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Xu W, Xu Y, Sun R, Rey Redondo E, Leung KK, Wan SH, Li J, Yung CCM. Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:176019. [PMID: 39236827 DOI: 10.1016/j.scitotenv.2024.176019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/15/2024] [Accepted: 09/02/2024] [Indexed: 09/07/2024]
Abstract
This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.
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Affiliation(s)
- Wenqian Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yangbing Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruixian Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Elvira Rey Redondo
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ka Kiu Leung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Siu Hei Wan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiying Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Charmaine C M Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
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2
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Kozak F, Brandis D, Pötzl C, Epasto LM, Reichinger D, Obrist D, Peterlik H, Polyansky A, Zagrovic B, Daus F, Geyer A, Becker CFW, Kurzbach D. An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401239. [PMID: 38874418 PMCID: PMC11321707 DOI: 10.1002/advs.202401239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.
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Affiliation(s)
- Fanny Kozak
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dörte Brandis
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Christopher Pötzl
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Ludovica M. Epasto
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dominik Obrist
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Herwig Peterlik
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5Vienna1090Austria
| | - Anton Polyansky
- Department of Structural and Computational BiologyMax Perutz LabsUniversity of ViennaCampus Vienna Biocenter 5ViennaA‐1030Austria
| | - Bojan Zagrovic
- Department of Structural and Computational BiologyMax Perutz LabsUniversity of ViennaCampus Vienna Biocenter 5ViennaA‐1030Austria
| | - Fabian Daus
- Faculty of ChemistryPhilipps‐Universität Marburg35032MarburgGermany
| | - Armin Geyer
- Faculty of ChemistryPhilipps‐Universität Marburg35032MarburgGermany
| | - Christian FW Becker
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 38Vienna109Austria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 42Vienna1090Austria
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3
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Thomassen AB, Jansen TLC, Weidner T. The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2024; 26:18538-18546. [PMID: 38888161 DOI: 10.1039/d4cp00970c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process has been a white whale for material scientists due to its potential in biomimetic applications, ranging from medical to microelectronic fields. Replicating diatom biosilicification will depend on a thorough understanding of the silaffin peptide structure during the reaction, yet existing models in the literature offer conflicting views on peptide folding during silicification. In our study, we employed two-dimensional infrared spectroscopy (2DIR) within the amide I region to determine the secondary structure of the silaffin repeat unit 5 (R5), both pre- and post-interaction with silica. The 2DIR experiments are complemented by molecular dynamics (MD) simulations of pure R5 reacting with silicate. Subsequently, theoretical 2DIR spectra calculated from these MD trajectories allowed us to compare calculated spectra with experimental data, and to determine the diverse structural poses of R5. Our findings indicate that unbound R5 predominantly forms β-strand structures alongside various atypical secondary structures. Post-silicification, there's a noticeable shift: a decrease in β-strands coupled with an increase in turn-type and bend-type configurations. We theorize that this structural transformation stems from silicate embedding within R5's hydrogen-bond network, prompting the peptide backbone to contract and adapt around the biosilica precursors.
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Affiliation(s)
- Asger Berg Thomassen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark.
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4
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Pick LM, Oehme V, Hartmann J, Wenzlaff J, Tang Q, Grogan G, Ansorge-Schumacher MB. SilE-R and SilE-S-DABB Proteins Catalying Enantiospecific Hydrolysis of Organosilyl Ethers. Angew Chem Int Ed Engl 2024; 63:e202404105. [PMID: 38630059 DOI: 10.1002/anie.202404105] [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: 02/28/2024] [Indexed: 06/11/2024]
Abstract
Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyse silyl ethers. They belong to the stress-response dimeric A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Å, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.
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Affiliation(s)
- Lisa M Pick
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Viviane Oehme
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Julia Hartmann
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Jessica Wenzlaff
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Qingyun Tang
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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5
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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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6
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Abdelhamid MAA, Ki MR, Pack SP. Biominerals and Bioinspired Materials in Biosensing: Recent Advancements and Applications. Int J Mol Sci 2024; 25:4678. [PMID: 38731897 PMCID: PMC11083057 DOI: 10.3390/ijms25094678] [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: 03/25/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Inspired by nature's remarkable ability to form intricate minerals, researchers have unlocked transformative strategies for creating next-generation biosensors with exceptional sensitivity, selectivity, and biocompatibility. By mimicking how organisms orchestrate mineral growth, biomimetic and bioinspired materials are significantly impacting biosensor design. Engineered bioinspired materials offer distinct advantages over their natural counterparts, boasting superior tunability, precise controllability, and the ability to integrate specific functionalities for enhanced sensing capabilities. This remarkable versatility enables the construction of various biosensing platforms, including optical sensors, electrochemical sensors, magnetic biosensors, and nucleic acid detection platforms, for diverse applications. Additionally, bioinspired materials facilitate the development of smartphone-assisted biosensing platforms, offering user-friendly and portable diagnostic tools for point-of-care applications. This review comprehensively explores the utilization of naturally occurring and engineered biominerals and materials for diverse biosensing applications. We highlight the fabrication and design strategies that tailor their functionalities to address specific biosensing needs. This in-depth exploration underscores the transformative potential of biominerals and materials in revolutionizing biosensing, paving the way for advancements in healthcare, environmental monitoring, and other critical fields.
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Affiliation(s)
- Mohamed A. A. Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
- Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
- Institute of Industrial Technology, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro 2511, Sejong 30019, Republic of Korea; (M.A.A.A.); (M.-R.K.)
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7
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Farfan GA, McKeown DA, Post JE. Mineralogical characterization of biosilicas versus geological analogs. GEOBIOLOGY 2023; 21:520-533. [PMID: 36849877 DOI: 10.1111/gbi.12553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/30/2023] [Accepted: 02/12/2023] [Indexed: 06/13/2023]
Abstract
Non-crystalline silica mineraloids are essential to life on Earth as they provide architectural structure to dominant primary producers, such as plants and phytoplankton, as well as to protists and sponges. Due to the difficulty in characterizing and quantifying the structure of highly disordered X-ray amorphous silica, relatively little has been done to understand the mineralogy of biogenic silica and how this may impact the material properties of biogenic silica, such as hardness and strength, or how biosilica might be identified and differentiated from its inorganic geological counterparts. Typically, geologically formed opal-A and hyalite opal-AN are regarded as analogs to biogenic silica, however, some spectroscopic and imaging studies suggest that this might not be a reasonable assumption. In this study, we use a variety of techniques (X-ray diffraction, Raman spectroscopy, and scanning electron microscopy) to compare differences in structural disorder and bonding environments of geologically formed hydrous silicas (Opal-A, hyalite, geyserite) and silica glass versus biogenic silicas from an array of organisms. Our results indicate differences in the levels of structural disorder and the Raman-observed bonding environments of the SiO2 network modes (D1 mode) and the Q-species modes (~1015 cm-1 ) between varieties of biogenic silicas and geologically formed silicas, which aligns with previous studies that suggest fundamental differences between biogenic and geologically formed silica. Biosilicas also differ structurally from one another by species of organism. Our mineralogical approach to characterizing biosilicas and differentiating them from other silicas may be expanded to future diagenesis studies, and potentially applied to astrobiology studies of Earth and other planets.
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Affiliation(s)
- Gabriela A Farfan
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - David A McKeown
- Vitreous State Laboratory, The Catholic University of America, Washington, District of Columbia, USA
| | - Jeffrey E Post
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
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8
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Golubeva A, Roychoudhury P, Dąbek P, Pałczyńska J, Pryshchepa O, Piszczek P, Pomastowski P, Gloc M, Dobrucka R, Feliczak-Guzik A, Nowak I, Kurzydłowski KJ, Buszewski B, Witkowski A. A novel effective bio-originated methylene blue adsorbent: the porous biosilica from three marine diatom strains of Nanofrustulum spp. (Bacillariophyta). Sci Rep 2023; 13:9168. [PMID: 37280270 PMCID: PMC10244400 DOI: 10.1038/s41598-023-36408-6] [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: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
In the present paper, for the first time the ability of the porous biosilica originated from three marine diatom strains of 'Nanofrustulum spp.' viz. N. wachnickianum (SZCZCH193), N. shiloi (SZCZM1342), N. cf. shiloi (SZCZP1809), to eliminate MB from aqueous solutions was investigated. The highest biomass was achieved under silicate enrichment for N. wachnickianum and N. shiloi (0.98 g L-1 DW and 0.93 g L-1 DW respectively), and under 15 °C for N. cf. shiloi (2.2 g L-1 DW). The siliceous skeletons of the strains were purified with hydrogen peroxide and characterized by SEM, EDS, the N2 adsorption/desorption, XRD, TGA, and ATR-FTIR. The porous biosilica (20 mg DW) obtained from the strains i.e. SZCZCH193, SZCZM1342, SZCZP1809, showed efficiency in 77.6%, 96.8%, and 98.1% of 14 mg L-1 MB removal under pH 7 for 180 min, and the maximum adsorption capacity was calculated as 8.39, 19.02, and 15.17 mg g-1, respectively. Additionally, it was possible to increase the MB removal efficiency in alkaline (pH = 11) conditions up to 99.08% for SZCZP1809 after 120 min. Modelling revealed that the adsorption of MB follows Pseudo-first order, Bangham's pore diffusion and Sips isotherm models.
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Affiliation(s)
- Aleksandra Golubeva
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383, Szczecin, Poland.
| | - Piya Roychoudhury
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383, Szczecin, Poland
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383, Szczecin, Poland
| | - Jagoda Pałczyńska
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Toruń, Poland
| | - Oleksandra Pryshchepa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland
| | - Piotr Piszczek
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland
| | - Michał Gloc
- Faculty of Materials Science and Engineering, Warsaw University of Technology, Wołoska 141, 02-507, Warsaw, Poland
| | - Renata Dobrucka
- Faculty of Materials Science and Engineering, Warsaw University of Technology, Wołoska 141, 02-507, Warsaw, Poland
- Department of Industrial Products and Packaging Quality, Institute of Quality Science, Poznań University of Economics and Business, al. Niepodległości 10, 61-875, Poznan, Poland
| | - Agnieszka Feliczak-Guzik
- Department of Applied Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Izabela Nowak
- Department of Applied Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Krzysztof J Kurzydłowski
- Faculty of Mechanical Engineering, Bialystok University of Technology, ul. Wiejska 45 c, 15-351, Bialystok, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Toruń, Poland
- Prof. Jan Czochralski Kuyavian-Pomeranian Research and Development Centre, Krasińskiego 4, 87-100, Toruń, Poland
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383, Szczecin, Poland
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9
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Golubeva A, Roychoudhury P, Dąbek P, Pryshchepa O, Pomastowski P, Pałczyńska J, Piszczek P, Gloc M, Dobrucka R, Feliczak-Guzik A, Nowak I, Buszewski B, Witkowski A. Removal of the Basic and Diazo Dyes from Aqueous Solution by the Frustules of Halamphora cf. salinicola (Bacillariophyta). Mar Drugs 2023; 21:md21050312. [PMID: 37233506 DOI: 10.3390/md21050312] [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: 05/08/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Industrial wastes with hazardous dyes serve as a major source of water pollution, which is considered to have an enormous impact on public health. In this study, an eco-friendly adsorbent, the porous siliceous frustules extracted from the diatom species Halamphora cf. salinicola, grown under laboratory conditions, has been identified. The porous architecture and negative surface charge under a pH of 7, provided by the various functional groups via Si-O, N-H, and O-H on these surfaces, revealed by SEM, the N2 adsorption/desorption isotherm, Zeta-potential measurement, and ATR-FTIR, respectively, made the frustules an efficient mean of removal of the diazo and basic dyes from the aqueous solutions, 74.9%, 94.02%, and 99.81% against Congo Red (CR), Crystal Violet (CV), and Malachite Green (MG), respectively. The maximum adsorption capacities were calculated from isotherms, as follows: 13.04 mg g-1, 41.97 mg g-1, and 33.19 mg g-1 against CR, CV, and MG, respectively. Kinetic and isotherm models showed a higher correlation to Pore diffusion and Sips models for CR, and Pseudo-Second Order and Freundlich models for CV and MG. Therefore, the cleaned frustules of the thermal spring-originated diatom strain Halamphora cf. salinicola could be used as a novel adsorbent of a biological origin against anionic and basic dyes.
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Affiliation(s)
- Aleksandra Golubeva
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
| | - Piya Roychoudhury
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
| | - Oleksandra Pryshchepa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Jagoda Pałczyńska
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
| | - Piotr Piszczek
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
| | - Michał Gloc
- Faculty of Materials Science and Engineering, Warsaw University of Technology, Wołoska 141, 02-507 Warsaw, Poland
| | - Renata Dobrucka
- Faculty of Materials Science and Engineering, Warsaw University of Technology, Wołoska 141, 02-507 Warsaw, Poland
- Department of Industrial Products and Packaging Quality, Institute of Quality Science, Poznań University of Economics and Business, al. Niepodległości 10, 61-875 Poznan, Poland
| | - Agnieszka Feliczak-Guzik
- Department of Applied Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Izabela Nowak
- Department of Applied Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
- Prof. Jan Czochralski Kuyavian-Pomeranian Research & Development Centre, Krasińskiego 4, 87-100 Toruń, Poland
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
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10
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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.
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11
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Merdy P, Meunier JD, Ziarelli F, Lucas Y. Evidence of humic acid-aluminium‑silicon complexes under controlled conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154601. [PMID: 35307449 DOI: 10.1016/j.scitotenv.2022.154601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
The chemistry of silicon (Si), the second most abundant element in soil after oxygen, is not yet fully understood in the soil-water-plant continuum. Although Si is widely accepted as an element that has little or no interaction with natural organic matter, some data seems to show the opposite. To identify a potential interaction between natural organic matter and Si, batch experiments were achieved at various pH and Si concentrations, involving also Al3+ as a common ion in soil and using humic acid (HA) as a typical model for natural organic matter. Several complementary techniques were used to characterize the possible complexes formed in the dissolved or solid phases: molecular fluorescence spectroscopy, 29Si solid-state NMR, Fourier transform infrared spectroscopy, quantification of Si, Al and organic carbon, and nanoparticle size distribution. These tools revealed that humic acid indeed interacts, but weakly, with Si alone. In the presence of Al, however, a ternary complex HA-Al-Si forms, likely with Al as the bridging atom. The presence of Si promotes the maintenance of both Al and dissolved organic matter (DOM) in solution, which is likely to modify the result or the kinetics of pedogenesis. Such complexes can also play a role in the control of Al toxicity towards plants and probably also exists with other metals, such as Fe or Mn, and other metalloids such as As.
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Affiliation(s)
- Patricia Merdy
- Université de Toulon, Aix Marseille Univ, CNRS, IM2NP, 83041 Toulon CEDEX 9, France.
| | | | - Fabio Ziarelli
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM, FR1739, 13013 Marseille, France
| | - Yves Lucas
- Université de Toulon, Aix Marseille Univ, CNRS, IM2NP, 83041 Toulon CEDEX 9, France
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12
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Zepernick BN, Gann ER, Martin RM, Pound HL, Krausfeldt LE, Chaffin JD, Wilhelm SW. Elevated pH Conditions Associated With Microcystis spp. Blooms Decrease Viability of the Cultured Diatom Fragilaria crotonensis and Natural Diatoms in Lake Erie. Front Microbiol 2021; 12:598736. [PMID: 33717001 PMCID: PMC7943883 DOI: 10.3389/fmicb.2021.598736] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacterial Harmful Algal Blooms (CyanoHABs) commonly increase water column pH to alkaline levels ≥9.2, and to as high as 11. This elevated pH has been suggested to confer a competitive advantage to cyanobacteria such as Microcystis aeruginosa. Yet, there is limited information regarding the restrictive effects bloom-induced pH levels may impose on this cyanobacterium’s competitors. Due to the pH-dependency of biosilicification processes, diatoms (which seasonally both precede and proceed Microcystis blooms in many fresh waters) may be unable to synthesize frustules at these pH levels. We assessed the effects of pH on the ecologically relevant diatom Fragilaria crotonensis in vitro, and on a Lake Erie diatom community in situ. In vitro assays revealed F. crotonensis monocultures exhibited lower growth rates and abundances when cultivated at a starting pH of 9.2 in comparison to pH 7.7. The suppressed growth trends in F. crotonensis were exacerbated when co-cultured with M. aeruginosa at pH conditions and cell densities that simulated a cyanobacteria bloom. Estimates demonstrated a significant decrease in silica (Si) deposition at alkaline pH in both in vitro F. crotonensis cultures and in situ Lake Erie diatom assemblages, after as little as 48 h of alkaline pH-exposure. These observations indicate elevated pH negatively affected growth rate and diatom silica deposition; in total providing a competitive disadvantage for diatoms. Our observations demonstrate pH likely plays a significant role in bloom succession, creating a potential to prolong summer Microcystis blooms and constrain diatom fall resurgence.
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Affiliation(s)
- Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Helena L Pound
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lauren E Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Justin D Chaffin
- F.T. Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put-in-Bay, OH, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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13
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Thangaraj S, Palanisamy SK, Zhang G, Sun J. Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress. Front Microbiol 2021; 11:554832. [PMID: 33519723 PMCID: PMC7841394 DOI: 10.3389/fmicb.2020.554832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Global warming is expected to reduce the nutrient concentration in the upper ocean and affect the physiology of marine diatoms, but the underlying molecular mechanisms controlling these physiological changes are currently unknown. To understand these mechanisms, here we investigated iTRAQ based proteomic profiling of diatom Skeletonema dohrnii in a multifactorial experimental with a combining change of temperature and silicate concentrations. In total, 3369 differently abundant proteins were detected in four different environmental conditions, and the function of all proteins was identified using Gene Ontology and KEGG pathway analysis. For discriminating the proteome variation among samples, multivariate statistical analysis (PCA, PLS-DA) was performed by comparing the protein ratio differences. Further, performing pathway analysis on diatom proteomes, we here demonstrated downregulation of photosynthesis, carbon metabolism, and ribosome biogenesis in the cellular process that leads to decrease the oxidoreductase activity and affects the cell cycle of the diatom. Using PLS-DA VIP score plot analysis, we identified 15 protein biomarkers for discriminating studied samples. Of these, five proteins or gene (rbcL, PRK, atpB, DNA-binding, and signal transduction) identified as key biomarkers, induced by temperature and silicate stress in diatom metabolism. Our results show that proteomic finger-printing of S. dohrnii with different environmental conditions adds biological information that strengthens marine phytoplankton proteome analysis.
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Affiliation(s)
| | - Satheesh Kumar Palanisamy
- Department of Zoology, School of Natural Science, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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14
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Abdelhamid MAA, Pack SP. Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications. Acta Biomater 2021; 120:38-56. [PMID: 32447061 DOI: 10.1016/j.actbio.2020.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea.
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15
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Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10238738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation.
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16
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Nawaz MA, Azeem F, Zakharenko AM, Lin X, Atif RM, Baloch FS, Chan TF, Chung G, Ham J, Sun S, Golokhvast KS. In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes. PLANTS 2020; 9:plants9111612. [PMID: 33233677 PMCID: PMC7709012 DOI: 10.3390/plants9111612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/29/2022]
Abstract
Silicon (Si) accumulation protects plants from biotic and abiotic stresses. It is transported and distributed within the plant body through a cooperative system of channel type (e.g., OsLsi1) and efflux (Lsi2s e.g., OsLsi2) Si transporters (SITs) that belong to Noduline-26 like intrinsic protein family of aquaporins and an uncharacterized anion transporter family, respectively. Si is deposited in plant tissues as phytoliths and the process is known as biosilicification but the knowledge about the proteins involved in this process is limited. In the present study, we explored channel type SITs and Lsi2s, and siliplant1 protein (Slp1) in 80 green plant species. We found 80 channel type SITs and 133 Lsi2s. The channel type SITs characterized by the presence of two NPA motifs, GSGR or STAR selectivity filter, and 108 amino acids between two NPA motifs were absent from Chlorophytes, while Streptophytes evolved two different types of channel type SITs with different selectivity filters. Both channel type SITs and Lsi2s evolved two types of gene structures each, however, Lsi2s are ancient and were also found in Chlorophyta. Homologs of Slp1 (225) were present in almost all Streptophytes regardless of their Si accumulation capacity. In Si accumulator plant species, the Slp1s were characterized by the presence of H, D-rich domain, P, K, E-rich domain, and P, T, Y-rich domain, while moderate Si accumulators lacked H, D-rich domain and P, T, Y-rich domains. The digital expression analysis and coexpression networks highlighted the role of channel type and Lsi2s, and how Slp1 homologs were ameliorating plants’ ability to withstand different stresses by co-expressing with genes related to structural integrity and signaling. Together, the in-silico exploration made in this study increases our knowledge of the process of biosilicification in plants.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Laboratory of Bio-Economics and Biotechnology, Department of Bio-Economics and Food Safety, School of Economics and Management, Far Eastern Federal University, 690950 Vladivostok, Russia;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | | | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey;
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Junghee Ham
- Department of Health Policy and Management, Wonkwang University, Iksan, Jeonbuk 54538, Korea;
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
- Correspondence: (S.S.); (K.S.G.)
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 42, 44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia;
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, FEB RAS, 7 Radio street, 690014 Vladivostok, Russia
- Correspondence: (S.S.); (K.S.G.)
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17
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Petkowski JJ, Bains W, Seager S. On the Potential of Silicon as a Building Block for Life. Life (Basel) 2020; 10:E84. [PMID: 32532048 PMCID: PMC7345352 DOI: 10.3390/life10060084] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Despite more than one hundred years of work on organosilicon chemistry, the basis for the plausibility of silicon-based life has never been systematically addressed nor objectively reviewed. We provide a comprehensive assessment of the possibility of silicon-based biochemistry, based on a review of what is known and what has been modeled, even including speculative work. We assess whether or not silicon chemistry meets the requirements for chemical diversity and reactivity as compared to carbon. To expand the possibility of plausible silicon biochemistry, we explore silicon's chemical complexity in diverse solvents found in planetary environments, including water, cryosolvents, and sulfuric acid. In no environment is a life based primarily around silicon chemistry a plausible option. We find that in a water-rich environment silicon's chemical capacity is highly limited due to ubiquitous silica formation; silicon can likely only be used as a rare and specialized heteroatom. Cryosolvents (e.g., liquid N2) provide extremely low solubility of all molecules, including organosilicons. Sulfuric acid, surprisingly, appears to be able to support a much larger diversity of organosilicon chemistry than water.
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Affiliation(s)
- Janusz Jurand Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; (W.B.); (S.S.)
| | - William Bains
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; (W.B.); (S.S.)
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; (W.B.); (S.S.)
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA
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18
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Michaelis M, Fayyaz A, Parambath M, Koeppen S, Ciacchi LC, Hanley QS, Perry CC. Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14230-14237. [PMID: 31609123 DOI: 10.1021/acs.langmuir.9b03085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC50), binding affinity (Ki), and binding free energy (ΔGads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | | | | | - Susan Koeppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
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19
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Nawaz MA, Zakharenko AM, Zemchenko IV, Haider MS, Ali MA, Imtiaz M, Chung G, Tsatsakis A, Sun S, Golokhvast KS. Phytolith Formation in Plants: From Soil to Cell. PLANTS (BASEL, SWITZERLAND) 2019; 8:E249. [PMID: 31357485 PMCID: PMC6724085 DOI: 10.3390/plants8080249] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/19/2023]
Abstract
Silica is deposited extra- and intracellularly in plants in solid form, as phytoliths. Phytoliths have emerged as accepted taxonomic tools and proxies for reconstructing ancient flora, agricultural economies, environment, and climate. The discovery of silicon transporter genes has aided in the understanding of the mechanism of silicon transport and deposition within the plant body and reconstructing plant phylogeny that is based on the ability of plants to accumulate silica. However, a precise understanding of the process of silica deposition and the formation of phytoliths is still an enigma and the information regarding the proteins that are involved in plant biosilicification is still scarce. With the observation of various shapes and morphologies of phytoliths, it is essential to understand which factors control this mechanism. During the last two decades, significant research has been done in this regard and silicon research has expanded as an Earth-life science superdiscipline. We review and integrate the recent knowledge and concepts on the uptake and transport of silica and its deposition as phytoliths in plants. We also discuss how different factors define the shape, size, and chemistry of the phytoliths and how biosilicification evolved in plants. The role of channel-type and efflux silicon transporters, proline-rich proteins, and siliplant1 protein in transport and deposition of silica is presented. The role of phytoliths against biotic and abiotic stress, as mechanical barriers, and their use as taxonomic tools and proxies, is highlighted.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia
| | | | | | - Muhammad Sajjad Haider
- Department of Forestry, College of Agriculture, University of Sargodha, 40100 Sargodha, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, 38040 Faisalabad, Pakistan
| | - Muhammad Imtiaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, 38040 Faisalabad, Pakistan
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, 59626 Yeosu-Si, Korea
| | - Aristides Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion GR-71003, Crete, Greece
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, 59626 Yeosu-Si, Korea.
| | - Kirill Sergeyevich Golokhvast
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia.
- Pacific Geographical Institute, FEB RAS, 7 Radio street, Vladivostok 690014, Russia.
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20
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Zhang Y, Lin X, Shi X, Lin L, Luo H, Li L, Lin S. Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom. Front Microbiol 2019; 10:590. [PMID: 30967855 PMCID: PMC6439486 DOI: 10.3389/fmicb.2019.00590] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
Diatoms and dinoflagellates dominate coastal marine phytoplankton communities as major players of marine biogeochemical cycles and their seasonal succession often leads to harmful algal blooms (HABs). What regulates their respective dominances and the development of the HABs remains elusive. Here we conducted time-sequential metatranscriptomic profiling on a natural assemblage that evolved from diatom dominance to a dinoflagellate bloom to interrogate the underlying major metabolic and ecological drivers. Data reveals similarity between diatoms and dinoflagellates in exhibiting high capacities of energy production, nutrient acquisition, and stress protection in their respective dominance stages. The diatom-to-dinoflagellate succession coincided with an increase in turbidity and sharp declines in silicate and phosphate availability, concomitant with the transcriptomic shift from expression of silicate uptake and urea utilization genes in diatoms to that of genes for light harvesting, diversified phosphorus acquisition and autophagy-based internal nutrient recycling in dinoflagellates. Furthermore, the diatom-dominant community featured strong potential to carbohydrate metabolism and a strikingly high expression of trypsin potentially promoting frustule building. In contrast, the dinoflagellate bloom featured elevated expression of xanthorhodopsin, and antimicrobial defensin genes, indicating potential importance of energy harnessing and microbial defense in bloom development. This study sheds light on mechanisms potentially governing diatom- and dinoflagellate-dominance and regulating bloom development in the natural environment and raises new questions to be addressed in future studies.
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Affiliation(s)
- Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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21
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Povarova NV, Barinov NA, Baranov MS, Markina NM, Varizhuk AM, Pozmogova GE, Klinov DV, Kozhemyako VB, Lukyanov KA. Efficient silica synthesis from tetra(glycerol)orthosilicate with cathepsin- and silicatein-like proteins. Sci Rep 2018; 8:16759. [PMID: 30425281 PMCID: PMC6233156 DOI: 10.1038/s41598-018-34965-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Silicateins play a key role in biosynthesis of spicules in marine sponges; they are also capable to catalyze formation of amorphous silica in vitro. Silicateins are highly homologous to cathepsins L – a family of cysteine proteases. Molecular mechanisms of silicatein activity remain controversial. Here site-directed mutagenesis was used to clarify significance of selected residues in silica polymerization. A number of mutations were introduced into two sponge proteins – silicatein A1 and cathepsin L from Latrunculia oparinae, as well as into human cathepsin L. First direction was alanine scanning of the proposed catalytic residues. Also, reciprocal mutations were introduced at selected positions that differ between cathepsins L and silicateins. Surprisingly, all the wild type and mutant proteins were capable to catalyze amorphous silica formation with a water-soluble silica precursor tetra(glycerol)orthosilicate. Some mutants possessed several-fold enhanced silica-forming activity and can potentially be useful for nanomaterial synthesis applications. Our findings contradict to the previously suggested mechanisms of silicatein action via a catalytic triad analogous to that in cathepsins L. Instead, a surface-templated biosilification by silicateins and related proteins can be proposed.
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Affiliation(s)
- Natalia V Povarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997, Moscow, Russia
| | - Nadezhda M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Valery B Kozhemyako
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022, Vladivostok, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
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Guo J, Ling S, Li W, Chen Y, Li C, Omenetto FG, Kaplan DL. Coding cell micropatterns through peptide inkjet printing for arbitrary biomineralized architectures. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1800228. [PMID: 32440260 PMCID: PMC7241601 DOI: 10.1002/adfm.201800228] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 05/20/2023]
Abstract
Well-designed micropatterns present in native tissues and organs involve changes in extracellular matrix compositions, cell types and mechanical properties to reflect complex biological functions. However, the design and fabrication of these micropatterns in vitro to meet task-specific biomedical applications remains a challenge. A de novo design strategy to code and synthesize functional micropatterns is presented to engineer cell alignment through the integration of aqueous-peptide inkjet printing and site-specific biomineralization. The inkjet printing provides direct writing of macroscopic biosilica selective peptide-R5 patterns with micrometer-scale resolution on the surface of a biopolymer (silk) hydrogel. This is combined with in situ biomineralization of the R5 peptide for site-specific growth of silica nanoparticles on the micropatterns, avoiding the use of harsh chemicals or complex processing. The functional micropatterned systems are used to align human mesenchymal stem cells and bovine serum albumin. This combination of peptide printing and site-specific biomineralization provides a new route for developing cost-effective micropatterns, with implications for broader materials designs. Coding cell micropatterns through peptide inkjet printing for arbitrary biomineralized architectures is demonstrated here. The functional micropatterned systems are used to align human mesenchymal stem cells and bovine serum albumin in vitro, avoiding the use of harsh chemicals or complex processing, while providing potential applications in developing cost-effective micropatterns to meet task-specific biomedical applications.
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Affiliation(s)
- Jin Guo
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
| | - Shengjie Ling
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
| | - Wenyi Li
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
| | - Chunmei Li
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
| | | | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, MA 02155, USA
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23
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Arinbasarova AY, Machulin AV, Biryukova EN, Sorokin VV, Medentsev AG, Suzina NE. Structural changes in the cell envelope of Yarrowia lipolytica yeast under stress conditions. Can J Microbiol 2018; 64:359-365. [PMID: 29444416 DOI: 10.1139/cjm-2018-0034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ultrastructural changes in the cell envelope of the yeast Yarrowia lipolytica as a stress response were examined using electron microscopy. The formation of new cellular surface structures, including membrane vesicles, pore channels, and wall surface globules, were shown for the first time under conditions of oxidative (endogenous and exogenous) or thermal stress. This demonstrates once again that under stress conditions the microorganisms reveal properties previously unknown for them. Particularly noteworthy is the accumulation of silicon in the surface globules, which was revealed by X-ray microanalysis of the elemental composition of thin sections of cells. A multilayered plasmalemma instead of a 3-layered one is also characteristic for stressed cells. The envelope modifications above were observed only as a stress response and were not detected in stationary-growth-phase yeast cells that assume different physiological states. A decrease in the intracellular level of cAMP allows us to assume that a common factor activates defensive mechanisms thus explaining the similarity of the response under different stress conditions. The data presented not only enable visualization of the yeast stress response and add to our awareness of the diversity of adaptive reactions, but they also raise questions about the interrelations of the stress phenomena and their functional necessity in the cell.
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Affiliation(s)
- Anna Yu Arinbasarova
- a G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow 142290, Russia
| | - Andrey V Machulin
- a G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow 142290, Russia
| | - Elena N Biryukova
- a G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow 142290, Russia
| | - Vladimir V Sorokin
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 33, Building Leninsky Avenue, Moscow 119071, Russia
| | - Alexander G Medentsev
- a G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow 142290, Russia
| | - Natalya E Suzina
- a G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow 142290, Russia
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Sprenger KG, Prakash A, Drobny G, Pfaendtner J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1199-1207. [PMID: 28981294 DOI: 10.1021/acs.langmuir.7b02868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
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25
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Song IW, Park H, Park JH, Kim H, Kim SH, Yi S, Jaworski J, Sang BI. Silica formation with nanofiber morphology via helical display of the silaffin R5 peptide on a filamentous bacteriophage. Sci Rep 2017; 7:16212. [PMID: 29176625 PMCID: PMC5701198 DOI: 10.1038/s41598-017-16278-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/09/2017] [Indexed: 11/17/2022] Open
Abstract
Biological systems often generate unique and useful structures, which can have industrial relevance either as direct components or as an inspiration for biomimetic materials. For fabrication of nanoscale silica structures, we explored the use of the silaffin R5 peptide from Cylindrotheca fusiformis expressed on the surface of the fd bacteriophage. By utilizing the biomineralizing peptide component displayed on the bacteriophage surface, we found that low concentrations (0.09 mg/mL of the R5 bacteriophage, below the concentration range used in other studies) could be used to create silica nanofibers. An additional benefit of this approach is the ability of our R5-displaying phage to form silica materials without the need for supplementary components, such as aminopropyl triethoxysilane, that are typically used in such processes. Because this method for silica formation can occur under mild conditions when implementing our R5 displaying phage system, we may provide a relatively simple, economical, and environmentally friendly process for creating silica nanomaterials.
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Affiliation(s)
- In-Wong Song
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hyojung Park
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jung Han Park
- Science&Technology Policy Coordination Division, Ministry of Science, ICT and Future Planning, 47 Gwanmun-ro, Gwacheon-si, Gyeonggi-do, 13809, Republic of Korea
| | - Hyunook Kim
- Department of Environmental Engineering, 163 Seoulsiripdaero, Dongdaemun-gu, The University of Seoul, Seoul, 02504, Republic of Korea
| | - Seong Hun Kim
- Department of Organic and Nano Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sung Yi
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Justyn Jaworski
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA.
| | - Byoung-In Sang
- Department of Fuel Cell and Hydrogen Technology, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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26
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Guo J, Li C, Ling S, Huang W, Chen Y, Kaplan DL. Multiscale design and synthesis of biomimetic gradient protein/biosilica composites for interfacial tissue engineering. Biomaterials 2017; 145:44-55. [PMID: 28843732 PMCID: PMC5610098 DOI: 10.1016/j.biomaterials.2017.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/16/2017] [Accepted: 08/14/2017] [Indexed: 01/13/2023]
Abstract
Continuous gradients present at tissue interfaces such as osteochondral systems, reflect complex tissue functions and involve changes in extracellular matrix compositions, cell types and mechanical properties. New and versatile biomaterial strategies are needed to create suitable biomimetic engineered grafts for interfacial tissue engineering. Silk protein-based composites, coupled with selective peptides with mineralization domains, were utilized to mimic the soft-to-hard transition in osteochondral interfaces. The gradient composites supported tunable mineralization and mechanical properties corresponding to the spatial concentration gradient of the mineralization domains (R5 peptide). The composite system exhibited continuous transitions in terms of composition, structure and mechanical properties, as well as cytocompatibility and biodegradability. The gradient silicified silk/R5 composites promoted and regulated osteogenic differentiation of human mesenchymal stem cells in an osteoinductive environment in vitro. The cells differentiated along the composites in a manner consistent with the R5-gradient profile. This novel biomimetic gradient biomaterial design offers a useful approach to meet a broad range of needs in regenerative medicine.
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Affiliation(s)
- Jin Guo
- Department of Chemical and Biological Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA; Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Chunmei Li
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Shengjie Ling
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA.
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27
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Spinthaki A, Zerfaß C, Paulsen H, Hobe S, Demadis KD. Pleiotropic Role of Recombinant Silaffin-Like Cationic Polypeptide P5S3: Peptide-Induced Silicic Acid Stabilization, Silica Formation and Inhibition of Silica Dissolution. ChemistrySelect 2016. [DOI: 10.1002/slct.201601086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Argyro Spinthaki
- Crystal Engineering, Growth and Design Laboratory; Department of Chemistry; University of Crete; Voutes Campus, Heraklion Crete 71003 Greece
| | - Christian Zerfaß
- Department of Biology; Institute of General Botany; University of Mainz; Johannes-von-Müllerweg 6 55099 Mainz Germany
- Graduate School Materials Science in Mainz; University of Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Harald Paulsen
- Department of Biology; Institute of General Botany; University of Mainz; Johannes-von-Müllerweg 6 55099 Mainz Germany
| | - Stephan Hobe
- Department of Biology; Institute of General Botany; University of Mainz; Johannes-von-Müllerweg 6 55099 Mainz Germany
| | - Konstantinos D. Demadis
- Crystal Engineering, Growth and Design Laboratory; Department of Chemistry; University of Crete; Voutes Campus, Heraklion Crete 71003 Greece
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28
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Dinjaski N, Ebrahimi D, Ling S, Shah S, Buehler MJ, Kaplan DL. Integrated Modeling and Experimental Approaches to Control Silica Modification of Design Silk-Based Biomaterials. ACS Biomater Sci Eng 2016; 3:2877-2888. [PMID: 33418709 DOI: 10.1021/acsbiomaterials.6b00236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mineralized polymeric biomaterials provide useful options toward mechanically robust systems for some tissue repairs. Silks as a mechanically robust protein-based material provide a starting point for biomaterial options, particularly when combined with silica toward organic-inorganic hybrid systems. To further understand the interplay between silk proteins and silica related to material properties, we systematically study the role of three key domains in bioengineered spider silk fusion proteins with respect to β-sheet formation and mineralization: (i) a core silk domain for materials assembly, (ii) a histidine tag for purification, and (iii) a silicification domain for mineralization. Computational simulations are used to identify the effect of each domain on the protein folding and accessibility of positively charged amino acids for silicification and predictions are then compared with experimental data. The results show that the addition of the silica and histidine domains reduces β-sheet structure in the materials, and increases solvent-accessible surface area to the positive charged amino acids, leading to higher levels of silica precipitation. Moreover, the simulations show that the location of the charged biomineralization domain has small effect on the protein folding and consequently surface exposure of charged amino acids. Those surfaces display correlation with the amount of silicification in experiments. The results demonstrate that the exposure of the positively charged amino acids impacts protein function related to mineralization. In addition, processing parameters (solvating agent, the method of β-sheet induction and temperature) affect protein secondary structure, folding and function. This integrated modeling and experimental approach provides insight into sequence-structure-function relationships for control of mineralized protein biomaterial structures.
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Affiliation(s)
- Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Davoud Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shengjie Ling
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Suraj Shah
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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Schröder HC, Grebenjuk VA, Wang X, Müller WEG. Hierarchical architecture of sponge spicules: biocatalytic and structure-directing activity of silicatein proteins as model for bioinspired applications. BIOINSPIRATION & BIOMIMETICS 2016; 11:041002. [PMID: 27452043 DOI: 10.1088/1748-3190/11/4/041002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Since the first description of the silicateins, a group of enzymes that mediate the formation of the amorphous, hydrated biosilica of the skeleton of the siliceous sponges, much progress has been achieved in the understanding of this biomineralization process. These discoveries include, beside the proof of the enzymatic nature of the sponge biosilica formation, the dual property of the enzyme, to act both as a structure-forming and structure-guiding protein, and the demonstration that the initial product of silicatein is a soft, gel-like material that has to undergo a maturation process during which it achieves its favorable physical-chemical properties allowing the development of various technological or medical applications. This process comprises the hardening of the material by the removal of water and ions, its cast-molding to specific morphologies, as well as the fusion of the biosilica nanoparticles through a biosintering mechanism. The discovery that the enzymatically formed biosilica is morphogenetically active and printable also opens new applications in rapid prototyping and three-dimensional bioprinting of customized scaffolds/implants for biomedical use.
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Affiliation(s)
- Heinz C Schröder
- Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
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30
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Şen EH, Ide S, Bayari SH, Hill M. Micro- and nano-structural characterization of six marine sponges of the class Demospongiae. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:831-842. [DOI: 10.1007/s00249-016-1127-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 10/22/2022]
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The C-Terminal Zwitterionic Sequence of CotB1 Is Essential for Biosilicification of the Bacillus cereus Spore Coat. J Bacteriol 2015; 198:276-82. [PMID: 26503850 DOI: 10.1128/jb.00447-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/15/2015] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Silica is deposited in and around the spore coat layer of Bacillus cereus, and enhances the spore's acid resistance. Several peptides and proteins, including diatom silaffin and silacidin peptides, are involved in eukaryotic silica biomineralization (biosilicification). Homologous sequence search revealed a silacidin-like sequence in the C-terminal region of CotB1, a spore coat protein of B. cereus. The negatively charged silacidin-like sequence is followed by a positively charged arginine-rich sequence of 14 amino acids, which is remarkably similar to the silaffins. These sequences impart a zwitterionic character to the C terminus of CotB1. Interestingly, the cotB1 gene appears to form a bicistronic operon with its paralog, cotB2, the product of which, however, lacks the C-terminal zwitterionic sequence. A ΔcotB1B2 mutant strain grew as fast and formed spores at the same rate as wild-type bacteria but did not show biosilicification. Complementation analysis showed that CotB1, but neither CotB2 nor C-terminally truncated mutants of CotB1, could restore the biosilicification activity in the ΔcotB1B2 mutant, suggesting that the C-terminal zwitterionic sequence of CotB1 is essential for the process. We found that the kinetics of CotB1 expression, as well as its localization, correlated well with the time course of biosilicification and the location of the deposited silica. To our knowledge, this is the first report of a protein directly involved in prokaryotic biosilicification. IMPORTANCE Biosilicification is the process by which organisms incorporate soluble silicate in the form of insoluble silica. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification was not studied until recently. We previously demonstrated that biosilicification occurs in Bacillus cereus and its close relatives, and that silica is deposited in and around a spore coat layer as a protective coating against acid. The present study reveals that a B. cereus spore coat protein, CotB1, which carried a C-terminal zwitterionic sequence, is essential for biosilicification. Our results provide the first insight into mechanisms required for biosilicification in prokaryotes.
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Lauritano C, Orefice I, Procaccini G, Romano G, Ianora A. Key genes as stress indicators in the ubiquitous diatom Skeletonema marinoi. BMC Genomics 2015; 16:411. [PMID: 26018764 PMCID: PMC4445783 DOI: 10.1186/s12864-015-1574-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The dense phytoplankton blooms that characterize productive regions and seasons in the oceans are dominated, from high to low latitudes and from coast line to open ocean, by comparatively few, often cosmopolitan species of diatoms. These key dominant species may undergo dramatic changes due to global climate change. RESULTS In order to identify molecular stress-indicators for the ubiquitous diatom species Skeletonema marinoi, we tested stress-related genes in different environmental conditions (i.e. nutrient starvation/depletion, CO2-enrichment and combined effects of these stressors) using RT-qPCR. The data show that these stressors impact algal growth rate, inducing early aging and profound changes in expression levels of the genes of interest. CONCLUSIONS Most analyzed genes (e.g. antioxidant-related and aldehyde dehydrogenases) were strongly down-regulated which may indicate a strategy to avoid unnecessary over-investment in their respective proteins. By contrast, key genes were activated (e.g. HSPs, GOX) which may allow the diatom species to better cope with adverse conditions. We propose the use of this panel of genes as early bio-indicators of environmental stress factors in a changing ocean.
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Affiliation(s)
- Chiara Lauritano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Ida Orefice
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | | | - Giovanna Romano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Adrianna Ianora
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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33
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Serine-rich protein is a novel positive regulator for silicon accumulation in mangrove. Gene 2014; 556:170-81. [PMID: 25479011 DOI: 10.1016/j.gene.2014.11.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 11/09/2014] [Accepted: 11/23/2014] [Indexed: 11/21/2022]
Abstract
Silicon (Si) plays an important role in reducing plant susceptibility against a variety of different biotic and abiotic stresses; and also has an important regulatory role in soil to avoid heavy metal toxicity and providing suitable growing conditions for plants. A full-length cDNAs of 696bp of serine-rich protein was cloned from mangrove plant (Rhizophora apiculata) by amplification of cDNA ends from an expressed sequence tag homologous to groundnut (Arachis hypogaea), submitted to NCBI (KF211374). This serine-rich protein gene encodes a deduced protein of 223 amino acids. The transcript titre of the serine-rich protein was found to be strongly enriched in roots compared with the leaves of two month old mangrove plants and expression level of this serine-rich protein was found to be strongly induced when the mangrove seedlings were exposed to SiO2. Expression of the serine-rich protein transgenic was detected in transgenic Arabidopsis thaliana, where the amount of serine increased from 1.02 to 37.8mg/g. The same trend was also seen in Si content in the roots (14.3%) and leaves (7.4%) of the transgenic A. thaliana compared to the wild-type plants under Si treatment. The biological results demonstrated that the accumulation of the serine amino acid in the vegetative tissues of the transgenic plants enhanced their ability to absorb and accumulate more Si in the roots and leaves and suggests that the serine-rich protein gene has potential for use in genetic engineering of different stress tolerance characteristics.
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Mladenović Ž, Johansson A, Willman B, Shahabi K, Björn E, Ransjö M. Soluble silica inhibits osteoclast formation and bone resorption in vitro. Acta Biomater 2014; 10:406-18. [PMID: 24016843 DOI: 10.1016/j.actbio.2013.08.039] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 11/18/2022]
Abstract
Several studies have suggested that silicon (Si) may be essential for the normal development of connective tissue and the skeleton. Positive effects of Si from the diet as well as from Si-containing biomaterials, such as bioactive glass 45S5 (BG), have been demonstrated. Studies have reported that Si stimulates osteoblast proliferation and differentiation. However, the effects of Si on osteoclasts have not been directly addressed. The purpose of the present in vitro study was to clarify if Si has regulatory effects on osteoclast formation and bone resorption. The effects of BG, BG dissolution extracts and Si containing cell culture medium were investigated in a mouse calvarial bone resorption assay and osteoclast formation assays (mouse bone marrow cultures and RAW264.7 cell cultures). We conclude from our results that Si causes significant inhibition of osteoclast phenotypic gene expressions, osteoclast formation and bone resorption in vitro. In conclusion, the present study suggests that Si has a dual nature in bone metabolism with stimulatory effects on osteoblasts and inhibitory effects on osteoclasts. This suggested property of Si might be interesting to further explore in future biomaterials for treatments of bone defects in patients.
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Affiliation(s)
- Živko Mladenović
- Department of Orthodontics, Institute of Odontology, Sahlgrenska Academy at University of Gothenburg, PO Box 450, SE-405 30 Göteborg, Sweden; Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, PO Box 412, SE-405 30 Göteborg, Sweden.
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Tokareva O, Jacobsen M, Buehler M, Wong J, Kaplan DL. Structure-function-property-design interplay in biopolymers: spider silk. Acta Biomater 2013; 10:1612-26. [PMID: 23962644 DOI: 10.1016/j.actbio.2013.08.020] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/06/2013] [Accepted: 08/12/2013] [Indexed: 11/17/2022]
Abstract
Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties.
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Affiliation(s)
- Olena Tokareva
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Matthew Jacobsen
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Markus Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joyce Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
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