised treatment of the dead in Wallacea.
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Affiliation(s)
- Stuart Hawkins
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia.
| | - Gabriella Ayang Zetika
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Rebecca Kinaston
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
- Griffith Centre for Social and Cultural Research, Griffith University, Nathan, QLD, Australia
- BioArch South, Waitati, 9085, New Zealand
| | - Yulio Ray Firmando
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Devi Mustika Sari
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Yuni Suniarti
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | - Mary Lucas
- Department of Archaeology, Max Planck Institute of Geoanthropology DE, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute of Geoanthropology DE, Jena, Germany
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Christian Reepmeyer
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute Division of Germany, Berlin, Germany
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society, and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Tim Maloney
- Griffith Centre for Social and Cultural Research, Griffith University, Southport, QLD, 4222, Australia
| | - Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
| | - Claudine Stirling
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - Malcolm Reid
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - David Barr
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, 9054, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Pratiwi Yuwono
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- Geoarchaeology and Archaeometry Research Group (GARG), Southern Cross University, Lismore, NSW, Australia
| | - Mirani Litster
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society, and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Muhammad Husni
- Balai Arkeologi Maluku, JI. Namalatu-Latuhalat, Ambon, Indonesia
| | - Marlon Ririmasse
- Balai Arkeologi Maluku, JI. Namalatu-Latuhalat, Ambon, Indonesia
| | - Mahirta
- Departemen Arkeologi Fakultas Ilmu Budaya, Universitas of Gadjah Mada, Yogyakarta, Indonesia
| | | | - Harriyadi
- Organisasi Riset Arkeologi Bahasa dan Sastra, Badan Riset dan Inovasi Nasional, Jakarta, Indonesia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, ANU College of Asia and the Pacific, Australian National University, Acton, ACT, 2601, Australia
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Rogers LM, Halcrow SE, Kleffmann T, King CL. Comparing Walker's (2008) skull trait sex estimation standard to proteomic sex estimation for a group of South Asian individuals. Forensic Sci Int Synerg 2024; 8:100450. [PMID: 38314398 PMCID: PMC10837481 DOI: 10.1016/j.fsisyn.2023.100450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024]
Abstract
This research assesses the potential for misidentification of sex in individuals of South Asian ancestry using the Walker (2008) morphological skull sex estimation standard [1]. Chromosomal sex was assessed using proteomic analysis targeting sex chromosome-specific amylogenic peptides. Results showed that the Walker method produced incorrect classification for 36.7 % of individuals. Overwhelmingly, those incorrectly assigned were chromosomally male. Misidentification was due to males within the group having lower trait scores (i.e., more gracile traits) than the standard would predict. There was also a high level of overlap in trait scores between male and females indicating reduced expression of sexual dimorphism. The use of established multivariate statistical techniques improved accuracy of sex estimation in some cases, but larger osteological data sets from South Asian individuals are required to develop population-specific standards. We suggest that peptide analysis may provide a useful tool for the forensic anthropologist when assessing sex in populations without population specific osteological standards.
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Affiliation(s)
- Laura M Rogers
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Siân E Halcrow
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Charlotte L King
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Sudron EL, Kinaston RL, Cawte H, Kleffmann T, Kumar A, Kramer R, Stirling C, Reid M, Barr D, McStay A, Lawrence M, King K, Halcrow SE. Extracting the truth through chemical analyses: Early life histories of Victorian-era dental patients in Aotearoa New Zealand. Am J Biol Anthropol 2024; 183:141-156. [PMID: 37925739 DOI: 10.1002/ajpa.24863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/15/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
OBJECTIVES There are few bioarcheological analyses of life experiences in colonial period Aotearoa New Zealand, despite this being a time of major adaptation and social change. In our study, early life histories are constructed from multi-isotope and enamel peptide analysis of permanent first molars associated with Victorian era dental practices operating between AD 1881 and 1905 in Invercargill. Chemical analyses of the teeth provide insight into the childhood feeding practices, diet, and mobility of the people who had their teeth extracted. MATERIALS AND METHODS Four permanent left mandibular first molars were analyzed from a cache of teeth discovered at the Leviathan Gift Depot site during excavations in 2019. The methods used were: (1) enamel peptide analysis to assess chromosomal sex; (2) bulk (δ13 Ccarbonate ) and incremental (δ13 Ccollagen and δ15 N) isotope analysis of dentin to assess childhood diet; and (3) strontium (87 Sr/86 Sr) and oxygen (δ18 O) isotope analysis of enamel to assess childhood residency. Two modern permanent first molars from known individuals were analyzed as controls. RESULTS The archaeological teeth were from three chromosomal males and one female. The protein and whole diets were predominately based on C3 -plants and domestic animal products (meat and milk). A breastfeeding signal was only identified in one historic male. All individuals likely had childhood residences in Aotearoa. DISCUSSION Unlike most bioarcheological studies that rely on the remains of the dead, the teeth analysed in this study were extracted from living people. We suggest that the dental patients were likely second or third generation colonists to Aotearoa, with fairly similar childhood diets. They were potentially lower-class individuals either living in, or passing through, the growing colonial center of Invercargill.
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Affiliation(s)
- Emma L Sudron
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Centre for Social and Cultural Research, Griffith University, Nathan, Australia
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Australia
| | - Rebecca L Kinaston
- Centre for Social and Cultural Research, Griffith University, Nathan, Australia
- BioArch South, Waitati, New Zealand
| | - Hayden Cawte
- New Zealand Heritage Properties, Dunedin and Invercargill, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Research Infrastructure Centre, University of Otago, Dunedin, New Zealand
| | - Abhishek Kumar
- North Region Environmental, California Department of Transportation, Los Angeles, California, USA
| | - Robyn Kramer
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, New Zealand
| | - Claudine Stirling
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, New Zealand
- Department of Geology, University of Otago, Dunedin, New Zealand
| | - Malcolm Reid
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, New Zealand
| | - David Barr
- Centre for Trace Element Analysis, Department of Geology, University of Otago, Dunedin, New Zealand
| | - Amy McStay
- New Zealand Heritage Properties, Dunedin and Invercargill, New Zealand
| | - Megan Lawrence
- New Zealand Heritage Properties, Dunedin and Invercargill, New Zealand
| | - Kathryn King
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Siân E Halcrow
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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Peppercorn K, Edgar CD, Kleffmann T, Tate WP. A pilot study on the immune cell proteome of long COVID patients shows changes to physiological pathways similar to those in myalgic encephalomyelitis/chronic fatigue syndrome. Sci Rep 2023; 13:22068. [PMID: 38086949 PMCID: PMC10716514 DOI: 10.1038/s41598-023-49402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Of those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ~ 10% develop the chronic post-viral debilitating condition, long COVID (LC). Although LC is a heterogeneous condition, about half of cases have typical post-viral fatigue with onset and symptoms that are very similar to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). A key question is whether these conditions are closely related. ME/CFS is a post-stressor fatigue condition that arises from multiple triggers. To investigate the pathophysiology of LC, a pilot study of patients (n = 6) and healthy controls (n = 5) has used quantitative proteomics to discover changes in peripheral blood mononuclear cell (PBMC) proteins. A principal component analysis separated all long COVID patients from healthy controls. Analysis of 3131 proteins identified 162 proteins differentially regulated, of which 37 were related to immune functions, and 21 to mitochondrial functions. Markov cluster analysis identified clusters involved in immune system processes, and two aspects of gene expression-spliceosome and transcription. These results were compared with an earlier dataset of 346 differentially regulated proteins in PBMC's from ME/CFS patients (n = 9) analysed by the same methodology. There were overlapping protein clusters and enriched molecular pathways particularly in immune functions, suggesting the two conditions have similar immune pathophysiology as a prominent feature, and mitochondrial functions involved in energy production were affected in both conditions.
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Affiliation(s)
- Katie Peppercorn
- Division of Health Sciences, Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Christina D Edgar
- Division of Health Sciences, Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Torsten Kleffmann
- Division of Health Sciences, Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Warren P Tate
- Division of Health Sciences, Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand.
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6
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Winterbourn CC, Peskin AV, Kleffmann T, Radi R, Pace PE. Carbon dioxide/bicarbonate is required for sensitive inactivation of mammalian glyceraldehyde-3-phosphate dehydrogenase by hydrogen peroxide. Proc Natl Acad Sci U S A 2023; 120:e2221047120. [PMID: 37098065 PMCID: PMC10161126 DOI: 10.1073/pnas.2221047120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 04/26/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) contains an active site Cys and is one of the most sensitive cellular enzymes to oxidative inactivation and redox regulation. Here, we show that inactivation by hydrogen peroxide is strongly enhanced in the presence of carbon dioxide/bicarbonate. Inactivation of isolated mammalian GAPDH by H2O2 increased with increasing bicarbonate concentration and was sevenfold faster in 25 mM (physiological) bicarbonate compared with bicarbonate-free buffer of the same pH. H2O2 reacts reversibly with CO2 to form a more reactive oxidant, peroxymonocarbonate (HCO4-), which is most likely responsible for the enhanced inactivation. However, to account for the extent of enhancement, we propose that GAPDH must facilitate formation and/or targeting of HCO4- to promote its own inactivation. Inactivation of intracellular GAPDH was also strongly enhanced by bicarbonate: treatment of Jurkat cells with 20 µM H2O2 in 25 mM bicarbonate buffer for 5 min caused almost complete GAPDH inactivation, but no loss of activity when bicarbonate was not present. H2O2-dependent GAPDH inhibition in bicarbonate buffer was observed even in the presence of reduced peroxiredoxin 2 and there was a significant increase in cellular glyceraldehyde-3-phosphate/dihydroxyacetone phosphate. Our results identify an unrecognized role for bicarbonate in enabling H2O2 to influence inactivation of GAPDH and potentially reroute glucose metabolism from glycolysis to the pentose phosphate pathway and NAPDH production. They also demonstrate what could be wider interplay between CO2 and H2O2 in redox biology and the potential for variations in CO2 metabolism to influence oxidative responses and redox signaling.
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Affiliation(s)
- Christine C. Winterbourn
- Mātai Hāora - Centre for Redox Biology & Medicine, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch8014, New Zealand
| | - Alexander V. Peskin
- Mātai Hāora - Centre for Redox Biology & Medicine, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch8014, New Zealand
| | - Torsten Kleffmann
- Research Infrastructure Centre, University of Otago, Dunedin9016, New Zealand
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800Montevideo, Uruguay
- Centro de Investigaciones Biomédicas, Facultad de Medicina, Universidad de la República, 11800Montevideo, Uruguay
| | - Paul E. Pace
- Mātai Hāora - Centre for Redox Biology & Medicine, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch8014, New Zealand
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Peppercorn K, Kleffmann T, Hughes SM, Tate WP. Secreted Amyloid Precursor Protein Alpha (sAPPα) Regulates the Cellular Proteome and Secretome of Mouse Primary Astrocytes. Int J Mol Sci 2023; 24:ijms24087165. [PMID: 37108327 PMCID: PMC10138557 DOI: 10.3390/ijms24087165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Secreted amyloid precursor protein alpha (sAPPα), processed from a parent mammalian brain protein, amyloid precursor protein, can modulate learning and memory. Recently it has been shown to modulate the transcriptome and proteome of human neurons, including proteins with neurological functions. Here, we analysed whether the acute administration of sAPPα facilitated changes in the proteome and secretome of mouse primary astrocytes in culture. Astrocytes contribute to the neuronal processes of neurogenesis, synaptogenesis and synaptic plasticity. Cortical mouse astrocytes in culture were exposed to 1 nM sAPPα, and changes in both the whole-cell proteome (2 h) and the secretome (6 h) were identified with Sequential Window Acquisition of All Theoretical Fragment Ion Spectra-Mass Spectrometry (SWATH-MS). Differentially regulated proteins were identified in both the cellular proteome and secretome that are involved with neurologically related functions of the normal physiology of the brain and central nervous system. Groups of proteins have a relationship to APP and have roles in the modulation of cell morphology, vesicle dynamics and the myelin sheath. Some are related to pathways containing proteins whose genes have been previously implicated in Alzheimer's disease (AD). The secretome is also enriched in proteins related to Insulin Growth Factor 2 (IGF2) signaling and the extracellular matrix (ECM). There is the promise that a more specific investigation of these proteins will help to understand the mechanisms of how sAPPα signaling affects memory formation.
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Affiliation(s)
- Katie Peppercorn
- Department of Biochemistry, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
| | - Torsten Kleffmann
- Research Infrastructure Centre, Division of Health Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie M Hughes
- Department of Biochemistry, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
- Genetics Otago, University of Otago, Dunedin 9016, New Zealand
| | - Warren P Tate
- Department of Biochemistry, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin 9016, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin 9016, New Zealand
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Templeton EM, Pilbrow AP, Kleffmann T, Pickering JW, Rademaker MT, Scott NJA, Ellmers LJ, Charles CJ, Endre ZH, Richards AM, Cameron VA, Lassé M. Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma. Int J Mol Sci 2023; 24:ijms24076290. [PMID: 37047281 PMCID: PMC10094439 DOI: 10.3390/ijms24076290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/30/2023] Open
Abstract
Mass spectrometry is a powerful technique for investigating renal pathologies and identifying biomarkers, and efficient protein extraction from kidney tissue is essential for bottom-up proteomic analyses. Detergent-based strategies aid cell lysis and protein solubilization but are poorly compatible with downstream protein digestion and liquid chromatography-coupled mass spectrometry, requiring additional purification and buffer-exchange steps. This study compares two well-established detergent-based methods for protein extraction (in-solution sodium deoxycholate (SDC); suspension trapping (S-Trap)) with the recently developed sample preparation by easy extraction and digestion (SPEED) method, which uses strong acid for denaturation. We compared the quantitative performance of each method using label-free mass spectrometry in both sheep kidney cortical tissue and plasma. In kidney tissue, SPEED quantified the most unique proteins (SPEED 1250; S-Trap 1202; SDC 1197). In plasma, S-Trap produced the most unique protein quantifications (S-Trap 150; SDC 148; SPEED 137). Protein quantifications were reproducible across biological replicates in both tissue (R2 = 0.85–0.90) and plasma (SPEED R2 = 0.84; SDC R2 = 0.76, S-Trap R2 = 0.65). Our data suggest SPEED as the optimal method for proteomic preparation in kidney tissue and S-Trap or SPEED as the optimal method for plasma, depending on whether a higher number of protein quantifications or greater reproducibility is desired.
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9
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Paget BW, Kleffmann T, Whiteman KE, Thomas MF, McMahon CD. Quantitative comparison of manuka and clover honey proteomes with royal jelly. PLoS One 2023; 18:e0272898. [PMID: 36763642 PMCID: PMC9916596 DOI: 10.1371/journal.pone.0272898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
Royal jelly and honey are two substances produced successively by the worker bee caste. Modern proteomics approaches have been used to explore the protein component of each substance independently, but to date none have quantitatively compared the protein profile of honey and royal jelly directly. Sequential window acquisition of all theoretical fragment-ion spectra mass spectrometry (SWATH-MS) was used to compare protein quantities of bee origin in mānuka and clover honey to royal jelly. Two analysis techniques identified 76 proteins in total. Peptide intensity was directly compared for a subset of 31 proteins that were identified with high confidence, and the relative changes in protein abundance were compared between each honey type and royal jelly. Major Royal Jelly Proteins (MRJPs) had similar profiles in both honeys, except MRJP6, which was significantly more abundant in clover honey. Proteins involved in nectar metabolism were more abundant in honey than in royal jelly as expected. However, the trend revealed a potential catalytic role for MRJP6 in clover honey and a nectar- or honey-specific role for uncharacterised protein LOC408608. The abundance of MRJP6 in mānuka honey was equivalent to royal jelly suggesting a potential effect of nectar type on expression of this protein. Data are available via ProteomeXchange with identifier PXD038889.
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Affiliation(s)
- Blake W. Paget
- Hamilton Laboratory, ManukaMed LP, Masterton, New Zealand
- * E-mail:
| | - Torsten Kleffmann
- Division of Health Sciences, Research Infrastructure Centre, University of Otago, Dunedin, New Zealand
| | | | - Mark F. Thomas
- Hamilton Laboratory, ManukaMed LP, Masterton, New Zealand
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Warring SL, Malone LM, Jayaraman J, Easingwood RA, Rigano LA, Frampton RA, Visnovsky SB, Addison SM, Hernandez L, Pitman AR, Lopez Acedo E, Kleffmann T, Templeton MD, Bostina M, Fineran PC. A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environ Microbiol 2022; 24:4834-4852. [PMID: 35912527 PMCID: PMC9796965 DOI: 10.1111/1462-2920.16106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.
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Affiliation(s)
- Suzanne L. Warring
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Lucia M. Malone
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
| | | | - Luciano A. Rigano
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Plant Health & Environment Laboratory, Biosecurity New ZealandMinistry for Primary IndustriesAucklandNew Zealand
| | - Rebekah A. Frampton
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Sandra B. Visnovsky
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Shea M. Addison
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Loreto Hernandez
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Andrew R. Pitman
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand,Foundation for Arable Research (FAR), TempletonChristchurchNew Zealand
| | - Elena Lopez Acedo
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand,School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Mihnea Bostina
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Otago Centre for Electron MicroscopyUniversity of OtagoDunedinNew Zealand
| | - Peter C. Fineran
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
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11
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Peppercorn K, Kleffmann T, Jones O, Hughes S, Tate W. Secreted Amyloid Precursor Protein Alpha, a Neuroprotective Protein in the Brain Has Widespread Effects on the Transcriptome and Proteome of Human Inducible Pluripotent Stem Cell-Derived Glutamatergic Neurons Related to Memory Mechanisms. Front Neurosci 2022; 16:858524. [PMID: 35692428 PMCID: PMC9179159 DOI: 10.3389/fnins.2022.858524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Secreted amyloid precursor protein alpha (sAPPα) processed from a parent human brain protein, APP, can modulate learning and memory. It has potential for development as a therapy preventing, delaying, or even reversing Alzheimer’s disease. In this study a comprehensive analysis to understand how it affects the transcriptome and proteome of the human neuron was undertaken. Human inducible pluripotent stem cell (iPSC)-derived glutamatergic neurons in culture were exposed to 1 nM sAPPα over a time course and changes in the transcriptome and proteome were identified with RNA sequencing and Sequential Window Acquisition of All THeoretical Fragment Ion Spectra-Mass Spectrometry (SWATH-MS), respectively. A large subset (∼30%) of differentially expressed transcripts and proteins were functionally involved with the molecular biology of learning and memory, consistent with reported links of sAPPα to memory enhancement, as well as neurogenic, neurotrophic, and neuroprotective phenotypes in previous studies. Differentially regulated proteins included those encoded in previously identified Alzheimer’s risk genes, APP processing related proteins, proteins involved in synaptogenesis, neurotransmitters, receptors, synaptic vesicle proteins, cytoskeletal proteins, proteins involved in protein and organelle trafficking, and proteins important for cell signalling, transcriptional splicing, and functions of the proteasome and lysosome. We have identified a complex set of genes affected by sAPPα, which may aid further investigation into the mechanism of how this neuroprotective protein affects memory formation and how it might be used as an Alzheimer’s disease therapy.
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Affiliation(s)
- Katie Peppercorn
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Division of Health Sciences, Research Infrastructure Centre, University of Otago, Dunedin, New Zealand
| | - Owen Jones
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Stephanie Hughes
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- *Correspondence: Warren Tate,
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12
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Templeton EM, Lassé M, Kleffmann T, Ellmers LJ, Palmer SC, Davidson T, Scott NJA, Pickering JW, Charles CJ, Endre ZH, Cameron VA, Richards AM, Rademaker MT, Pilbrow AP. Identifying Candidate Protein Markers of Acute Kidney Injury in Acute Decompensated Heart Failure. Int J Mol Sci 2022; 23:ijms23021009. [PMID: 35055195 PMCID: PMC8778509 DOI: 10.3390/ijms23021009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/15/2021] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
One-quarter of patients with acute decompensated heart failure (ADHF) experience acute kidney injury (AKI)—an abrupt reduction or loss of kidney function associated with increased long-term mortality. There is a critical need to identify early and real-time markers of AKI in ADHF; however, to date, no protein biomarkers have exhibited sufficient diagnostic or prognostic performance for widespread clinical uptake. We aimed to identify novel protein biomarkers of AKI associated with ADHF by quantifying changes in protein abundance in the kidneys that occur during ADHF development and recovery in an ovine model. Relative quantitative protein profiling was performed using sequential window acquisition of all theoretical fragment ion spectra–mass spectrometry (SWATH–MS) in kidney cortices from control sheep (n = 5), sheep with established rapid-pacing-induced ADHF (n = 8), and sheep after ~4 weeks recovery from ADHF (n = 7). Of the 790 proteins quantified, we identified 17 candidate kidney injury markers in ADHF, 1 potential kidney marker of ADHF recovery, and 2 potential markers of long-term renal impairment (differential abundance between groups of 1.2–2.6-fold, adjusted p < 0.05). Among these 20 candidate protein markers of kidney injury were 6 candidates supported by existing evidence and 14 novel candidates not previously implicated in AKI. Proteins of differential abundance were enriched in pro-inflammatory signalling pathways: glycoprotein VI (activated during ADHF development; adjusted p < 0.01) and acute phase response (repressed during recovery from ADHF; adjusted p < 0.01). New biomarkers for the early detection of AKI in ADHF may help us to evaluate effective treatment strategies to prevent mortality and improve outcomes for patients.
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Affiliation(s)
- Evelyn M. Templeton
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
- Correspondence: ; Tel.: +64-03-364-12-53
| | - Moritz Lassé
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - Torsten Kleffmann
- Research Infrastructure Centre, Division of Health Sciences, University of Otago, Dunedin 9016, New Zealand;
| | - Leigh J. Ellmers
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - Suetonia C. Palmer
- Department of Medicine, University of Otago, Christchurch 8014, New Zealand;
| | - Trent Davidson
- Department of Anatomical Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia;
| | - Nicola J. A. Scott
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - John W. Pickering
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - Christopher J. Charles
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - Zoltan H. Endre
- Department of Nephrology, Prince of Wales Hospital, Sydney, NSW 2031, Australia;
| | - Vicky A. Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - A. Mark Richards
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
- Cardiovascular Research Institute, Department of Cardiology, National University of Singapore, Singapore 119077, Singapore
| | - Miriam T. Rademaker
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
| | - Anna P. Pilbrow
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch 8014, New Zealand; (M.L.); (L.J.E.); (N.J.A.S.); (J.W.P.); (C.J.C.); (V.A.C.); (A.M.R.); (M.T.R.); (A.P.P.)
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13
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Templeton E, Lassé M, Cameron V, Pickering J, Kleffmann T, Hertzberg D, Frampton C, Ellmers L, Palmer S, Davidson T, Scott N, Charles C, Endre Z, Richards M, Doughty R, Troughton R, Rademaker M, Pilbrow A. Harnessing the Power of “Omics”: Discovering Novel microRNA and Protein Biomarkers of Acute Kidney Injury in Acute Heart Failure. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Johnson SL, Borziak K, Kleffmann T, Rosengrave P, Dorus S, Gemmell NJ. Ovarian fluid proteome variation associates with sperm swimming speed in an externally fertilizing fish. J Evol Biol 2020; 33:1783-1794. [PMID: 33034086 PMCID: PMC7719593 DOI: 10.1111/jeb.13717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/02/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022]
Abstract
Sperm velocity is a key trait that predicts the outcome of sperm competition. By promoting or impeding sperm velocity, females can control fertilization via postcopulatory cryptic female choice. In Chinook salmon, ovarian fluid (OF), which surrounds the ova, mediates sperm velocity according to male and female identity, biasing the outcome of sperm competition towards males with faster sperm. Past investigations have revealed proteome variation in OF, but the specific components of OF that differentially mediate sperm velocity have yet to be characterized. Here we use quantitative proteomics to investigate whether OF protein composition explains variation in sperm velocity and fertilization success. We found that OF proteomes from six females robustly clustered into two groups and that these groups are distinguished by the abundance of a restricted set of proteins significantly associated with sperm velocity. Exposure of sperm to OF from females in group I had faster sperm compared to sperm exposed to the OF of group II females. Overall, OF proteins that distinguished between these groups were enriched for vitellogenin and calcium ion interactions. Our findings suggest that these proteins may form the functional basis for cryptic female choice via the biochemical and physiological mediation of sperm velocity.
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Affiliation(s)
- Sheri L. Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Kirill Borziak
- Biology Department, Center for Reproductive Evolution, Syracuse University, Syracuse, NY, USA
| | - Torsten Kleffmann
- Department of Biochemistry, Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Patrice Rosengrave
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- AgResearch, Biocontrol and Biosecurity, Christchurch, New Zealand
| | - Steve Dorus
- Biology Department, Center for Reproductive Evolution, Syracuse University, Syracuse, NY, USA
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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15
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Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G. Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Sci Rep 2020; 10:16301. [PMID: 33004869 PMCID: PMC7530986 DOI: 10.1038/s41598-020-73199-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/11/2020] [Indexed: 01/21/2023] Open
Abstract
Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
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Affiliation(s)
- Eileen L. Murphy
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Kavindra V. Singh
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Bryant Avila
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Torsten Kleffmann
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Steven T. Gregory
- grid.20431.340000 0004 0416 2242Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881 USA
| | - Barbara E. Murray
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Kurt L. Krause
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Reza Khayat
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Gerwald Jogl
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
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16
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Sweetman E, Kleffmann T, Edgar C, de Lange M, Vallings R, Tate W. A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction. J Transl Med 2020; 18:365. [PMID: 32972442 PMCID: PMC7512220 DOI: 10.1186/s12967-020-02533-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and ‘post-exertional malaise’, exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology. Methods To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. Results A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < −0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. Conclusions The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.
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Affiliation(s)
- Eiren Sweetman
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Christina Edgar
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Michel de Lange
- Centre for Biostatistics, University of Otago, Dunedin, 9016, New Zealand
| | | | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.
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17
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Mehta S, Algie M, Al-Jabry T, McKinney C, Kannan S, Verma CS, Ma W, Zhang J, Bartolec TK, Masamsetti VP, Parker K, Henderson L, Gould ML, Bhatia P, Harfoot R, Chircop M, Kleffmann T, Cohen SB, Woolley AG, Cesare AJ, Braithwaite A. Critical Role for Cold Shock Protein YB-1 in Cytokinesis. Cancers (Basel) 2020; 12:cancers12092473. [PMID: 32882852 PMCID: PMC7565962 DOI: 10.3390/cancers12092473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Y-box-binding protein-1, YB-1, plays an important role in regulating the cell cycle, although precisely how it does the is unknown. Using live cell imaging, we show that YB-1 is essential for initiating the last step of cell division (cytokinesis), required for creation of two daughter cells. Using confocal microscopy we showed that YB-1 regulates the spatial distribution of key proteins essential for cytokinesis to occur and that this required YB-1 to be phosphorylated on several residues. In-silico modeling demonstrated that modifications at these residues resulted in conformational changes in YB-1 protein allowing it to interact with proteins essential for cytokinesis. As many cancers have high levels YB-1 and these are associated with poor prognosis, our data suggest developing small molecule inhibitors to block YB-1 phosphorylation could be a novel approach to cancer therapy. Abstract High levels of the cold shock protein Y-box-binding protein-1, YB-1, are tightly correlated with increased cell proliferation and progression. However, the precise mechanism by which YB-1 regulates proliferation is unknown. Here, we found that YB-1 depletion in several cancer cell lines and in immortalized fibroblasts resulted in cytokinesis failure and consequent multinucleation. Rescue experiments indicated that YB-1 was required for completion of cytokinesis. Using confocal imaging we found that YB-1 was essential for orchestrating the spatio-temporal distribution of the microtubules, β-actin and the chromosome passenger complex (CPC) to define the cleavage plane. We show that phosphorylation at six serine residues was essential for cytokinesis, of which novel sites were identified using mass spectrometry. Using atomistic modelling we show how phosphorylation at multiple sites alters YB-1 conformation, allowing it to interact with protein partners. Our results establish phosphorylated YB-1 as a critical regulator of cytokinesis, defining precisely how YB-1 regulates cell division.
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Affiliation(s)
- Sunali Mehta
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
- Maurice Wilkins Centre for Biodiscovery, University of Otago, 9016 Dunedin, New Zealand
- Correspondence: ; Tel.: +64-3-4797169
| | - Michael Algie
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
- Centre for Protein Research, Department of Biochemistry, University of Otago, 9054 Dunedin, New Zealand;
| | - Tariq Al-Jabry
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Cushla McKinney
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
| | - Srinivasaraghavan Kannan
- Department of Biomolecular Modelling and Design, Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore; (S.K.); (C.S.V.)
| | - Chandra S Verma
- Department of Biomolecular Modelling and Design, Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore; (S.K.); (C.S.V.)
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117543, Singapore
| | - Weini Ma
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Jessie Zhang
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Tara K. Bartolec
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - V. Pragathi Masamsetti
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Kim Parker
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
| | - Luke Henderson
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
- Maurice Wilkins Centre for Biodiscovery, University of Otago, 9016 Dunedin, New Zealand
| | - Maree L Gould
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
| | - Puja Bhatia
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
| | - Rhodri Harfoot
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
| | - Megan Chircop
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, 9054 Dunedin, New Zealand;
| | - Scott B Cohen
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Adele G Woolley
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
- Maurice Wilkins Centre for Biodiscovery, University of Otago, 9016 Dunedin, New Zealand
| | - Anthony J Cesare
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
| | - Antony Braithwaite
- Department of Pathology, University of Otago, 9016 Dunedin, New Zealand; (M.A.); (C.M.); (K.P.); (L.H.); (M.L.G.); (P.B.); (R.H.); (A.G.W.); (A.B.)
- Maurice Wilkins Centre for Biodiscovery, University of Otago, 9016 Dunedin, New Zealand
- Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; (T.S.-J.); (W.M.); (J.Z.); (T.K.B.); (V.P.M.); (M.C.); (S.B.C.); (A.J.C.)
- Malaghan Institute of Medical Research, 6242 Wellington, New Zealand
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18
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Lee Isla Crake R, Phillips E, Kleffmann T, Currie MJ. Co-culture With Human Breast Adipocytes Differentially Regulates Protein Abundance in Breast Cancer Cells. Cancer Genomics Proteomics 2020; 16:319-332. [PMID: 31467226 DOI: 10.21873/cgp.20137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/15/2019] [Accepted: 07/25/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND/AIM Recent research highlights the role of cancer-associated adipocytes (CAA) in promoting breast cancer cell migration, invasion and resistance to therapy. This study aimed at identifying cellular proteins differentially regulated in breast cancer cells co-cultured with CAA. MATERIALS AND METHODS Adipocytes isolated from human breast adipose tissue were co-cultured with hormone receptor-positive (MCF-7) or -negative (MDA-MB-231) breast cancer cells using a transwell co-culture system. Proteomes of co-cultured and control breast cancer cells were compared quantitatively using iTRAQ labelling and tandem mass spectrometry, and the results were validated by western blotting. RESULTS A total of 1,126 and 1,218 proteins were identified in MCF-7 and MDA-MB-231 cells, respectively. Among these, 85 (MCF-7) and 63 (MDA-MB-231) had an average fold change >1.5 following co-culture. Pathway analysis revealed that CAA-induced enrichment of proteins involved in metabolism, the ubiquitin proteasome, and purine synthesis. CONCLUSION This study provides a proteomic platform for investigating the paracrine role of CAA in promoting breast cancer cell metastasis and resistance to therapy.
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Affiliation(s)
- Rebekah Lee Isla Crake
- Department of Pathology and Biomedical Science, Mackenzie Cancer Research Group, University of Otago Christchurch, Christchurch, New Zealand
| | - Elisabeth Phillips
- Department of Pathology and Biomedical Science, Mackenzie Cancer Research Group, University of Otago Christchurch, Christchurch, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Margaret Jane Currie
- Department of Pathology and Biomedical Science, Mackenzie Cancer Research Group, University of Otago Christchurch, Christchurch, New Zealand
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19
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Herbison R, Evans S, Doherty JF, Algie M, Kleffmann T, Poulin R. A molecular war: convergent and ontogenetic evidence for adaptive host manipulation in related parasites infecting divergent hosts. Proc Biol Sci 2019; 286:20191827. [PMID: 31744433 DOI: 10.1098/rspb.2019.1827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mermithids (phylum Nematoda) and hairworms (phylum Nematomorpha) somehow drive their arthropod hosts into water, which is essential for the worms' survival after egression. The mechanisms behind this behavioural change have been investigated in hairworms, but not in mermithids. Establishing a similar mechanistic basis for host behavioural change between these two distantly related parasitic groups would provide strong convergent evidence for adaptive manipulation and insight into how these parasites modify and/or create behaviour. Here, we search for this convergence, and also contrast changes in physiology between hosts infected with immature and mature mermithids to provide the first ontogenetic evidence for adaptive manipulation by disentangling host response and pathology from the parasite's apparent manipulative effects. We used SWATH-mass spectrometry on brains of Forficula auricularia (earwig) and Bellorchestia quoyana (sandhopper), infected with the mermithids Mermis nigrescens and Thaumamermis zealandica, respectively, at both immature and mature stages of infection, to quantify proteomic changes resulting from mermithid infection. Across both hosts (and hairworm-infected hosts, from earlier studies), the general function of dysregulated proteins was conserved. Proteins involved in energy generation/mobilization were dysregulated, corroborating reports of erratic/hyperactive behaviour in infected hosts. Dysregulated proteins involved in axon/dendrite and synapse modulation were also common to all hosts, suggesting neuronal manipulation is involved in inducing positive hydrotaxis. Furthermore, downregulation of CamKII and associated proteins suggest manipulation of memory also contributes to the behavioural shift.
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Affiliation(s)
- Ryan Herbison
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Steven Evans
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | | | - Michael Algie
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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20
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Jogl G, Khayat R, Murphy E, Kleffmann T, Singh K, Murray B, Krause K. 164. Reporting the High-resolution Structure of the Enterococcal Ribosome: A New Template for Antibiotic Discovery. Open Forum Infect Dis 2018. [PMCID: PMC6253141 DOI: 10.1093/ofid/ofy209.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background The ribosome is a rich target for antibiotic design and its structural secrets have been described at the atomic level over the past 2 decades. However, most bacterial ribosome structures come from nonpathogenic species of Archaea or thermophilic bacteria. To aid in the development of modern antibiotics against the enterococcus, we report the structure of the ribosome from Enterococcus faecalis at 3.5 Å resolution using cryo-electron microscopy. Methods E. faecalis strain OG1 was grown in liquid culture, collected and lysed using a French press. 70S ribosomes were purified using centrifugation through a sucrose cushion followed by column chromatography and sucrose gradient centrifugation. 70S particles were diluted in buffer and applied to a holey carbon grid and using an FEI vitrobot were flash-frozen in liquid ethane. Data were collected on an FEI Titan Krios operating at 300 kV acceleration voltage. The particles classified into 6 distinct structures based on their composition. Completed maps were utilized for structure modelling using Coot and were then refined using real space refinement within Phenix. Results High-quality maps of the 70S ribosome were obtained at up to 3.5 Å resolution in several distinct conformations. The 23S, 16S, and 5S RNA structures were almost completely built into maps with clear density. All but 2 ribosome proteins L25 and L33 have been placed in density. The A, P, and E sites were built into unambiguous density and found to be consistent with other bacterial structures. Notably, 1 EM density map contains an uncharged t-RNA molecule in the E site. The sites identified for current antibiotics are also well defined and interpretable. This 70S structural platform is suitable for structural analysis of antibiotic binding sites, especially for those antibiotics directed specifically against the enterococcal ribosome. Conclusion For the first time, the structure of the ribosome from the important human pathogen Enterococcus faecalis has been determined. The maps were obtained at high resolution and found to be suitable for antibiotic design. It is anticipated that the continued determination of the structures of ribosomes from pathogens will aid in the discovery of new treatments for infectious diseases. Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Gerwald Jogl
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Reza Khayat
- Chemistry and Biochemistry, City College of New York, New York, New York
| | - Eileen Murphy
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | | | - Kavindra Singh
- Internal Medicine, University of Texas McGovern Medical School at Houston, Houston, Texas
| | - Barbara Murray
- Internal Medicine, University of Texas McGovern Medical School at Houston, Houston, Texas
| | - Kurt Krause
- Biochemistry, University of Otago, Dunedin, New Zealand
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21
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Parakra RD, Kleffmann T, Jameson GNL, Ledgerwood EC. The proportion of Met80-sulfoxide dictates peroxidase activity of human cytochrome c. Dalton Trans 2018; 47:9128-9135. [PMID: 29944150 DOI: 10.1039/c8dt02185f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The peroxidase activity of cytochrome c is proposed to contribute to apoptosis by peroxidation of cardiolipin in the mitochondrial inner membrane. However, cytochrome c heme is hexa-coordinate with a methionine (Met80) on the distal side, stopping it from acting as an efficient peroxidase. The first naturally occurring variant of cytochrome c discovered, G41S, has higher peroxidase activity than wild-type. To understand the basis for this increase and gain insight into the peroxidase activity of wild-type, we have studied wild-type, G41S and the unnatural variant G41T. Through a combined kinetic and mass spectrometric analysis, we have shown that hydrogen peroxide specifically oxidizes Met80 to the sulfoxide. In the absence of substrate this can be further oxidized to the sulfone, leading to a decrease in peroxidase activity. Peroxidase activity can be correlated with the proportion of sulfoxide present and if fully in that form, all variants have the same activity without a lag phase caused by activation of the protein.
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Affiliation(s)
- Rinky D Parakra
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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22
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Phillips E, Kleffmann T, Morrin H, Robinson B, Currie M. PO-307 Differential secretome analysis of cancer-associated adipocytes (CAA) and mature adipocytes to identify adipocyte-driven micro-environmental regulators of breast cancer progression. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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23
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McCormick S, Porteous C, Sharma M, Jones G, Legge M, Kleffmann T, Rodger E. Proteomic Analysis of Liver from Human Lipoprotein(a) Transgenic Mice Shows an Oxidative Stress and Lipid Export Response. ATHEROSCLEROSIS SUPP 2018. [DOI: 10.1016/j.atherosclerosissup.2018.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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24
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Lim CS, T. Wardell SJ, Kleffmann T, Brown CM. The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res 2018; 46:4575-4591. [PMID: 29684192 PMCID: PMC5961209 DOI: 10.1093/nar/gky282] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/28/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Introns in mRNA leaders are common in complex eukaryotes, but often overlooked. These introns are spliced out before translation, leaving exon-exon junctions in the mRNA leaders (leader EEJs). Our multi-omic approach shows that the number of leader EEJs inversely correlates with the main protein translation, as does the number of upstream open reading frames (uORFs). Across the five species studied, the lowest levels of translation were observed for mRNAs with both leader EEJs and uORFs (29%). This class of mRNAs also have ribosome footprints on uORFs, with strong triplet periodicity indicating uORF translation. Furthermore, the positions of both leader EEJ and uORF are conserved between human and mouse. Thus, the uORF, in combination with leader EEJ predicts lower expression for nearly one-third of eukaryotic proteins.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Samuel J T. Wardell
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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25
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González-Miró M, Rodríguez-Noda LM, Fariñas-Medina M, Cedré-Marrero B, Madariaga-Zarza S, Zayas-Vignier C, Hernández-Cedeño M, Kleffmann T, García-Rivera D, Vérez-Bencomo V, Rehm BHA. Bioengineered polyester beads co-displaying protein and carbohydrate-based antigens induce protective immunity against bacterial infection. Sci Rep 2018; 8:1888. [PMID: 29382864 PMCID: PMC5789850 DOI: 10.1038/s41598-018-20205-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/15/2018] [Indexed: 12/17/2022] Open
Abstract
The efficacy of protein and carbohydrate antigens as vaccines can be improved via particulate delivery strategies. Here, protein and carbohydrate antigens used in formulations of vaccines against Neisseria menigitidis were displayed on in vivo assembled polyester beads using a combined bioengineering and conjugation approach. An endotoxin-free mutant of Escherichia coli was engineered to produce translational fusions of antigens (Neisseria adhesin A (NadA) and factor H binding protein (fHbp) derived from serogroup B) to the polyhydroxybutyrate synthase (PhaC), in order to intracellularly assemble polyester beads displaying the respective antigens. Purified beads displaying NadA showed enhanced immunogenicity compared to soluble NadA. Both soluble and particulate NadA elicited functional antibodies with bactericidal activity associated with protective immunity. To expand the antigen repertoire and to design a more broadly protective vaccine, NadA-PhaC beads were additionally conjugated to the capsular polysaccharide from serogroup C. Co-delivery of surface displayed NadA and the capsular polysaccharide induced a strong and specific Th1/Th17 mediated immune response associated with functional bactericidal antibodies. Our findings provide the foundation for the design of multivalent antigen-coated polyester beads as suitable carriers for protein and polysaccharide antigens in order to induce protective immunity.
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Affiliation(s)
- Majela González-Miró
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Finlay Vaccine Institute, La Havana, Cuba
| | | | | | | | | | | | | | | | | | | | - Bernd H A Rehm
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.
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26
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Muhsin-Sharafaldine MR, Saunderson SC, Dunn AC, Faed JM, Kleffmann T, McLellan AD. Procoagulant and immunogenic properties of melanoma exosomes, microvesicles and apoptotic vesicles. Oncotarget 2018; 7:56279-56294. [PMID: 27462921 PMCID: PMC5302914 DOI: 10.18632/oncotarget.10783] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/17/2016] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EV) are lipid particles released from eukaryotic cells into the extracellular fluid. Depending on the cell type or mechanism of release, vesicles vary in form and function and exert distinct functions in coagulation and immunity. Tumor cells may constitutively shed vesicles known as exosomes or microvesicles (MV). Alternatively, apoptosis induces the release of apoptotic blebs or vesicles (ApoV) from the plasma membrane. EV have been implicated in thrombotic events (the second highest cause of death in cancer patients) and tumor vesicles contribute to the anti-cancer immune response. In this study, we utilized the well characterized B16 melanoma model to determine the molecular composition and procoagulant and immunogenic potential of exosomes, MV and ApoV. Distinct patterns of surface and cytoplasmic molecules (tetraspanins, integrins, heat shock proteins and histones) were expressed between the vesicle types. Moreover, in vitro coagulation assays revealed that membrane-derived vesicles, namely MV and ApoV, were more procoagulant than exosomes–with tissue factor and phosphatidylserine critical for procoagulant activity. Mice immunized with antigen-pulsed ApoV and challenged with B16 tumors were protected out to 60 days, while lower protection rates were afforded by MV and exosomes. Together the results demonstrate distinct phenotypic and functional differences between vesicle types, with important procoagulant and immunogenic functions emerging for membrane-derived MV and ApoV versus endosome-derived exosomes. This study highlights the potential of EV to contribute to the prothrombotic state, as well as to anti-cancer immunity.
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Affiliation(s)
| | - Sarah C Saunderson
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Amy C Dunn
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - James M Faed
- Department of Pathology, University of Otago, Dunedin, Otago, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, Dunedin, Otago, New Zealand
| | - Alexander D McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand.,Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, Otago, New Zealand
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27
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Mortuza R, Aung HL, Taiaroa G, Opel-Reading HK, Kleffmann T, Cook GM, Krause KL. Overexpression of a newly identified d-amino acid transaminase inMycobacterium smegmatiscomplements glutamate racemase deletion. Mol Microbiol 2017; 107:198-213. [DOI: 10.1111/mmi.13877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Roman Mortuza
- Department of Biochemistry; University of Otago; Otago New Zealand
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Htin Lin Aung
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - George Taiaroa
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | | | | | - Gregory M. Cook
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Kurt L. Krause
- Department of Biochemistry; University of Otago; Otago New Zealand
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28
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Tong M, Kleffmann T, Pradhan S, Johansson CL, DeSousa J, Stone PR, James JL, Chen Q, Chamley LW. Proteomic characterization of macro-, micro- and nano-extracellular vesicles derived from the same first trimester placenta: relevance for feto-maternal communication. Hum Reprod 2016; 31:687-99. [PMID: 26839151 DOI: 10.1093/humrep/dew004] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/02/2016] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION What proteins are carried by extracellular vesicles (EVs) released from normal first trimester placentae? SUMMARY ANSWER One thousand five hundred and eighty-five, 1656 and 1476 proteins were characterized in macro-, micro- and nano-vesicles, respectively, from first trimester placentae, with all EV fractions being enriched for proteins involved in vesicle transport and inflammation. WHAT IS KNOWN ALREADY Placental EVs are being increasingly recognized as important mediators of both healthy and pathological pregnancies. However, current research has focused on detecting changes in specific proteins in particular fractions of vesicles during disease. This is the first study to investigate the full proteome of different-sized fractions of EVs from the same first trimester placenta and highlights the differences/similarities between the vesicle fractions. STUDY DESIGN, SIZE, DURATION A well-established ex vivo placental explant culture model was used to generate macro-, micro- and nano-vesicles from 56 first trimester placentae. Vesicle fractions were collected by differential ultracentrifugation, quantified and characterized. PARTICIPANTS/MATERIALS, SETTING, METHODS Placental macro-, micro- and nano-vesicles were characterized by microscopy, dynamic light scattering and nanoparticle tracking analysis. The proteome of each EV fraction was interrogated using liquid chromatography-coupled tandem mass spectrometry. Results were validated by semi-quantitative western blotting. MAIN RESULTS AND THE ROLE OF CHANCE A total of 1585, 1656 and 1476 proteins were identified in macro-, micro- and nano-vesicles, respectively. One thousand one hundred and twenty-five proteins were shared between all three fractions while up to 223 proteins were unique to each fraction. Gene Ontology pathway analysis showed an enrichment of proteins involved in vesicle transport and inflammation in all three fractions of EVs. The expression levels of proteins involved in internalization of vesicles (annexin V, calreticulin, CD31, CD47), the complement pathway [C3, decay-accelerating factor (DAF), membrane cofactor protein (MCP), protectin] and minor histocompatibility antigens [ATP-dependent RNA helicase (DDX3), ribosomal protein S4 (RPS4)] were different between different-sized EVs. LIMITATIONS, REASONS FOR CAUTION This study is largely hypothesis-generating in nature. It is important to validate these findings using EVs isolated from maternal plasma and the function of the different EV fractions would need further investigation. WIDER IMPLICATIONS OF THE FINDINGS Our results support the concept that various EV factions can interact with different maternal cells and have unique effects to mediate feto-maternal communication during early pregnancy. This study also provides a list of candidate proteins, which may inform the identification of robust markers that can be used to isolate placental vesicles from the maternal blood in the future. STUDY FUNDING/COMPETING INTERESTS M.T. is a recipient of the University of Auckland Health Research Doctoral Scholarship and the Freemasons Postgraduate Scholarship. This project was supported by a School of Medicine Performance-based research fund (PBRF) grant awarded to L.W.C. No authors have any conflicts of interest to disclose.
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Affiliation(s)
- Mancy Tong
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Shantanu Pradhan
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Caroline L Johansson
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-581 83, Sweden
| | - Joana DeSousa
- Maternal Fetal Medicine, Auckland City Hospital, Auckland 1023, New Zealand
| | - Peter R Stone
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand Maternal Fetal Medicine, Auckland City Hospital, Auckland 1023, New Zealand
| | - Joanna L James
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Qi Chen
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Larry W Chamley
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
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29
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Kohn YY, Symonds JE, Kleffmann T, Nakagawa S, Lagisz M, Lokman PM. Proteomic analysis of early-stage embryos: implications for egg quality in hapuku (Polyprion oxygeneios). Fish Physiol Biochem 2015; 41:1403-1417. [PMID: 26183261 DOI: 10.1007/s10695-015-0095-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 07/06/2015] [Indexed: 06/04/2023]
Abstract
In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function/pathway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.
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Affiliation(s)
- Yair Y Kohn
- Department of Zoology, University of Otago, PO Box 56, 340 Great King St., Dunedin, 9016, New Zealand
- Bream Bay Aquaculture Park, NIWA, PO Box 147, Ruakaka, 0151, New Zealand
- Arava Research and Development Station, Hatzeva, Israel
| | - Jane E Symonds
- Bream Bay Aquaculture Park, NIWA, PO Box 147, Ruakaka, 0151, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - P Mark Lokman
- Department of Zoology, University of Otago, PO Box 56, 340 Great King St., Dunedin, 9016, New Zealand.
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Pantham P, Viall CA, Chen Q, Kleffmann T, Print CG, Chamley LW. Antiphospholipid antibodies bind syncytiotrophoblast mitochondria and alter the proteome of extruded syncytial nuclear aggregates. Placenta 2015; 36:1463-73. [PMID: 26506561 DOI: 10.1016/j.placenta.2015.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/28/2015] [Accepted: 10/11/2015] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Antiphospholipid antibodies (aPL) are autoantibodies that increase the risk of women developing the hypertensive disorder pre-eclampsia. aPL are internalised by the syncytiotrophoblast and increase extrusion of necrotic multinucleated syncytial nuclear aggregates (SNAs), which may trigger endothelial dysfunction in pre-eclampsia. The mechanisms by which aPL alter death processes in the syncytiotrophoblast leading to extrusion of SNAs are unknown. METHODS First trimester human placentae (n = 10) were dissected into explants and cultured either with aPL (50 μg/mL), isotype-matched control antibody (50 μg/mL), or media for 24 h. Harvested SNAs underwent iTRAQ proteomic analysis. Mitochondria in syncytiotrophoblast treated with aPL labelled with FluoroNanogold were visualised using transmission electron microscopy (TEM). RESULTS aPL altered the expression of 72 proteins in SNAs. Thirteen proteins were involved in mitochondrial function. TEM demonstrated that aPL bind to mitochondria in the syncytiotrophoblast and may cause mitochondrial swelling. DISCUSSION aPL disrupt mitochondria increasing the extrusion of SNAs with an altered proteome from the syncytiotrophoblast. These altered SNAs may trigger endothelial dysfunction and pre-eclampsia in these pregnancies.
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Affiliation(s)
- Priyadarshini Pantham
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand; Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Chez A Viall
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Qi Chen
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand; Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics & Gynaecology, The University of Auckland, Auckland, New Zealand
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Cardno TS, Shimaki Y, Sleebs BE, Lackovic K, Parisot JP, Moss RM, Crowe-McAuliffe C, Mathew SF, Edgar CD, Kleffmann T, Tate WP. HIV-1 and Human PEG10 Frameshift Elements Are Functionally Distinct and Distinguished by Novel Small Molecule Modulators. PLoS One 2015; 10:e0139036. [PMID: 26447468 PMCID: PMC4598141 DOI: 10.1371/journal.pone.0139036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 09/07/2015] [Indexed: 11/19/2022] Open
Abstract
Frameshifting during translation of viral or in rare cases cellular mRNA results in the synthesis of proteins from two overlapping reading frames within the same mRNA. In HIV-1 the protease, reverse transcriptase, and integrase enzymes are in a second reading frame relative to the structural group-specific antigen (gag), and their synthesis is dependent upon frameshifting. This ensures that a strictly regulated ratio of structural proteins and enzymes, which is critical for HIV-1 replication and viral infectivity, is maintained during protein synthesis. The frameshift element in HIV-1 RNA is an attractive target for the development of a new class of anti HIV-1 drugs. However, a number of examples are now emerging of human genes using −1 frameshifting, such as PEG10 and CCR5. In this study we have compared the HIV-1 and PEG10 frameshift elements and shown they have distinct functional characteristics. Frameshifting occurs at several points within each element. Moreover, frameshift modulators that were isolated by high-throughput screening of a library of 114,000 lead-like compounds behaved differently with the PEG10 frameshift element. The most effective compounds affecting the HIV-1 element enhanced frameshifting by 2.5-fold at 10 μM in two different frameshift reporter assay systems. HIV-1 protease:gag protein ratio was affected by a similar amount in a specific assay of virally-infected cultured cell, but the modulation of frameshifting of the first-iteration compounds was not sufficient to show significant effects on viral infectivity. Importantly, two compounds did not affect frameshifting with the human PEG10 element, while one modestly inhibited rather than enhanced frameshifting at the human element. These studies indicate that frameshift elements have unique characteristics that may allow targeting of HIV-1 and of other viruses specifically for development of antiviral therapeutic molecules without effect on human genes like PEG10 that use the same generic mechanism.
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Affiliation(s)
- Tony S. Cardno
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Yosuke Shimaki
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Kurt Lackovic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John P. Parisot
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Rebecca M. Moss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | | | - Suneeth F. Mathew
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Torsten Kleffmann
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Warren P. Tate
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- * E-mail:
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Tchesnokov EP, Fellner M, Siakkou E, Kleffmann T, Martin LW, Aloi S, Lamont IL, Wilbanks SM, Jameson GNL. The cysteine dioxygenase homologue from Pseudomonas aeruginosa is a 3-mercaptopropionate dioxygenase. J Biol Chem 2015; 290:24424-37. [PMID: 26272617 PMCID: PMC4591825 DOI: 10.1074/jbc.m114.635672] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 08/02/2015] [Indexed: 02/02/2023] Open
Abstract
Thiol dioxygenation is the initial oxidation step that commits a thiol to important catabolic or biosynthetic pathways. The reaction is catalyzed by a family of specific non-heme mononuclear iron proteins each of which is reported to react efficiently with only one substrate. This family of enzymes includes cysteine dioxygenase, cysteamine dioxygenase, mercaptosuccinate dioxygenase, and 3-mercaptopropionate dioxygenase. Using sequence alignment to infer cysteine dioxygenase activity, a cysteine dioxygenase homologue from Pseudomonas aeruginosa (p3MDO) has been identified. Mass spectrometry of P. aeruginosa under standard growth conditions showed that p3MDO is expressed in low levels, suggesting that this metabolic pathway is available to the organism. Purified recombinant p3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. We therefore describe this enzyme as a 3-mercaptopropionate dioxygenase. Mössbauer spectroscopy suggests that substrate binding to the ferrous iron is through the thiol but indicates that each substrate could adopt different coordination geometries. Crystallographic comparison with mammalian cysteine dioxygenase shows that the overall active site geometry is conserved but suggests that the different substrate specificity can be related to replacement of an arginine by a glutamine in the active site.
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Affiliation(s)
| | | | | | - Torsten Kleffmann
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Lois W Martin
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | - Iain L Lamont
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Sigurd M Wilbanks
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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Frampton RA, Acedo EL, Young VL, Chen D, Tong B, Taylor C, Easingwood RA, Pitman AR, Kleffmann T, Bostina M, Fineran PC. Genome, Proteome and Structure of a T7-Like Bacteriophage of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae. Viruses 2015; 7:3361-79. [PMID: 26114474 PMCID: PMC4517105 DOI: 10.3390/v7072776] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/08/2015] [Accepted: 06/16/2015] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (Actinidia sp.). Bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. A variety of bacteriophages were previously isolated that infect P. syringae pv. actinidiae, and their basic properties were characterized to provide a framework for formulation of these phages as biocontrol agents. Here, we have examined in more detail φPsa17, a phage with the capacity to infect a broad range of P. syringae pv. actinidiae strains and the only member of the Podoviridae in this collection. Particle morphology was visualized using cryo-electron microscopy, the genome was sequenced, and its structural proteins were analysed using shotgun proteomics. These studies demonstrated that φPsa17 has a 40,525 bp genome, is a member of the T7likevirus genus and is closely related to the pseudomonad phages φPSA2 and gh-1. Eleven structural proteins (one scaffolding) were detected by proteomics and φPsa17 has a capsid of approximately 60 nm in diameter. No genes indicative of a lysogenic lifecycle were identified, suggesting the phage is obligately lytic. These features indicate that φPsa17 may be suitable for formulation as a biocontrol agent of P. syringae pv. actinidiae.
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Affiliation(s)
- Rebekah A Frampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
- New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand.
| | - Elena Lopez Acedo
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
- Departamento de Genetica, Universidad de Extremadura, Badajoz 06080, Spain.
| | - Vivienne L Young
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Danni Chen
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Brian Tong
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Corinda Taylor
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Richard A Easingwood
- Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Andrew R Pitman
- New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand.
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
- Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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Johnson SL, Villarroel M, Rosengrave P, Carne A, Kleffmann T, Lokman PM, Gemmell NJ. Proteomic analysis of chinook salmon (Oncorhynchus tshawytscha) ovarian fluid. PLoS One 2014; 9:e104155. [PMID: 25089903 PMCID: PMC4121310 DOI: 10.1371/journal.pone.0104155] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022] Open
Abstract
The ovarian, or coelomic, fluid that is released with the egg mass of many fishes is increasingly found to play an important role in several biological processes crucial for reproductive success. These include maintenance of oocyte fertility and developmental competence, prolonging of sperm motility, and enhancing sperm swimming speed. Here we examined if and how the proteome of chinook salmon (Oncorhynchus tshawytscha) ovarian fluid varied among females and then sought to examine the composition of this fluid. Ovarian fluid in chinook salmon was analyzed using 1D SDS PAGE and LC-MS/MS tryptic digest screened against Mascot and Sequest databases. We found marked differences in the number and concentrations of proteins in salmon ovarian fluid across different females. A total of 174 proteins were identified in ovarian fluid, 47 of which were represented by six or more peptides, belonging to one of six Gene Ontology pathways. The response to chemical stimulus and response to hypoxia pathways were best represented, accounting for 26 of the 174 proteins. The current data set provides a resource that furthers our understanding of those factors that influence successful egg production and fertilisation in salmonids and other species.
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Affiliation(s)
- Sheri L. Johnson
- Allan Wilson Centre for Molecular Ecology and Evolution and Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Marsha Villarroel
- Allan Wilson Centre for Molecular Ecology and Evolution and Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Patrice Rosengrave
- Allan Wilson Centre for Molecular Ecology and Evolution and Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Alan Carne
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - P. Mark Lokman
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Neil J. Gemmell
- Allan Wilson Centre for Molecular Ecology and Evolution and Department of Anatomy, University of Otago, Dunedin, New Zealand
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Pemberton CJ, Siriwardena M, Kleffmann T, Richards AM. C-type natriuretic peptide (CNP) signal peptide fragments are present in the human circulation. Biochem Biophys Res Commun 2014; 449:301-6. [DOI: 10.1016/j.bbrc.2014.05.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/09/2014] [Indexed: 11/24/2022]
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von Zychlinski A, Williams M, McCormick S, Kleffmann T. Absolute quantification of apolipoproteins and associated proteins on human plasma lipoproteins. J Proteomics 2014; 106:181-90. [DOI: 10.1016/j.jprot.2014.04.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
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Marchalant Y, Brownjohn PW, Bonnet A, Kleffmann T, Ashton JC. Validating Antibodies to the Cannabinoid CB2 Receptor: Antibody Sensitivity Is Not Evidence of Antibody Specificity. J Histochem Cytochem 2014; 62:395-404. [PMID: 24670796 PMCID: PMC4174627 DOI: 10.1369/0022155414530995] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Antibody-based methods for the detection and quantification of membrane integral proteins, in particular, the G protein-coupled receptors (GPCRs), have been plagued with issues of primary antibody specificity. In this report, we investigate one of the most commonly utilized commercial antibodies for the cannabinoid CB2 receptor, a GPCR, using immunoblotting in combination with mass spectrometry. In this way, we were able to develop powerful negative and novel positive controls. By doing this, we are able to demonstrate that it is possible for an antibody to be sensitive for a protein of interest—in this case CB2—but still cross-react with other proteins and therefore lack specificity. Specifically, we were able to use western blotting combined with mass spectrometry to unequivocally identify CB2 protein in over-expressing cell lines. This shows that a common practice of validating antibodies with positive controls only is insufficient to ensure antibody reliability. In addition, our work is the first to develop a label-free method of protein detection using mass spectrometry that, with further refinement, could provide unequivocal identification of CB2 receptor protein in native tissues.
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Affiliation(s)
- Yannick Marchalant
- Aix-Marseille University, Neurobiologie des Interactions Cellulaires et Neurophysiopathologie, Marseille, France (YM,AB)Department of Pharmacology and Toxicology (PWB,JCA)Centre for Protein Research, Biochemistry Department, University of Otago, Dunedin, New Zealand (TK)
| | - Philip W Brownjohn
- Aix-Marseille University, Neurobiologie des Interactions Cellulaires et Neurophysiopathologie, Marseille, France (YM,AB)Department of Pharmacology and Toxicology (PWB,JCA)Centre for Protein Research, Biochemistry Department, University of Otago, Dunedin, New Zealand (TK)
| | - Amandine Bonnet
- Aix-Marseille University, Neurobiologie des Interactions Cellulaires et Neurophysiopathologie, Marseille, France (YM,AB)Department of Pharmacology and Toxicology (PWB,JCA)Centre for Protein Research, Biochemistry Department, University of Otago, Dunedin, New Zealand (TK)
| | - Torsten Kleffmann
- Aix-Marseille University, Neurobiologie des Interactions Cellulaires et Neurophysiopathologie, Marseille, France (YM,AB)Department of Pharmacology and Toxicology (PWB,JCA)Centre for Protein Research, Biochemistry Department, University of Otago, Dunedin, New Zealand (TK)
| | - John C Ashton
- Aix-Marseille University, Neurobiologie des Interactions Cellulaires et Neurophysiopathologie, Marseille, France (YM,AB)Department of Pharmacology and Toxicology (PWB,JCA)Centre for Protein Research, Biochemistry Department, University of Otago, Dunedin, New Zealand (TK)
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Souness RJ, Kleffmann T, Tchesnokov EP, Wilbanks SM, Jameson GB, Jameson GNL. Mechanistic implications of persulfenate and persulfide binding in the active site of cysteine dioxygenase. Biochemistry 2013; 52:7606-17. [PMID: 24084026 DOI: 10.1021/bi400661a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Describing the organization of substrates and substrate analogues in the active site of cysteine dioxygenase identifies potential intermediates in this critical yet poorly understood reaction, the oxidation of cysteine to cysteine sulfinic acid. The fortuitous formation of persulfides under crystallization conditions has allowed their binding in the active site of cysteine dioxygenase to be studied. The crystal structures of cysteine persulfide and 3-mercaptopropionic acid persulfide bound to iron(II) in the active site show that binding of the persulfide occurs via the distal sulfide and, in the case of the cysteine persulfide, the amine also binds. Persulfide was detected by mass spectrometry in both the crystal and the drop, suggesting its origin is chemical rather than enzymatic. A mechanism involving the formation of the relevant disulfide from sulfide produced by hydrolysis of dithionite is proposed. In comparison, persulfenate {observed bound to cysteine dioxygenase [Simmons, C. R., et al. (2008) Biochemistry 47, 11390]} is shown through mass spectrometry to occur only in the crystal and not in the surrounding drop, suggesting that in the crystalline state the persulfenate does not lie on the reaction pathway. Stabilization of both the persulfenate and the persulfides does, however, suggest the position in which dioxygen binds during catalysis.
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Affiliation(s)
- Richard J Souness
- Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology and ‡Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand
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Kumar V, Kleffmann T, Hampton MB, Cannell MB, Winterbourn CC. Redox proteomics of thiol proteins in mouse heart during ischemia/reperfusion using ICAT reagents and mass spectrometry. Free Radic Biol Med 2013; 58:109-17. [PMID: 23376233 DOI: 10.1016/j.freeradbiomed.2013.01.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/10/2013] [Accepted: 01/16/2013] [Indexed: 02/07/2023]
Abstract
There is strong evidence for the involvement of reactive oxygen species in ischemia/reperfusion injury. Although oxidation of individual thiol proteins has been reported, more extensive redox proteomics of hearts subjected to ischemia/reperfusion has not been performed. We have carried out an exploratory study using mass spectrometry with isotope-coded affinity tags (ICAT) aimed at identifying reversible oxidative changes to protein thiols in Langendorff perfused isolated mouse hearts subjected to 20 min ischemia with or without aerobic reperfusion for 5 or 30 min. Reduced thiols were blocked by adding N-ethylmaleimide during protein extraction, then reversibly oxidized thiols in extracts of control perfused and treated hearts were reduced and labeled with the light and heavy ICAT reagents, respectively. Protein extracts were mixed in equal amounts and relative proportions of the isotope-labeled peaks were used to quantify oxidative changes between the control and the treated groups. Approximately 300 peptides with ICAT signatures were reliably identified in each sample, with 181 peptides from 118 proteins common to all treatments. A proportion showed elevated ICAT ratios, consistent with reversible thiol oxidation. This was most evident after early reperfusion, with apparent reversal after longer reperfusion. In comparison, there was gradual accumulation of protein carbonyls and loss of GSH with longer reperfusion. Many of the thiol changes were in mitochondrial proteins, including components of electron transport complexes and enzymes involved in lipid metabolism. The results are consistent with mitochondria being a major site of oxidant generation during early cardiac reperfusion and mitochondrial thiol proteins being targets for oxidation.
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Affiliation(s)
- Vikas Kumar
- Department of Pathology, University of Otago Christchurch, Christchurch 8140, New Zealand
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Pemberton CJ, Siriwardena M, Kleffmann T, Ruygrok P, Palmer SC, Yandle TG, Richards AM. First Identification of Circulating Prepro–A-Type Natriuretic Peptide (PreproANP) Signal Peptide Fragments in Humans: Initial Assessment as Cardiovascular Biomarkers. Clin Chem 2012; 58:757-67. [DOI: 10.1373/clinchem.2011.176990] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
New biomarkers are needed to assist clinical decision making in cardiovascular disease. We have recently shown that signal peptides may represent a novel biomarker target in cardiovascular diseases.
METHODS
We developed a novel immunoassay for the signal peptide of preproANP (ANPsp) and used it to document cardiac tissue levels of ANPsp in explant human hearts (n = 9), circulating venous concentrations of ANPsp in healthy volunteers (n = 65), temporal ANPsp concentrations in patients with ST-elevation myocardial infarction (STEMI) <4 h after chest pain onset (n = 23), and regional plasma ANPsp concentrations in patients undergoing clinically indicated catheterization (n = 10). We analyzed the structure and sequence of circulating ANPsp by tandem mass spectrometry (MS/MS).
RESULTS
ANPsp levels in human heart tissue were 50–1000 times lower than those of ANP/NT-proANP. ANPsp was detectable in control human plasma at concentrations comparable with ANP itself (approximately 20 ng/L). In STEMI patients, plasma concentrations of ANPsp rose to peak values at 5 h after symptom onset, significantly earlier than myoglobin, creatine kinase-MB, and troponin (P < 0.001). There were significant arteriovenous increases in ANPsp concentrations (P < 0.05) across the heart and kidney; arterial and coronary sinus concentrations of ANPsp both negatively correlated with systolic and mean arterial blood pressures (both P < 0.01). MS/MS verified circulating ANPsp to be preproANP(16–25) and preproANP(18–25).
CONCLUSIONS
ANPsp is a novel circulating natriuretic peptide with potential to act as a cardiovascular biomarker. The rapid increase of plasma ANPsp in STEMI and its significant relationship with blood pressure encourage further study of its potential clinical utility.
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Affiliation(s)
- Chris J Pemberton
- Christchurch Cardioendocrine Research Group, University of Otago, Christchurch, New Zealand
| | - Maithri Siriwardena
- Christchurch Cardioendocrine Research Group, University of Otago, Christchurch, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, Department of Biochemistry, University of Otago, New Zealand
| | - Peter Ruygrok
- Green Lane Cardiovascular Service, Auckland City Hospital, Auckland, New Zealand
| | - Suetonia C Palmer
- Christchurch Cardioendocrine Research Group, University of Otago, Christchurch, New Zealand
| | - Tim G Yandle
- Christchurch Cardioendocrine Research Group, University of Otago, Christchurch, New Zealand
| | - A Mark Richards
- Christchurch Cardioendocrine Research Group, University of Otago, Christchurch, New Zealand
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Rodger EJ, Suetani RJ, Jones GT, Kleffmann T, Carne A, Legge M, McCormick SPA. Proteomic analysis of aortae from human lipoprotein(a) transgenic mice shows an early metabolic response independent of atherosclerosis. PLoS One 2012; 7:e30383. [PMID: 22276189 PMCID: PMC3261968 DOI: 10.1371/journal.pone.0030383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/15/2011] [Indexed: 01/23/2023] Open
Abstract
Background Elevated low density lipoprotein (LDL) and lipoprotein(a) are independent risk factors for the development of atherosclerosis. Using a proteomic approach we aimed to determine early changes in arterial protein expression in transgenic mice containing both human LDL and lipoprotein(a) in circulation. Methods and Results Plasma lipid analyses showed the lipoprotein(a) transgenic mice had significantly higher lipid levels than wildtype, including a much increased LDL and high density lipoprotein (HDL) cholesterol. Analysis of aortae from lipoprotein(a) mice showed lipoprotein(a) accumulation but no lipid accumulation or foam cells, leaving the arteries essentially atherosclerosis free. Using two-dimensional gel electrophoresis and mass spectrometry, we identified 34 arterial proteins with significantly altered abundance (P<0.05) in lipoprotein(a) transgenic mice compared to wildtype including 17 that showed a ≥2 fold difference. Some proteins of interest showed a similarly altered abundance at the transcript level. These changes collectively indicated an initial metabolic response that included a down regulation in energy, redox and lipid metabolism proteins and changes in structural proteins at a stage when atherosclerosis had not yet developed. Conclusions Our study shows that human LDL and lipoprotein(a) promote changes in the expression of a unique set of arterial proteins which may be early indicators of the metabolic disturbances preceding atherosclerosis.
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Affiliation(s)
- Euan J. Rodger
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Rachel J. Suetani
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Gregory T. Jones
- Department of Surgical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research, University of Otago, Dunedin, New Zealand
| | - Alan Carne
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Michael Legge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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von Zychlinski A, Kleffmann T, Williams MJA, McCormick SP. Proteomics of Lipoprotein(a) identifies a protein complement associated with response to wounding. J Proteomics 2011; 74:2881-91. [PMID: 21802535 DOI: 10.1016/j.jprot.2011.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/06/2011] [Accepted: 07/11/2011] [Indexed: 10/18/2022]
Abstract
Lipoprotein(a) [Lp(a)] is a major independent risk factor for cardiovascular disease. Twenty percent of the general population exhibit levels above the risk threshold highlighting the importance for clinical and basic research. Comprehensive proteomics of human Lp(a) will provide significant insights into Lp(a) physiology and pathogenicity. Using liquid chromatography-coupled mass spectrometry, we established a high confidence Lp(a) proteome of 35 proteins from highly purified particles. Protein interaction network analysis and functional clustering revealed proteins assigned to the two major biological processes of lipid metabolism and response to wounding. The latter includes the processes of coagulation, complement activation and inflammatory response. Furthermore, absolute protein quantification of apoB-100, apo(a), apoA1, complement C3 and PON1 gave insights into the compositional stoichiometry of associated proteins per particle. Our proteomics study has identified Lp(a)-associated proteins that support a suggested role of Lp(a) in response to wounding which points to mechanisms of Lp(a) pathogenicity at sites of vascular injury and atherosclerotic lesions. This study has identified a high confidence Lp(a) proteome and provides an important basis for further comparative and quantitative analyses of Lp(a) isolated from greater numbers of plasma samples to investigate the significance of associated proteins and their dynamics for Lp(a) pathogenicity.
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43
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Dickerhof N, Kleffmann T, Jack R, McCormick S. Bacitracin inhibits the reductive activity of protein disulfide isomerase by disulfide bond formation with free cysteines in the substrate-binding domain. FEBS J 2011; 278:2034-43. [PMID: 21481187 DOI: 10.1111/j.1742-4658.2011.08119.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peptide antibiotic bacitracin is widely used as an inhibitor of protein disulfide isomerase (PDI) to demonstrate the role of the protein-folding catalyst in a variety of molecular pathways. Commercial bacitracin is a mixture of at least 22 structurally related peptides. The inhibitory activity of individual bacitracin analogs on PDI is unknown. For the present study, we purified the major bacitracin analogs, A, B, H, and F, and tested their ability to inhibit the reductive activity of PDI by use of an insulin aggregation assay. All analogs inhibited PDI, but the activity (IC(50) ) ranged from 20 μm for bacitracin F to 1050 μm for bacitracin B. The mechanism of PDI inhibition by bacitracin is unknown. Here, we show, by MALDI-TOF/TOF MS, a direct interaction of bacitracin with PDI, involving disulfide bond formation between an open thiol form of the bacitracin thiazoline ring and cysteines in the substrate-binding domain of PDI.
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Affiliation(s)
- Nina Dickerhof
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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44
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Park SJ, Kleffmann T, Hessian PA. The G82S polymorphism promotes glycosylation of the receptor for advanced glycation end products (RAGE) at asparagine 81: comparison of wild-type rage with the G82S polymorphic variant. J Biol Chem 2011; 286:21384-92. [PMID: 21511948 DOI: 10.1074/jbc.m111.241281] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Interaction between the receptor for advanced glycation end products (RAGE) and its ligands amplifies the proinflammatory response. N-Linked glycosylation of RAGE plays an important role in the regulation of ligand binding. Two potential sites for N-linked glycosylation, at Asn(25) and Asn(81), are implicated, one of which is potentially influenced by a naturally occurring polymorphism that substitutes Gly(82) with Ser. This G82S polymorphic RAGE variant displays increased ligand binding and downstream signaling. We hypothesized that the G82S polymorphism affects RAGE glycosylation and thereby affects ligand binding. WT or various mutant forms of RAGE protein, including N25Q, N81Q, N25Q/G82S, and N25Q/N81Q, were produced by transfecting HEK293 cells. The glycosylation patterns of expressed proteins were compared. Enzymatic deglycosylation showed that WT RAGE and the G82S polymorphic variant are glycosylated to the same extent. Our data also revealed N-linked glycosylation of N25Q and N81Q mutants, suggesting that both Asn(25) and Asn(81) can be utilized for N-linked glycosylation. Using mass spectrometry analysis, we found that Asn(81) may or may not be glycosylated in WT RAGE, whereas in G82S RAGE, Asn(81) is always glycosylated. Furthermore, RAGE binding to S100B ligand is affected by Asn(81) glycosylation, with consequences for NF-κB activation. Therefore, the G82S polymorphism promotes N-linked glycosylation of Asn(81), which has implications for the structure of the ligand binding region of RAGE and might explain the enhanced function associated with the G82S polymorphic RAGE variant.
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Affiliation(s)
- Sun Jin Park
- Department of Physiology, University of Otago, Dunedin 9054, New Zealand
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45
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P. Kafka A, Kleffmann T, Rades T, McDowell A. Characterization of Peptide Polymer Interactions in Poly(alkylcyanoacrylate) Nanoparticles: A Mass Spectrometric Approach. Curr Drug Deliv 2010. [DOI: 10.2174/156720110791560937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kafka AP, Kleffmann T, Rades T, McDowell A. Characterization of Peptide Polymer Interactions in Poly(alkylcyanoacrylate) Nanoparticles: A Mass Spectrometric Approach. Curr Drug Deliv 2010; 7:208-215. [PMID: 20497104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Drug/polymer interactions occur during in situ polymerization of poly(alkylcyanoacrylate) (PACA) formulations. We have used MALDI ionization coupled tandem time-of-flight (TOF) mass spectrometry as an accurate method to characterize covalent peptide/polymer interactions of PACA nanoparticles with the bioactives D-Lys6-GnRH, insulin, [Asn1-Val5]-angiotensin II, and fragments of insulin-like growth factor 1 (IGF-1 (1-3)) and human adrenocorticotropic hormone (h-ACTH, (18-39)) at the molecular level. Covalent interactions of peptide with alkylcyanoacrylate were identified for D-Lys6-GnRH, [Asn1-Val5]-angiotensin II and IGF-1 (1-3). D-Lys6-GnRH and [Asn1-Val5]-angiotensin II were modified at their histidine side chain within the peptide, whilst IGF-1 (1-3) was modified at the C-terminal glutamic acid residue. The more complex protein insulin was not modified despite the presence of 2 histidine residues. This might be explained by the engagement of histidine residues in the folding and sterical arrangement of insulin under polymerization conditions. As expected, h-ACTH (18-39) that does not contain histidine residues did not interfere in the polymerization process. Lowering the pH did not prevent the covalent association of PACA with D-Lys6-GnRH or IGF-1 (1-3). Conclusively, protein and peptide bioactives are potentially reactive towards alkylcyanoacrylate monomers via various mechanisms with limited interference of pH. Histidines and C-terminal glutamic acid residues have been identified as potential sites of interaction. The likelihood of their engagement in the polymerization process (initiators), however, seems dependent on their sterical availability. The reactivity of nucleophilic functional groups should always be considered and bioactives examined for their potential to covalently interfere with alkylcyanoacrylate monomers, especially when designing PACA delivery systems for protein and peptide biopharmaceuticals.
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Affiliation(s)
| | | | | | - Arlene McDowell
- University of Otago, School of Pharmacy, 18 Frederick Street, P.O. Box 56, 9054 Dunedin, New Zealand.
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Kafka AP, Kleffmann T, Rades T, McDowell A. Characterization of Peptide Polymer Interactions in Poly(alkylcyanoacrylate) Nanoparticles: A Mass Spectrometric Approach. Curr Drug Deliv 2010:BSP-CDD-EPUB-00042. [PMID: 20158486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/28/2010] [Indexed: 05/28/2023]
Abstract
Drug/polymer interactions occur during in situ polymerization of poly(alkylcyanoacrylate) (PACA) formulations. We have used MALDI ionization coupled tandem time-of-flight (TOF) mass spectrometry as an accurate method to characterize covalent peptide/polymer interactions of PACA nanoparticles with the bioactives D-Lys6-GnRH, insulin, [Asn1-Val5]-angiotensin II, and fragments of insulin-like growth factor 1 (IGF-1 (1-3)) and human adrenocorticotropic hormone (h-ACTH, (18-39)) at the molecular level. Covalent interactions of peptide with alkylcyanoacrylate were identified for D-Lys6-GnRH, [Asn1-Val5]-angiotensin II and IGF-1 (1-3). D-Lys6-GnRH and [Asn1-Val5]-angiotensin II were modified at their histidine side chain within the peptide, whilst IGF-1 (1-3) was modified at the C-terminal glutamic acid residue. The more complex protein insulin was not modified despite the presence of 2 histidine residues. This might be explained by the engagement of histidine residues in the folding and sterical arrangement of insulin under polymerization conditions. As expected, h-ACTH (18-39) that does not contain histidine residues did not interfere in the polymerisation process. Lowering the pH did not prevent the covalent association of PACA with D-Lys6-GnRH or IGF-1 (1-3). Conclusively, protein and peptide bioactives are potentially reactive towards alkylcyanoacrylate monomers via various mechanisms with limited interference of pH. Histidines and C-terminal glutamic acid residues have been identified as potential sites of interaction. The likelihood of their engagement in the polymerisation process (initiators), however, seems dependant on their sterical availability. The reactivity of nucleophilic functional groups should always be considered and bioactives examined for their potential to covalently interfere with alkylcyanoacrylate monomers, especially when designing PACA delivery systems for protein and peptide biopharmaceuticals.
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Affiliation(s)
- Alexandra P Kafka
- University of Otago, School of Pharmacy, 18 Frederick Street, PO Box 56, 9054 Dunedin, New Zealand.
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Kafka AP, Kleffmann T, Rades T, McDowell A. Histidine Residues in the Peptide d-Lys6-GnRH: Potential for Copolymerization in Polymeric Nanoparticles. Mol Pharm 2009; 6:1483-91. [DOI: 10.1021/mp900043e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra P. Kafka
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand, and Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Torsten Kleffmann
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand, and Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Thomas Rades
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand, and Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Arlene McDowell
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand, and Centre for Protein Research, Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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Kleffmann T, Jongkees SAK, Fairweather G, Wilbanks SM, Jameson GNL. Mass-spectrometric characterization of two posttranslational modifications of cysteine dioxygenase. J Biol Inorg Chem 2009; 14:913-21. [DOI: 10.1007/s00775-009-0504-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 04/06/2009] [Indexed: 12/01/2022]
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50
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Clark MB, Jänicke M, Gottesbühren U, Kleffmann T, Legge M, Poole ES, Tate WP. Mammalian Gene PEG10 Expresses Two Reading Frames by High Efficiency –1 Frameshifting in Embryonic-associated Tissues. J Biol Chem 2007; 282:37359-69. [DOI: 10.1074/jbc.m705676200] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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