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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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Kubo A, Kawarasaki K, Hara H. Silica removal at sewage treatment plants causes new silica deficiency. Sci Rep 2022; 12:8141. [PMID: 35581363 PMCID: PMC9114124 DOI: 10.1038/s41598-022-12272-8] [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: 03/29/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
The dissolved silicate (DSi) concentration in coastal waters has decreased due to anthropogenic activities. Many studies have indicated that dam construction is a main reason for this reduction. However, recently, dam construction alone has not been sufficient to explain the DSi reduction in some coastal waters. In this study, we focused on silica removal at sewage treatment plants (STPs). DSi and particulate silica (PSi) concentrations were measured in STP influent and effluent waters from September 2020 to September 2021. Dissolution experiments on PSi were also conducted to estimate the fraction of soluble PSi in the STP influent. DSi and PSi were removed by 29.5% and 96.9%, respectively, at the STP. In addition, the soluble PSi in the STP influent accounted for 20.3% of the PSi removed. Therefore, in addition to the DSi removal in STPs, removal of soluble PSi can also cause potential DSi depletion in downstream and coastal waters. In addition to the effect of dams, the silica supply delivered to coastal waters may be further reduced in the future due to the progress of sewage treatment development in coastal areas.
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Affiliation(s)
- Atsushi Kubo
- Department of Geosciences, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Koki Kawarasaki
- Department of Geosciences, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hiroshi Hara
- Sewer Water Quality Section, Water Quality Management Division, Waterworks Department, Waterworks and Sewerage Bureau, Shizuoka City Hall, Shizuoka, Japan
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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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de Moraes ACP, Ribeiro LDS, de Camargo ER, Lacava PT. The potential of nanomaterials associated with plant growth-promoting bacteria in agriculture. 3 Biotech 2021; 11:318. [PMID: 34194902 PMCID: PMC8190246 DOI: 10.1007/s13205-021-02870-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023] Open
Abstract
The impacts of chemical fertilizers and pesticides have raised public concerns regarding the sustainability and security of food supplies, prompting the investigation of alternative methods that have combinations of both agricultural and environmental benefits, such as the use of biofertilizers involving microbes. These types of microbial inoculants are living microorganisms that colonize the soil or plant tissues when applied to the soil, seeds, or plant surfaces, facilitating plant nutrient acquisition. They can enhance plant growth by transforming nutrients into a form assimilable by plants and by acting as biological control agents, known as plant growth-promoting bacteria. The potential use of bacteria as biofertilizers in agriculture constitutes an economical and eco-friendly way to reduce the use of chemical fertilizers and pesticides. In this context, nanotechnology has emerged as a new source of quality enrichment for the agricultural sector. The use of nanoparticles can be an effective method to meet the challenges regarding the effectiveness of biofertilizers in natural environments. Given the novel sustainable strategies applied in agricultural systems, this review addresses the effects of nanoparticles on beneficial plant bacteria for promoting plant growth.
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Affiliation(s)
- Amanda Carolina Prado de Moraes
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
- Biotechnology Graduation Program (PPG-Biotec), Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Lucas da Silva Ribeiro
- Interdisciplinary Laboratory of Electrochemistry and Ceramics, Department of Chemistry, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Emerson Rodrigues de Camargo
- Interdisciplinary Laboratory of Electrochemistry and Ceramics, Department of Chemistry, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Paulo Teixeira Lacava
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
- Biotechnology Graduation Program (PPG-Biotec), Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
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5
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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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6
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Abdelhamid MAA, Pack SP. Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications. Acta Biomater 2021; 120:38-56. [PMID: 32447061 DOI: 10.1016/j.actbio.2020.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea.
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7
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Shah AA, Yasin NA, Akram K, Ahmad A, Khan WU, Akram W, Akbar M. Ameliorative role of Bacillus subtilis FBL-10 and silicon against lead induced stress in Solanum melongena. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:486-496. [PMID: 33298367 DOI: 10.1016/j.plaphy.2020.11.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/20/2020] [Indexed: 05/28/2023]
Abstract
The continuous deterioration of arable lands by metal pollution compels finding suitable strategies to increase plant tolerance under contaminated regimes. Current study was designed to examine the synergistic role of Bacillus subtilis FBL-10 and silicon (Si) with respect to mitigation of lead (Pb) induced phytotoxicity in Solanum melongena L. Lead stress (75 mg kg-1) reduced chlorophyll (Chl) content, photosynthetic rate and gas exchange characteristics of S. melongena plants. The Si and B. subtilis FBL-10 individually upgraded all the above-mentioned growth attributes. However, co-application of Si (50 mg kg-1) and B. subtilis FBL-10 significantly improved biochemical and growth attributes of Pb challenged plants. The abridged levels of oxidative markers including hydrogen peroxide (H2O2), and malondialdehyde (MDA) besides reduced Pb accumulation in foliage tissues, were recorded in Si and microbe assisted plants. Furthermore, plants inoculated with B. subtilis FBL-10 alone or in combination with Si showed increment in total soluble proteins, photosynthetic rate and gas exchange attributes. The inoculated plants treated with Si exhibited higher level of auxins and improved activity of antioxidant enzymes under Pb stress. Present research elucidates interactive role of B. subtilis FBL-10 and Si in reduction of Pb toxicity in S. melongena plants. Alone application of Si or B. subtilis FBL-10 was less effective for attenuation of Pb stress; however, synergism between both phyto-protectants demonstrated fabulous ability for Pb stress assuagement. Consequently, executions of field studies become indispensable to comprehend the efficacy of Si applied alone or in combination with plant growth promoting bacteria (PGPB) like B. subtilis FBL-10. From current research, it is concluded that the interaction of Si and PGPB seems an auspicious technique and eco-friendly approach to enhance metal tolerance in crop plants.
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Affiliation(s)
- Anis Ali Shah
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Nasim Ahmad Yasin
- Guangdong Academy of Agricultural Sciences, Guangzhou, China; SSG, RO-II Department, University of the Punjab, Lahore, Pakistan.
| | - Kanwal Akram
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Aqeel Ahmad
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Waheed Ullah Khan
- College of Earth and Environmental Sciences, University of the Punjab, Lahore, Pakistan; Department of Environmental Science, The Islamia University of Bahawalpur, Pakistan.
| | - Waheed Akram
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Ebe S, Ohike T, Okanami M, Ano T. Components of rice husk biochar in promoting the growth, sporulation and iturin A production of Bacillus sp. strain IA. ACTA ACUST UNITED AC 2019; 74:211-217. [PMID: 30917107 DOI: 10.1515/znc-2018-0223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/02/2019] [Indexed: 11/15/2022]
Abstract
In a previously study, the Bacillus sp. strain IA was successfully isolated with high sensitivity to rice husk biochar (RHB). Moreover, RHB promoted an antibiotic iturin A production by strain IA. In order to develop the biocontrol agent, we attempted to reveal the functions of the RHB in promoting the production of iturin A by strain IA. The promotion effects of growth, sporulation and iturin A production of strain IA by the RHB were explained as follows. First, the manganese ion, released from RHB, promoted the sporulation and iturin A production of strain IA. Second, the silicon dioxide contained in RHB adsorbed the metabolic inhibitor(s) and promoted the iturin A production of strain IA. Finally, the combination of manganese ion and silicon dioxide promoted the growth, sporulation and iturin A production of the Bacillus sp. strain IA. To culture strain IA in the medium combining manganese ion and silicon dioxide, the total cells, spore cells and iturin A production increased 15 times, 10,000 times and 18 times higher than the control medium, respectively.
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Affiliation(s)
- Shohei Ebe
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Tatsuya Ohike
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Masahiro Okanami
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Takashi Ano
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
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9
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Nguyen PQ, Courchesne NMD, Duraj-Thatte A, Praveschotinunt P, Joshi NS. Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704847. [PMID: 29430725 PMCID: PMC6309613 DOI: 10.1002/adma.201704847] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/25/2017] [Indexed: 05/20/2023]
Abstract
Vast potential exists for the development of novel, engineered platforms that manipulate biology for the production of programmed advanced materials. Such systems would possess the autonomous, adaptive, and self-healing characteristics of living organisms, but would be engineered with the goal of assembling bulk materials with designer physicochemical or mechanical properties, across multiple length scales. Early efforts toward such engineered living materials (ELMs) are reviewed here, with an emphasis on engineered bacterial systems, living composite materials which integrate inorganic components, successful examples of large-scale implementation, and production methods. In addition, a conceptual exploration of the fundamental criteria of ELM technology and its future challenges is presented. Cradled within the rich intersection of synthetic biology and self-assembling materials, the development of ELM technologies allows the power of biology to be leveraged to grow complex structures and objects using a palette of bio-nanomaterials.
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Affiliation(s)
- Peter Q. Nguyen
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Noémie-Manuelle Dorval Courchesne
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Anna Duraj-Thatte
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Pichet Praveschotinunt
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Neel S. Joshi
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
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10
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Novoselov AA, Silva D, Schneider J, Abrevaya XC, Chaffin MS, Serrano P, Navarro MS, Conti MJ, Souza Filho CRD. Geochemical constraints on the Hadean environment from mineral fingerprints of prokaryotes. Sci Rep 2017; 7:4008. [PMID: 28638074 PMCID: PMC5479841 DOI: 10.1038/s41598-017-04161-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed. Here we present new data on the elemental compositions and mineral fingerprints of both Bacteria and Archaea, using these data to constrain the environment in which life formed. The cradle solution that produced this elemental signature was saturated in barite, sphene, chalcedony, apatite, and clay minerals. The presence of these minerals, as well as other chemical features, suggests that the cradle environment of life may have been a weathering fluid interacting with dry-land silicate rocks. The specific mineral assemblage provides evidence for a moderate Hadean climate with dry and wet seasons and a lower atmospheric abundance of CO2 than is present today.
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Affiliation(s)
- Alexey A Novoselov
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil.
- University of Concepción, Institute of Applied Economic Geology, Concepción, Casilla 160-C, Chile.
| | - Dailto Silva
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil
| | - Jerusa Schneider
- University of Campinas, School of Civil Engineering, Architecture and Urban Design, Campinas, 13083-889, Brazil
| | - Ximena Celeste Abrevaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EHA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Astronomía y Física del Espacio (IAFE), Buenos Aires, C1428ZAA, Argentina
| | | | - Paloma Serrano
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, 14473, Germany
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The Influence of Silicon Oxide Nanoparticles on Morphometric Parameters of Monocotyledons and Dicotyledons in Soil and Climatic Conditions of Western Siberia, as well as on Microbiological Soil Properties. BIONANOSCIENCE 2017. [DOI: 10.1007/s12668-017-0419-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Abdelhamid MAA, Ikeda T, Motomura K, Tanaka T, Ishida T, Hirota R, Kuroda A. Application of volcanic ash particles for protein affinity purification with a minimized silica-binding tag. J Biosci Bioeng 2016; 122:633-638. [PMID: 27212265 DOI: 10.1016/j.jbiosc.2016.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
We recently reported that the spore coat protein, CotB1 (171 amino acids), from Bacillus cereus mediates silica biomineralization and that the polycationic C-terminal sequence of CotB1 (14 amino acids), designated CotB1p, serves as a silica-binding tag when fused to other proteins. Here, we reduced the length of this silica-binding tag to only seven amino acids (SB7 tag: RQSSRGR) while retaining its affinity for silica. Alanine scanning mutagenesis indicated that the three arginine residues in the SB7 tag play important roles in binding to a silica surface. Monomeric l-arginine, at concentrations of 0.3-0.5 M, was found to serve as a competitive eluent to release bound SB7-tagged proteins from silica surfaces. To develop a low-cost, silica-based affinity purification procedure, we used natural volcanic ash particles with a silica content of ∼70%, rather than pure synthetic silica particles, as an adsorbent for SB7-tagged proteins. Using green fluorescent protein, mCherry, and mKate2 as model proteins, our purification method achieved 75-90% recovery with ∼90% purity. These values are comparable to or even higher than that of the commonly used His-tag affinity purification. In addition to low cost, another advantage of our method is the use of l-arginine as the eluent because its protein-stabilizing effect would help minimize alteration of the intrinsic properties of the purified proteins. Our approach paves the way for the use of naturally occurring materials as adsorbents for simple, low-cost affinity purification.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Kei Motomura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Tatsuya Tanaka
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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Abstract
Spores of various Bacillus and Clostridium species are among the most resistant life forms known. Since the spores of some species are causative agents of much food spoilage, food poisoning, and human disease, and the spores of Bacillus anthracis are a major bioweapon, there is much interest in the mechanisms of spore resistance and how these spores can be killed. This article will discuss the factors involved in spore resistance to agents such as wet and dry heat, desiccation, UV and γ-radiation, enzymes that hydrolyze bacterial cell walls, and a variety of toxic chemicals, including genotoxic agents, oxidizing agents, aldehydes, acid, and alkali. These resistance factors include the outer layers of the spore, such as the thick proteinaceous coat that detoxifies reactive chemicals; the relatively impermeable inner spore membrane that restricts access of toxic chemicals to the spore core containing the spore's DNA and most enzymes; the low water content and high level of dipicolinic acid in the spore core that protect core macromolecules from the effects of heat and desiccation; the saturation of spore DNA with a novel group of proteins that protect the DNA against heat, genotoxic chemicals, and radiation; and the repair of radiation damage to DNA when spores germinate and return to life. Despite their extreme resistance, spores can be killed, including by damage to DNA, crucial spore proteins, the spore's inner membrane, and one or more components of the spore germination apparatus.
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14
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The C-Terminal Zwitterionic Sequence of CotB1 Is Essential for Biosilicification of the Bacillus cereus Spore Coat. J Bacteriol 2015; 198:276-82. [PMID: 26503850 DOI: 10.1128/jb.00447-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/15/2015] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Silica is deposited in and around the spore coat layer of Bacillus cereus, and enhances the spore's acid resistance. Several peptides and proteins, including diatom silaffin and silacidin peptides, are involved in eukaryotic silica biomineralization (biosilicification). Homologous sequence search revealed a silacidin-like sequence in the C-terminal region of CotB1, a spore coat protein of B. cereus. The negatively charged silacidin-like sequence is followed by a positively charged arginine-rich sequence of 14 amino acids, which is remarkably similar to the silaffins. These sequences impart a zwitterionic character to the C terminus of CotB1. Interestingly, the cotB1 gene appears to form a bicistronic operon with its paralog, cotB2, the product of which, however, lacks the C-terminal zwitterionic sequence. A ΔcotB1B2 mutant strain grew as fast and formed spores at the same rate as wild-type bacteria but did not show biosilicification. Complementation analysis showed that CotB1, but neither CotB2 nor C-terminally truncated mutants of CotB1, could restore the biosilicification activity in the ΔcotB1B2 mutant, suggesting that the C-terminal zwitterionic sequence of CotB1 is essential for the process. We found that the kinetics of CotB1 expression, as well as its localization, correlated well with the time course of biosilicification and the location of the deposited silica. To our knowledge, this is the first report of a protein directly involved in prokaryotic biosilicification. IMPORTANCE Biosilicification is the process by which organisms incorporate soluble silicate in the form of insoluble silica. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification was not studied until recently. We previously demonstrated that biosilicification occurs in Bacillus cereus and its close relatives, and that silica is deposited in and around a spore coat layer as a protective coating against acid. The present study reveals that a B. cereus spore coat protein, CotB1, which carried a C-terminal zwitterionic sequence, is essential for biosilicification. Our results provide the first insight into mechanisms required for biosilicification in prokaryotes.
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15
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Abdelhamid MAA, Motomura K, Ikeda T, Ishida T, Hirota R, Kuroda A. Affinity purification of recombinant proteins using a novel silica-binding peptide as a fusion tag. Appl Microbiol Biotechnol 2014; 98:5677-84. [PMID: 24756322 DOI: 10.1007/s00253-014-5754-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/02/2014] [Accepted: 04/04/2014] [Indexed: 01/30/2023]
Abstract
We recently reported that silica is deposited on the coat of Bacillus cereus spores as a layer of nanometer-sized particles (Hirota et al. 2010 J Bacteriol 192: 111-116). Gene disruption analysis revealed that the spore coat protein CotB1 mediates the accumulation of silica (our unpublished results). Here, we report that B. cereus CotB1 (171 amino acids [aa]) and its C-terminal 14-aa region (corresponding to residues 158-171, designated CotB1p) show strong affinity for silica particles, with dissociation constants at pH 8.0 of 2.09 and 1.24 nM, respectively. Using CotB1 and CotB1p as silica-binding tags, we developed a silica-based affinity purification method in which silica particles are used as an adsorbent for CotB1/CotB1p fusion proteins. Small ubiquitin-like modifier (SUMO) technology was employed to release the target proteins from the adsorbed fusion proteins. SUMO-protease-mediated site-specific cleavage at the C-terminus of the fused SUMO sequence released the tagless target proteins into the liquid phase while leaving the tag region still bound to the solid phase. Using the fluorescent protein mCherry as a model, our purification method achieved 85 % recovery, with a purity of 95 % and yields of 0.60 ± 0.06 and 1.13 ± 0.13 mg per 10-mL bacterial culture for the CotB1-SUMO-mCherry and CotB1p-SUMO-mCherry fusions, respectively. CotB1p, a short 14-aa peptide, which demonstrates high affinity for silica, could be a promising fusion tag for both affinity purification and enzyme immobilization on silica supports.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
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16
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Bacillus thuringiensis as a surrogate for Bacillus anthracis in aerosol research. World J Microbiol Biotechnol 2013; 30:1453-61. [PMID: 24338558 DOI: 10.1007/s11274-013-1576-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
Characterization of candidate surrogate spores prior to experimental use is critical to confirm that the surrogate characteristics are as closely similar as possible to those of the pathogenic agent of interest. This review compares the physical properties inherent to spores of Bacillus anthracis (Ba) and Bacillus thuringiensis (Bt) that impact their movement in air and interaction with surfaces, including size, shape, density, surface morphology, structure and hydrophobicity. Also evaluated is the impact of irradiation on the physical properties of both Bacillus species. Many physical features of Bt and Ba have been found to be similar and, while Bt is considered typically non-pathogenic, it is in the B. cereus group, as is Ba. When cultured and sporulated under similar conditions, both microorganisms share a similar cylindrical pellet shape, an aerodynamic diameter of approximately 1 μm (in the respirable size range), have an exosporium with a hairy nap, and have higher relative hydrophobicities than other Bacillus species. While spore size, morphology, and other physical properties can vary among strains of the same species, the variations can be due to growth/sporulation conditions and may, therefore, be controlled. Growth and sporulation conditions are likely among the most important factors that influence the representativeness of one species, or preparation, to another. All Bt spores may, therefore, not be representative of all Ba spores. Irradiated spores do not appear to be a good surrogate to predict the behavior of non-irradiated spores due to structural damage caused by the irradiation. While the use of Bt as a surrogate for Ba in aerosol testing appears to be well supported, this review does not attempt to narrow selection between Bt strains. Comparative studies should be performed to test the hypothesis that viable Ba and Bt spores will behave similarly when suspended in the air (as an aerosol) and to compare the known microscale characteristics versus the macroscale response.
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Karunakaran G, Suriyaprabha R, Manivasakan P, Yuvakkumar R, Rajendran V, Prabu P, Kannan N. Effect of nanosilica and silicon sources on plant growth promoting rhizobacteria, soil nutrients and maize seed germination. IET Nanobiotechnol 2013; 7:70-7. [PMID: 24028804 DOI: 10.1049/iet-nbt.2012.0048] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The study was aimed at evaluating the effect of nanosilica and different sources of silicon on soil properties, total bacterial population and maize seed germination. Nanosilica was synthesised using rice husk and characterised. Silica powder was amorphous (50 nm) with >99.9% purity. Sodium silicate treated soil inhibited plant growth promoting rhizobacteria in contrast to nanosilica and other bulk sources. Surface property and effect of soil nutrient content of nanosilica treatment were improved. Colony forming unit (CFU) was doubled in the presence of nanosilica from 4 × 105 CFU (control) to 8 × 105 CFU per gram of soil. The silica and protein content of bacterial biomass clearly showed an increase in uptake of silica with an increase in nanosilica concentration. Nanosilica promoted seed germination percentage (100%) in maize than conventional Si sources. These studies show that nanosilica has favourable effect on beneficial bacterial population and nutrient value of soil.
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18
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Li AG, Xing Y, Burggraf LW. Thermal effects on surface structures and properties of Bacillus anthracis spores on nanometer scales. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8343-8354. [PMID: 23742662 DOI: 10.1021/la400992q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial spores, one of the hardiest forms of life known, can survive severe environmental stresses such as high temperature. Using thermal atomic force microscopy (AFM), we show that the surface structures and properties of Bacillus anthracis spores when exposed to elevated temperatures undergo substantial changes on nanometer scales. Thermal-blister-like nanostructures, which grow in size with increasing temperature, are formed on the spore surface when it is heated by a thermal tip. Although thermal damage to the spore surface is persistent upon cooling heat-treated spores to room temperature, thermal effects on surface properties of the spores are complex. The thermally induced nanostructures show a lower surface-tip adhesion and a higher modulus than the surrounding spore surface. The overall trend is for the adhesion to decrease with increasing temperature. However, the adhesion of heat-treated spores may be smaller than, equal to, or larger than that of untreated spores, depending upon the degree of surface damage induced by heat. Although the overall spore dimensions show few changes during and after heat treatment, the size of the spore substructures decreases significantly. In addition, we demonstrate a nanoscratch AFM method for imaging the subsurface structures of spores.
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Affiliation(s)
- Alex G Li
- Department of Engineering Physics, Air Force Institute of Technology, 2950 Hobson Way, Wright-Patterson AFB Ohio 45433-7765, United States.
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Isolation and characterization of a soluble and thermostable phosphite dehydrogenase from Ralstonia sp. strain 4506. J Biosci Bioeng 2011; 113:445-50. [PMID: 22197497 DOI: 10.1016/j.jbiosc.2011.11.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 11/21/2011] [Accepted: 11/24/2011] [Indexed: 11/21/2022]
Abstract
Phosphite dehydrogenase (PtxD), which catalyzes the nearly irreversible oxidation of phosphite to phosphate with the concomitant reduction of NAD(+) to NADH, has great potential for NADH regeneration in industrial biocatalysts. Here, we isolated a soil bacterium, Ralstonia sp. strain 4506, that grew at 45°C on a minimal medium containing phosphite as the sole source of phosphorus. A recombinant PtxD of Ralstonia sp. (PtxD(R4506)) appeared in the soluble fraction in Escherichia coli. The purified PtxD(R4506) showed 6.7-fold greater catalytic efficiency (V(max)/K(m)) than the first characterized PtxD of Pseudomonas stutzeri (PtxD(PS)). Moreover, the purified PtxD(R4506) showed maximum activity at 50°C, and its half-life of thermal inactivation at 45°C was 80.5h, which is approximately 3,450-fold greater than that of PtxD(PS). Therefore, we concluded that PtxD(R4506), which shows high catalytic efficiency, solubility, and thermostability, would be useful for NADH regeneration applications.
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