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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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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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Li Y, He J, Zhang X, Deng X. The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification. BMC Genomics 2024; 25:560. [PMID: 38840265 PMCID: PMC11151724 DOI: 10.1186/s12864-024-10479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification. RESULTS In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima. CONCLUSIONS Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.
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Affiliation(s)
- Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
| | - Jinman He
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiuxia Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiaodong Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
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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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Ikeda T, Nakasugi Y, Nakagawa M, Matsuura SI, Ikeda T, Ishida T, Funabashi H, Hirota R, Kuroda A. Discovery of long-chain polyamines embedded in the biosilica on the Bacillus cereus spore coat. J Biosci Bioeng 2024; 137:254-259. [PMID: 38342665 DOI: 10.1016/j.jbiosc.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/13/2024]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification has only recently begun to be studied. We previously reported that biosilicification occurs in the gram-positive, spore-forming bacterium Bacillus cereus, and that silica is intracellularly deposited on the spore coat as a protective coating against acids, although the underlying mechanism is not yet fully understood. In eukaryotic biosilicifying organisms, such as diatoms and siliceous sponges, several relevant biomolecules are embedded in biogenic silica (biosilica). These biomolecules include peptides, proteins, and long-chain polyamines. In this study, we isolated organic compounds embedded in B. cereus biosilica to investigate the biomolecules involved in the prokaryotic biosilicification process and identified long-chain polyamines with a chemical structure of H2N-(CH2)4-[NH-(CH2)3]n-NH2 (n: up to 55). Our results demonstrate the common presence of long-chain polyamines in different evolutionary lineages of biosilicifying organisms, i.e., diatoms, siliceous sponges, and B. cereus, suggesting a common mechanism underlying eukaryotic and prokaryotic biosilicification.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Yukihide Nakasugi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Miki Nakagawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Shun-Ichi Matsuura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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Osorio-Rodriguez D, Metcalfe KS, McGlynn SE, Yu H, Dekas AE, Ellisman M, Deerinck T, Aristilde L, Grotzinger JP, Orphan VJ. Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation. Proc Natl Acad Sci U S A 2023; 120:e2302156120. [PMID: 38079551 PMCID: PMC10743459 DOI: 10.1073/pnas.2302156120] [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: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.
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Affiliation(s)
- Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Kyle S. Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Shawn E. McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo152-8550, Japan
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- College of Urban and Environmental Sciences, Peking University, Beijing100871, China
| | - Anne E. Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Earth System Science, Stanford University, Stanford, CA94305
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Tom Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL60208
| | - John P. Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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Wang L, Sun Y, Zhang R, Pan K, Li Y, Wang R, Zhang L, Zhou C, Li J, Li Y, Zhu B, Han J. Enhancement of hemostatic properties of Cyclotella cryptica frustule through genetic manipulation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:136. [PMID: 37710352 PMCID: PMC10503012 DOI: 10.1186/s13068-023-02389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND The silicified cell wall of diatoms, also known as frustule, shows huge potential as an outstanding bio-nanomaterial for hemostatic applications due to its high hemostatic efficiency, good biocompatibility, and ready availability. As the architectural features of the frustule determine its hemostatic performance, it is of great interest to develop an effective method to modify the frustule morphology into desired patterns to further improve hemostatic efficiency. RESULTS In this study, the gene encoding Silicalemma Associated Protein 2 (a silicalemma-spanning protein) of Cyclotella cryptica (CcSAP2) was identified as a key gene in frustule morphogenesis. Thus, it was overexpressed and knocked down, respectively. The frustule of the overexpress lines showed no obvious alteration in morphology compared to the wild type (WT), while the size, specific surface area (BET), pore volume, and pore diameter of the knockdown strains changed greatly. Particularly, the knockdown frustules achieved a more pronounced coagulation effect and in vivo hemostatic performance than the WT strains. Such observations suggested that silicalemma proteins are ideal genetic encoding targets for manipulating frustule morphology associated hemostatic properties. Furthermore, the Mantel test was adopted to identify the key morphologies associated with C. cryptica bleeding control. Finally, based on our results and recent advances, the mechanism of frustule morphogenesis was discussed. CONCLUSION This study explores a new strategy for enhancing the hemostatic efficiency of the frustule based on genetic morphology modification and may provide insights into a better understanding of the frustule morphogenesis mechanism.
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Affiliation(s)
- Lulu Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yan Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China
| | - Ruihao Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kehou Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Laoshan Laboratory, Qingdao, 266237, China
| | - Yuhang Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
| | - Lin Zhang
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315200, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China
| | - Jian Li
- School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Baohua Zhu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jichang Han
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China.
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Belshaw N, Grouneva I, Aram L, Gal A, Hopes A, Mock T. Efficient gene replacement by CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2023; 238:438-452. [PMID: 36307966 DOI: 10.1111/nph.18587] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
CRISPR/Cas enables targeted genome editing in many different plant and algal species including the model diatom Thalassiosira pseudonana. However, efficient gene targeting by homologous recombination (HR) to date is only reported for photosynthetic organisms in their haploid life-cycle phase. Here, a CRISPR/Cas construct, assembled using Golden Gate cloning, enabled highly efficient HR in a diploid photosynthetic organism. Homologous recombination was induced in T. pseudonana using sequence-specific CRISPR/Cas, paired with a dsDNA donor matrix, generating substitution of the silacidin, nitrate reductase and urease genes by a resistance cassette (FCP:NAT). Up to c. 85% of NAT-resistant T. pseudonana colonies screened positive for HR by nested PCR. Precise integration of FCP:NAT at each locus was confirmed using an inverse PCR approach. The knockout of the nitrate reductase and urease genes impacted growth on nitrate and urea, respectively, while the knockout of the silacidin gene in T. pseudonana caused a significant increase in cell size, confirming the role of this gene for cell-size regulation in centric diatoms. Highly efficient gene targeting by HR makes T. pseudonana as genetically tractable as Nannochloropsis and Physcomitrella, hence rapidly advancing functional diatom biology, bionanotechnology and biotechnological applications targeted on harnessing the metabolic potential of diatoms.
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Affiliation(s)
- Nigel Belshaw
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Irina Grouneva
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lior Aram
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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10
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Fattorini N, Maier UG. Targeting motifs in frustule-associated proteins from the centric diatom Thalassiosira pseudonana. FRONTIERS IN PLANT SCIENCE 2022; 13:1006072. [PMID: 36388477 PMCID: PMC9650480 DOI: 10.3389/fpls.2022.1006072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
The frustule of diatoms has an exceptional structure composed of inorganic and organic molecules. In the organic fraction, protein families were identified whose members are expected to have a complex cellular targeting to their final location within the frustule. Here we investigated for frustule-targeting signals two representatives of the cingulin family, the proteins CinY2 and CinW2; beside an already known, classical signal peptide, we have identified further regions involved in cellular targeting. By using these regions as a search criteria we were able to identify two new frustule proteins. In addition, we showed that the temporal regulation of the gene expression determines the final location of one cingulin. Our results therefore point to a sophisticated cellular and extracellular targeting of frustule components to build the fascinating frustule structure of a diatom.
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Affiliation(s)
- Neri Fattorini
- Department of Biology, Laboratory for Cell Biology Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Department of Biology, Laboratory for Cell Biology Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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11
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Modeling the elemental stoichiometry and silica accumulation in diatoms. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100164. [DOI: 10.1016/j.crmicr.2022.100164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Schwarz P, Steinem C. The role of the transmembrane domain of silicanin-1: Reconstitution of the full-length protein in artificial membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183921. [PMID: 35367203 DOI: 10.1016/j.bbamem.2022.183921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Biosilica formation in diatoms is a membrane-confined process that occurs in so-called silica deposition vesicles (SDVs). As SDVs have as yet not been successfully isolated, the impact of the SDV membrane on silica morphogenesis is not well understood. However, recently the first SDV transmembrane protein, silicanin-1 (Sin1) has been identified that appears to be involved in biosilica formation. In this study, we recombinantly expressed and isolated full-length Sin1 from E. coli and investigated its reconstitution behavior in artificial membranes. A reconstitution efficiency in vesicles of up to 80% was achieved by a co-micellization method. By using a chymotrypsin digest, the orientation of Sin1 in unilamellar vesicles was analyzed indicating a positioning of the large N-terminal domain to the outside of the vesicles. These proteoliposomes were capable of precipitating silica in the presence of long-chain polyamines. Supported lipid bilayers were produced by proteoliposome spreading on lipid monolayers to form continuous lipid bilayers with Sin1 confined to the membrane. Successful Sin1 reconstitution into these planar membranes was shown by means of immunostaining with purified primary anti-Sin1 and secondary fluorescent antibodies. The established planar model membrane system, amenable for surface sensitive and microscopy techniques, will pave the way to investigate SDV-membrane interactions with other SDV associated biomolecules and its role in silica biogenesis.
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Affiliation(s)
- Philipp Schwarz
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Claudia Steinem
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany; Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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13
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Danilovtseva EN, Palshin VA, Strelova MS, Lopatina IN, Kaneva EV, Zakharova NV, Annenkov VV. Functional polymers for modeling the formation of biogenic calcium carbonate and the design of new materials. POLYM ADVAN TECHNOL 2022. [DOI: 10.1002/pat.5764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elena N. Danilovtseva
- Limnological Institute Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
| | - Viktor A. Palshin
- Limnological Institute Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
| | - Mariya S. Strelova
- Limnological Institute Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
| | - Irina N. Lopatina
- Limnological Institute Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
| | - Ekaterina V. Kaneva
- Vinogradov Institute of Geochemistry Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
| | - Nataliya V. Zakharova
- Institute of Macromolecular Compounds of the Russian Academy of Sciences Saint Petersburg Russian Federation
| | - Vadim V. Annenkov
- Limnological Institute Siberian Branch of Russian Academy of Sciences Irkutsk Russian Federation
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14
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Li J, Liu P, Menguy N, Zhang X, Wang J, Benzerara K, Feng L, Sun L, Zheng Y, Meng F, Gu L, Leroy E, Hao J, Chu X, Pan Y. Intracellular silicification by early-branching magnetotactic bacteria. SCIENCE ADVANCES 2022; 8:eabn6045. [PMID: 35559677 PMCID: PMC9106300 DOI: 10.1126/sciadv.abn6045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/31/2022] [Indexed: 06/13/2023]
Abstract
Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Xingliang Zhang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life and Environments and Department of Geology, Northwest University, Xi’an 710069, China
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, SK S7N 2V3, Canada
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Lianjun Feng
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Sun
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Fanqi Meng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lin Gu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Eric Leroy
- ICMPE, University Paris East, UMR 7182, CNRS, 2-8 Rue Henri Dunant, Thiais, Cedex 94320, France
| | - Jialong Hao
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuelei Chu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Sciences, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Daus F, Xie X, Geyer A. The silica mineralisation properties of synthetic Silaffin-1A 1 ( synSil-1A 1). Org Biomol Chem 2022; 20:3387-3396. [PMID: 35362502 DOI: 10.1039/d2ob00390b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthetic monodisperse pentadecapeptide synSil-1A1 is a representative of the microdisperse mixture of the native silaffin natSil-1A1 produced by the diatom Cylindrotheca fusiformis. The octaphosphorylated zwitterionic synSil-1A1 is able to mineralise silica under slightly acidic conditions at pH 5.5, which is the physiologically relevant pH range assumed. Like the posttranslational modifications of the native silaffins, synSil-1A1 is functionalised on all four lysine and phosphorylated on all seven serine residues. We describe the synthesis of a trimethyl-δ-hydroxy-L-lysine building block, the incorporation of this choline-type amino acid in peptide synthesis and its phosphorylation, together with all further posttranslational modifications observed in the native silaffins. Quantitative structure-activity relationships from silicification experiments at high dilution reveal the unique mineralisation properties of the hyperphosphorylated peptide as a single substance and in interaction with long-chain polyamines (LCPA). Diffusion-ordered spectroscopy (DOSY) experiments reveal the formation of polyelectrolyte complexes (PEC) between synSil-1A1 and long-chain polyamines, which promotes the silicification process. The microdroplets have an overall balanced ratio of 100-150 cationic and the same number of anionic charges. The unique zwitterionic synSil-1A1 confirms the prevailing molecular model of biosilicification and validates it with quantitative data based on a single phosphopeptide species, avoiding the usual unphysiologically high concentrations of phosphate of many previous in vitro silicification experiments.
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Affiliation(s)
- Fabian Daus
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Xiulan Xie
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
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16
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Bialas F, Reichinger D, Becker CF. Biomimetic and biopolymer-based enzyme encapsulation. Enzyme Microb Technol 2021; 150:109864. [DOI: 10.1016/j.enzmictec.2021.109864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/02/2021] [Accepted: 06/29/2021] [Indexed: 12/25/2022]
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17
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Reid A, Buchanan F, Julius M, Walsh PJ. A review on diatom biosilicification and their adaptive ability to uptake other metals into their frustules for potential application in bone repair. J Mater Chem B 2021; 9:6728-6737. [PMID: 34346480 DOI: 10.1039/d1tb00322d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diatoms are unicellular eukaryotic algae that have a distinctive siliceous cell wall (frustule) with unique architectures. The nanotopography of the frustule is perfectly replicated between generations, offering a source of highly intricate and identical silica microparticles. In recent years, the ability to alter their cell wall chemistry both in terms of functionalisation with organic moieties or by incorporation of the metal ions in their frustules has increased interest in their utility for catalysis technologies, and semiconductor and biomedical applications. Herein we review the fundamental biological mechanisms in which diatoms produce their frustule and their ability to substitute different metal ions in their frustule fabrication process. The review focuses on the potential of diatom frustules as a naturally derived biomaterial in bone tissue engineering applications and how their cell walls, comprising biogenic silica, could either partially or fully incorporate other bone therapeutic metal ions, e.g., titanium or calcium, into their frustule. The use of diatom frustules in bone repair also potentially offers a 'greener', more environmentally friendly, biomaterial as they can naturally synthesise oxides of silicon and other metals into their frustules under ambient conditions at a relatively neutral pH. This process would negate the use of harsh organic chemicals and high-temperature processing conditions, often used in the fabrication of silica based biomaterials, e.g., bioactive glass.
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Affiliation(s)
- A Reid
- School of Chemistry & Chemical Engineering, Queen's University, Belfast, UK.
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18
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Ikeda T. Bacterial biosilicification: a new insight into the global silicon cycle. Biosci Biotechnol Biochem 2021; 85:1324-1331. [PMID: 33877302 DOI: 10.1093/bbb/zbab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/08/2021] [Indexed: 11/13/2022]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Biosilicifying eukaryotes, including diatoms, siliceous sponges, and higher plants, have been the targets of intense research to study the molecular mechanisms underlying biosilicification. By contrast, prokaryotic biosilicification has been less well studied, partly because the biosilicifying capability of well-known bacteria was not recognized until recently. This review summarizes recent findings on bacterial extracellular and intracellular biosilicification, the latter of which has been demonstrated only recently in bacteria. The topics discussed herein include bacterial (and archaeal) extracellular biosilicification in geothermal environments, encapsulation of Bacillus spores within a silica layer, and silicon accumulation in marine cyanobacteria. The possible contribution of bacterial biosilicification to the global silicon cycle is also discussed.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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19
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Can sustainable, monodisperse, spherical silica be produced from biomolecules? A review. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01869-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Cassarino L, Curnow P, Hendry KR. A biomimetic peptide has no effect on the isotopic fractionation during in vitro silica precipitation. Sci Rep 2021; 11:9698. [PMID: 33958622 PMCID: PMC8102562 DOI: 10.1038/s41598-021-88881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/14/2021] [Indexed: 11/25/2022] Open
Abstract
The stable isotopic composition of diatom silica is used as a proxy for nutrient utilisation in natural waters. This approach provides essential insight into the current and historic links between biological production, carbon cycling and climate. However, estimates of isotopic fractionation during diatom silica production from both laboratory and field studies are variable, and the biochemical pathways responsible remain unknown. Here, we investigate silicon isotopic fractionation through a series of chemical precipitation experiments that are analogous to the first stages of intracellular silica formation within the diatom silicon deposition vesicle. The novelty of our experiment is the inclusion of the R5 peptide, which is closely related to a natural biomolecule known to play a role in diatom silicification. Our results suggest that the presence of R5 induces a systematic but non-significant difference in fractionation behaviour. It thus appears that silicon isotopic fractionation in vitro is largely driven by an early kinetic fractionation during rapid precipitation that correlates with the initial amount of dissolved silica in the system. Our findings raise the question of how environmental changes might impact silicon isotopic fractionation in diatoms, and whether frustule archives record information in addition to silica consumption in surface water.
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Affiliation(s)
- Lucie Cassarino
- University of Bristol, School of Earth Sciences, Wills Memorial Building, Queen's Road, Brsitol, BS8 1RJ, UK.
| | - Paul Curnow
- University of Bristol, School of Biochemistry, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Katharine R Hendry
- University of Bristol, School of Earth Sciences, Wills Memorial Building, Queen's Road, Brsitol, BS8 1RJ, UK
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21
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Curley R, Banta RA, Garvey S, Holmes JD, Flynn EJ. Biomimetic spherical silica production using phosphatidylcholine and soy lecithin. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01839-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Annenkov VV, Aseyev V, Zelinskiy SN, Danilovtseva EN. Imidazole-phosphate polymers: Acid-base properties, association with oligonucleotides and oligosilicates. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Wang Y, Chen H, Huang Z, Yang M, Yu H, Peng M, Yang Z, Chen S. Structural characterization of cystathionine γ-lyase smCSE enables aqueous metal quantum dot biosynthesis. Int J Biol Macromol 2021; 174:42-51. [PMID: 33497694 DOI: 10.1016/j.ijbiomac.2021.01.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/25/2022]
Abstract
The development and utilization of inorganic material biosynthesis have evolved into single macromolecular systems. A putative cystathionine γ-lyase of bacteria Stenotrophomonas maltophilia (smCSE) is a newly identified biomolecule that enables the synthesis of nanomaterials. Due to the lack of structural information, the mechanism of smCSE biosynthesis remains unclear. Herein, we obtain two atomic-resolution smCSE-form X-ray structures and confirm that the conformational changes of Tyr108 and Lys206 within the enzyme active sites are critical for the protein-driven synthesis of metal sulfide quantum dots (QDs). The structural stability of tetramer and the specificity of surface amino acids are the basis for smCSE to synthesize quantum dots. The size of QD products can be regulated by predesigned amino acids and the morphology can be controlled through proteolytic treatments. The growth rate is enhanced by the stabilization of a flexible loop in the active site, as shown by the X-ray structure of the engineered protein which fused with a dodecapeptide. We further prove that the smCSE-driven route can be applied to the general synthesis of other metal sulfide nanoparticles. These results provide a better understanding of the mechanism of QD biosynthesis and a new perspective on the control of this biosynthesis by protein modification.
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Affiliation(s)
- Yutong Wang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China
| | - Huai Chen
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Zhaoxia Huang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China
| | - Mei Yang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China
| | - Hailing Yu
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China
| | - Maochen Peng
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China
| | - Zhenyu Yang
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China.
| | - Shoudeng Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai 519000, Guangdong, China.
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24
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Kumar S, Adiram-Filiba N, Blum S, Sanchez-Lopez JA, Tzfadia O, Omid A, Volpin H, Heifetz Y, Goobes G, Elbaum R. Siliplant1 protein precipitates silica in sorghum silica cells. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6830-6843. [PMID: 32485738 DOI: 10.1093/jxb/eraa258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/26/2020] [Indexed: 05/26/2023]
Abstract
Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume using an unknown biological factor. Using bioinformatics tools, we identified a previously uncharacterized protein in Sorghum bicolor, which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell types. Our results show that Slp1 precipitates silica in sorghum silica cells.
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Affiliation(s)
- Santosh Kumar
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Shula Blum
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Javier Arturo Sanchez-Lopez
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Oren Tzfadia
- Bioinformatics and Systems Biology, VIB/Ghent University, Gent, Belgium
| | - Ayelet Omid
- Danziger Innovations Limited, Mishmar Hashiva, Israel
| | - Hanne Volpin
- Danziger Innovations Limited, Mishmar Hashiva, Israel
| | - Yael Heifetz
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Rivka Elbaum
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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25
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Skordalou G, Korey M, Youngblood JP, Demadis KD. Pleiotropic action of pH-responsive poly(pyridine/PEG) copolymers in the stabilization of silicic acid or the enhancement of its polycondensation. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Nishi M, Kobayashi H, Amano T, Sakate Y, Bito T, Arima J, Shimizu K. Identification of the Domains Involved in Promotion of Silica Formation in Glassin, a Protein Occluded in Hexactinellid Sponge Biosilica, for Development of a Tag for Purification and Immobilization of Recombinant Proteins. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:739-747. [PMID: 32291549 DOI: 10.1007/s10126-020-09967-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Glassin, a protein occluded in biosilica of the hexactinellid sponge Euplectela, promotes silica formation from silicic acid at room temperature and neutral pH and is characterized by its primary structure which consists of a tandem repeat carrying three distinct domains, histidine and aspartic acid-rich (HD) domain, proline-rich (P) domain, and histidine and threonine-rich (HT) domain. The present study aims to clarify the domain responsible for the promotion of silica formation and to demonstrate usefulness of glassin and its domain as a tag for purification and immobilization of recombinant proteins. When each domain was mixed with silicic acid at neutral pH, silica was formed with HD domain as well as glassin, or a single repeat, but not with P or HT domain. Neither of amino or carboxy-terminal half of HD domain induced silica formation. The amount of silica formed with HD domain was significantly lower than that of glassin or a single repeat. HD domain fused with HT domain raised the amount of silica formed, while a HD domain fused with P domain, a mixture of HD and P domains, or a mixture of HD and HT domains has little effect on the promotion of silica formation. Collectively, a minimum sequence for promotion of silica formation is HD domain, whose activity can be enhanced by HT domain through a topological effect. In addition, practicality of glassin and HD domain was demonstrated by fusion of these sequences to green fluorescent protein which was successfully purified with Ni affinity chromatography and immobilized on silica.
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Affiliation(s)
- Michika Nishi
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Hiroki Kobayashi
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Taro Amano
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Yuto Sakate
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Tomohiro Bito
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Jiro Arima
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Katsuhiko Shimizu
- Platform for Community-based Research and Education, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8550, Japan.
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27
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Protein-driven biomineralization: Comparing silica formation in grass silica cells to other biomineralization processes. J Struct Biol 2020; 213:107665. [PMID: 33227416 DOI: 10.1016/j.jsb.2020.107665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/20/2022]
Abstract
Biomineralization is a common strategy adopted by organisms to support their body structure. Plants practice significant silicon and calcium based biomineralization in which silicon is deposited as silica in cell walls and intracellularly in various cell-types, while calcium is deposited mostly as calcium oxalate in vacuoles of specialized cells. In this review, we compare cellular processes leading to protein-dependent mineralization in plants, diatoms and sponges (phylum Porifera). The mechanisms of biomineralization in these organisms are inherently different. The composite silica structure in diatoms forms inside the cytoplasm in a membrane bound vesicle, which after maturation is exocytosed to the cell surface. In sponges, separate vesicles with the mineral precursor (silicic acid), an inorganic template, and organic molecules, fuse together and are extruded to the extracellular space. In plants, calcium oxalate mineral precipitates in vacuolar crystal chambers containing a protein matrix which is never exocytosed. Silica deposition in grass silica cells takes place outside the cell membrane when the cells secrete the mineralizing protein into the apoplasm rich with silicic acid (the mineral precursor molecules). Our review infers that the organism complexity and precursor reactivity (calcium and oxalate versus silicic acid) are main driving forces for the evolution of varied mineralization mechanisms.
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28
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Montagna M, Brückner SI, Dianat A, Gutierrez R, Daus F, Geyer A, Brunner E, Cuniberti G. Interactions of Long-Chain Polyamines with Silica Studied by Molecular Dynamics Simulations and Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11600-11609. [PMID: 32924496 DOI: 10.1021/acs.langmuir.0c02157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The investigation of molecular interactions between silica phases and organic components is crucial for elucidating the main steps involved in the biosilica mineralization process. In this respect, the structural characterization of the organic/inorganic interface is particularly useful for a deeper understanding of the dominant mechanisms of biomineralization. In this work, we have investigated the interaction of selectively 13C- and 15N-labeled atoms of organic long-chain polyamines (LCPAs) with 29Si-labeled atoms of a silica layer at the molecular level. In particular, silica/LCPA nanocomposites were analyzed by solid-state NMR spectroscopy in combination with all-atom molecular dynamics simulations. Solid-state NMR experiments allow the determination of 29Si-15N and 29Si-13C internuclear distances, providing the parameters for direct verification of atomistic simulations. Our results elucidate the relevant molecular conformations as well as the nature of the interaction between the LCPA and a silica substrate. Specifically, distances and second moments suggest a picture compatible with (i) LCPA completely embedded in the silica phase and (ii) the charged amino groups located in close vicinity of silanol groups.
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Affiliation(s)
- Maria Montagna
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Stephan Ingmar Brückner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Arezoo Dianat
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Rafael Gutierrez
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
| | - Fabian Daus
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062 Dresden, Germany
- Dresden Center for Computational Materials Science, TU Dresden, 01062 Dresden, Germany
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29
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Nemoto M, Iwaki S, Moriya H, Monden Y, Tamura T, Inagaki K, Mayama S, Obuse K. Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:551-563. [PMID: 32488507 DOI: 10.1007/s10126-020-09976-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.
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Affiliation(s)
- Michiko Nemoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
| | - Sayako Iwaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenji Inagaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shigeki Mayama
- Department of Biology, Tokyo Gakugei University, Tokyo, 184-8511, Japan
| | - Kiori Obuse
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
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30
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Kolbe F, Daus F, Geyer A, Brunner E. Phosphate-Silica Interactions in Diatom Biosilica and Synthetic Composites Studied by Rotational Echo Double Resonance (REDOR) NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4332-4338. [PMID: 32233513 DOI: 10.1021/acs.langmuir.0c00336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biosilica is a biogenic composite material produced by organisms like diatoms. Various biomolecules are tightly attached or incorporated into biosilica. Examples are special proteins termed silaffins and long-chain polyamines (LCPAs). Presumably, these biomolecules are involved in the biosilica formation process. Silaffins are highly phosphorylated zwitterions with LCPAs post-translationally attached to lysine residues. In the present work, we use distance-dependent solid-state NMR experiments, especially the 31P{29Si} Rotational Echo Double Resonance (REDOR) technique, to study the environment of phosphate moieties in biosilica and in vitro synthesized SiO2-based composites. In contrast to the heterogeneous mixtures of biomolecules found in native biosilica, the described in vitro silicification experiments make use of a single synthetic phosphopeptide and an LCPA of well-defined and uniform structure. The heteronuclear correlations measured from these silica composites provide reliable 31P-29Si dipolar second moments and information about the distribution of the phosphopeptide within the silica material. The calculated second moment indicates close contact between phosphopeptides and silica. The phosphopeptides are incorporated into the silica composite in a disperse manner. Moreover, the REDOR data acquired for diatom biosilica also imply that phosphate groups are part of the silica-organic interface in this material.
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Affiliation(s)
- Felicitas Kolbe
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Fabian Daus
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Eike Brunner
- Chair of Bioanalytical Chemistry, Faculty of Chemistry and Food Chemistry, TU Dresden, 01062 Dresden, Germany
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31
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Singh R, Khan MJ, Rane J, Gajbhiye A, Vinayak V, Joshi KB. Biofabrication of Diatom Surface by Tyrosine‐Metal Complexes:Smart Microcontainers to Inhibit Bacterial Growth. ChemistrySelect 2020. [DOI: 10.1002/slct.201904248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ramesh Singh
- Department of ChemistrySchool of Chemical Science and TechnologyDr. Harisingh Gour Central University Sagar MP 470003 India
| | - Mohd Jahir Khan
- Diatom Nanoengineering and Metabolism Lab (DNM)School of Applied SciencesDr. Harisingh Gour Central University Sagar MP 470003 India
| | - Jagdish Rane
- Department of Pharmaceutical SciencesDr. Harisingh Gour Central University Sagar MP 470003 India
| | - Ashmita Gajbhiye
- Department of Pharmaceutical SciencesDr. Harisingh Gour Central University Sagar MP 470003 India
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Lab (DNM)School of Applied SciencesDr. Harisingh Gour Central University Sagar MP 470003 India
| | - Khashti Ballabh Joshi
- Department of ChemistrySchool of Chemical Science and TechnologyDr. Harisingh Gour Central University Sagar MP 470003 India
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32
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Daus F, Pfeifer E, Seipp K, Hampp N, Geyer A. The role of phosphopeptides in the mineralisation of silica. Org Biomol Chem 2020; 18:700-706. [DOI: 10.1039/c9ob02438g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of hyperphosphorylated peptides and the investigation of theirin vitrosilicification activity in combination with long-chain polyamines (LCPA) at high dilution and mildly acidic conditions.
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Affiliation(s)
- Fabian Daus
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Erik Pfeifer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Kevin Seipp
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Norbert Hampp
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Armin Geyer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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33
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Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ, Liang J. Distinct genome‐wide alternative polyadenylation during the response to silicon availability in the marine diatom
Thalassiosira pseudonana. THE PLANT JOURNAL 2019; 99:67-80. [PMID: 30844106 DOI: 10.1111/tpj.14309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/15/2019] [Accepted: 02/27/2019] [Indexed: 05/28/2023]
Affiliation(s)
- Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Peng Wang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Xiaohui Wu
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Xiaoxuan Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Guoli Ji
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Yahui Gao
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA 91766 USA
| | - Junrong Liang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
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34
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Görlich S, Pawolski D, Zlotnikov I, Kröger N. Control of biosilica morphology and mechanical performance by the conserved diatom gene Silicanin-1. Commun Biol 2019; 2:245. [PMID: 31286062 PMCID: PMC6599040 DOI: 10.1038/s42003-019-0436-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/17/2019] [Indexed: 11/18/2022] Open
Abstract
The species-specifically patterned biosilica cell walls of diatoms are paradigms for biological mineral morphogenesis and the evolution of lightweight materials with exceptional mechanical performance. Biosilica formation is a membrane-mediated process that occurs in intracellular compartments, termed silica deposition vesicles (SDVs). Silicanin-1 (Sin1) is a highly conserved protein of the SDV membrane, but its role in biosilica formation has remained elusive. Here we generate Sin1 knockout mutants of the diatom Thalassiosira pseudonana. Although the mutants grow normally, they exhibit reduced biosilica content and morphological aberrations, which drastically compromise the strength and stiffness of their cell walls. These results identify Sin1 as essential for the biogenesis of mechanically robust diatom cell walls, thus providing an explanation for the conservation of this gene throughout the diatom realm. This insight paves the way for genetic engineering of silica architectures with desired structures and mechanical performance.
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Affiliation(s)
- Stefan Görlich
- B CUBE Center of Molecular Bioengineering, CMCB, TU Dresden, Am Tatzberg 41, 01307 Dresden, Germany
| | - Damian Pawolski
- B CUBE Center of Molecular Bioengineering, CMCB, TU Dresden, Am Tatzberg 41, 01307 Dresden, Germany
| | - Igor Zlotnikov
- B CUBE Center of Molecular Bioengineering, CMCB, TU Dresden, Am Tatzberg 41, 01307 Dresden, Germany
| | - Nils Kröger
- B CUBE Center of Molecular Bioengineering, CMCB, TU Dresden, Am Tatzberg 41, 01307 Dresden, Germany
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35
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Panwar V, Dutta T. Diatom Biogenic Silica as a Felicitous Platform for Biochemical Engineering: Expanding Frontiers. ACS APPLIED BIO MATERIALS 2019; 2:2295-2316. [DOI: 10.1021/acsabm.9b00050] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Varsha Panwar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Tanmay Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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36
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Bedoshvili Y, Gneusheva K, Popova M, Morozov A, Likhoshway Y. Anomalies in the valve morphogenesis of the centric diatom alga Aulacoseira islandica caused by microtubule inhibitors. Biol Open 2018; 7:bio035519. [PMID: 30037970 PMCID: PMC6124563 DOI: 10.1242/bio.035519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Of all unicellular organisms possessing a cell wall, diatoms are the most adept at micro- and nanoscale embellishment of their frustules. Elements of their cell walls are formed inside the cell under cytoskeletal control. In this work, we used laser scanning microscopy and electron microscopy to describe the major stages of cell wall formation in the centric diatom algae Aulacoseira islandica and to study the effect of various microtubule inhibitors on the morphogenesis of frustule elements. Our results show that colchicine inhibits karyokinesis and cytokinesis in A. islandica colonies. In contrast, valve morphogenesis is changed, rather than inhibited altogether. In normal cells, this process starts simultaneously in both daughter cells, beginning with the formation of two adjacent discs that later become valve faces and connecting spines. Under colchicine treatment, however, the cleavage furrow is blocked and a single lateral valve forms on the side of the cylindrical frustule. As a result, a single hollow pipe forms instead of two separate drinking glass-shaped frustules; such pipes can form up to 35% of all forming frustules. Colchicine inhibits the formation of connecting spines, whereas paclitaxel causes spines to form a complex, branching shape. At the same time, inhibitors do not affect the formation of areolae (openings) in the frustule. We discuss the possibility that various processes of the diatom frustule morphogenesis are controlled by two different mechanisms: membrane-related micromorphogenesis and cytoskeleton-mediated macromorphogenesis.
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Affiliation(s)
- Yekaterina Bedoshvili
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Ksenia Gneusheva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Maria Popova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Alexey Morozov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Yelena Likhoshway
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
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37
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Kirkham AR, Richthammer P, Schmidt K, Wustmann M, Maeda Y, Hedrich R, Brunner E, Tanaka T, van Pée KH, Falciatore A, Mock T. A role for the cell-wall protein silacidin in cell size of the diatom Thalassiosira pseudonana. THE ISME JOURNAL 2017; 11:2452-2464. [PMID: 28731468 PMCID: PMC5649158 DOI: 10.1038/ismej.2017.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 01/06/2023]
Abstract
Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana. In particular, the targeted deregulation of the expression of the cell-wall protein silacidin caused a significant increase in valve diameter. Remarkably, the natural downregulation of the silacidin gene transcript due to experimental evolution under low temperature also correlated with cell-size increase. Our data give first evidence for a genetically controlled regulation of cell size in T. pseudonana and possibly other centric diatoms as they also encode the silacidin gene in their genomes.
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Affiliation(s)
- Amy R Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Yoshiaki Maeda
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - René Hedrich
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Eike Brunner
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Tsuyoshi Tanaka
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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38
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Tesson B, Lerch SJL, Hildebrand M. Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica. Sci Rep 2017; 7:13457. [PMID: 29044150 PMCID: PMC5647440 DOI: 10.1038/s41598-017-13613-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/25/2017] [Indexed: 01/27/2023] Open
Abstract
Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.
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Affiliation(s)
- Benoit Tesson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
| | - Sarah J L Lerch
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
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39
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Kotzsch A, Gröger P, Pawolski D, Bomans PHH, Sommerdijk NAJM, Schlierf M, Kröger N. Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization. BMC Biol 2017; 15:65. [PMID: 28738898 PMCID: PMC5525289 DOI: 10.1186/s12915-017-0400-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological mineral formation (biomineralization) proceeds in specialized compartments often bounded by a lipid bilayer membrane. Currently, the role of membranes in biomineralization is hardly understood. RESULTS Investigating biomineralization of SiO2 (silica) in diatoms we identified Silicanin-1 (Sin1) as a conserved diatom membrane protein present in silica deposition vesicles (SDVs) of Thalassiosira pseudonana. Fluorescence microscopy of GFP-tagged Sin1 enabled, for the first time, to follow the intracellular locations of a biomineralization protein during silica biogenesis in vivo. The analysis revealed incorporation of the N-terminal domain of Sin1 into the biosilica via association with the organic matrix inside the SDVs. In vitro experiments showed that the recombinant N-terminal domain of Sin1 undergoes pH-triggered assembly into large clusters, and promotes silica formation by synergistic interaction with long-chain polyamines. CONCLUSIONS Sin1 is the first identified SDV transmembrane protein, and is highly conserved throughout the diatom realm, which suggests a fundamental role in the biomineralization of diatom silica. Through interaction with long-chain polyamines, Sin1 could serve as a molecular link by which the SDV membrane exerts control on the assembly of biosilica-forming organic matrices in the SDV lumen.
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Affiliation(s)
- Alexander Kotzsch
- B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany
| | - Philip Gröger
- B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany
| | - Damian Pawolski
- B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany
| | - Paul H H Bomans
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry & Center of Multiscale Electron Microscopy, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Nico A J M Sommerdijk
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry & Center of Multiscale Electron Microscopy, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Michael Schlierf
- B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany
| | - Nils Kröger
- B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany. .,Department of Chemistry and Food Chemistry, TU Dresden, 01062, Dresden, Germany.
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40
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De Tommasi E, Gielis J, Rogato A. Diatom Frustule Morphogenesis and Function: a Multidisciplinary Survey. Mar Genomics 2017; 35:1-18. [PMID: 28734733 DOI: 10.1016/j.margen.2017.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023]
Abstract
Diatoms represent the major component of phytoplankton and are responsible for about 20-25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions. In the present article the main reported data related to frustule morphogenesis and functionalities with contributions from fundamental biology, genetics, mathematics, geometry and physics are reviewed.
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Affiliation(s)
- Edoardo De Tommasi
- Institute for Microelectronics and Microsystems, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Johan Gielis
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Alessandra Rogato
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy; Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy.
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41
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Brembu T, Chauton MS, Winge P, Bones AM, Vadstein O. Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs. Sci Rep 2017; 7:4865. [PMID: 28687794 PMCID: PMC5501833 DOI: 10.1038/s41598-017-04921-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.
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Affiliation(s)
- Tore Brembu
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway.
| | | | - Per Winge
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Atle M Bones
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Olav Vadstein
- Biotechnology and Food Science, N-7491, Trondheim, Norway
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42
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Bella A, Ray S, Ryadnov MG. Linear and orthogonal peptide templating of silicified protein fibres. Org Biomol Chem 2017; 15:5380-5385. [PMID: 28620669 DOI: 10.1039/c7ob01134b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biomineralisation is essential for biology. Specialist proteins use peptide motifs that catalyse mineral deposition into nano-to-microscale inorganic materials. Unlike in native proteins, the motifs incorporated into self-assembled fibres can persistently propagate on the microscopic scale enabling empirically defined silica nanostructures. Herein we show that the two main modes of motif templating - linear and orthogonal - in self-assembling, fibre-forming peptide sequences effectively silicify protein fibres. We show that the mere charge and morphology of protein fibres are not sufficient for silica deposition, but it is the synergy between fibrillogenesis and silica-specific motifs regularly spaced in fibres that ensures silica templating, regardless of the relative orientation of the motifs.
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Affiliation(s)
- Angelo Bella
- National Physical Laboratory, Teddington, Middlesex TW11 0LW, UK.
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43
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Abstract
The application of biocatalytic or chemoenzymatic techniques in silicon chemistry serves two roles: it provides a greater understanding of the processing of silicon species by natural systems, such as plants, diatoms, and sponges, as well opening up avenues to green methodologies in the field. In the latter case, biocatalytic approaches have been applied to the synthesis of small-molecule systems and polymeric materials. Often these biocatalytic approaches allow access to molecular structures under mild conditions and, in some cases, molecular structures that are not accessible through traditional chemical methodologies. A review of recent advances in the applications of biocatalysis in silicon chemistry is presented.
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Affiliation(s)
- Mark B Frampton
- School of Biosciences, Loyalist College, 376 Wallbridge-Loyalist Road, Belleville, ON, K89 5B9, Canada
| | - Paul M Zelisko
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
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44
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Annenkov V, Danilovtseva EN, Pal'shin VA, Verkhozina ON, Zelinskiy SN, Krishnan UM. Silicic acid condensation under the influence of water-soluble polymers: from biology to new materials. RSC Adv 2017. [DOI: 10.1039/c7ra01310h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Silicic acid condensation under the influence of functional polymers is reviewed starting from biology to new materials.
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Affiliation(s)
- Vadim V. Annenkov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
- Irkutsk
- Russia
| | - Elena N. Danilovtseva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
- Irkutsk
- Russia
| | - Viktor A. Pal'shin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
- Irkutsk
- Russia
| | - Ol'ga N. Verkhozina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
- Irkutsk
- Russia
| | - Stanislav N. Zelinskiy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
- Irkutsk
- Russia
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB)
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur – 613401
- India
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45
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Establishing super-resolution imaging for proteins in diatom biosilica. Sci Rep 2016; 6:36824. [PMID: 27827427 PMCID: PMC5101815 DOI: 10.1038/srep36824] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/21/2016] [Indexed: 11/17/2022] Open
Abstract
The intricate, genetically controlled biosilica nano- and micropatterns produced by diatoms are a testimony for biology’s ability to control mineral formation (biomineralization) at the nanoscale and regarded as paradigm for nanotechnology. Previously, several protein families involved in diatom biosilica formation have been identified, and many of them remain tightly associated with the final biosilica structure. Determining the locations of biosilica-associated proteins with high precision is, therefore expected to provide clues to their roles in biosilica morphogenesis. To achieve this, we introduce here single-molecule localization microscopy to diatoms based on photo-activated light microscopy (PALM) to overcome the diffraction limit. We identified six photo-convertible fluorescent proteins (FPs) that can be utilized for PALM in the cytoplasm of model diatom Thalassiosira pseudonana. However, only three FPs were also functional when embedded in diatom biosilica. These were employed for PALM-based localization of the diatom biosilica-associated protein Silaffin-3 (tpSil3) with a mean precision of 25 nm. This allowed for the identification of distinct accumulation areas of Sil3 in the biosilica, which cannot be resolved by confocal fluorescence microscopy. The enhanced microscopy technique introduced here for diatoms will aid in elucidating the molecular mechanism of silica biomineralization as well as other aspects of diatom cell biology.
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46
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Ravera E, Martelli T, Geiger Y, Fragai M, Goobes G, Luchinat C. Biosilica and bioinspired silica studied by solid-state NMR. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Hyde EDER, Seyfaee A, Neville F, Moreno-Atanasio R. Colloidal Silica Particle Synthesis and Future Industrial Manufacturing Pathways: A Review. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b01839] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Emily D. E. R. Hyde
- School of Engineering, and ‡School of Environmental
and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Ahmad Seyfaee
- School of Engineering, and ‡School of Environmental
and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Frances Neville
- School of Engineering, and ‡School of Environmental
and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Roberto Moreno-Atanasio
- School of Engineering, and ‡School of Environmental
and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
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48
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Knight MJ, Senior L, Nancolas B, Ratcliffe S, Curnow P. Direct evidence of the molecular basis for biological silicon transport. Nat Commun 2016; 7:11926. [PMID: 27305972 PMCID: PMC4912633 DOI: 10.1038/ncomms11926] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/11/2016] [Indexed: 12/19/2022] Open
Abstract
Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na+/silicic acid symporters with a 1:1 protein: substrate stoichiometry and KM for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials. Diatoms sheath themselves in a self-made casing of silica, which requires the function of silicic acid transporters. Here, the authors identify versions of these transporters that are experimentally tractable, and develop a fluorescence method to study silicic acid transport in vitro.
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Affiliation(s)
- Michael J Knight
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Laura Senior
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Bethany Nancolas
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sarah Ratcliffe
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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49
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Kotzsch A, Pawolski D, Milentyev A, Shevchenko A, Scheffel A, Poulsen N, Shevchenko A, Kröger N. Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana. J Biol Chem 2016; 291:4982-97. [PMID: 26710847 PMCID: PMC4777836 DOI: 10.1074/jbc.m115.706440] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis.
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Affiliation(s)
| | | | - Alexander Milentyev
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Anna Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - André Scheffel
- the Max-Planck-Institute of Plant Physiology, 14476 Potsdam, Germany
| | | | - Andrej Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Nils Kröger
- From the B CUBE Center for Molecular Bioengineering and the Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01307 Dresden, Germany,
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50
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Jantschke A, Koers E, Mance D, Weingarth M, Brunner E, Baldus M. Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:15069-73. [DOI: 10.1002/anie.201507327] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 01/23/2023]
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