1
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Kalka M, Bielak K, Ptak M, Stolarski J, Dobryszycki P, Wojtas M. Calcium carbonate polymorph selection in fish otoliths: A key role of phosphorylation of Starmaker-like protein. Acta Biomater 2024; 174:437-446. [PMID: 38061675 DOI: 10.1016/j.actbio.2023.11.039] [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: 09/05/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Fish otoliths are calcium carbonate biominerals found in the inner ear commonly used for tracking fish biochronologies and as a model system for biomineralization. The process of fish otolith formation is biologically controlled by numerous biomacromolecules which not only affect crystal size, shape, mechanical properties, but also selection of calcium carbonate polymorph (e.g., aragonite, vaterite). The proteinaceous control over calcium carbonate polymorph selection occurs in many other species (e.g., corals, mollusks, echinoderms) but the exact mechanism of protein interactions with calcium and carbonate ions - constituents of CaCO3 - are not fully elucidated. Herein, we focus on a native Starmaker-like protein isolated from vaterite asteriscus otoliths from Cyprinus carpio. The proteomic studies show the presence of the phosphorylated protein in vaterite otoliths. In a series of in vitro mineralization experiments with Starmaker-like, we show that native phosphorylation is a crucial determinant for the selection of a crystal's polymorphic form. This is the first report showing that the switch in calcium carbonate phase depends on the phosphorylation pattern of a single isolated protein. STATEMENT OF SIGNIFICANCE: Calcium carbonate has numerous applications in industry and medicine. However, we still do not understand the mechanism of biologically driven polymorph selection which results in specific biomineral properties. Previous work on calcium carbonate biominerals showed that either several macromolecular factors or high magnesium concentration (non-physiological) are required for proper polymorph selection (e.g., in mollusk shells, corals and otoliths). In this work, we showed for the first time that protein phosphorylation is a crucial factor for controlling the calcium carbonate crystal phase. This is important because a single protein from the otolith organic matrix could switch between polymorphs depending on the phosphorylation level. It seems that protein post-translational modifications (native, not artificial) are more important for biomolecular control of crystal growth than previously considered.
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Affiliation(s)
- Marta Kalka
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław, Poland
| | - Klaudia Bielak
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław, Poland
| | - Maciej Ptak
- Division of Optical Spectroscopy, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Wrocław, Poland
| | | | - Piotr Dobryszycki
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław, Poland
| | - Magdalena Wojtas
- Wroclaw University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Molecular Biology and Biotechnology, Wrocław, Poland.
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2
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Różycka MO, Bielak K, Ptak M, Jost B, Melo Rodriguez G, Schoelkopf J, Stolarski J, Dobryszycki P, Ożyhar A. Effect of Gel Exposition on Calcium and Carbonate Ions Determines the Stm-l Effect on the Crystal Morphology of Calcium Carbonate. Biomacromolecules 2023; 24:4042-4050. [PMID: 37605889 PMCID: PMC10498444 DOI: 10.1021/acs.biomac.3c00395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/22/2023] [Indexed: 08/23/2023]
Abstract
Biomineralization of fish otoliths is regulated by macromolecules, such as proteins, whose presence is crucial for the functionality and properties of these mineralized structures. Special regulatory effects are exerted by intrinsically disordered proteins, such as the polyanionic Starmaker-like protein from medaka, a homolog of zebrafish Starmaker. In this study, we employed a set of bioinspired mineralization experiments with a single diffusion system to investigate the effect of the Starmaker-like protein on calcium carbonate biominerals with regards to the prior exposition of the protein to calcium or carbonate ions. Interestingly, the bioinspired minerals grown in the presence of the Starmaker-like protein in calcium- or carbonate-type experiments differ significantly in terms of morphology and protein distribution within the crystals. Our deeper analysis shows that the Starmaker-like protein action is a result of the environmental conditions to which it is exposed. These findings may be of special interest in the areas of biomineralization process pathways and biomaterial sciences.
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Affiliation(s)
- Mirosława O. Różycka
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Klaudia Bielak
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Maciej Ptak
- Institute
of Low Temperature and Structure Research, Polish Academy of Sciences, Wroclaw 50-422, Poland
| | | | | | | | - Jarosław Stolarski
- Institute
of Paleobiology, Polish Academy of Sciences, Warsaw 00-818, Poland
| | - Piotr Dobryszycki
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Andrzej Ożyhar
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
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3
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Bielak K, Benkowska-Biernacka D, Ptak M, Stolarski J, Kalka M, Ożyhar A, Dobryszycki P. Otolin-1, an otolith- and otoconia-related protein, controls calcium carbonate bioinspired mineralization. Biochim Biophys Acta Gen Subj 2023; 1867:130327. [PMID: 36791829 DOI: 10.1016/j.bbagen.2023.130327] [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: 12/15/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Otoliths and otoconia are calcium carbonate biomineral structures that form in the inner ear of fish and humans, respectively. The formation of these structures is tightly linked to the formation of an organic matrix framework with otolin-1, a short collagen-like protein from the C1q family as one of its major constituents. METHODS In this study, we examined the activity of recombinant otolin-1 originating from Danio rerio and Homo sapiens on calcium carbonate bioinspired mineralization with slow-diffusion method and performed crystals characterization with scanning electron microscopy, two-photon excited fluorescence microscopy, confocal laser scanning microscopy and micro-Raman spectroscopy. RESULTS We show that both proteins are embedded in the core of CaCO3 crystals that form through the slow-diffusion mineralization method. Both of them influence the morphology but do not change the polymorphic mineral phase. D.rerio otolin-1 also closely adheres to the crystal surface. GENERAL SIGNIFICANCE The results suggest, that otolin-1 is not a passive scaffold, but is directly involved in regulating the morphology of the resulting calcium carbonate biocrystals.
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Affiliation(s)
- Klaudia Bielak
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Dominika Benkowska-Biernacka
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Ptak
- Division of Optical Spectroscopy, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, ul. Okólna 2, 50-422 Wroclaw, Poland
| | - Jarosław Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland
| | - Marta Kalka
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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4
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First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host. Sci Rep 2023; 13:3822. [PMID: 36882485 PMCID: PMC9992438 DOI: 10.1038/s41598-023-30537-8] [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: 11/09/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex insoluble collagen-like protein and soluble non-collagenous protein assemblages; many of these proteins are incorporated into their aragonite crystal structure. However, in the fossil record these proteins are considered lost through diagenetic processes, hampering studies of past biomineralization mechanisms. Here we report the presence of 11 fish-specific proteins (and several isoforms) in Miocene (ca. 14.8-14.6 Ma) phycid hake otoliths. These fossil otoliths were preserved in water-impermeable clays and exhibit microscopic and crystallographic features indistinguishable from modern representatives, consistent with an exceptionally pristine state of preservation. Indeed, these fossil otoliths retain ca. 10% of the proteins sequenced from modern counterparts, including proteins specific to inner ear development, such as otolin-1-like proteins involved in the arrangement of the otoliths into the sensory epithelium and otogelin/otogelin-like proteins that are located in the acellular membranes of the inner ear in modern fish. The specificity of these proteins excludes the possibility of external contamination. Identification of a fraction of identical proteins in modern and fossil phycid hake otoliths implies a highly conserved inner ear biomineralization process through time.
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Yarawsky AE, Ori AL, English LR, Whitten ST, Herr AB. Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523059. [PMID: 36711672 PMCID: PMC9881980 DOI: 10.1101/2023.01.06.523059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Staphylococcus epidermidis and S. aureus are highly problematic bacteria in hospital settings. This stems, at least in part, from strong abilities to form biofilms on abiotic or biotic surfaces. Biofilms are well-organized multicellular aggregates of bacteria, which, when formed on indwelling medical devices, lead to infections that are difficult to treat. Cell wall-anchored (CWA) proteins are known to be important players in biofilm formation and infection. Many of these proteins have putative stalk-like regions or regions of low complexity near the cell wall-anchoring motif. Recent work demonstrated the strong propensity of the stalk region of the S. epidermidis accumulation-associated protein (Aap) to remain highly extended under solution conditions that typically induce compaction or other significant conformational changes. This behavior is consistent with the expected function of a stalk-like region that is covalently attached to the cell wall peptidoglycan and projects the adhesive domains of Aap away from the cell surface. In this study, we evaluate whether the ability to resist compaction is a common theme among stalk regions from various staphylococcal CWA proteins. Circular dichroism spectroscopy was used to examine secondary structure changes as a function of temperature and cosolvents along with sedimentation velocity analytical ultracentrifugation and SAXS to characterize structural characteristics in solution. All stalk regions tested are intrinsically disordered, lacking secondary structure beyond random coil and polyproline type II helix, and they all sample highly extended conformations. Remarkably, the Ser-Asp dipeptide repeat region of SdrC exhibited nearly identical behavior in solution when compared to the Aap Pro/Gly-rich region, despite highly divergent sequence patterns, indicating conservation of function by various distinct staphylococcal CWA protein stalk regions.
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Affiliation(s)
- Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrea L. Ori
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Medical Sciences Baccalaureate Program, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Lance R. English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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6
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Tarczewska A, Bielak K, Zoglowek A, Sołtys K, Dobryszycki P, Ożyhar A, Różycka M. The Role of Intrinsically Disordered Proteins in Liquid–Liquid Phase Separation during Calcium Carbonate Biomineralization. Biomolecules 2022; 12:biom12091266. [PMID: 36139105 PMCID: PMC9496343 DOI: 10.3390/biom12091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Some animal organs contain mineralized tissues. These so-called hard tissues are mostly deposits of calcium salts, usually in the form of calcium phosphate or calcium carbonate. Examples of this include fish otoliths and mammalian otoconia, which are found in the inner ear, and they are an essential part of the sensory system that maintains body balance. The composition of ear stones is quite well known, but the role of individual components in the nucleation and growth of these biominerals is enigmatic. It is sure that intrinsically disordered proteins (IDPs) play an important role in this aspect. They have an impact on the shape and size of otoliths. It seems probable that IDPs, with their inherent ability to phase separate, also play a role in nucleation processes. This review discusses the major theories on the mechanisms of biomineral nucleation with a focus on the importance of protein-driven liquid–liquid phase separation (LLPS). It also presents the current understanding of the role of IDPs in the formation of calcium carbonate biominerals and predicts their potential ability to drive LLPS.
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7
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Bielak K, Hołubowicz R, Zoglowek A, Żak A, Kędzierski P, Ożyhar A, Dobryszycki P. N'-terminal- and Ca 2+-induced stabilization of high-order oligomers of full-length Danio rerio and Homo sapiens otolin-1. Int J Biol Macromol 2022; 209:1032-1047. [PMID: 35447266 DOI: 10.1016/j.ijbiomac.2022.04.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023]
Abstract
Otolin-1 is a C1q family member and a major component of the organic matrix of fish otoliths and human otoconia. To date, the protein molecular properties have not been characterized. In this work, we describe biochemical characterization and comparative studies on saccular-specific otolin-1 derived from Danio rerio and Homo sapiens. Due to the low abundance of proteins in the otoconial matrix, we developed a production and purification method for both recombinant homologues of otolin-1. Danio rerio and Homo sapiens otolin-1 forms higher-order oligomers that can be partially disrupted under reducing conditions. The presence of Ca2+ stabilizes the oligomers and significantly increases the thermal stability of the proteins. Despite the high sequence coverage, the oligomerization of Danio rerio otolin-1 is more affected by the reducing conditions and presence of Ca2+ than the human homologue. The results show differences in molecular behaviour, which may be reflected in Danio rerio and Homo sapiens otolin-1 role in otolith and otoconia formation.
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Affiliation(s)
- Klaudia Bielak
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Anna Zoglowek
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Andrzej Żak
- Electron Microscopy Laboratory, Faculty of Mechanical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Paweł Kędzierski
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland.
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8
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Song N, Li J, Li B, Pan E, Gao J, Ma Y. In vitro crystallization of calcium carbonate mediated by proteins extracted from P. placenta shells. CrystEngComm 2022. [DOI: 10.1039/d2ce00692h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ASM extracted from the shells of P. placenta can stabilize ACC and inhibit secondary nucleation for 10 hours, and an explosive secondary nucleation and quick crystal growth from 50 nm to 10 μm can be finished on the shell surface in one hour.
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Affiliation(s)
- Ningjing Song
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jiangfeng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Baosheng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ercai Pan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Juan Gao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yurong Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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9
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Molecular mechanism of calcium induced trimerization of C1q-like domain of otolin-1 from human and zebrafish. Sci Rep 2021; 11:12778. [PMID: 34140580 PMCID: PMC8211825 DOI: 10.1038/s41598-021-92129-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
The C1q superfamily includes proteins involved in innate immunity, insulin sensitivity, biomineralization and more. Among these proteins is otolin-1, which is a collagen-like protein that forms a scaffold for the biomineralization of inner ear stones in vertebrates. The globular C1q-like domain (gC1q), which is the most conserved part of otolin-1, binds Ca2+ and stabilizes its collagen-like triple helix. The molecular details of the assembly of gC1q otolin-1 trimers are not known. Here, we substituted putative Ca2+-binding acidic residues of gC1q otolin-1 with alanine to analyse how alanine influences the formation of gC1q trimers. We used human and zebrafish gC1q otolin-1 to assess how evolutionary changes affected the function of the protein. Surprisingly, the mutated forms of gC1q otolin-1 trimerized even in the absence of Ca2+, although they were less stable than native proteins saturated with Ca2+. We also found that the zebrafish gC1q domain was less stable than the human homologue under all tested conditions and became stabilized at higher concentrations of Ca2+, which showed that specific interactions leading to the neutralization of the negative charge at the axis of a gC1q trimer by Ca2+ are required for the trimers to form. Moreover, human gC1q otolin-1 seems to be optimized to function at lower concentrations of Ca2+, which is consistent with reported Ca2+ concentrations in the endolymphs of fish and mammals. Our results allow us to explain the molecular mechanism of assembly of proteins from the C1q superfamily, the modulating role of Ca2+ and expand the knowledge of biomineralization of vertebrate inner ear stones: otoliths and otoconia.
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10
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Sołtys K, Wycisk K, Ożyhar A. Liquid-liquid phase separation of the intrinsically disordered AB region of hRXRγ is driven by hydrophobic interactions. Int J Biol Macromol 2021; 183:936-949. [PMID: 33971237 DOI: 10.1016/j.ijbiomac.2021.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that are regulated endogenously by small lipophilic ligands. Recently, liquid-liquid phase separation (LLPS) has appeared as a new aspect of NR function. In the human retinoid X receptor γ (hRXRγ), the inherently disordered AB region undergoes LLPS via homotypic multivalent interactions. To better understand the functions of liquid condensates, a clear view of the molecular interactions underlying the LLPS are required. The phase separation propensity of the AB region of hRXRγ (AB_hRXG) at a high NaCl concentration, a lower critical solution temperature behavior, and also sensitivity to kosmotropic salts and 1,6-hexanediol, which all indicate the importance of hydrophobic interactions in the formation of AB_hRXG liquid condensates, is presented in the paper. Additionally, molecular crowding agents and TMAO shift the equilibrium, in turn enabling phase transition at lower AB_hRXG concentrations. Although the LLPS of the proteins can lead to aggregation, AB_hRXG liquid condensates are not aggregation prone. Interestingly, the formation of AB_hRXG liquid condensates has an impact on the rest of the receptor, as AB_hRXG liquid condensates recruit the remaining fragment of hRXRγ into the droplets. The ability of AB_hRXG to undergo LLPS might be important for gene expression regulation.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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11
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Jedrychowska J, Gasanov EV, Korzh V. Kcnb1 plays a role in development of the inner ear. Dev Biol 2020; 471:65-75. [PMID: 33316259 DOI: 10.1016/j.ydbio.2020.12.007] [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: 04/05/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
The function of the inner ear depends on the maintenance of high concentrations of K+ ions. The slow-inactivating delayed rectifier Kv2.1/KCNB1 channel works in the inner ear in mammals. The kcnb1 gene is expressed in the otic vesicle of developing zebrafish, suggesting its role in development of the inner ear. In the present study, we found that a Kcnb1 loss-of-function mutation affected development of the inner ear at multiple levels, including otic vesicle expansion, otolith formation, and the proliferation and differentiation of mechanosensory cells. This resulted in defects of kinocilia and stereocilia and abnormal function of the inner ear detected by behavioral assays. The quantitative transcriptional analysis of 75 genes demonstrated that the kcnb1 mutation affected the transcription of genes that are involved in K+ metabolism, cell proliferation, cilia development, and intracellular protein trafficking. These results demonstrate a role for Kv2.1/Kcnb1 channels in development of the inner ear in zebrafish.
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Affiliation(s)
- Justyna Jedrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Poland; Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Eugene V Gasanov
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland.
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12
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Porębska A, Różycka M, Hołubowicz R, Szewczuk Z, Ożyhar A, Dobryszycki P. Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals. FASEB J 2020; 34:6147-6165. [PMID: 32190922 DOI: 10.1096/fj.201901999r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.
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Affiliation(s)
- Aleksandra Porębska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mirosława Różycka
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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13
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Różycka M, Coronado I, Brach K, Olesiak‐Bańska J, Samoć M, Zarębski M, Dobrucki J, Ptak M, Weber E, Polishchuk I, Pokroy B, Stolarski J, Ożyhar A. Lattice Shrinkage by Incorporation of Recombinant Starmaker-Like Protein within Bioinspired Calcium Carbonate Crystals. Chemistry 2019; 25:12740-12750. [PMID: 31241793 PMCID: PMC6790713 DOI: 10.1002/chem.201902157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 11/16/2022]
Abstract
The biological mediation of mineral formation (biomineralization) is realized through diverse organic macromolecules that guide this process in a spatial and temporal manner. Although the role of these molecules in biomineralization is being gradually revealed, the molecular basis of their regulatory function is still poorly understood. In this study, the incorporation and distribution of the model intrinsically disordered starmaker-like (Stm-l) protein, which is active in fish otoliths biomineralization, within calcium carbonate crystals, is revealed. Stm-l promotes crystal nucleation and anisotropic tailoring of crystal morphology. Intracrystalline incorporation of Stm-l protein unexpectedly results in shrinkage (and not expansion, as commonly described in biomineral and bioinspired crystals) of the crystal lattice volume, which is described herein, for the first time, for bioinspired mineralization. A ring pattern was observed in crystals grown for 48 h; this was composed of a protein-enriched region flanked by protein-depleted regions. It can be explained as a result of the Ostwald-like ripening process and intrinsic properties of Stm-l, and bears some analogy to the daily growth layers of the otolith.
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Affiliation(s)
- Mirosława Różycka
- Department of BiochemistryFaculty of ChemistryWroclaw University of Science and TechnologyWroclaw50-370Poland
| | - Ismael Coronado
- Institute of PaleobiologyPolish Academy of SciencesWarsaw00-818Poland
| | - Katarzyna Brach
- Advanced Materials Engineering and Modelling GroupFaculty of ChemistryWroclaw University of Science and TechnologyWroclaw50-370Poland
| | - Joanna Olesiak‐Bańska
- Advanced Materials Engineering and Modelling GroupFaculty of ChemistryWroclaw University of Science and TechnologyWroclaw50-370Poland
| | - Marek Samoć
- Advanced Materials Engineering and Modelling GroupFaculty of ChemistryWroclaw University of Science and TechnologyWroclaw50-370Poland
| | - Mirosław Zarębski
- Department of Cell BiophysicsFaculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityKrakow30-387Poland
| | - Jerzy Dobrucki
- Department of Cell BiophysicsFaculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityKrakow30-387Poland
| | - Maciej Ptak
- Institute of Low Temperature and Structure ResearchPolish Academy of SciencesWroclaw50-422Poland
| | - Eva Weber
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology InstituteTechnion Israel Institute of TechnologyHaifa32000Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology InstituteTechnion Israel Institute of TechnologyHaifa32000Israel
| | - Boaz Pokroy
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology InstituteTechnion Israel Institute of TechnologyHaifa32000Israel
| | | | - Andrzej Ożyhar
- Department of BiochemistryFaculty of ChemistryWroclaw University of Science and TechnologyWroclaw50-370Poland
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14
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Kalka M, Markiewicz N, Ptak M, Sone ED, Ożyhar A, Dobryszycki P, Wojtas M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization. FASEB J 2019; 33:6877-6886. [PMID: 30840836 DOI: 10.1096/fj.201802268r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Otoliths are one of the biominerals whose formation is highly controlled by proteins. The first protein discovered to be involved in otolith biomineralization in zebrafish was starmaker (Stm). Previously, Stm was shown to be responsible for the preferential formation of aragonite, a polymorph of calcium carbonate, in otoliths. In this work, proteomic analysis of adult zebrafish otoliths was performed. Stm is the only highly phosphorylated protein found in our studies. Besides previously studied otolith proteins, we discovered several dozens of unknown proteins that reveal the likely mechanism of biomineralization. A comparison of aragonite and vaterite otoliths showed similarities in protein composition. We observed the presence of Stm in both types of otoliths. In vitro studies of 2 characteristic Stm fragments indicated that the DS-rich region has a special biomineralization activity, especially after phosphorylation.-Kalka, M., Markiewicz, N., Ptak, M., Sone, E. D., Ożyhar, A., Dobryszycki, P., Wojtas, M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.
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Affiliation(s)
- Marta Kalka
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Natalia Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Maciej Ptak
- Division of Optical Spectroscopy, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Wrocław, Poland; and
| | - Eli D Sone
- Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
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15
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Thomas ORB, Swearer SE, Kapp EA, Peng P, Tonkin‐Hill GQ, Papenfuss A, Roberts A, Bernard P, Roberts BR. The inner ear proteome of fish. FEBS J 2018; 286:66-81. [DOI: 10.1111/febs.14715] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/30/2018] [Accepted: 12/03/2018] [Indexed: 01/28/2023]
Affiliation(s)
| | - Stephen E. Swearer
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Eugene A. Kapp
- The Florey Institute of Neuroscience and Mental Health The University of Melbourne Parkville Vic. Australia
- The Walter and Eliza Hall Institute of Medical Research Parkville Vic. Australia
| | - Po Peng
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Gerry Q. Tonkin‐Hill
- The Walter and Eliza Hall Institute of Medical Research Parkville Vic. Australia
| | - Anthony Papenfuss
- The Walter and Eliza Hall Institute of Medical Research Parkville Vic. Australia
| | - Anne Roberts
- The Florey Institute of Neuroscience and Mental Health The University of Melbourne Parkville Vic. Australia
| | - Pascal Bernard
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Blaine R. Roberts
- The Florey Institute of Neuroscience and Mental Health The University of Melbourne Parkville Vic. Australia
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16
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Ruggeri F, Krishnan M. Entropic Trapping of a Singly Charged Molecule in Solution. NANO LETTERS 2018; 18:3773-3779. [PMID: 29688720 DOI: 10.1021/acs.nanolett.8b01011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate the ability to confine a single molecule in solution by spatial modulation of its local configurational entropy. Previously we established electrostatic trapping of a charged macromolecule by geometric tailoring of a repulsive electrical interaction potential in a parallel plate system. However, since the lifetime of the trapped state depends exponentially on the electrical charge of the molecule, the electrostatic interaction alone is often insufficient in magnitude to stably confine molecules carrying a net charge of magnitude ≤5 e. Here we show that the configurational entropy of a thermally fluctuating molecule in a geometrically modulated system can be exploited to spatially confine weakly charged molecules in solution. Measurement of the configurational entropy contribution reveals good agreement with theoretical expectations. This additional translational contribution to the total free energy facilitates direct optical imaging and measurement of the effective charge of molecules on the size scale of ∼1 nm and a charge as low as 1 e, physical properties comparable with those of a monovalent ion in solution.
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Affiliation(s)
- Francesca Ruggeri
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
| | - Madhavi Krishnan
- Department of Chemistry , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
- Department of Physics , University of Zürich , Winterthurerstrasse 190 , CH 8057 Zürich , Switzerland
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17
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Zhang W, Xu J, Liu D, Liu H, Lu X, Yu W. Characterization of an α-agarase from Thalassomonas sp. LD5 and its hydrolysate. Appl Microbiol Biotechnol 2018; 102:2203-2212. [PMID: 29353307 DOI: 10.1007/s00253-018-8762-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/19/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
It has been a long time since the first α-agarase was discovered. However, only two α-agarases have been cloned and partially characterized so far and the study of α-agarases has lagged far behind that of β-agarases. Here, we report an α-agarase, AgaD, cloned from marine bacterium Thalassomonas sp. LD5. Its cDNA consists of 4401 bp, encoding a protein of 1466 amino acids. Based on amino acid similarity, AgaD is classified into glycoside hydrolase (GH) family GH96. The recombinant enzyme gave a molecular weight of about 180 kDa on SDS-PAGE and 360 kDa on Native-PAGE indicating it acted as a dimer. However, the recombinant enzyme is labile and easy to be fractured into series of small active fragments, of which the smallest one is about 70 kDa, matching the size of catalytic module. The enzyme has maximal activity at 35 °C and pH 7.4, and shows a strong dependence on the presence of calcium ions. AgaD degrades agarose to yield agarotetraose as the predominate end product. However, the hydrolysates are rapidly degraded to odd-numbered oligosaccharides under strong alkaline condition. The spectra of ESI-MS and 1H-NMR proved that the main hydrolysate agarotetraose is degraded into neoagarotriose, bearing the sequence of G-A-G (G, D-galactose; A, 3,6-anhydro-α-L-galactose). Unlike the alkaline condition, the hydrolysates are further hydrolyzed into smaller degree polymerization (DP) of agaro-oligosaccharides (AOS) in dilute strong acid. Therefore, this study provides more insights into the properties for both the α-agarases and the AOS.
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Affiliation(s)
- Weibin Zhang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Jingnan Xu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Dan Liu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Huan Liu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Xinzhi Lu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China.
| | - Wengong Yu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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18
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Ruggeri F, Krishnan M. Lattice diffusion of a single molecule in solution. Phys Rev E 2017; 96:062406. [PMID: 29347432 DOI: 10.1103/physreve.96.062406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 05/28/2023]
Abstract
The ability to trap a single molecule in an electrostatic potential well in solution has opened up new possibilities for the use of molecular electrical charge to study macromolecular conformation and dynamics at the level of the single entity. Here we study the diffusion of a single macromolecule in a two-dimensional lattice of electrostatic traps in solution. We report the ability to measure both the size and effective electrical charge of a macromolecule by observing single-molecule transport trajectories, typically a few seconds in length, using fluorescence microscopy. While, as shown previously, the time spent by the molecule in a trap is a strong function of its effective charge, we demonstrate here that the average travel time between traps in the landscape yields its hydrodynamic radius. Tailoring the pitch of the lattice thus yields two different experimentally measurable time scales that together uniquely determine both the size and charge of the molecule. Since no information is required on the location of the molecule between consecutive departure and arrival events at lattice sites, the technique is ideally suited to measurements on weakly emitting entities such as single molecules.
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Affiliation(s)
- Francesca Ruggeri
- Department of Chemistry, University of Zürich,Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
| | - Madhavi Krishnan
- Department of Chemistry, University of Zürich,Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
- Department of Physics, University of Zürich,Winterthurerstrasse 190, CH 8057 Zürich, Switzerland
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19
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Hołubowicz R, Wojtas M, Taube M, Kozak M, Ożyhar A, Dobryszycki P. Effect of calcium ions on structure and stability of the C1q-like domain of otolin-1 from human and zebrafish. FEBS J 2017; 284:4278-4297. [DOI: 10.1111/febs.14308] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/17/2017] [Accepted: 10/24/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Rafał Hołubowicz
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Magdalena Wojtas
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Michał Taube
- Department of Macromolecular Physics; Faculty of Physics; A. Mickiewicz University; Poznan Poland
| | - Maciej Kozak
- Department of Macromolecular Physics; Faculty of Physics; A. Mickiewicz University; Poznan Poland
| | - Andrzej Ożyhar
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Piotr Dobryszycki
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
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20
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Poznar M, Hołubowicz R, Wojtas M, Gapiński J, Banachowicz E, Patkowski A, Ożyhar A, Dobryszycki P. Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1358-1371. [PMID: 28866388 DOI: 10.1016/j.bbapap.2017.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/28/2017] [Indexed: 01/28/2023]
Abstract
Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed.
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Affiliation(s)
- Monika Poznar
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Rafał Hołubowicz
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Wojtas
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jacek Gapiński
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Ewa Banachowicz
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Adam Patkowski
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Andrzej Ożyhar
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Piotr Dobryszycki
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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21
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Ruggeri F, Zosel F, Mutter N, Różycka M, Wojtas M, Ożyhar A, Schuler B, Krishnan M. Single-molecule electrometry. NATURE NANOTECHNOLOGY 2017; 12:488-495. [PMID: 28288117 DOI: 10.1038/nnano.2017.26] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/31/2017] [Indexed: 05/22/2023]
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22
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Yarawsky AE, English LR, Whitten ST, Herr AB. The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. J Mol Biol 2017; 429:261-279. [PMID: 27890783 PMCID: PMC5363081 DOI: 10.1016/j.jmb.2016.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022]
Abstract
Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a 135-aa-long, proline/glycine-rich region (PGR) that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the PGR using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide with unusually high polyproline type II helix propensity. In contrast to many intrinsically disordered polypeptides, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon the addition of the osmolyte trimethylamine N-oxide or the cosolvent 2,2,2-trifluoroethanol. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B Herr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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23
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Boskey AL, Villarreal-Ramirez E. Intrinsically disordered proteins and biomineralization. Matrix Biol 2016; 52-54:43-59. [PMID: 26807759 DOI: 10.1016/j.matbio.2016.01.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/19/2016] [Accepted: 01/19/2016] [Indexed: 01/21/2023]
Abstract
In vertebrates and invertebrates, biomineralization is controlled by the cell and the proteins they produce. A large number of these proteins are intrinsically disordered, gaining some secondary structure when they interact with their binding partners. These partners include the component ions of the mineral being deposited, the crystals themselves, the template on which the initial crystals form, and other intrinsically disordered proteins and peptides. This review speculates why intrinsically disordered proteins are so important for biomineralization, providing illustrations from the SIBLING (small integrin binding N-glycosylated) proteins and their peptides. It is concluded that the flexible structure, and the ability of the intrinsically disordered proteins to bind to a multitude of surfaces is crucial, but details on the precise-interactions, energetics and kinetics of binding remain to be determined.
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Affiliation(s)
- Adele L Boskey
- Musculoskeletal Integrity Program, Hospital for Special Surgery, New York, NY 10021, USA.
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24
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Weigele J, Franz-Odendaal TA, Hilbig R. Not All Inner Ears are the Same: Otolith Matrix Proteins in the Inner Ear of Sub-Adult Cichlid Fish,Oreochromis Mossambicus, Reveal Insights Into the Biomineralization Process. Anat Rec (Hoboken) 2015; 299:234-45. [DOI: 10.1002/ar.23289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Jochen Weigele
- Zoological Institute, University of Stuttgart-Hohenheim; Garbenstrasse 30 Stuttgart 73734 Germany
- Department of Biology; Mount Saint Vincent University; 166 Bedford Highway Halifax Nova Scotia B3M 2J6 Canada
| | - Tamara A. Franz-Odendaal
- Department of Biology; Mount Saint Vincent University; 166 Bedford Highway Halifax Nova Scotia B3M 2J6 Canada
| | - Reinhard Hilbig
- Zoological Institute, University of Stuttgart-Hohenheim; Garbenstrasse 30 Stuttgart 73734 Germany
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25
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Correction: Intrinsically disordered and pliable starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PLoS One 2015; 10:e0119969. [PMID: 25793297 PMCID: PMC4368191 DOI: 10.1371/journal.pone.0119969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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