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Joshi A, Nigam A, Narayan Mudgal L, Mondal B, Basak T. ColPTMScape: An open access knowledge base for tissue-specific collagen PTM maps. Matrix Biol Plus 2024; 22:100144. [PMID: 38469247 PMCID: PMC10926295 DOI: 10.1016/j.mbplus.2024.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Collagen is a key component of the extracellular matrix (ECM). In the remodeling of ECM, a remarkable variation in collagen post-translational modifications (PTMs) occurs. This makes collagen a potential target for understanding extracellular matrix remodeling during pathological conditions. Over the years, scientists have gathered a huge amount of data about collagen PTM during extracellular matrix remodeling. To make such information easily accessible in a consolidated space, we have developed ColPTMScape (https://colptmscape.iitmandi.ac.in/), a dedicated knowledge base for collagen PTMs. The identified site-specific PTMs, quantitated PTM sites, and PTM maps of collagen chains are deliverables to the scientific community, especially to matrix biologists. Through this knowledge base, users can easily gain information related to the difference in the collagen PTMs across different tissues in different organisms.
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Affiliation(s)
- Ashutosh Joshi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Ayush Nigam
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Lalit Narayan Mudgal
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Bhaskar Mondal
- School of Chemical Sciences, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
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2
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Thomas P, Peele EE, Yopak KE, Sulikowski JA, Kinsey ST. Lectin binding to pectoral fin of neonate little skates reared under ambient and projected-end-of-century temperature regimes. J Morphol 2024; 285:e21698. [PMID: 38669130 PMCID: PMC11064730 DOI: 10.1002/jmor.21698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
The glycosylation of macromolecules can vary both among tissue structural components and by adverse conditions, potentially providing an alternative marker of stress in organisms. Lectins are proteins that bind carbohydrate moieties and lectin histochemistry is a common method to visualize microstructures in biological specimens and diagnose pathophysiological states in human tissues known to alter glycan profiles. However, this technique is not commonly used to assess broad-spectrum changes in cellular glycosylation in response to environmental stressors. In addition, the binding of various lectins has not been studied in elasmobranchs (sharks, skates, and rays). We surveyed the binding tissue structure specificity of 14 plant-derived lectins, using both immunoblotting and immunofluorescence, in the pectoral fins of neonate little skates (Leucoraja erinacea). Skates were reared under present-day or elevated (+5°C above ambient) temperature regimes and evaluated for lectin binding as an indicator of changing cellular glycosylation and tissue structure. Lectin labeling was highly tissue and microstructure specific. Dot blots revealed no significant changes in lectin binding between temperature regimes. In addition, lectins only detected in the elevated temperature treatment were Canavalia ensiformis lectin (Concanavalin A) in spindle cells of muscle and Ricinus communis agglutinin in muscle capillaries. These results provide a reference for lectin labeling in elasmobranch tissue that may aid future investigations.
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Affiliation(s)
- Peyton Thomas
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - Emily E. Peele
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - Kara E. Yopak
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
| | - James A. Sulikowski
- 2030 SE Marine Science Drive, Coastal Oregon Marine Experiment Station, Oregon State University, Corvallis, OR 97365, USA
| | - Stephen T. Kinsey
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, 28403, USA
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3
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Morais MRPT, Tian P, O'cualain R, Lawless C, Lennon R. Protocol to characterize basement membranes during kidney development using mass spectrometry-based label-free quantitative proteomics. STAR Protoc 2023; 4:102741. [PMID: 38039136 PMCID: PMC10722381 DOI: 10.1016/j.xpro.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Basement membranes are specialized extracellular matrices formed by highly insoluble structural proteins and extracellular matrix (ECM)-bound components that provide structural and signaling support to tissues and are dynamic during development. Here, we present a mass spectrometry-based label-free quantitative proteomics protocol to investigate basement membranes and define their composition using samples from human kidney organoids and mouse fetal kidneys. This protocol facilitates the study of basement membrane and other ECM components during development to improve our understanding of matrix regulation and function. For complete details on the use and execution of this protocol, please refer to Morais et al.1.
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Affiliation(s)
- Mychel R P T Morais
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK.
| | - Ronan O'cualain
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK.
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4
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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5
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Ambli M, Deracinois B, Jenequin AS, Ravallec R, Cudennec B, Flahaut C. Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish. Foods 2023; 12:2524. [PMID: 37444262 DOI: 10.3390/foods12132524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the mass measurement accuracy of the instrument and the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software algorithms are able to identify a large number of post-translational modifications (PTMs). However, peptide and PTM identifications are challenging in the agrofood field due to non-specific cleavage sites of physiological- or food-grade enzymes and the number and location of PTMs. In this study, we show the importance of customized software programming to obtain a better peptide and PTM identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork, and fish), each digested by simulated gastrointestinal digestion, MS-grade trypsin, or both, were used to perform the comparisons. Two main points are illustrated: (i) the impact of the set-up of specific enzyme versus no specific enzyme use and (ii) the impact of a maximum of six PTMs allowed per peptide versus the standard of three. Prior knowledge of the composition of the raw proteins is an important asset for better identification of peptide sequences.
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Affiliation(s)
- Mouna Ambli
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Anne-Sophie Jenequin
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Rozenn Ravallec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Benoit Cudennec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Christophe Flahaut
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
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Sarohi V, Basak T. Perturbed post-translational modification (PTM) network atlas of collagen I during stent-induced neointima formation. J Proteomics 2023; 276:104842. [PMID: 36775122 DOI: 10.1016/j.jprot.2023.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/30/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Myocardial infarction (MI) leading to heart failure contributes to almost 85% of deaths associated with CVDs. MI results from plaque formation in the coronary artery which leads to a lack of oxygen and nutrients in the myocardium. To date, stenting is a widely used gold-standard technique to maintain the proper blood flow through coronary circulation in the myocardium. Bare metal stents (BMS) and drug-eluting stents (DES) are majorly used in implantation. However, BMS and DES both can induce neointima formation by depositing excessive collagens in the coronary arteries leading to restenosis. Identification and quantitative analysis of site-specific post-translational modifications (PTMs) of deposited COL1A1 from neointima ECM are not known. Applying our in-house workflow, we re-analyzed a previously published mass-spectrometry data set to comprehensively map site-specific prolyl-hydroxylation, lysyl hydroxylation, and O-glycosylation sites in COL1A1 from neointima ECM. Furthermore, we quantitated the occupancy level of 9 3-hydroxyproline (3-HyP) sites, 2 hydroxylysine sites, and glycosylation microheterogeneity on 6 lysine sites of COL1A1. Although the total level of COL1A1 was decreased in DES-induced neointima, the occupancy levels of 2 3-HyP sites (P872, and P881) and 2 HyK (K435 and K768) sites of COL1A1 were significantly (p < 0.05) elevated in DES-induced neointima compared to BMS-induced neointima. We also found O-glycosylation to be significantly elevated on 3 lysine sites (K573, K339, and K and K849) of COL1A1 in DES-induced neointima compared to BMS-induced neointima. Taken together, our first comprehensive PTM analysis of COL1A1 reflected significant site-specific alterations that may play a very important role in the ECM remodeling during stent-induced neointima formation in MI patients. SIGNIFICANCE: The knowledge about site-specific post-translational modifications (PTMs) of collagen 1 deposited in the neointima ECM during the post-stenting restenosis process is absent. Here for the first time, we report the altered levels of COL1A1 PTMs during metal stent and drug-eluting stent-induced neointima formation. Our study showcases a novel ECM remodeling through site-specific collagen PTMs during stent-induced restenosis.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering (SBB), Indian Institute of Technology (IIT)- Mandi, India; BioX Center, IIT-Mandi, Himachal Pradesh 175075, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering (SBB), Indian Institute of Technology (IIT)- Mandi, India; BioX Center, IIT-Mandi, Himachal Pradesh 175075, India.
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7
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Tassara E, Orel B, Ilan M, Cavallo D, Dodero A, Castellano M, Vicini S, Giovine M, Pozzolini M. Seasonal Molecular Difference in Fibrillar Collagen Extracts Derived from the Marine Sponge Chondrosia reniformis (Nardo, 1847) and Their Impact on Its Derived Biomaterials. Mar Drugs 2023; 21:md21040210. [PMID: 37103350 PMCID: PMC10141479 DOI: 10.3390/md21040210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Chondrosia reniformis (Nardo, 1847) is a marine sponge of high biotechnological interest both for its natural compound content and for its peculiar collagen, which is suitable for the production of innovative biomaterials in the form, for instance, of 2D membranes and hydrogels, exploitable in the fields of tissue engineering and regenerative medicine. In this study, the molecular and chemical-physical properties of fibrillar collagen extracted from specimens collected in different seasons are studied to evaluate the possible impact of sea temperature on them. Collagen fibrils were extracted from sponges harvested by the Sdot Yam coast (Israel) during winter (sea temperature: 17 °C) and during summer (sea temperature: 27 °C). The total AA composition of the two different collagens was evaluated, together with their thermal stability and glycosylation level. The results showed a lower lysyl-hydroxylation level, lower thermal stability, and lower protein glycosylation level in fibrils extracted from 17 °C animals compared to those from 27 °C animals, while no differences were noticed in the GAGs content. Membranes obtained with fibrils deriving from 17 °C samples showed a higher stiffness if compared to the 27 °C ones. The lower mechanical properties shown by 27 °C fibrils are suggestive of some unknown molecular changes in collagen fibrils, perhaps related to the creeping behavior of C. reniformis during summer. Overall, the differences in collagen properties gain relevance as they can guide the intended use of the biomaterial.
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Affiliation(s)
- Eleonora Tassara
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Boaz Orel
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Ilan
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dario Cavallo
- Department of Chemistry and Industrial Chemistry (DCCI), University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Andrea Dodero
- Department of Chemistry and Industrial Chemistry (DCCI), University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
- Adolphe Merkle Institute (AMI), University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Maila Castellano
- Department of Chemistry and Industrial Chemistry (DCCI), University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Silvia Vicini
- Department of Chemistry and Industrial Chemistry (DCCI), University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Marco Giovine
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
- Correspondence: (M.G.); (M.P.)
| | - Marina Pozzolini
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
- Correspondence: (M.G.); (M.P.)
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8
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Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Mol Cell Proteomics 2023; 22:100528. [PMID: 36918099 PMCID: PMC10152135 DOI: 10.1016/j.mcpro.2023.100528] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural scaffold of multicellular organisms. In addition to its structural role, the ECM conveys signals orchestrating cellular phenotypes. Alterations of ECM composition, abundance, structure, or mechanics, have been linked to diseases and disorders affecting all physiological systems, including fibrosis and cancer. Deciphering the protein composition of the ECM and how it changes in pathophysiological contexts is thus the first step toward understanding the roles of the ECM in health and disease and toward the development of therapeutic strategies to correct disease-causing ECM alterations. Potentially, the ECM also represents a vast, yet untapped reservoir of disease biomarkers. ECM proteins are characterized by unique biochemical properties that have hindered their study: they are large, heavily and uniquely post-translationally modified, and highly insoluble. Overcoming these challenges, we and others have devised mass-spectrometry-based proteomic approaches to define the ECM composition, or "matrisome", of tissues. This review provides a historical overview of ECM proteomics research and presents the latest advances that now allow the profiling of the ECM of healthy and diseased tissues. The second part highlights recent examples illustrating how ECM proteomics has emerged as a powerful discovery pipeline to identify prognostic cancer biomarkers. The third part discusses remaining challenges limiting our ability to translate findings to clinical application and proposes approaches to overcome them. Last, the review introduces readers to resources available to facilitate the interpretation of ECM proteomics datasets. The ECM was once thought to be impenetrable. MS-based proteomics has proven to be a powerful tool to decode the ECM. In light of the progress made over the past decade, there are reasons to believe that the in-depth exploration of the matrisome is within reach and that we may soon witness the first translational application of ECM proteomics.
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Affiliation(s)
- Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA.
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9
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Visser DR, Loo TS, Norris GE, Parry DAD. Potential implications of the glycosylation patterns in collagen α1(I) and α2(I) chains for fibril assembly and growth. J Struct Biol 2023; 215:107938. [PMID: 36641113 DOI: 10.1016/j.jsb.2023.107938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
O-Glycosylation of hydroxylysine (Hyl) in collagen occurs at an early stage of biosynthesis before the triple-helix has formed. This simple post-translational modification (PTM) of lysine by either a galactosyl or glucosylgalactosyl moiety is highly conserved in collagens and depends on the species, type of tissue and the collagen amino acid sequence. The structural/functional reason why only specific lysines are modified is poorly understood, and has led to increased efforts to map the sites of PTMs on collagen sequences from different species and to ascertain their potential role in vivo. To investigate this, we purified collagen type I (Col1) from the skins of four animals, then used mass spectrometry and proteomic techniques to identify lysines that were oxidised, galactosylated, glucosylgalactosylated, or glycated in its mature sequence. We found 18 out of the 38 lysines in collagen type Iα1, (Col1A1) and 7 of the 30 lysines in collagen type Iα2 (Col1A2) were glycosylated. Six of these modifications had not been reported before, and included a lysine involved in crosslinking collagen molecules. A Fourier transform analysis of the positions of the glycosylated hydroxylysines showed they display a regular axial distribution with the same d-period observed in collagen fibrils. The significance of this finding in terms of the assembly of collagen molecules into fibrils and of potential restrictions on the growth of the collagen fibrils is discussed.
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Affiliation(s)
- D R Visser
- School of Natural Sciences, Massey University, New Zealand
| | - T S Loo
- School of Natural Sciences, Massey University, New Zealand
| | - G E Norris
- School of Natural Sciences, Massey University, New Zealand.
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10
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Characterization of Galectin Fusion Proteins with Glycoprotein Affinity Columns and Binding Assays. Molecules 2023; 28:molecules28031054. [PMID: 36770718 PMCID: PMC9919667 DOI: 10.3390/molecules28031054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
Galectins are β-galactosyl-binding proteins that fulfill essential physiological functions. In the biotechnological field, galectins are versatile tools, such as in the development of biomaterial coatings or the early-stage diagnosis of cancer diseases. Recently, we introduced galectin-1 (Gal-1) and galectin-3 (Gal-3) as fusion proteins of a His6-tag, a SNAP-tag, and a fluorescent protein. We characterized their binding in ELISA-type assays and their application in cell-surface binding. In the present study, we have constructed further fusion proteins of galectins with fluorescent protein color code. The fusion proteins of Gal-1, Gal-3, and Gal-8 were purified by affinity chromatography. For this, we have prepared glycoprotein affinity resins based on asialofetuin (ASF) and fetuin and combined this in a two-step purification with Immobilized Metal Affinity chromatography (IMAC) to get pure and active galectins. Purified galectin fractions were analyzed by size-exclusion chromatography. The binding characteristics to ASF of solely His6-tagged galectins and galectin fusion proteins were compared. As an example, we demonstrate a 1.6-3-fold increase in binding efficiency for HSYGal-3 (His6-SNAP-yellow fluorescent protein-Gal-3) compared to the HGal-3 (His6-Gal-3). Our results reveal an apparent higher binding efficiency for galectin SNAP-tag fusion proteins compared to His6-tagged galectins, which are independent of the purification mode. This is also demonstrated by the binding of galectin fusion proteins to extracellular glycoconjugates laminin, fibronectin, and collagen IV. Our results indicate the probable involvement of the SNAP-tag in apparently higher binding signals, which we discuss in this study.
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11
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Staab-Weijnitz CA, Onursal C, Nambiar D, Vanacore R. Assessment of Collagen in Translational Models of Lung Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1413:213-244. [PMID: 37195533 DOI: 10.1007/978-3-031-26625-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The extracellular matrix (ECM) plays an important role in lung health and disease. Collagen is the main component of the lung ECM, widely used for the establishment of in vitro and organotypic models of lung disease, and as scaffold material of general interest for the field of lung bioengineering. Collagen also is the main readout for fibrotic lung disease, where collagen composition and molecular properties are drastically changed and ultimately result in dysfunctional "scarred" tissue. Because of the central role of collagen in lung disease, quantification, determination of molecular properties, and three-dimensional visualization of collagen is important for both development and characterization of translational models of lung research. In this chapter, we provide a comprehensive overview on the various methodologies currently available for quantification and characterization of collagen including their detection principles, advantages, and disadvantages.
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Affiliation(s)
- Claudia A Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany.
| | - Ceylan Onursal
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany
| | - Deepika Nambiar
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roberto Vanacore
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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12
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Sarohi V, Chakraborty S, Basak T. Exploring the cardiac ECM during fibrosis: A new era with next-gen proteomics. Front Mol Biosci 2022; 9:1030226. [PMID: 36483540 PMCID: PMC9722982 DOI: 10.3389/fmolb.2022.1030226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 10/24/2023] Open
Abstract
Extracellular matrix (ECM) plays a critical role in maintaining elasticity in cardiac tissues. Elasticity is required in the heart for properly pumping blood to the whole body. Dysregulated ECM remodeling causes fibrosis in the cardiac tissues. Cardiac fibrosis leads to stiffness in the heart tissues, resulting in heart failure. During cardiac fibrosis, ECM proteins get excessively deposited in the cardiac tissues. In the ECM, cardiac fibroblast proliferates into myofibroblast upon various kinds of stimulations. Fibroblast activation (myofibroblast) contributes majorly toward cardiac fibrosis. Other than cardiac fibroblasts, cardiomyocytes, epithelial/endothelial cells, and immune system cells can also contribute to cardiac fibrosis. Alteration in the expression of the ECM core and ECM-modifier proteins causes different types of cardiac fibrosis. These different components of ECM culminated into different pathways inducing transdifferentiation of cardiac fibroblast into myofibroblast. In this review, we summarize the role of different ECM components during cardiac fibrosis progression leading to heart failure. Furthermore, we highlight the importance of applying mass-spectrometry-based proteomics to understand the key changes occurring in the ECM during fibrotic progression. Next-gen proteomics studies will broaden the potential to identify key targets to combat cardiac fibrosis in order to achieve precise medicine-development in the future.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Sanchari Chakraborty
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
- BioX Center, Indian Institute of Technology (IIT)- Mandi, Himachal Pradesh, India
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13
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Ishikawa Y, Taga Y, Coste T, Tufa SF, Keene DR, Mizuno K, Tournier-Lasserve E, Gould DB. Lysyl hydroxylase 3-mediated post-translational modifications are required for proper biosynthesis of collagen α1α1α2(IV). J Biol Chem 2022; 298:102713. [PMID: 36403858 PMCID: PMC9761383 DOI: 10.1016/j.jbc.2022.102713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
Collagens are the most abundant proteins in the body and among the most biosynthetically complex. A molecular ensemble of over 20 endoplasmic reticulum resident proteins participates in collagen biosynthesis and contributes to heterogeneous post-translational modifications. Pathogenic variants in genes encoding collagens cause connective tissue disorders, including osteogenesis imperfecta, Ehlers-Danlos syndrome, and Gould syndrome (caused by mutations in COL4A1 and COL4A2), and pathogenic variants in genes encoding proteins required for collagen biosynthesis can cause similar but overlapping clinical phenotypes. Notably, pathogenic variants in lysyl hydroxylase 3 (LH3) cause a multisystem connective tissue disorder that exhibits pathophysiological features of collagen-related disorders. LH3 is a multifunctional collagen-modifying enzyme; however, its precise role(s) and substrate specificity during collagen biosynthesis has not been defined. To address this critical gap in knowledge, we generated LH3 KO cells and performed detailed quantitative and molecular analyses of collagen substrates. We found that LH3 deficiency severely impaired secretion of collagen α1α1α2(IV) but not collagens α1α1α2(I) or α1α1α1(III). Amino acid analysis revealed that LH3 is a selective LH for collagen α1α1α2(IV) but a general glucosyltransferase for collagens α1α1α2(IV), α1α1α2(I), and α1α1α1(III). Importantly, we identified rare variants that are predicted to be pathogenic in the gene encoding LH3 in two of 113 fetuses with intracranial hemorrhage-a cardinal feature of Gould syndrome. Collectively, our findings highlight a critical role of LH3 in α1α1α2(IV) biosynthesis and suggest that LH3 pathogenic variants might contribute to Gould syndrome.
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Affiliation(s)
- Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, California, USA.
| | - Yuki Taga
- Nippi Research Institute of Biomatrix, Ibaraki, Japan
| | - Thibault Coste
- Université Paris Cité, Inserm Neurodiderot, AP-HP Paris, France
| | - Sara F Tufa
- Research Department, Shriners Hospital for Children, Portland, Oregon, USA
| | - Douglas R Keene
- Research Department, Shriners Hospital for Children, Portland, Oregon, USA
| | | | | | - Douglas B Gould
- Department of Ophthalmology, University of California San Francisco, School of Medicine, California, USA; Department Anatomy, Cardiovascular Research Institute, Bakar Aging Research Institute, and Institute for Human Genetics, University of California, San Francisco, California, USA.
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14
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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15
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Sarohi V, Srivastava S, Basak T. Comprehensive Mapping and Dynamics of Site-Specific Prolyl-Hydroxylation, Lysyl-Hydroxylation and Lysyl O-Glycosylation of Collagens Deposited in ECM During Zebrafish Heart Regeneration. Front Mol Biosci 2022; 9:892763. [PMID: 35782869 PMCID: PMC9245515 DOI: 10.3389/fmolb.2022.892763] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Cardiac fibrosis-mediated heart failure (HF) is one of the major forms of end-stage cardiovascular diseases (CVDs). Cardiac fibrosis is an adaptive response of the myocardium upon any insult/injury. Excessive deposition of collagen molecules in the extracellular matrix (ECM) is the hallmark of fibrosis. This fibrotic response initially protects the myocardium from ventricular rupture. Although in mammals this fibrotic response progresses towards scar-tissue formation leading to HF, some fishes and urodeles have mastered the art of cardiac regeneration following injury-mediated fibrotic response. Zebrafish have a unique capability to regenerate the myocardium after post-amputation injury. Following post-amputation, the ECM of the zebrafish heart undergoes extensive remodeling and deposition of collagen. Being the most abundant protein of ECM, collagen plays important role in the assembly and cell-matrix interactions. However, the mechanism of ECM remodeling is not well understood. Collagen molecules undergo heavy post-translational modifications (PTMs) mainly hydroxylation of proline, lysine, and glycosylation of lysine during biosynthesis. The critical roles of these PTMs are emerging in several diseases, embryonic development, cell behavior regulation, and cell-matrix interactions. The site-specific identification of these collagen PTMs in zebrafish heart ECM is not known. As these highly modified peptides are not amenable to mass spectrometry (MS), the site-specific identification of these collagen PTMs is challenging. Here, we have implemented our in-house proteomics analytical pipeline to analyze two ECM proteomics datasets (PXD011627, PXD010092) of the zebrafish heart during regeneration (post-amputation). We report the first comprehensive site-specific collagen PTM map of zebrafish heart ECM. We have identified a total of 36 collagen chains (19 are reported for the first time here) harboring a total of 95 prolyl-3-hydroxylation, 108 hydroxylysine, 29 galactosyl-hydroxylysine, and 128 glucosylgalactosyl-hydroxylysine sites. Furthermore, we comprehensively map the three chains (COL1A1a, COL1A1b, and COL1A2) of collagen I, the most abundant protein in zebrafish heart ECM. We achieved more than 95% sequence coverage for all the three chains of collagen I. Our analysis also revealed the dynamics of prolyl-3-hydroxylation occupancy oscillations during heart regeneration at these sites. Moreover, quantitative site-specific analysis of lysine-O-glycosylation microheterogeneity during heart regeneration revealed a significant (p < 0.05) elevation of site-specific (K1017) glucosylgalactosyl-hydroxylysine on the col1a1a chain. Taken together, these site-specific PTM maps and the dynamic changes of site-specific collagen PTMs in ECM during heart regeneration will open up new avenues to decode ECM remodeling and may lay the foundation to tinker the cardiac regeneration process with new approaches.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
- BioX Center, IIT-Mandi, Mandi, India
| | - Shriya Srivastava
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
- BioX Center, IIT-Mandi, Mandi, India
- *Correspondence: Trayambak Basak,
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16
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Piñeiro-Llanes J, Rodriguez CD, Farhadi SA, Hudalla GA, Sarntinoranont M, Simmons CS. Experimental and Computational Models of Transport of Galectin-3 Through Glycosylated Matrix. Ann Biomed Eng 2022; 50:703-715. [PMID: 35352215 PMCID: PMC10621651 DOI: 10.1007/s10439-022-02949-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/09/2022] [Indexed: 11/01/2022]
Abstract
Altered extracellular matrix (ECM) production is a hallmark of many fibroproliferative diseases, including certain cancers. The high incidence of glycan-rich components within altered ECM makes the use of glycan-binding proteins such as Galectin-3 (G3) a promising therapeutic strategy. The complexity of ECM as a rich 3D network of proteins with varied glycosylation states makes it challenging to determine the retention of glycan-binding proteins in altered ECM environments. Computational models capable of predicting the transport of glycan-binding proteins in altered ECM can benefit the design and testing of such proteins and associated novel therapeutic strategies. However, such computational models require many kinetic parameters that cannot be estimated from traditional 2D pharmacokinetic assays. To validate transport properties of G3 in 3D ECM constructs, we developed a species transport model that includes diffusion and matrix-binding components to predict retention of G3 fusion proteins in glycan-rich ECM. By iteratively comparing our computational model to experimental results, we are able to determine a reasonable range of parameters for a robust computational model of G3 transport. We anticipate this overall approach to building a data-driven model is translatable to other ECM-targeting therapeutic strategies.
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Affiliation(s)
- Janny Piñeiro-Llanes
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Camille D Rodriguez
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Shaheen A Farhadi
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Malisa Sarntinoranont
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Chelsey S Simmons
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA.
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32611, USA.
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17
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Identification and In Silico Characterization of a Novel COLGALT2 Gene Variant in a Child with Mucosal Rectal Prolapse. Int J Mol Sci 2022; 23:ijms23073670. [PMID: 35409030 PMCID: PMC8999070 DOI: 10.3390/ijms23073670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Rectal prolapse is influenced by many factors including connective tissue dysfunction. Currently, there is no data about genetic contribution in the etiology of this disorder. In this study, we performed trio whole-exome sequencing in an 11-year-old girl with mucosal rectal prolapse and her parents and sibling. Genetic testing revealed a novel heterozygous missense variant c.1406G>T; p.G469V in exon 11 of the COLGALT2 gene encoding the GLT25 D2 enzyme. Sanger sequencing confirmed this variant only in the patient while the mother, father and sister showed a wild-type sequence. The pathogenicity of the novel variant was predicted using 10 different in silico tools that classified it as pathogenic. Further, in silico prediction, according to Phyre2, Project HOPE, I-Mutant3.0 and MutPred2 showed that the missense variant can decrease protein stability and cause alterations in the physical properties of amino acids resulting in structural and functional changes of the GLT25D2 protein. In conclusion, the present study identifies a previously unknown missense mutation in the COLGALT2 gene that encodes the enzyme involved in collagen glycosylation. The clinical features observed in the patient and the results of in silico analysis suggest that the new genetic variant can be pathogenic.
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18
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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19
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Glasgow JE, Byrnes JR, Barbee SD, Moreau JM, Rosenblum MD, Wells JA. Identifying and antagonizing the interactions between layilin and glycosylated collagens. Cell Chem Biol 2022; 29:597-604.e7. [PMID: 35104453 DOI: 10.1016/j.chembiol.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/19/2021] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Layilin is a small type I transmembrane receptor thought to bridge extracellular ligands with the cytoskeleton through its intracellular interactions with the scaffolding protein talin. Recent bulk- and single-cell RNA sequencing experiments have repeatedly found layilin to be highly upregulated in key T cell sub-populations in multiple disease states, suggesting its importance to the adaptive immune response. Despite this prevalence, little is known about layilin's precise role in mediating extracellular interactions or how these interactions can be modulated in disease states. Here we take advantage of layilin's dependence on calcium ions to discover its interactions with highly glycosylated type II, IV, V, and VI collagens. Toward exploring layilin's role in disease, we exploited the Ca2+ dependence in a differential phage display strategy to engineer species cross-reactive antibodies that block this interaction.
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Affiliation(s)
- Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Joshua M Moreau
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael D Rosenblum
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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20
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Staab-Weijnitz CA. Fighting the Fiber: Targeting Collagen in Lung Fibrosis. Am J Respir Cell Mol Biol 2021; 66:363-381. [PMID: 34861139 DOI: 10.1165/rcmb.2021-0342tr] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Organ fibrosis is characterized by epithelial injury and aberrant tissue repair, where activated effector cells, mostly fibroblasts and myofibroblasts, excessively deposit collagen into the extracellular matrix. Fibrosis frequently results in organ failure and has been estimated to contribute to at least one third of all global deaths. Also lung fibrosis, in particular idiopathic pulmonary fibrosis (IPF), is a fatal disease with rising incidence worldwide. As current treatment options targeting fibrogenesis are insufficient, there is an urgent need for novel therapeutic strategies. During the last decade, several studies have proposed to target intra- and extracellular components of the collagen biosynthesis, maturation, and degradation machinery. This includes intra- and extracellular targets directly acting on collagen gene products, but also such that anabolize essential building blocks of collagen, in particular glycine and proline biosynthetic enzymes. Collagen, however, is a ubiquitous molecule in the body and fulfils essential functions as a macromolecular scaffold, growth factor reservoir, and receptor binding site in virtually every tissue. This review summarizes recent advances and future directions in this field. Evidence for the proposed therapeutic targets and where they currently stand in terms of clinical drug development for treatment of fibrotic disease is provided. The drug targets are furthermore discussed in light of (1) specificity for collagen biosynthesis, maturation and degradation, and (2) specificity for disease-associated collagen. As therapeutic success and safety of these drugs may largely depend on targeted delivery, different strategies for specific delivery to the main effector cells and to the extracellular matrix are discussed.
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Affiliation(s)
- Claudia A Staab-Weijnitz
- Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Gesundheit und Umwelt, 9150, Comprehensive Pneumology Center/Institute of Lung Biology and Disease, Member of the German Center of Lung Research (DZL), München, Germany;
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21
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The role of basement membranes in cardiac biology and disease. Biosci Rep 2021; 41:229516. [PMID: 34382650 PMCID: PMC8390786 DOI: 10.1042/bsr20204185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Basement membranes are highly specialised extracellular matrix structures that within the heart underlie endothelial cells and surround cardiomyocytes and vascular smooth muscle cells. They generate a dynamic and structurally supportive environment throughout cardiac development and maturation by providing physical anchorage to the underlying interstitium, structural support to the tissue, and by influencing cell behaviour and signalling. While this provides a strong link between basement membrane dysfunction and cardiac disease, the role of the basement membrane in cardiac biology remains under-researched and our understanding regarding the mechanistic interplay between basement membrane defects and their morphological and functional consequences remain important knowledge-gaps. In this review we bring together emerging understanding of basement membrane defects within the heart including in common cardiovascular pathologies such as contractile dysfunction and highlight some key questions that are now ready to be addressed.
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22
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Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR. Sequence-dependent mechanics of collagen reflect its structural and functional organization. Biophys J 2021; 120:4013-4028. [PMID: 34390685 DOI: 10.1016/j.bpj.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 01/06/2023] Open
Abstract
Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semiflexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain.
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Affiliation(s)
- Alaa Al-Shaer
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Aaron Lyons
- Department of Physics, Burnaby, British Columbia, Canada
| | - Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, California
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee; Department of Cell and Developmental Biology, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee
| | - Nancy R Forde
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada; Department of Physics, Burnaby, British Columbia, Canada; Department of Chemistry, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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23
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Han S, Zhao K, Cai S, Jiang M, Huang X, Chen S, Li S, Zhao M, Duan JA, Liu R. Discovery of peptide biomarkers by label-free peptidomics for discrimination of horn gelatin and hide gelatin from Cervus nippon Temminck. Food Chem 2021; 363:130347. [PMID: 34147893 DOI: 10.1016/j.foodchem.2021.130347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/20/2022]
Abstract
Gelatin and gelatin-based derivatives have been attracting worldwide attention as health-food ingredients. Deer horn gelatin (DCG), a well-known and expensive gelatin food in Asia, has suffered adulterants by adding deer-hide gelatin (DHG) in it. However, robust and effective methods which could differentiate DCG from DHG are still unavailable. This study is committed to discover peptide biomarkers to distinguish DCG from DHG using label-free peptidomics by nanoLC-MS/MS. Multivariate statistical analysis combined with glycosylation sites analysis of peptides was applied to visualize the difference between DCG and DHG. As a result, four peptide biomarkers for distinguishing DCG and DHG were confirmed and validated by UPLC-MS/MS and MRM mode, which was also used to calculate adulteration percentage in commercial samples. The presented strategy may be also particularly helpful in the in-depth authentication of food gelatins from different tissues of the same species.
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Affiliation(s)
- Shuying Han
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Kexuan Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Shuo Cai
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Mengtong Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Xiaozheng Huang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Shengjun Chen
- Jiangyin Tianjiang Pharmaceutical Co. LTD., Jiangyin 214434, PR China; Key Technology Laboratory for Preparation and Quality Control of Traditional Chinese Medicine Granules in Jiangsu. Jiangyin 214434, PR China
| | - Song Li
- Jiangyin Tianjiang Pharmaceutical Co. LTD., Jiangyin 214434, PR China; Key Technology Laboratory for Preparation and Quality Control of Traditional Chinese Medicine Granules in Jiangsu. Jiangyin 214434, PR China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Rui Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, PR China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
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24
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Li L, Galichon P, Xiao X, Figueroa-Ramirez AC, Tamayo D, Lee JJK, Kalocsay M, Gonzalez-Sanchez D, Chancay MS, McCracken KW, Lee NN, Ichimura T, Mori Y, Valerius MT, Wilflingseder J, Lemos DR, Edelman ER, Bonventre JV. Orphan nuclear receptor COUP-TFII enhances myofibroblast glycolysis leading to kidney fibrosis. EMBO Rep 2021; 22:e51169. [PMID: 34031962 DOI: 10.15252/embr.202051169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/28/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
Recent studies demonstrate that metabolic disturbance, such as augmented glycolysis, contributes to fibrosis. The molecular regulation of this metabolic perturbation in fibrosis, however, has been elusive. COUP-TFII (also known as NR2F2) is an important regulator of glucose and lipid metabolism. Its contribution to organ fibrosis is undefined. Here, we found increased COUP-TFII expression in myofibroblasts in human fibrotic kidneys, lungs, kidney organoids, and mouse kidneys after injury. Genetic ablation of COUP-TFII in mice resulted in attenuation of injury-induced kidney fibrosis. A non-biased proteomic study revealed the suppression of fatty acid oxidation and the enhancement of glycolysis pathways in COUP-TFII overexpressing fibroblasts. Overexpression of COUP-TFII in fibroblasts also induced production of alpha-smooth muscle actin (αSMA) and collagen 1. Knockout of COUP-TFII decreased glycolysis and collagen 1 levels in fibroblasts. Chip-qPCR revealed the binding of COUP-TFII on the promoter of PGC1α. Overexpression of COUP-TFII reduced the cellular level of PGC1α. Targeting COUP-TFII serves as a novel treatment approach for mitigating fibrosis in chronic kidney disease and potentially fibrosis in other organs.
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Affiliation(s)
- Li Li
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre Galichon
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiaoyan Xiao
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Diana Tamayo
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jake J-K Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Maria S Chancay
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kyle W McCracken
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nathan N Lee
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Takaharu Ichimura
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yutaro Mori
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - M Todd Valerius
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | | | - Dario R Lemos
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elazer R Edelman
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph V Bonventre
- Division of Renal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
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25
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Jud MC, Lowry J, Padilla T, Clifford E, Yang Y, Fennell F, Miller AK, Hamill D, Harvey AM, Avila-Zavala M, Shao H, Nguyen Tran N, Bao Z, Bowerman B. A genetic screen for temperature-sensitive morphogenesis-defective Caenorhabditis elegans mutants. G3-GENES GENOMES GENETICS 2021; 11:6169531. [PMID: 33713117 PMCID: PMC8133775 DOI: 10.1093/g3journal/jkab026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022]
Abstract
Morphogenesis involves coordinated cell migrations and cell shape changes that generate tissues and organs, and organize the body plan. Cell adhesion and the cytoskeleton are important for executing morphogenesis, but their regulation remains poorly understood. As genes required for embryonic morphogenesis may have earlier roles in development, temperature-sensitive embryonic-lethal mutations are useful tools for investigating this process. From a collection of ∼200 such Caenorhabditis elegans mutants, we have identified 17 that have highly penetrant embryonic morphogenesis defects after upshifts from the permissive to the restrictive temperature, just prior to the cell shape changes that mediate elongation of the ovoid embryo into a vermiform larva. Using whole genome sequencing, we identified the causal mutations in seven affected genes. These include three genes that have roles in producing the extracellular matrix, which is known to affect the morphogenesis of epithelial tissues in multicellular organisms: the rib-1 and rib-2 genes encode glycosyltransferases, and the emb-9 gene encodes a collagen subunit. We also used live imaging to characterize epidermal cell shape dynamics in one mutant, or1219ts, and observed cell elongation defects during dorsal intercalation and ventral enclosure that may be responsible for the body elongation defects. These results indicate that our screen has identified factors that influence morphogenesis and provides a platform for advancing our understanding of this fundamental biological process.
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Affiliation(s)
- Molly C Jud
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Josh Lowry
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Thalia Padilla
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Erin Clifford
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Yuqi Yang
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Francesca Fennell
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Alexander K Miller
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Danielle Hamill
- Department of Zoology, Ohio Wesleyan University, Delaware, OH, 43015, USA
| | - Austin M Harvey
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Martha Avila-Zavala
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
| | - Hong Shao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Nhan Nguyen Tran
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Bruce Bowerman
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97402, USA
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26
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Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis. Int J Mol Sci 2021; 22:ijms22083896. [PMID: 33918807 PMCID: PMC8069486 DOI: 10.3390/ijms22083896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Prolyl 3-hydroxylase 2 (P3H2) catalyzes the post-translational formation of 3-hydroxyproline on collagens, mainly on type IV. Its activity has never been directly associated to angiogenesis. Here, we identified P3H2 gene through a deep-sequencing transcriptome analysis of human umbilical vein endothelial cells (HUVECs) stimulated with vascular endothelial growth factor A (VEGF-A). Differently from many previous studies we carried out the stimulation not on starved HUVECs, but on cells grown to maintain the best condition for their in vitro survival and propagation. We showed that P3H2 is induced by VEGF-A in two primary human endothelial cell lines and that its transcription is modulated by VEGF-A/VEGF receptor 2 (VEGFR-2) signaling pathway through p38 mitogen-activated protein kinase (MAPK). Then, we demonstrated that P3H2, through its activity on type IV Collagen, is essential for angiogenesis properties of endothelial cells in vitro by performing experiments of gain- and loss-of-function. Immunofluorescence studies showed that the overexpression of P3H2 induced a more condensed status of Collagen IV, accompanied by an alignment of the cells along the Collagen IV bundles, so towards an evident pro-angiogenic status. Finally, we found that P3H2 knockdown prevents pathological angiogenesis in vivo, in the model of laser-induced choroid neovascularization. Together these findings reveal that P3H2 is a new molecular player involved in new vessels formation and could be considered as a potential target for anti-angiogenesis therapy.
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27
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Collagen hydroxylysine glycosylation: non-conventional substrates for atypical glycosyltransferase enzymes. Biochem Soc Trans 2021; 49:855-866. [PMID: 33704379 DOI: 10.1042/bst20200767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/22/2022]
Abstract
Collagen is a major constituent of the extracellular matrix (ECM) that confers fundamental mechanical properties to tissues. To allow proper folding in triple-helices and organization in quaternary super-structures, collagen molecules require essential post-translational modifications (PTMs), including hydroxylation of proline and lysine residues, and subsequent attachment of glycan moieties (galactose and glucose) to specific hydroxylysine residues on procollagen alpha chains. The resulting galactosyl-hydroxylysine (Gal-Hyl) and less abundant glucosyl-galactosyl-hydroxylysine (Glc-Gal-Hyl) are amongst the simplest glycosylation patterns found in nature and are essential for collagen and ECM homeostasis. These collagen PTMs depend on the activity of specialized glycosyltransferase enzymes. Although their biochemical reactions have been widely studied, several key biological questions about the possible functions of these essential PTMs are still missing. In addition, the lack of three-dimensional structures of collagen glycosyltransferase enzymes hinders our understanding of the catalytic mechanisms producing this modification, as well as the impact of genetic mutations causing severe connective tissue pathologies. In this mini-review, we summarize the current knowledge on the biochemical features of the enzymes involved in the production of collagen glycosylations and the current state-of-the-art methods for the identification and characterization of this important PTM.
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28
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Wu Y, Cao Y, Xu K, Zhu Y, Qiao Y, Wu Y, Chen J, Li C, Zeng R, Ge G. Dynamically remodeled hepatic extracellular matrix predicts prognosis of early-stage cirrhosis. Cell Death Dis 2021; 12:163. [PMID: 33558482 PMCID: PMC7870969 DOI: 10.1038/s41419-021-03443-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/17/2022]
Abstract
Liver cirrhosis remains major health problem. Despite the progress in diagnosis of asymptomatic early-stage cirrhosis, prognostic biomarkers are needed to identify cirrhotic patients at high risk developing advanced stage disease. Liver cirrhosis is the result of deregulated wound healing and is featured by aberrant extracellular matrix (ECM) remodeling. However, it is not comprehensively understood how ECM is dynamically remodeled in the progressive development of liver cirrhosis. It is yet unknown whether ECM signature is of predictive value in determining prognosis of early-stage liver cirrhosis. In this study, we systematically analyzed proteomics of decellularized hepatic matrix and identified four unique clusters of ECM proteins at tissue damage/inflammation, transitional ECM remodeling or fibrogenesis stage in carbon tetrachloride-induced liver fibrosis. In particular, basement membrane (BM) was heavily deposited at the fibrogenesis stage. BM component minor type IV collagen α5 chain expression was increased in activated hepatic stellate cells. Knockout of minor type IV collagen α5 chain ameliorated liver fibrosis by hampering hepatic stellate cell activation and promoting hepatocyte proliferation. ECM signatures were differentially enriched in the biopsies of good and poor prognosis early-stage liver cirrhosis patients. Clusters of ECM proteins responsible for homeostatic remodeling and tissue fibrogenesis, as well as basement membrane signature were significantly associated with disease progression and patient survival. In particular, a 14-gene signature consisting of basement membrane proteins is potent in predicting disease progression and patient survival. Thus, the ECM signatures are potential prognostic biomarkers to identify cirrhotic patients at high risk developing advanced stage disease.
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Affiliation(s)
- Yuexin Wu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuyan Cao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Keren Xu
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yue Zhu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuemei Qiao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanjun Wu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Jianfeng Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China
| | - Chen Li
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
- School of Life Science and Technology, Shanghai Tech University, 201210, Shanghai, China.
| | - Gaoxiang Ge
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
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29
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Ouni E, Ruys SPD, Dolmans MM, Herinckx G, Vertommen D, Amorim CA. Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization. Int J Mol Sci 2020; 21:E9141. [PMID: 33266304 PMCID: PMC7730167 DOI: 10.3390/ijms21239141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/29/2022] Open
Abstract
Currently, the extracellular matrix (ECM) is considered a pivotal complex meshwork of macromolecules playing a plethora of biomolecular functions in health and disease beyond its commonly known mechanical role. Only by unraveling its composition can we leverage related tissue engineering and pharmacological efforts. Nevertheless, its unbiased proteomic identification still encounters some limitations mainly due to partial ECM enrichment by precipitation, sequential fractionation using unfriendly-mass spectrometry (MS) detergents, and resuspension with harsh reagents that need to be entirely removed prior to analysis. These methods can be technically challenging and labor-intensive, which affects the reproducibility of ECM identification and induces protein loss. Here, we present a simple new method applicable to tissue fragments of 10 mg and more. The technique has been validated on human ovarian tissue and involves a standardized procedure for sample processing with an MS-compatible detergent and combined centrifugation. This two-step protocol eliminates the need for laborious sample clarification and divides our samples into 2 fractions, soluble and insoluble, successively enriched with matrisome-associated (ECM-interacting) and core matrisome (structural ECM) proteins.
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Affiliation(s)
- Emna Ouni
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium; (E.O.); (M.-M.D.)
| | - Sébastien Pyr dit Ruys
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (S.P.d.R.); (G.H.); (D.V.)
| | - Marie-Madeleine Dolmans
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium; (E.O.); (M.-M.D.)
- Gynecology and Andrology Department, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Gaëtan Herinckx
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (S.P.d.R.); (G.H.); (D.V.)
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (S.P.d.R.); (G.H.); (D.V.)
| | - Christiani A. Amorim
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium; (E.O.); (M.-M.D.)
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30
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Gardelli C, Russo L, Cipolla L, Moro M, Andriani F, Rondinone O, Nicotra F, Sozzi G, Bertolini G, Roz L. Differential glycosylation of collagen modulates lung cancer stem cell subsets through β1 integrin-mediated interactions. Cancer Sci 2020; 112:217-230. [PMID: 33068069 PMCID: PMC7780011 DOI: 10.1111/cas.14700] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
In lung cancer, CD133+ cells represent the subset of cancer stem cells (CSC) able to sustain tumor growth and metastatic dissemination. CSC function is tightly regulated by specialized niches composed of both stromal cells and extracellular matrix (ECM) proteins, mainly represented by collagen. The relevance of collagen glycosylation, a fundamental post-translational modification controlling several biological processes, in regulating tumor cell phenotype remains, however, largely unexplored. To investigate the bioactive effects of differential ECM glycosylation on lung cancer cells, we prepared collagen films functionalized with glucose (Glc-collagen) and galactose (Gal-collagen) exploiting a neoglycosylation approach based on a reductive amination of maltose and lactose with the amino residues of collagen lysines. We demonstrate that culturing of tumor cells on collagen determines a glycosylation-dependent positive selection of CSC and triggers their expansion/generation. The functional relevance of CD133+ CSC increase was validated in vivo, proving an augmented tumorigenic and metastatic potential. High expression of integrin β1 in its active form is associated with an increased proficiency of tumor cells to sense signaling from glycosylated matrices (glyco-collagen) and to acquire stemness features. Accordingly, inhibition of integrin β1 in tumor cells prevents CSC enrichment, suggesting that binding of integrin β1 to Glc-collagen subtends CSC expansion/generation. We provide evidence suggesting that collagen glycosylation could play an essential role in modulating the creation of a niche favorable for the generation and selection/survival of lung CSC. Interfering with this crosstalk may represent an innovative therapeutic strategy for lung cancer treatment.
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Affiliation(s)
- Cecilia Gardelli
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Laura Russo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Laura Cipolla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Moro
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Andriani
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ornella Rondinone
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesco Nicotra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Bertolini
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Roz
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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31
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Salo AM, Myllyharju J. Prolyl and lysyl hydroxylases in collagen synthesis. Exp Dermatol 2020; 30:38-49. [PMID: 32969070 DOI: 10.1111/exd.14197] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Collagens are the most abundant proteins in the extracellular matrix. They provide a framework to build organs and tissues and give structural support to make them resistant to mechanical load and forces. Several intra- and extracellular modifications are needed to make functional collagen molecules, intracellular post-translational modifications of proline and lysine residues having key roles in this. In this article, we provide a review on the enzymes responsible for the proline and lysine modifications, that is collagen prolyl 4-hydroxylases, 3-hydroxylases and lysyl hydroxylases, and discuss their biological functions and involvement in diseases.
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Affiliation(s)
- Antti M Salo
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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32
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Mutgan AC, Jandl K, Kwapiszewska G. Endothelial Basement Membrane Components and Their Products, Matrikines: Active Drivers of Pulmonary Hypertension? Cells 2020; 9:cells9092029. [PMID: 32899187 PMCID: PMC7563239 DOI: 10.3390/cells9092029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a vascular disease that is characterized by elevated pulmonary arterial pressure (PAP) due to progressive vascular remodeling. Extracellular matrix (ECM) deposition in pulmonary arteries (PA) is one of the key features of vascular remodeling. Emerging evidence indicates that the basement membrane (BM), a specialized cluster of ECM proteins underlying the endothelium, may be actively involved in the progression of vascular remodeling. The BM and its steady turnover are pivotal for maintaining appropriate vascular functions. However, the pathologically elevated turnover of BM components leads to an increased release of biologically active short fragments, which are called matrikines. Both BM components and their matrikines can interfere with pivotal biological processes, such as survival, proliferation, adhesion, and migration and thus may actively contribute to endothelial dysfunction. Therefore, in this review, we summarize the emerging role of the BM and its matrikines on the vascular endothelium and further discuss its implications on lung vascular remodeling in pulmonary hypertension.
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Affiliation(s)
- Ayse Ceren Mutgan
- Otto Loewi Research Center, Division of Physiology, Medical University of Graz, 8010 Graz, Austria;
| | - Katharina Jandl
- Ludwig Boltzmann Institute for Lung Vascular Research, 8010 Graz, Austria;
- Otto Loewi Research Center, Division of Pharmacology, Medical University of Graz, 8010 Graz, Austria
| | - Grazyna Kwapiszewska
- Otto Loewi Research Center, Division of Physiology, Medical University of Graz, 8010 Graz, Austria;
- Ludwig Boltzmann Institute for Lung Vascular Research, 8010 Graz, Austria;
- Correspondence:
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33
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van Huizen NA, Ijzermans JNM, Burgers PC, Luider TM. Collagen analysis with mass spectrometry. MASS SPECTROMETRY REVIEWS 2020; 39:309-335. [PMID: 31498911 DOI: 10.1002/mas.21600] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.
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Affiliation(s)
- Nick A van Huizen
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Peter C Burgers
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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34
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Taga Y, Kusubata M, Mizuno K. Quantitative Analysis of the Positional Distribution of Hydroxyproline in Collagenous Gly-Xaa-Yaa Sequences by LC-MS with Partial Acid Hydrolysis and Precolumn Derivatization. Anal Chem 2020; 92:8427-8434. [PMID: 32437599 DOI: 10.1021/acs.analchem.0c01098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Collagen is extensively modified by various enzymes, including prolyl hydroxylases. Pro residues at the Yaa position of repeating Gly-Xaa-Yaa amino acid sequences are mostly hydroxylated to 4-hydroxyproline (4Hyp), which is essential for the thermal stability of collagen triple helix. In contrast, Pro residues at the Xaa position are rarely modified to 3Hyp and 4Hyp, the biological function of which is poorly understood. Overall estimation of prolyl hydroxylation with discrimination of the position (Xaa or Yaa) and hydroxylation type (4Hyp or 3Hyp) has been difficult to perform using traditional methods. In the present study, we developed a novel position-specific analytical method featuring LC-MS detection of collagenous Gly-containing dipeptides, including Gly-Pro, Pro-Gly, Gly-4Hyp, Gly-3Hyp, and 4Hyp-Gly, after partial acid hydrolysis and precolumn derivatization using 3-aminopyridyl-N-hydroxysuccinimidyl carbamate (APDS). We performed acid hydrolysis at 55 °C with HCl/trifluoroacetic acid/water (2:1:1, v/v) to avoid peptide inversion and imbalanced peptide generation observed for collagenous model peptides. The positional distribution of Pro, 4Hyp, and 3Hyp can be calculated from the relative concentrations of the APDS-derivatized dipeptides, and in combination with amino acid analysis, we can determine their absolute contents at the Xaa and Yaa positions. Bovine type I, III, and V collagens were analyzed by the established method, and the amount of 4Hyp was higher than that of 3Hyp at the Xaa position in type I and III collagens. In addition, we clearly showed that collagen extracted from earthworm cuticles has an extremely high content of Xaa position 4Hyp, reaching over 10% of the total amino acids.
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Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Masashi Kusubata
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
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35
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Schiller JL, Fogle MM, Bussey O, Kissner WJ, Hill DB, Lai SK. Antibody-mediated trapping in biological hydrogels is governed by sugar-sugar hydrogen bonds. Acta Biomater 2020; 107:91-101. [PMID: 32147470 DOI: 10.1016/j.actbio.2020.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/07/2020] [Accepted: 03/02/2020] [Indexed: 02/08/2023]
Abstract
N-glycans on IgG and IgM antibodies (Ab) facilitate Ab-mediated crosslinking of viruses and nanoparticles to the major structural elements of mucus and basement membranes. Nevertheless, the chemical moieties in these biological hydrogel matrices to which Ab can bind remain poorly understood. To gain insights into the chemistries that support Ab-matrix interactions, we systematically evaluated IgG- and IgM-mediated trapping of nanoparticles in different polysaccharide-based biogels with unique chemical features. In agarose, composed of alternating d-galactose and 3,6-anhydro-l-galactopyranose (i.e. hydroxyl groups only), anti-PEG IgM but not anti-PEG IgG trapped PEGylated nanoparticles. In alginate, comprised of homopolymeric blocks of mannuronate and guluronate (i.e. both hydroxyl and carboxyl groups), both IgG and IgM trapped PEGylated nanoparticles. In contrast, chitosan, comprised primarily of glucosamine (i.e. both hydroxyl and primary amine groups), did not facilitate either IgG- or IgM-mediated trapping. IgG-mediated trapping in alginate was abrogated upon removal of IgG N-glycans, whereas IgM-mediated trapping was eliminated in agarose but not alginate upon desialylation. These results led us to propose a model in which hydrogen bonding between carboxyl and hydroxyl groups of glycans on both Ab and matrix facilitates Ab-mediated trapping of pathogens in biogels. Our work here offers a blueprint for designing de novo hydrogels that could harness Ab-matrix interactions for various biomedical and biological applications. STATEMENT OF SIGNIFICANCE: Here, we interrogated the molecular mechanism of antibody-mediated trapping to address what are the chemical moieties on biogels that are essential for facilitating trapping in biogels. We systematically evaluated the potencies of IgG and IgM to trap nanoparticles in different polysaccharide-based biogels with unique and highly defined chemical moieties: hydroxyl groups (agarose), amine groups (chitosan), and carboxyl groups (alginate). We discovered that only hydroxyl/carboxyl hydrogen bonds (and stronger) are sufficiently strong enough to facilitate antibody-mediated trapping; weaker hydroxyl/hydroxyl bonds or hydroxyl/amine bonds fail to adequately slow particles. Our findings presents the first blueprint for how to engineer de novo biogels that are capable of harnessing antibodies to immobilize foreign entities in the biogels, for applications ranging from infectious disease to contraception to purification processes.
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36
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Seifried BM, Qi W, Yang YJ, Mai DJ, Puryear WB, Runstadler JA, Chen G, Olsen BD. Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry. Bioconjug Chem 2020; 31:554-566. [PMID: 32078297 DOI: 10.1021/acs.bioconjchem.9b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.
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Affiliation(s)
- Brian M Seifried
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenjing Qi
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Macromolecular Science, Fudan University, Shanghai 200000, China
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37
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Wu Y, Ge G. Complexity of type IV collagens: from network assembly to function. Biol Chem 2019; 400:565-574. [PMID: 30864416 DOI: 10.1515/hsz-2018-0317] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/02/2018] [Indexed: 02/06/2023]
Abstract
Collagens form complex networks in the extracellular space that provide structural support and signaling cues to cells. Network-forming type IV collagens are the key structural components of basement membranes. In this review, we discuss how the complexity of type IV collagen networks is established, focusing on collagen α chain selection in type IV collagen protomer and network formation; covalent crosslinking in type IV collagen network stabilization; and the differences between solid-state type IV collagen in the extracellular matrix and soluble type IV collagen fragments. We further discuss how complex type IV collagen networks exert their physiological and pathological functions through cell surface integrin and nonintegrin receptors.
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Affiliation(s)
- Yuexin Wu
- State Key Laboratory of Cell Biology, CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Gaoxiang Ge
- State Key Laboratory of Cell Biology, CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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38
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Abstract
Fibrosis is the abnormal deposition of extracellular matrix, which can lead to organ dysfunction, morbidity, and death. The disease burden caused by fibrosis is substantial, and there are currently no therapies that can prevent or reverse fibrosis. Metabolic alterations are increasingly recognized as an important pathogenic process that underlies fibrosis across many organ types. As a result, metabolically targeted therapies could become important strategies for fibrosis reduction. Indeed, some of the pathways targeted by antifibrotic drugs in development - such as the activation of transforming growth factor-β and the deposition of extracellular matrix - have metabolic implications. This Review summarizes the evidence to date and describes novel opportunities for the discovery and development of drugs for metabolic reprogramming, their associated challenges, and their utility in reducing fibrosis. Fibrotic therapies are potentially relevant to numerous common diseases such as cirrhosis, non-alcoholic steatohepatitis, chronic renal disease, heart failure, diabetes, idiopathic pulmonary fibrosis, and scleroderma.
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39
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Chiusa M, Hu W, Liao HJ, Su Y, Borza CM, de Caestecker MP, Skrypnyk NI, Fogo AB, Pedchenko V, Li X, Zhang MZ, Hudson BG, Basak T, Vanacore RM, Zent R, Pozzi A. The Extracellular Matrix Receptor Discoidin Domain Receptor 1 Regulates Collagen Transcription by Translocating to the Nucleus. J Am Soc Nephrol 2019; 30:1605-1624. [PMID: 31383731 PMCID: PMC6727269 DOI: 10.1681/asn.2018111160] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The discoidin domain receptor 1 (DDR1) is activated by collagens, upregulated in injured and fibrotic kidneys, and contributes to fibrosis by regulating extracellular matrix production, but how DDR1 controls fibrosis is poorly understood. DDR1 is a receptor tyrosine kinase (RTK). RTKs can translocate to the nucleus via a nuclear localization sequence (NLS) present on the receptor itself or a ligand it is bound to. In the nucleus, RTKs regulate gene expression by binding chromatin directly or by interacting with transcription factors. METHODS To determine whether DDR1 translocates to the nucleus and whether this event is mediated by collagen-induced DDR1 activation, we generated renal cells expressing wild-type or mutant forms of DDR1 no longer able to bind collagen. Then, we determined the location of the DDR1 upon collagen stimulation. Using both biochemical assays and immunofluorescence, we analyzed the steps involved in DDR1 nuclear translocation. RESULTS We show that although DDR1 and its natural ligand, collagen, lack an NLS, DDR1 is present in the nucleus of injured human and mouse kidney proximal tubules. We show that DDR1 nuclear translocation requires collagen-mediated receptor activation and interaction of DDR1 with SEC61B, a component of the Sec61 translocon, and nonmuscle myosin IIA and β-actin. Once in the nucleus, DDR1 binds to chromatin to increase the transcription of collagen IV, a major collagen upregulated in fibrosis. CONCLUSIONS These findings reveal a novel mechanism whereby activated DDR1 translates to the nucleus to regulate synthesis of profibrotic molecules.
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Affiliation(s)
- Manuel Chiusa
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Wen Hu
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Hong-Jun Liao
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Yan Su
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Corina M Borza
- Division of Nephrology and Hypertension, Department of Medicine, and
| | | | | | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Vadim Pedchenko
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Xiyue Li
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Ming-Zhi Zhang
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Billy G Hudson
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Trayambak Basak
- Division of Nephrology and Hypertension, Department of Medicine, and
| | | | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, and
- Department of Veterans Affairs, Nashville, Tennessee
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, and
- Department of Veterans Affairs, Nashville, Tennessee
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40
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Exploring the extracellular matrix in health and disease using proteomics. Essays Biochem 2019; 63:417-432. [DOI: 10.1042/ebc20190001] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins that constitutes the scaffold of multicellular organisms. In addition to providing architectural and mechanical support to the surrounding cells, it conveys biochemical signals that regulate cellular processes including proliferation and survival, fate determination, and cell migration. Defects in ECM protein assembly, decreased ECM protein production or, on the contrary, excessive ECM accumulation, have been linked to many pathologies including cardiovascular and skeletal diseases, cancers, and fibrosis. The ECM thus represents a potential reservoir of prognostic biomarkers and therapeutic targets. However, our understanding of the global protein composition of the ECM and how it changes during pathological processes has remained limited until recently.
In this mini-review, we provide an overview of the latest methodological advances in sample preparation and mass spectrometry-based proteomics that have permitted the profiling of the ECM of now dozens of normal and diseased tissues, including tumors and fibrotic lesions.
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41
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Geister KA, Lopez-Jimenez AJ, Houghtaling S, Ho TH, Vanacore R, Beier DR. Loss of function of Colgalt1 disrupts collagen post-translational modification and causes musculoskeletal defects. Dis Model Mech 2019; 12:dmm.037176. [PMID: 31101663 PMCID: PMC6602307 DOI: 10.1242/dmm.037176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
In a screen for organogenesis defects in N-ethyl-N-nitrosourea (ENU)-induced mutant mice, we discovered a line carrying a mutation in Colgalt1 [collagen beta(1-O)galactosyltransferase type 1], which is required for proper galactosylation of hydroxylysine residues in a number of collagens. Colgalt1 mutant embryos have not been previously characterized; here, we show that they exhibit skeletal and muscular defects. Analysis of mutant-derived embryonic fibroblasts reveals that COLGALT1 acts on collagen IV and VI, and, while collagen VI appears stable and its secretion is not affected, collagen IV accumulates inside of cells and within the extracellular matrix, possibly due to instability and increased degradation. We also generated mutant zebrafish that do not express the duplicated orthologs of mammalian Colgalt1. The double-homozygote mutants have muscle defects; they are viable through the larvae stage but do not survive to 10 days post-fertilization. We hypothesize that the Colgalt1 mutant could serve as a model of a human connective tissue disorder and/or congenital muscular dystrophy or myopathy. Summary: The authors characterized a novel mouse mutant that has a defect in collagen glycosylation, which appears to affect muscle development. There is very little functional characterization of the affected gene, but this study provides analysis of its embryonic phenotype and the biochemistry of the null mutant, as well as the phenotype of null-mutant zebrafish.
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Affiliation(s)
- Krista A Geister
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA.,Department of Pediatrics, Division of Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alberto Jose Lopez-Jimenez
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Scott Houghtaling
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Tzu-Hua Ho
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Roberto Vanacore
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA .,Department of Pediatrics, Division of Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
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42
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Maity PP, Dutta D, Ganguly S, Kapat K, Dixit K, Chowdhury AR, Samanta R, Das NC, Datta P, Das AK, Dhara S. Isolation and mass spectrometry based hydroxyproline mapping of type II collagen derived from Capra hircus ear cartilage. Commun Biol 2019; 2:146. [PMID: 31044171 PMCID: PMC6488623 DOI: 10.1038/s42003-019-0394-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/18/2019] [Indexed: 11/19/2022] Open
Abstract
Collagen II (COLII), the most abundant protein in vertebrates, helps maintain the structural and functional integrity of cartilage. Delivery of COLII from animal sources could improve cartilage regeneration therapies. Here we show that COLII can be purified from the Capra ear cartilage, a commonly available bio-waste product, with a high yield. MALDI-MS/MS analysis evidenced post-translational modifications of the signature triplet, Glycine-Proline-Hydroxyproline (G-P-Hyp), in alpha chain of isolated COLII (COLIIA1). Additionally, thirty-two peptides containing 59 Hyp residues and a few G-X-Y triplets with positional alterations of Hyp in COLIIA1 are also identified. Furthermore, we show that an injectable hydrogel formulation containing the isolated COLII facilitates chondrogenic differentiation towards cartilage regeneration. These findings show that COLII can be isolated from Capra ear cartilage and that positional alteration of Hyp in its structural motif, as detected by newly developed mass spectrometric method, might be an early marker of cartilage disorder.
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Affiliation(s)
- Priti Prasanna Maity
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Debabrata Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Sayan Ganguly
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Kausik Kapat
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Krishna Dixit
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Amit Roy Chowdhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Ramapati Samanta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Narayan Chandra Das
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Pallab Datta
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
| | - Santanu Dhara
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302 India
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43
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Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis. Matrix Biol Plus 2019; 1:100005. [PMID: 33543004 PMCID: PMC7852317 DOI: 10.1016/j.mbplus.2019.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Lung fibrosis is characterized by excessive deposition of extracellular matrix (ECM), in particular collagens, by fibroblasts in the interstitium. Transforming growth factor-β1 (TGF-β1) alters the expression of many extracellular matrix (ECM) components produced by fibroblasts, but such changes in ECM composition as well as modulation of collagen post-translational modification (PTM) levels have not been comprehensively investigated. Here, we performed mass spectrometry (MS)-based proteomics analyses to assess changes in the ECM deposited by cultured lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients upon stimulation with transforming growth factor β1 (TGF-β1). In addition to the ECM changes commonly associated with lung fibrosis, MS-based label-free quantification revealed profound effects on enzymes involved in ECM crosslinking and turnover as well as multiple positive and negative feedback mechanisms of TGF-β1 signaling. Notably, the ECM changes observed in this in vitro model correlated significantly with ECM changes observed in patient samples. Because collagens are subject to multiple PTMs with major implications in disease, we implemented a new bioinformatic platform to analyze MS data that allows for the comprehensive mapping and site-specific quantitation of collagen PTMs in crude ECM preparations. These analyses yielded a comprehensive map of prolyl and lysyl hydroxylations as well as lysyl glycosylations for 15 collagen chains. In addition, site-specific PTM analysis revealed novel sites of prolyl-3-hydroxylation and lysyl glycosylation in type I collagen. Interestingly, the results show, for the first time, that TGF-β1 can modulate prolyl-3-hydroxylation and glycosylation in a site-specific manner. Taken together, this proof of concept study not only reveals unanticipated TGF-β1 mediated regulation of collagen PTMs and other ECM components but also lays the foundation for dissecting their key roles in health and disease. The proteomic data has been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with the data set identifier MSV000082958. Quantitative proteomics of TGF-β-induced changes in ECM composition and collagen PTM in pulmonary fibroblasts TGF-β promotes crosslinking and turnover as well as complex feedback mechanisms that alter fibroblast ECM homeostasis. A novel bioinformatic workflow for MS data analysis enabled global mapping and quantitation of known and novel collagen PTMs Quantitative assessment of prolyl-3-hydroxylation site occupancy and lysine-O-glycosylation microheterogeneity TGF-β1 modulates collagen PTMs in a site-specific manner that may favor collagen accumulation in lung fibrosis
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Key Words
- 3-HyP, 3-hydroxyproline
- 4-HyP, 4-hydroxyproline
- AGC, automatic gain control
- ANXA11, annexin A11
- BGN, biglycan
- COL1A1, collagen-I alpha 1 chain
- Collagen
- Collagen post-translational modifications
- DCN, decorin
- ECM, extracellular matrix
- Extracellular matrix
- FN1, fibronectin 1
- G-HyK, galactosylhydroxylysine
- GG-HyK, glucosylgalactosylhydroxylysine
- HyK, hydroxylysine
- HyP, hydroxyproline
- ILD, interstitial lung disease
- IPF, idiopathic pulmonary fibrosis
- LH, lysyl hydroxylase
- LOX(L), lysyl oxidase(-like)
- LTBP2, latent-transforming growth factor β -binding protein 2
- Lysyl glycosylation
- Lysyl hydroxylation
- P3H, prolyl-3-hydroxylase
- P4H, prolyl-4-hydroxylase
- PAI1, plasminogen activator inhibitor 1
- PCA, principal component analysis
- PLOD (LH), procollagen-lysine,2-oxoglutarate 5-dioxygenases (lysyl hydroxylases)
- PTM, post-translational modification
- Prolyl hydroxylation
- Pulmonary fibrosis
- SEMA7A, semaphorin 7a
- TGF-β, transforming growth factor β
- TGM2, transglutaminase 1
- Transforming growth factor-β
- VCAN, versican
- Xaa, Xaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- Yaa, Yaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- α-SMA, α-smooth muscle actin
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44
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van Huizen NA, Burgers PC, Saintmont F, Brocorens P, Gerbaux P, Stingl C, Dekker LJM, IJzermans JNM, Luider TM. Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry. J Proteome Res 2019; 18:2045-2051. [PMID: 30945869 DOI: 10.1021/acs.jproteome.8b00930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 41 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 45 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, that is, 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).
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Affiliation(s)
| | | | - Fabrice Saintmont
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP) , University of Mons - UMONS , 23 Place du Parc , 7000 Mons , Belgium.,Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials , University of Mons, UMONS , 23 Place du Parc , 7000 Mons , Belgium
| | - Patrick Brocorens
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials , University of Mons, UMONS , 23 Place du Parc , 7000 Mons , Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP) , University of Mons - UMONS , 23 Place du Parc , 7000 Mons , Belgium
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45
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Collagen glycosylation. Curr Opin Struct Biol 2019; 56:131-138. [PMID: 30822656 DOI: 10.1016/j.sbi.2019.01.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/04/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023]
Abstract
Despite the ubiquity of collagens in the animal kingdom, little is known about the biology of the disaccharide Glc(α1-2)Gal(β1-O) bound to hydroxylysine across collagens from sponges to mammals. The extent of collagen glycosylation varies by the types of collagen, with basement membrane collagen type IV being more glycosylated than fibrillar collagens. Beyond true collagens, proteins including collagen domains such as the complement protein 1Q and the hormone adiponectin also feature glycosylated hydroxylysine. Collagen glycosylation is initiated in the endoplasmic reticulum by the galactosyltransferases COLGALT1 and COLGALT2. Mutations in the COLGALT1 gene cause cerebral small vessel abnormality and porencephaly, which are common in collagen type IV deficiency. Beyond the strongly conserved Glc(α1-2)Gal(β1-O) glycan, additional forms of collagen glycosylation have been described in the deep-sea worm Riftia pachyptila and in the giant virus Mimivirus, thereby suggesting that further forms of collagen glycosylation are likely to be identified in the future.
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Montgomery NT, Zientek KD, Pokidysheva EN, Bächinger HP. Post-translational modification of type IV collagen with 3-hydroxyproline affects its interactions with glycoprotein VI and nidogens 1 and 2. J Biol Chem 2018; 293:5987-5999. [PMID: 29491144 DOI: 10.1074/jbc.ra117.000406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/15/2018] [Indexed: 01/18/2023] Open
Abstract
Type IV collagen is a major component of the basement membrane and interacts with numerous other basement membrane proteins. Many of these interactions are poorly characterized. Type IV collagen is abundantly post-translationally modified with 3-hydroxyproline (3-Hyp), but 3-Hyp's biochemical role in type IV collagen's interactions with other proteins is not well established. In this work, we present binding data consistent with a major role of 3-Hyp in interactions of collagen IV with glycoprotein VI and nidogens 1 and 2. The increased binding interaction between type IV collagen without 3-Hyp and glycoprotein VI has been the subject of some controversy, which we sought to explore, whereas the lack of binding of nidogens to type IV collagen without 3-Hyp is novel. Using tandem MS, we show that the putative glycoprotein VI-binding site is 3-Hyp-modified in WT PFHR-9 type IV collagen, but not in PFHR-9 cells in which prolyl-3-hydroxylase 2 (P3H2) has been knocked out (KO). Moreover, we observed altered 3-Hyp occupancy across many other sites. Using amino acid analysis of type IV collagen from the WT and P3H2 KO cell lines, we confirm that P3H2 is the major, but not the only 3-Hyp-modifying enzyme of type IV collagen. These findings underscore the importance of post-translational modifications of type IV collagen for interactions with other proteins.
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Affiliation(s)
- Nathan T Montgomery
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239.,the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239, and
| | - Keith D Zientek
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239
| | - Elena N Pokidysheva
- the Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University, Nashville, Tennessee 37232
| | - Hans Peter Bächinger
- From the Research Department, Shriners Hospital for Children, Portland, Oregon 97239, .,the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239, and
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Brown KL, Cummings CF, Vanacore RM, Hudson BG. Building collagen IV smart scaffolds on the outside of cells. Protein Sci 2017; 26:2151-2161. [PMID: 28845540 DOI: 10.1002/pro.3283] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 12/22/2022]
Abstract
Collagen IV scaffolds assemble through an intricate pathway that begins intracellularly and is completed extracellularly. Multiple intracellular enzymes act in concert to assemble collagen IV protomers, the building blocks of collagen IV scaffolds. After being secreted from cells, protomers are activated to initiate oligomerization, forming insoluble networks that are structurally reinforced with covalent crosslinks. Within these networks, embedded binding sites along the length of the protomer lead to the "decoration" of collagen IV triple helix with numerous functional molecules. We refer to these networks as "smart" scaffolds, which as a component of the basement membrane enable the development and function of multicellular tissues in all animal phyla. In this review, we present key molecular mechanisms that drive the assembly of collagen IV smart scaffolds.
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Affiliation(s)
- Kyle L Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | | | - Roberto M Vanacore
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Billy G Hudson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
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Taga Y, Tanaka K, Hamada C, Kusubata M, Ogawa-Goto K, Hattori S. Hydroxyhomocitrulline Is a Collagen-Specific Carbamylation Mark that Affects Cross-link Formation. Cell Chem Biol 2017; 24:1276-1284.e3. [DOI: 10.1016/j.chembiol.2017.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 10/18/2022]
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López-Jiménez AJ, Basak T, Vanacore RM. Proteolytic processing of lysyl oxidase-like-2 in the extracellular matrix is required for crosslinking of basement membrane collagen IV. J Biol Chem 2017; 292:16970-16982. [PMID: 28864775 DOI: 10.1074/jbc.m117.798603] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/16/2017] [Indexed: 12/13/2022] Open
Abstract
Lysyl oxidase-like-2 (LOXL2) is an enzyme secreted into the extracellular matrix that crosslinks collagens by mediating oxidative deamination of lysine residues. Our previous work demonstrated that this enzyme crosslinks the 7S domain, a structural domain that stabilizes collagen IV scaffolds in the basement membrane. Despite its relevant role in extracellular matrix biosynthesis, little is known about the structural requirements of LOXL2 that enable collagen IV crosslinking. In this study, we demonstrate that LOXL2 is processed extracellularly by serine proteases, generating a 65-kDa form lacking the first two scavenger receptor cysteine-rich domains. Site-specific mutagenesis to prevent proteolytic processing generated a full-length enzyme that is active in vitro toward a soluble substrate, but fails to crosslink insoluble collagen IV within the extracellular matrix. In contrast, the processed form of LOXL2 binds to collagen IV and crosslinks the 7S domain. Together, our data demonstrate that proteolytic processing is an important event that allows LOXL2-mediated crosslinking of basement membrane collagen IV.
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Affiliation(s)
- Alberto J López-Jiménez
- From the Department of Medicine, Division of Nephrology and Hypertension and.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Trayambak Basak
- From the Department of Medicine, Division of Nephrology and Hypertension and.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Roberto M Vanacore
- From the Department of Medicine, Division of Nephrology and Hypertension and .,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
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50
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Ishikawa Y, Mizuno K, Bächinger HP. Ziploc-ing the structure 2.0: Endoplasmic reticulum-resident peptidyl prolyl isomerases show different activities toward hydroxyproline. J Biol Chem 2017; 292:9273-9282. [PMID: 28385890 DOI: 10.1074/jbc.m116.772657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular matrix proteins are biosynthesized in the rough endoplasmic reticulum (rER), and the triple-helical protein collagen is the most abundant extracellular matrix component in the human body. Many enzymes, molecular chaperones, and post-translational modifiers facilitate collagen biosynthesis. Collagen contains a large number of proline residues, so the cis/trans isomerization of proline peptide bonds is the rate-limiting step during triple-helix formation. Accordingly, the rER-resident peptidyl prolyl cis/trans isomerases (PPIases) play an important role in the zipper-like triple-helix formation in collagen. We previously described this process as "Ziploc-ing the structure" and now provide additional information on the activity of individual rER PPIases. We investigated the substrate preferences of these PPIases in vitro using type III collagen, the unhydroxylated quarter fragment of type III collagen, and synthetic peptides as substrates. We observed changes in activity of six rER-resident PPIases, cyclophilin B (encoded by the PPIB gene), FKBP13 (FKBP2), FKBP19 (FKBP11), FKBP22 (FKBP14), FKBP23 (FKBP7), and FKBP65 (FKBP10), due to posttranslational modifications of proline residues in the substrate. Cyclophilin B and FKBP13 exhibited much lower activity toward post-translationally modified substrates. In contrast, FKBP19, FKBP22, and FKBP65 showed increased activity toward hydroxyproline-containing peptide substrates. Moreover, FKBP22 showed a hydroxyproline-dependent effect by increasing the amount of refolded type III collagen in vitro and FKBP19 seems to interact with triple helical type I collagen. Therefore, we propose that hydroxyproline modulates the rate of Ziploc-ing of the triple helix of collagen in the rER.
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Affiliation(s)
- Yoshihiro Ishikawa
- From the Department of Biochemistry and Molecular Biology, Oregon Health & Science University and.,Research Department, Shriners Hospital for Children, Portland, Oregon 97239
| | - Kazunori Mizuno
- Research Department, Shriners Hospital for Children, Portland, Oregon 97239
| | - Hans Peter Bächinger
- From the Department of Biochemistry and Molecular Biology, Oregon Health & Science University and .,Research Department, Shriners Hospital for Children, Portland, Oregon 97239
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