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Pilakka Veedu A, Nakashima K, Shiga H, Sato T, Godigamuwa K, Hiroyoshi N, Kawasaki S. Functional modification of mussel adhesive protein to control solubility and adhesion property. J Biosci Bioeng 2023:S1389-1723(23)00135-4. [PMID: 37246136 DOI: 10.1016/j.jbiosc.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/16/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
Abstract
Marine mussels produce strong underwater adhesives called mussel adhesive proteins (MAPs) that can adhere to a variety of surfaces under physiological conditions. Thus, MAPs have been investigated as a potentially sustainable alternative to conventional petrochemical-based adhesives. Recombinant MAPs would be promising for large-scale production and commercialization; however, MAPs are intrinsically adhesive, aggregative, and insoluble in water. In this study, we have developed a solubilization method for the control of MAP adhesion by fusion protein technique. Foot protein 1 (Fp1), a kind of MAP, was fused with the highly water-soluble protein, which is the C-terminal domain of ice-nucleation protein K (InaKC), separated by a protease cleaving site. The fusion protein exhibited low adhesion but high solubility and stability. Notably, Fp1 recovered its adhesive property after removal from the InaKC moiety by protease cleaving, which was evaluated and confirmed by the agglomeration of magnetite particles in water. The ability to control adhesion and agglomeration makes MAPs favorable prospects for bio-based adhesives.
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Affiliation(s)
- Anju Pilakka Veedu
- Division of Sustainable Resources Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
| | - Kazunori Nakashima
- Division of Sustainable Resources Engineering, Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan.
| | - Hayahide Shiga
- Division of Sustainable Resources Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
| | - Takahiro Sato
- Division of Sustainable Resources Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
| | - Kasun Godigamuwa
- Division of Sustainable Resources Engineering, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
| | - Naoki Hiroyoshi
- Division of Sustainable Resources Engineering, Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
| | - Satoru Kawasaki
- Division of Sustainable Resources Engineering, Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-Ku, Sapporo 060-8628, Japan
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Zhang A, Hou Y, Wang Y, Wang Q, Shan X, Liu J. Highly efficient low-temperature biodegradation of polyethylene microplastics by using cold-active laccase cell-surface display system. BIORESOURCE TECHNOLOGY 2023; 382:129164. [PMID: 37207695 DOI: 10.1016/j.biortech.2023.129164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
To eliminate efficiency restriction of polyethylene microplastics low-temperature biodegradation, a novel InaKN-mediated Escherichia coli surface display platform for cold-active degrading laccase PsLAC production was developed. Display efficiency of 88.0% for engineering bacteria BL21/pET-InaKN-PsLAC was verified via subcellular extraction and protease accessibility, exhibiting an activity load of 29.6 U/mg. Cell growth and membrane integrity revealed BL21/pET-InaKN-PsLAC maintained stable growth and intact membrane structure during the display process. The favorable applicability was confirmed, with 50.0% activity remaining in 4 days at 15 °C, and 39.0% activity recovery retention after 15 batches of activity substrate oxidation reactions. Moreover, BL21/pET-InaKN-PsLAC possessed high polyethylene low-temperature depolymerizing capacity. Bioremediation experiments proved that the degradation rate was 48.0% within 48 h at 15 °C, and reached 66.0% after 144 h. Collectively, cold-active PsLAC functional surface display technology and its significant contributions to polyethylene microplastics low-temperature degradation constitute an effective improvement strategy for biomanufacturing and microplastics cold remediation.
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Affiliation(s)
- Ailin Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yanhua Hou
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Yatong Wang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Quanfu Wang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Xuejing Shan
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Jianan Liu
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
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Identification of phenotypic and genotypic properties and cold adaptive mechanisms of novel freeze–thaw stress-resistant strain Pseudomonas mandelii from Antarctica. Polar Biol 2023. [DOI: 10.1007/s00300-023-03114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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Arango RA, Schoville SD, Currie CR, Carlos-Shanley C. Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar). Front Microbiol 2021; 12:632715. [PMID: 34079527 PMCID: PMC8166220 DOI: 10.3389/fmicb.2021.632715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/15/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding the effects of environmental disturbances on insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts are known to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. In this study, subterranean termites [Reticulitermes flavipes (Kollar)] were exposed to three different temperature treatments characterized as low (15°C), medium (27°C), and high (35°C). Results suggested that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites also showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termite's physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.
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Affiliation(s)
- Rachel A. Arango
- USDA Forest Service, Forest Products Laboratory, Madison, WI, United States
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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Yuan YC, Bai XL, Liu YM, Tang XY, Yuan H, Liao X. Ligand fishing based on cell surface display of enzymes for inhibitor screening. Anal Chim Acta 2021; 1156:338359. [PMID: 33781459 DOI: 10.1016/j.aca.2021.338359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 11/19/2022]
Abstract
Ligand fishing for screening of enzyme inhibitors from complex chemical systems using baits prepared by cell surface display of the enzyme is herein demonstrated for the first time. Tyrosine phosphatase 1B (PTP1B), used as a model enzyme in this work, is displayed on the surface of E. coli cells by using ice nucleation protein (INP) as the anchoring motif. Infusion of PTP1B is characterized by western blot, immunofluorescence, proteinase K accessibility, and enzyme activity assays. Surface displayed PTP1B exhibits a maximum of 5.62 ± 0.251 U/OD600 enzymatic activity and a better stability compared with free enzyme. PTP1B displayed cells are used as solid-phase extraction adsorbent in combination with HPLC-MS to screen the inhibitors from the extracts of Rhodiola rosea, a traditional Chinese medicinal plant. Among many well-known active ingredients only arbutin is fished out with an IC50 value of 20.5 ± 0.873 μM, showing the inhibitor screening is highly selective. Furthermore, the equilibrium dissociation constant (KD) of the complex of arbutin and PTP1B was determined to be 79.6 μM by localized surface plasma resonance (LSPR) assay. The proposed ligand fishing technique using recombinant cells as baits opens a new avenue for screening of active compounds from natural products with accuracy and specificity.
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Affiliation(s)
- Yun-Cong Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Lin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yi-Ming Liu
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA.
| | - Xiao-Yue Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Nicchi S, Giuliani M, Giusti F, Pancotto L, Maione D, Delany I, Galeotti CL, Brettoni C. Decorating the surface of Escherichia coli with bacterial lipoproteins: a comparative analysis of different display systems. Microb Cell Fact 2021; 20:33. [PMID: 33531008 PMCID: PMC7853708 DOI: 10.1186/s12934-021-01528-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background The display of recombinant proteins on cell surfaces has a plethora of applications including vaccine development, screening of peptide libraries, whole-cell biocatalysts and biosensor development for diagnostic, industrial or environmental purposes. In the last decades, a wide variety of surface display systems have been developed for the exposure of recombinant proteins on the surface of Escherichia coli, such as autotransporters and outer membrane proteins. Results In this study, we assess three approaches for the surface display of a panel of heterologous and homologous mature lipoproteins in E. coli: four from Neisseria meningitidis and four from the host strain that are known to be localised in the inner leaflet of the outer membrane. Constructs were made carrying the sequences coding for eight mature lipoproteins, each fused to the delivery portion of three different systems: the autotransporter adhesin involved in diffuse adherence-I (AIDA-I) from enteropathogenic E. coli, the Lpp’OmpA chimaera and a truncated form of the ice nucleation protein (INP), InaK-NC (N-terminal domain fused with C-terminal one) from Pseudomonas syringae. In contrast to what was observed for the INP constructs, when fused to the AIDA-I or Lpp’OmpA, most of the mature lipoproteins were displayed on the bacterial surface both at 37 and 25 °C as demonstrated by FACS analysis, confocal and transmission electron microscopy. Conclusions To our knowledge this is the first study that compares surface display systems using a number of passenger proteins. We have shown that the experimental conditions, including the choice of the carrier protein and the growth temperature, play an important role in the translocation of mature lipoproteins onto the bacterial surface. Despite all the optimization steps performed with the InaK-NC anchor motif, surface exposure of the passenger proteins used in this study was not achieved. For our experimental conditions, Lpp’OmpA chimaera has proved to be an efficient surface display system for the homologous passenger proteins although cell lysis and phenotype heterogeneity were observed. Finally, AIDA-I was found to be the best surface display system for mature lipoproteins (especially heterologous ones) in the E. coli host strain with no inhibition of growth and only limited phenotype heterogeneity.
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Affiliation(s)
- Sonia Nicchi
- GSK, via Fiorentina 1, 53100, Siena, Italy.,Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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Furhan J. Adaptation, production, and biotechnological potential of cold-adapted proteases from psychrophiles and psychrotrophs: recent overview. J Genet Eng Biotechnol 2020; 18:36. [PMID: 32725297 PMCID: PMC7387391 DOI: 10.1186/s43141-020-00053-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
Background Proteases or peptidases are an imperative class of hydrolytic enzymes capable of hydrolyzing large proteins into smaller peptides. The cold-adapted proteases show higher catalytic capacity in low temperatures as well as stability in alkaline conditions and appear as strong contenders for various applications in special industries. Main body In the past few decades, the interest in cold-adapted microorganisms producing cold-adapted proteases has increased at an exciting rate, and many of them have emerged as important biotechnological and industrial candidates. Industrial proteases are largely supplied from various types of microorganisms than plant or animal sources. Among diverse microbial sources, psychrophiles and psychrotrophs inhabiting permanently or partially cold environments have appeared as rich sources of cold-adapted proteases. Short conclusion The present review focuses on recent sources of cold-adapted protease producers along with the molecular adaptation of psychrotrophs and psychrophiles. The recent knowledge on production, kinetic properties, purification, and substrate specificity of cold-adapted proteases has been summarized. Recent advances in cold-adapted protease gene cloning and structural studies are also described. Moreover, the prospective applications of cold-adapted proteases are discussed which can help in evaluating their industrial potential.
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Affiliation(s)
- Junaid Furhan
- Department of Microbiology, SKIMS Medical College-Hospital, Bemina, Srinagar, Jammu and Kashmir, 190017, India.
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Chen X, Shi X, Cai X, Yang F, Li L, Wu J, Wang S. Ice-binding proteins: a remarkable ice crystal regulator for frozen foods. Crit Rev Food Sci Nutr 2020; 61:3436-3449. [PMID: 32715743 DOI: 10.1080/10408398.2020.1798354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ice crystal growth during cold storage presents a quality problem in frozen foods. The development of appropriate technical conditions and ingredient formulations is an effective method for frozen food manufacturers to inhibit ice crystals generated during storage and distribution. Ice-binding proteins (IBPs) have great application potential as ice crystal growth inhibitors. The ability of IBPs to retard the growth of ice crystals suggests that IBPs can be used as a natural ice conditioner for a variety of frozen products. In this review, we first discussed the damage caused by ice crystals in frozen foods during freezing and frozen storage. Next, the methods and technologies for production, purification and evaluation of IBPs were summarized. Importantly, the present review focused on the characteristics, structural diversity and mechanisms of IBPs, and the application advances of IBPs in food industry. Finally, the challenges and future perspectives of IBPs are also discussed. This review may provide a better understanding of IBPs and their applications in frozen products, providing some valuable information for further research and application of IBPs.
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Affiliation(s)
- Xu Chen
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Xiaodan Shi
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Xixi Cai
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Fujia Yang
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China.,College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Ling Li
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoyun Wang
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian, China
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Freezing from the inside: Ice nucleation in Escherichia coli and Escherichia coli ghosts by inner membrane bound ice nucleation protein InaZ. Biointerphases 2020; 15:031003. [PMID: 32429672 DOI: 10.1116/1.5142174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ice nucleation (IN) active bacteria such as Pseudomonas syringae promote the growth of ice crystals more effectively than any material known. Using the specialized ice nucleation protein (INP) InaZ, P. syringae-the well studied epiphytic plant pathogen-attacks plants by frost damage and, likewise fascinating, drives ice nucleation within clouds when airborne in the atmosphere by linkage to the Earth's water cycle. While ice nucleation proteins play a tremendous role for life on the planet, the molecular details of their activity on the bacterial membrane surface are largely unknown. Bacterial ghosts (BGs) derived from Escherichia coli can be used as simplified model systems to study the mode of action of InaZ. In this work, the authors used BGs to study the role of InaZ localization on the luminal side of the bacterial inner membrane. Naturally, P. syringae INPs are displayed on the surface of the outer membrane; so in contrast, the authors engineered an N-terminal truncated form of inaZ lacking the transport sequence for anchoring of InaZ on the outer membrane. This construct was fused to N- and C-terminal inner membrane anchors and expressed in Escherichia coli C41. The IN activity of the corresponding living recombinant E. coli catalyzing interfacial ice formation of supercooled water at high subzero temperatures was tested by a droplet-freezing assay and surface spectroscopy. The median freezing temperature (T50) of the parental living E. coli C41 cells without INP was detected at -20.1 °C and with inner membrane anchored INPs at a T50 value between -7 and -9 °C, demonstrating that the induction of IN from the inside of the bacterium by inner membrane anchored INPs facing the luminal inner membrane side is very similar to IN induced by bacterial INPs located at the outer membrane. Bacterial ghosts derived from these different constructs showed first droplet freezing values between -6 and -8 °C, whereas E. coli C41 BGs alone without carrying inner membrane anchored INPs exhibit a T50 of -18.9 °C. Sum frequency generation spectroscopy showed structural ordered water at the BG/water interface, which increased close to the water melting point. Together, this indicates that the more efficient IN of INP-BGs compared to their living parental strains can be explained by the free access of inner membrane anchored INP constructs to ultrapure water filling the inner space of the BGs.
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Zhang Q, Chen X, Luo W, Wu H, Liu X, Chen W, Tang J, Zhang L. Effects of Temperature on the Characteristics of Nitrogen Removal and Microbial Community in Post Solid-Phase Denitrification Biofilter Process. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16224466. [PMID: 31766298 PMCID: PMC6888237 DOI: 10.3390/ijerph16224466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 11/18/2022]
Abstract
In order to solve the problems of high energy consumption, complex process and low nitrogen removal efficiency in the currently available low carbon source wastewater treatment processes, a novel coagulation sedimentation/post-solid-phase denitrification biofilter process (CS-BAF-SPDB) was proposed. The effect of temperature on the nitrogen removal performance of BAF-SPDB was intensively studied, and the mechanism of the effect of temperature on nitrogen removal performance was analyzed from the perspective of microbial community structure by using the polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). The results showed that, to realize favorable nitrifying and denitrifying performance simultaneously in the BAF-SPDB unit, the operation temperature should be set above 18 °C. In addition, the influence of the macro operation parameters on the performance of the BAF and SPDB has a direct relationship with the dynamic changes of the micro microbial community. The influence of temperature on nitrification performance in BAF was mainly embodied in the change of composition, amount and activity of ammonia oxidizing bacteria Candidatus Nitrospira defluvii and nitrite oxidizing bacteria Nitrosomonas sp. Nm47, while that on denitrification performance in SPDB is mainly embodied in the change of composition and amount of solid carbon substrate degrading denitrifying bacteria Pseudomonas sp., Myxobacterium AT3-03 and heterotrophic denitrifying bacteria Dechloromonas agitate, Thauera aminoaromatica, Comamonas granuli and Rubrivivax gelatinosus.
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Affiliation(s)
- Qian Zhang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Xue Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Wandong Luo
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Heng Wu
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Xiangyang Liu
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Wang Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Jianhong Tang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China; (Q.Z.); (X.C.); (W.L.); (H.W.); (X.L.); (W.C.); (J.T.)
| | - Lijie Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
- Correspondence: ; Tel.: +86-177-2519-9400
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Abstract
Despite the typical human notion that the Earth is a habitable planet, over three quarters of our planet is uninhabitable by us without assistance. The organisms that live and thrive in these “inhospitable” environments are known by the name extremophiles and are found in all Domains of Life. Despite our general lack of knowledge about them, they have already assisted humans in many ways and still have much more to give. In this review, I describe how they have adapted to live/thrive/survive in their niches, helped scientists unlock major scientific discoveries, advance the field of biotechnology, and inform us about the boundaries of Life and where we might find it in the Universe.
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Affiliation(s)
- James A Coker
- Department of Sciences, University of Maryland Global Campus, Adelphi, MD, USA
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15
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Liu Q, Liu HC, Zhou YG, Xin YH. Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers. Front Microbiol 2019; 10:1069. [PMID: 31178833 PMCID: PMC6538692 DOI: 10.3389/fmicb.2019.01069] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous mountain glaciers located on the Tibetan Plateau are inhabited by abundant microorganisms. The microorganisms on the glacier surface are exposed to the cold, barren, and high-ultraviolet radiation environments. Although the microbial community composition on glaciers has been revealed by high-throughput sequencing, little is known about the microevolution and adaptive strategy of certain bacterial populations. In this study, we used a polyphasic approach to determine the taxonomic status of 11 psychrophilic Flavobacterium strains isolated from glaciers on the Tibetan Plateau and performed a comparative genomic analysis. The phylogenetic tree based on the concatenated single-copy gene sequences showed the 11 strains clustered together, forming a distinct and novel clade in the genus Flavobacterium. The average nucleotide identity (ANI) values among these strains were higher than 96%. However, the values much lower than 90% between them and related species indicated that they represent a novel species and the name Flavobacterium bomense sp. nov. is proposed. The core and accessory genomes of strains in this new Flavobacterium species showed diverse distinct patterns of gene content and metabolism pathway. In order to infer the driving evolutionary forces of the core genomes, homologous recombination was found to contribute twice as much to nucleotide substitutions as mutations. A series of genes encoding proteins with known or predicted roles in cold adaptation were found in their genomes, for example, cold-shock protein, proteorhodopsin, osmoprotection, and membrane-related proteins. A comparative analysis of the group with optimal growth temperature (OGT) ≤ 20°C and the group with OGT > 20°C of the 32 Flavobacterium type strains and 11 new strains revealed multiple amino acid substitutions, including the decrease of the proline and glutamine content and the increase of the methionine and isoleucine content in the group with OGT ≤ 20°C, which may contribute to increased protein flexibility at low temperatures. Thus, this study discovered a novel Flavobacterium species in glaciers, which has high intraspecific diversity and multiple adaptation mechanisms that enable them to cope and thrive in extreme habitats.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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16
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Khudyakov AN, Kuleshova LG, Zaitseva OO, Sergushkina MI, Vetoshkin KA, Polezhaeva TV. Effect of Pectins on Water Crystallization Pattern and Integrity of Cells During Freezing. Biopreserv Biobank 2019; 17:52-57. [DOI: 10.1089/bio.2018.0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Andrey Nikolayevich Khudyakov
- Laboratory of Cryophysiology of Blood, Institute of Physiology, Komi Scientific Center of the Russian Academy of Sciences, Komi Republic, Syktyvkar, Russian Federation
| | - Larisa Georgievna Kuleshova
- Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Oksana Olegovna Zaitseva
- Laboratory of Cryophysiology of Blood, Institute of Physiology, Komi Scientific Center of the Russian Academy of Sciences, Komi Republic, Syktyvkar, Russian Federation
| | - Marta Igorevna Sergushkina
- Laboratory of Cryophysiology of Blood, Institute of Physiology, Komi Scientific Center of the Russian Academy of Sciences, Komi Republic, Syktyvkar, Russian Federation
| | | | - Tatyana Vitalyevna Polezhaeva
- Laboratory of Cryophysiology of Blood, Institute of Physiology, Komi Scientific Center of the Russian Academy of Sciences, Komi Republic, Syktyvkar, Russian Federation
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17
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Nakatani H, Kanie J, Hori K. On‐fiber display of a functional peptide at sites distant from the cell surface using a long bacterionanofiber of a trimeric autotransporter adhesin. Biotechnol Bioeng 2018; 116:239-249. [DOI: 10.1002/bit.26857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/20/2018] [Accepted: 10/30/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Hajime Nakatani
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
| | - Junichi Kanie
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
| | - Katsutoshi Hori
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
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18
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Bacteria Associated with Marine Benthic Invertebrates from Polar Environments: Unexplored Frontiers for Biodiscovery? DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ecological function of bacteria-invertebrate interactions in Polar areas remains poorly understood, despite increasing evidence that microbial metabolites may play pivotal roles in host-associated chemical defense and in shaping the symbiotic community structure. The metabolic and physiological changes that these organisms undergo in response to adapting to extreme conditions result in the production of structurally and functionally novel biologically active molecules. Deepening our knowledge on the interactions between bacteria and their invertebrate host would be highly helpful in providing the rationale for why (e.g., competition or cooperative purpose) and which (whether secondary metabolites, enzymes, or proteins) bioactive compounds are produced. To date, cold-adapted bacteria associated with marine invertebrates from the Arctic and Antarctica have not been given the attention they deserve and the versatility of their natural products remains virtually unexplored, even if they could represent a new attractive frontier in the search for novel natural compounds. This review is aimed at showcasing the diversity of cold-adapted bacteria associated with benthic invertebrates from Polar marine areas, highlighting the yet unexplored treasure they represent for biodiscovery.
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19
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Tagawa E, Ura M, Nakatsuka E, Hirono Y, Kawahara H. Anti-Ice Nucleation Activities of Tyrosine Peptide. Biocontrol Sci 2018; 23:81-83. [PMID: 29910213 DOI: 10.4265/bio.23.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
We investigated whether trimers of serine, threonine, tyrosine, and phenylalanine which may interact with water molecules and ice, show anti-ice nucleation activity. Only tyrosine trimer had high levels of anti-ice nucleation activity (10.10±0.74℃) at a final concentration of 0.2 mM. This was constant at an activity of 2.0℃ between the 0.01-0.1 mM concentrations, and rapidly increased at 0.1 mM or more. At the final concentration of 0.2 mM or more, the activity of the tyrosine trimer was almost constant (from 9.2℃ to 10.2℃). Although it is lower than the activity against silver iodide, the tyrosine trimer showed an effect on the activity of the ice nucleating bacteria. This is the first report that revealed that trimer of amino acid, especially tyrosine has the supercooling-facilitating activity.
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Affiliation(s)
- Eri Tagawa
- Department of Life Science and Biotechnology, Kansai University
| | - Mayumi Ura
- Department of Life Science and Biotechnology, Kansai University
| | - Eri Nakatsuka
- Department of Chemistry and Materials Engineering, Kansai University
| | - Yoshiaki Hirono
- Department of Chemistry and Materials Engineering, Kansai University
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20
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Glatz B, Sarupria S. Heterogeneous Ice Nucleation: Interplay of Surface Properties and Their Impact on Water Orientations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1190-1198. [PMID: 29020452 DOI: 10.1021/acs.langmuir.7b02859] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ice is ubiquitous in nature, and heterogeneous ice nucleation is the most common pathway of ice formation. How surface properties affect the propensity to observe ice nucleation on that surface remains an open question. We present results of molecular dynamics studies of heterogeneous ice nucleation on model surfaces. The models surfaces considered emulate the chemistry of kaolinite, an abundant component of mineral dust. We investigate the interplay of surface lattice and hydrogen bonding properties in affecting ice nucleation. We find that lattice matching and hydrogen bonding are necessary but not sufficient conditions for observing ice nucleation at these surfaces. We correlate this behavior to the orientations sampled by the metastable supercooled water in contact with the surfaces. We find that ice is observed in cases where water molecules not only sample orientations favorable for bilayer formation but also do not sample unfavorable orientations. This distribution depends on both surface-water and water-water interactions and can change with subtle modifications to the surface properties. Our results provide insights into the diverse behavior of ice nucleation observed at different surfaces and highlight the complexity in elucidating heterogeneous ice nucleation.
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Affiliation(s)
- Brittany Glatz
- Department of Chemical & Biomolecular Engineering, Clemson University , Clemson, South Carolina 29634, United States
| | - Sapna Sarupria
- Department of Chemical & Biomolecular Engineering, Clemson University , Clemson, South Carolina 29634, United States
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21
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Stelmach KB, Neveu M, Vick-Majors TJ, Mickol RL, Chou L, Webster KD, Tilley M, Zacchei F, Escudero C, Flores Martinez CL, Labrado A, Fernández EJG. Secondary Electrons as an Energy Source for Life. ASTROBIOLOGY 2018; 18:73-85. [PMID: 29314901 DOI: 10.1089/ast.2016.1510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Life on Earth is found in a wide range of environments as long as the basic requirements of a liquid solvent, a nutrient source, and free energy are met. Previous hypotheses have speculated how extraterrestrial microbial life may function, among them that particle radiation might power living cells indirectly through radiolytic products. On Earth, so-called electrophilic organisms can harness electron flow from an extracellular cathode to build biomolecules. Here, we describe two hypothetical mechanisms, termed "direct electrophy" and "indirect electrophy" or "fluorosynthesis," by which organisms could harness extracellular free electrons to synthesize organic matter, thus expanding the ensemble of potential habitats in which extraterrestrial organisms might be found in the Solar System and beyond. The first mechanism involves the direct flow of secondary electrons from particle radiation to a microbial cell to power the organism. The second involves the indirect utilization of impinging secondary electrons and a fluorescing molecule, either biotic or abiotic in origin, to drive photosynthesis. Both mechanisms involve the attenuation of an incoming particle's energy to create low-energy secondary electrons. The validity of the hypotheses is assessed through simple calculations showing the biomass density attainable from the energy supplied. Also discussed are potential survival strategies that could be used by organisms living in possible habitats with a plentiful supply of secondary electrons, such as near the surface of an icy moon. While we acknowledge that the only definitive test for the hypothesis is to collect specimens, we also describe experiments or terrestrial observations that could support or nullify the hypotheses. Key Words: Radiation-Electrophiles-Subsurface life. Astrobiology 18, 73-85.
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Affiliation(s)
- Kamil B Stelmach
- 1 Department of Chemistry and Biochemistry, George Mason University , Fairfax, Virginia, USA
| | - Marc Neveu
- 2 School of Earth and Space Exploration, Arizona State University , Tempe, Arizona, USA
| | - Trista J Vick-Majors
- 3 Department of Land Resources and Environmental Sciences, Montana State University , Bozeman, Montana, USA
- 4 Département des sciences biologiques, Université du Québec à Montréal , Montréal, Canada
| | - Rebecca L Mickol
- 5 Arkansas Center for Space and Planetary Sciences, University of Arkansas , Fayetteville, Arkansas, USA
| | - Luoth Chou
- 6 Department of Earth and Environmental Sciences, University of Illinois at Chicago , Chicago, Illinois, USA
| | - Kevin D Webster
- 7 Department of Ecology and Evolutionary Biology, University of Arizona , Tucson, Arizona, USA
- 8 School of Natural Resources and the Environment, University of Arizona , Tucson, Arizona, USA
| | - Matt Tilley
- 9 Department of Earth and Space Sciences, University of Washington , Seattle, Washington, USA
| | - Federica Zacchei
- 10 Instituut voor Sterrenkunde, University of Leuven , Leuven, Belgium
| | | | | | - Amanda Labrado
- 13 Department of Geosciences, The Pennsylvania State University , University Park, Pennsylvania, USA
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22
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Xu Q, Ni P, Liu D, Yin Y, Li Q, Zhang J, Wu Q, Tian P, Shi X, Wang D. A Bacterial Surface Display System Expressing Cleavable Capsid Proteins of Human Norovirus: A Novel System to Discover Candidate Receptors. Front Microbiol 2017; 8:2405. [PMID: 29270155 PMCID: PMC5723664 DOI: 10.3389/fmicb.2017.02405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/20/2017] [Indexed: 12/02/2022] Open
Abstract
Human noroviruses (HuNoVs) are the dominant cause of food-borne outbreaks of acute gastroenteritis. However, fundamental researches on HuNoVs, such as identification of viral receptors have been limited by the currently immature system to culture HuNoVs and the lack of efficient small animal models. Previously, we demonstrated that the recombinant protruding domain (P domain) of HuNoVs capsid proteins were successfully anchored on the surface of Escherichia coli BL21 cells after the bacteria were transformed with a plasmid expressing HuNoVs P protein fused with bacterial transmembrane anchor protein. The cell-surface-displayed P proteins could specifically recognize and bind to histo-blood group antigens (HBGAs, receptors of HuNoVs). In this study, an upgraded bacterial surface displayed system was developed as a new platform to discover candidate receptors of HuNoVs. A thrombin-susceptible “linker” sequence was added between the sequences of bacterial transmembrane anchor protein and P domain of HuNoV (GII.4) capsid protein in a plasmid that displays the functional P proteins on the surface of bacteria. In this new system, the surface-displayed HuNoV P proteins could be released by thrombin treatment. The released P proteins self-assembled into small particles, which were visualized by electron microscopy. The bacteria with the surface-displayed P proteins were incubated with pig stomach mucin which contained HBGAs. The bacteria-HuNoV P proteins-HBGAs complex could be collected by low speed centrifugation. The HuNoV P proteins-HBGAs complex was then separated from the recombinant bacterial surface by thrombin treatment. The released viral receptor was confirmed by using the monoclonal antibody against type A HBGA. It demonstrated that the new system was able to capture and easily isolate receptors of HuNoVs. This new strategy provides an alternative, easier approach for isolating unknown receptors/ligands of HuNoVs from different samples including mammalian cell lines, oysters, and fresh produce.
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Affiliation(s)
- Qian Xu
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pei'en Ni
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Danlei Liu
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Yin
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianqian Li
- Department of Bioengineering, Shanghai Institute of Technology, Shanghai, China
| | - Jvmei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service - United States Department of Agriculture, Albany, CA, United States
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Redesigning of Microbial Cell Surface and Its Application to Whole-Cell Biocatalysis and Biosensors. Appl Biochem Biotechnol 2017; 185:396-418. [PMID: 29168153 DOI: 10.1007/s12010-017-2662-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Microbial cell surface display technology can redesign cell surfaces with functional proteins and peptides to endow cells some unique features. Foreign peptides or proteins are transported out of cells and immobilized on cell surface by fusing with anchoring proteins, which is an effective solution to avoid substance transfer limitation, enzyme purification, and enzyme instability. As the most frequently used prokaryotic and eukaryotic protein surface display system, bacterial and yeast surface display systems have been widely applied in vaccine, biocatalysis, biosensor, bioadsorption, and polypeptide library screening. In this review of bacterial and yeast surface display systems, different cell surface display mechanisms and their applications in biocatalysis as well as biosensors are described with their strengths and shortcomings. In addition to single enzyme display systems, multi-enzyme co-display systems are presented here. Finally, future developments based on our and other previous reports are discussed.
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24
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Bore EK, Apostel C, Halicki S, Kuzyakov Y, Dippold MA. Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling. Front Microbiol 2017; 8:946. [PMID: 28611748 PMCID: PMC5447017 DOI: 10.3389/fmicb.2017.00946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
Although biogeochemical models designed to simulate carbon (C) and nitrogen (N) dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: +5 (control), -5, and -20°C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC) after 1, 3, and 10 days and also after 30 days for samples at -20°C. Compared to +5°C, CO2 decreased 3- and 10-fold at -5 and -20°C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at +5°C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at -5 than +5°C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at -20°C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.
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Affiliation(s)
- Ezekiel K. Bore
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Carolin Apostel
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Sara Halicki
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
- Institute of Environmental Sciences, Kazan Federal UniversityKazan, Russia
| | - Michaela A. Dippold
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
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25
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Zhai H, Xu P, Ning M, Cheng Q, Mandal J, Yang Y. A Flexible Solid Composite Electrolyte with Vertically Aligned and Connected Ion-Conducting Nanoparticles for Lithium Batteries. NANO LETTERS 2017; 17:3182-3187. [PMID: 28409638 DOI: 10.1021/acs.nanolett.7b00715] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Replacing flammable organic liquid electrolytes with solid Li-ion conductors is a promising approach to realize safe rechargeable batteries with high energy density. Composite solid electrolytes, which are comprised of a polymer matrix with ceramic Li-ion conductors dispersed inside, are attractive, since they combine the flexibility of polymer electrolytes and high ionic conductivities of ceramic electrolytes. However, the high conductivity of ceramic fillers is largely compromised by the low conductivity of the matrix, especially when nanoparticles (NPs) are used. Therefore, optimizations of the geometry of ceramic fillers are critical to further enhance the conductivity of composite electrolytes. Here we report the vertically aligned and connected Li1+xAlxTi2-x(PO4)3 (LATP) NPs in the poly(ethylene oxide) (PEO) matrix to maximize the ionic conduction, while maintaining the flexibility of the composite. This vertically aligned structure can be fabricated by an ice-templating-based method, and its conductivity reaches 0.52 × 10-4 S/cm, which is 3.6 times that of the composite electrolyte with randomly dispersed LATP NPs. The composite electrolyte also shows enhanced thermal and electrochemical stability compared to the pure PEO electrolyte. This method opens a new approach to optimize ion conduction in composite solid electrolytes for next-generation rechargeable batteries.
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Affiliation(s)
- Haowei Zhai
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
| | - Pengyu Xu
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
| | - Mingqiang Ning
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
- School of Materials Science & Engineering, Beijing Institute of Technology , Beijing, 100081, China
| | - Qian Cheng
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
| | - Jyotirmoy Mandal
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
| | - Yuan Yang
- Program of Materials Science and Engineering, Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10025, United States
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27
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Glatz B, Sarupria S. The surface charge distribution affects the ice nucleating efficiency of silver iodide. J Chem Phys 2016; 145:211924. [DOI: 10.1063/1.4966018] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Brittany Glatz
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, USA
| | - Sapna Sarupria
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, USA
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28
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Surface Immobilization of Human Arginase-1 with an Engineered Ice Nucleation Protein Display System in E. coli. PLoS One 2016; 11:e0160367. [PMID: 27479442 PMCID: PMC4968799 DOI: 10.1371/journal.pone.0160367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/18/2016] [Indexed: 01/18/2023] Open
Abstract
Ice nucleation protein (INP) is frequently used as a surface anchor for protein display in gram-negative bacteria. Here, MalE and TorA signal peptides, and three charged polypeptides, 6×Lys, 6×Glu and 6×Asp, were anchored to the N-terminus of truncated INP (InaK-N) to improve its surface display efficiency for human Arginase1 (ARG1). Our results indicated that the TorA signal peptide increased the surface translocation of non-protein fused InaK-N and human ARG1 fused InaK-N (InaK-N/ARG1) by 80.7% and 122.4%, respectively. Comparably, the MalE signal peptide decreased the display efficiencies of both the non-protein fused InaK-N and InaK-N/ARG1. Our results also suggested that the 6×Lys polypeptide significantly increased the surface display efficiency of K6-InaK-N/ARG1 by almost 2-fold, while also practically abolishing the surface translocation of non-protein fused InaK-N, indicating the interesting roles of charged polypeptides in bacteria surface display systems. Cell surface-immobilized K6-InaK-N/ARG1 presented an arginase activity of 10.7 U/OD600 under the optimized conditions of 40°C, pH 10.0 and 1 mM Mn2+, which could convert more than 95% of L-Arginine (L-Arg) to L-Ornithine (L-Orn) in 16 hours. The engineered InaK-Ns expanded the INP surface display system, which aided in the surface immobilization of human ARG1 in E. coli cells.
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Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools. J Microbiol Methods 2016; 120:23-8. [DOI: 10.1016/j.mimet.2015.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022]
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Bäumer A, Duman JG, Havenith M. Ice nucleation of an insect lipoprotein ice nucleator (LPIN) correlates with retardation of the hydrogen bond dynamics at the myo-inositol ring. Phys Chem Chem Phys 2016; 18:19318-23. [DOI: 10.1039/c6cp02399a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Remarkably little is known about the mechanism of action of ice nucleation proteins (INPs), although their ability to trigger ice nucleation could be used in a broad variety of applications.
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Affiliation(s)
- Alexander Bäumer
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität
- 44801 Bochum
- Germany
| | - John G. Duman
- Department of Biological Sciences
- University of Notre Dame
- Notre Dame
- USA
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität
- 44801 Bochum
- Germany
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Niu M, Yu Q, Tian P, Gao Z, Wang D, Shi X. Engineering Bacterial Surface Displayed Human Norovirus Capsid Proteins: A Novel System to Explore Interaction Between Norovirus and Ligands. Front Microbiol 2015; 6:1448. [PMID: 26733983 PMCID: PMC4686607 DOI: 10.3389/fmicb.2015.01448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/04/2015] [Indexed: 01/24/2023] Open
Abstract
Human noroviruses (HuNoVs) are major contributors to acute nonbacterial gastroenteritis outbreaks. Many aspects of HuNoVs are poorly understood due to both the current inability to culture HuNoVs, and the lack of efficient small animal models. Surrogates for HuNoVs, such as recombinant viral like particles (VLPs) expressed in eukaryotic system or P particles expressed in prokaryotic system, have been used for studies in immunology and interaction between the virus and its receptors. However, it is difficult to use VLPs or P particles to collect or isolate potential ligands binding to these recombinant capsid proteins. In this study, a new strategy was used to collect HuNoVs binding ligands through the use of ice nucleation protein (INP) to display recombinant capsid proteins of HuNoVs on bacterial surfaces. The viral protein-ligand complex could be easily separated by a low speed centrifugation step. This system was also used to explore interaction between recombinant capsid proteins of HuNoVs and their receptors. In this system, the VP1 capsid encoding gene (ORF2) and the protruding domain (P domain) encoding gene (3′ terminal fragment of ORF2) of HuNoVs GI.1 and GII.4 were fused with 5′ terminal fragment of INP encoding gene (inaQn). The results demonstrated that the recombinant VP1 and P domains of HuNoVs were expressed and anchored on the surface of Escherichia coli BL21 cells after the bacteria were transformed with the corresponding plasmids. Both cell surface displayed VP1 and P domains could be recognized by HuNoVs specific antibodies and interact with the viral histo-blood group antigens receptors. In both cases, displayed P domains had better binding abilities than VP1. This new strategy of using displayed HuNoVs capsid proteins on the bacterial surface could be utilized to separate HuNoVs binding components from complex samples, to investigate interaction between the virus and its receptors, as well as to develop an oral vaccine for HuNoVs.
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Affiliation(s)
- Mengya Niu
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qianqian Yu
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture Albany, CA, USA
| | - Zhiyong Gao
- Beijing Center for Diseases Prevention and Control Beijing, China
| | - Dapeng Wang
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Xianming Shi
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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32
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Deciphering EGFP production via surface display and self-cleavage intein system in different hosts. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2015.03.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Congdon T, Dean BT, Kasperczak-Wright J, Biggs CI, Notman R, Gibson MI. Probing the Biomimetic Ice Nucleation Inhibition Activity of Poly(vinyl alcohol) and Comparison to Synthetic and Biological Polymers. Biomacromolecules 2015; 16:2820-6. [PMID: 26258729 PMCID: PMC4577968 DOI: 10.1021/acs.biomac.5b00774] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/08/2015] [Indexed: 12/13/2022]
Abstract
Nature has evolved many elegant solutions to enable life to flourish at low temperatures by either allowing (tolerance) or preventing (avoidance) ice formation. These processes are typically controlled by ice nucleating proteins or antifreeze proteins, which act to either promote nucleation, prevent nucleation or inhibit ice growth depending on the specific need, respectively. These proteins can be expensive and their mechanisms of action are not understood, limiting their translation, especially into biomedical cryopreservation applications. Here well-defined poly(vinyl alcohol), synthesized by RAFT/MADIX polymerization, is investigated for its ice nucleation inhibition (INI) activity, in contrast to its established ice growth inhibitory properties and compared to other synthetic polymers. It is shown that ice nucleation inhibition activity of PVA has a strong molecular weight dependence; polymers with a degree of polymerization below 200 being an effective inhibitor at just 1 mg.mL(-1). Other synthetic and natural polymers, both with and without hydroxyl-functional side chains, showed negligible activity, highlighting the unique ice/water interacting properties of PVA. These findings both aid our understanding of ice nucleation but demonstrate the potential of engineering synthetic polymers as new biomimetics to control ice formation/growth processes.
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Affiliation(s)
- Thomas Congdon
- Department of Chemistry, University
of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Bethany T. Dean
- Department of Chemistry, University
of Warwick, Coventry, CV4 7AL, United Kingdom
| | | | - Caroline I. Biggs
- Department of Chemistry, University
of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Rebecca Notman
- Department of Chemistry, University
of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department of Chemistry, University
of Warwick, Coventry, CV4 7AL, United Kingdom
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Wu J, Rong Y, Wang Z, Zhou Y, Wang S, Zhao B. Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction. Food Chem 2015; 174:621-9. [DOI: 10.1016/j.foodchem.2014.11.100] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/21/2014] [Accepted: 11/17/2014] [Indexed: 02/03/2023]
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Bao S, Yu S, Guo X, Zhang F, Sun Y, Tan L, Duan Y, Lu F, Qiu X, Ding C. Construction of a cell-surface display system based on the N-terminal domain of ice nucleation protein and its application in identification of mycoplasma
adhesion proteins. J Appl Microbiol 2015; 119:236-44. [DOI: 10.1111/jam.12824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
Affiliation(s)
- S. Bao
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - S. Yu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - X. Guo
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - F. Zhang
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Sun
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - L. Tan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Duan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - F. Lu
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - X. Qiu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - C. Ding
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
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Rice CV, Middaugh A, Wickham JR, Friedline A, Thomas KJ, Scull E, Johnson K, Zachariah M, Garimella R. Bacterial lipoteichoic acid enhances cryosurvival. Extremophiles 2014; 19:297-305. [PMID: 25477208 DOI: 10.1007/s00792-014-0714-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022]
Abstract
Antifreeze proteins in fish, plants, and insects provide protection to a few degrees below freezing. Microbes have been found to survive at even lower temperatures, and with a few exceptions, antifreeze proteins are missing. We show that lipoteichoic acid (LTA), a biopolymer in the cell wall of Gram-positive bacteria, can be added to B. subtilis cultures and increase freeze tolerance. At 1 % w/v, LTA enables a 50 % survival rate, similar to the results obtained with 1 % w/v glycerol as measured with the resazurin cell viability assay. In the absence of added LTA or glycerol, a very small number of B. subtilis cells survive freezing. This suggests that an innate freeze tolerance mechanism exists. While cryoprotection can be provided by extracellular polymeric substances, our data demonstrate a role for LTA in cryoprotection. Currently, the exact mode of action for LTA cryoprotection is unknown. With a molecular weight of 3-5 kDa, it is unlikely to enter the cell cytoplasm. However, low temperature microscopy data show small ice crystals aligned along channels of liquid water. Our observations suggest that teichoic acids could protect liquid water within biofilms and planktonic bacteria, augmenting the role of brine while also raising the possibility for survival without brine present.
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Affiliation(s)
- Charles V Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA,
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Perturbation of bacterial ice nucleation activity by a grass antifreeze protein. Biochem Biophys Res Commun 2014; 452:636-41. [DOI: 10.1016/j.bbrc.2014.08.138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 11/21/2022]
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De Maayer P, Anderson D, Cary C, Cowan DA. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 2014; 15:508-17. [PMID: 24671034 DOI: 10.1002/embr.201338170] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
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40
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Ganji S, Jenkins JN, Wubben MJ. Molecular characterization of the reniform nematode C-type lectin gene family reveals a likely role in mitigating environmental stresses during plant parasitism. Gene 2014; 537:269-78. [PMID: 24424511 DOI: 10.1016/j.gene.2013.12.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/26/2022]
Abstract
The reniform nematode, Rotylenchulus reniformis, is a damaging semi-endoparasitic pathogen of more than 300 plant species. Transcriptome sequencing of R. reniformis parasitic females revealed an enrichment for sequences homologous to C-type lectins (CTLs), an evolutionarily ancient family of Ca(+2)-dependent carbohydrate-binding proteins that are involved in the innate immune response. To gain further insight as to the potential role of CTLs in facilitating plant parasitism by R. reniformis, we performed a comprehensive assessment of the CTL gene family. 5'- and 3'-RACE experiments identified a total of 11 R. reniformis CTL transcripts (Rr-ctl-1 through Rr-ctl-11) that ranged in length from 1083 to 1,194 bp and showed 93-99% identity with one another. An alignment of cDNA and genomic sequences revealed three introns with the first intron residing within the 5'-untranslated region. BLAST analyses showed the closest homologs belonging to the parasitic nematodes Heligmosomoides polygyrus and Heterodera glycines. Rr-ctl-1, -2, and -3 were expressed throughout the R. reniformis life cycle; whereas, the remaining Rr-ctl genes showed life stage-specific expression. Quantitative real time RT-PCR determined that Rr-ctl transcripts were 839-fold higher in sedentary female nematodes than the next most abundant life stage. Predicted Rr-CTL peptides ranged from 301 to 338 amino acids long, possessed an N-terminal signal peptide for secretion, and contained a conserved CLECT domain, including the mannose-binding motifs EPN and EPD and the conserved WND motif that is required for binding Ca(+2). In addition, Rr-CTL peptides harbored repeats of a novel 17-mer motif within their C-terminus that showed similarity to motifs associated with bacterial ice nucleation proteins. In situ hybridization of Rr-ctl transcripts within sedentary females showed specific accumulation within the hypodermis of the body regions exposed to the soil environment; those structures embedded within the root during parasitism did not show Rr-ctl expression. A phylogenetic analysis of the Rr-CTL CLECT domain with homologous domains from other nematode species suggested that CTLs from animal- and plant-parasitic genera may have evolved in order to play an active role in the parasitic process.
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Affiliation(s)
- Satish Ganji
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Johnie N Jenkins
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS 39762, USA; USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, Mississippi State, MS 39762, USA.
| | - Martin J Wubben
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS 39762, USA; USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit, Mississippi State, MS 39762, USA.
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41
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Soukoulis C, Fisk I. Innovative Ingredients and Emerging Technologies for Controlling Ice Recrystallization, Texture, and Structure Stability in Frozen Dairy Desserts: A Review. Crit Rev Food Sci Nutr 2014; 56:2543-2559. [DOI: 10.1080/10408398.2013.876385] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Over the past three decades, a powerful array of techniques has been developed for expressing heterologous proteins and saccharides on the surface of bacteria. Surface-engineered bacteria, in turn, have proven useful in a variety of settings, including high-throughput screening, biofuel production, and vaccinology. In this chapter, we provide a comprehensive review of methods for displaying polypeptides and sugars on the bacterial cell surface, and discuss the many innovative applications these methods have found to date. While already an important biotechnological tool, we believe bacterial surface display may be further improved through integration with emerging methodology in other fields, such as protein engineering and synthetic chemistry. Ultimately, we envision bacterial display becoming a multidisciplinary platform with the potential to transform basic and applied research in bacteriology, biotechnology, and biomedicine.
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Kwak Y, Lee SE, Shin JH. Expression of organophosphorus hydrolase in Escherichia coli for use as whole-cell biocatalyst. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Singh P, Hanada Y, Singh SM, Tsuda S. Antifreeze protein activity in Arctic cryoconite bacteria. FEMS Microbiol Lett 2013; 351:14-22. [PMID: 24283367 DOI: 10.1111/1574-6968.12345] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/23/2013] [Accepted: 11/24/2013] [Indexed: 11/30/2022] Open
Abstract
Fourteen Arctic bacterial strains belonging to five genera, Cryobacterium, Leifsonia, Polaromonas, Pseudomonas, and Subtercola isolated from sediments found in cryoconite holes of Arctic glaciers, were subjected to screening for antifreeze proteins (AFPs). Eight strains showed AFP activity, and six strains of four species were further characterized. Pseudomonas ficuserectae exhibited a high thermal hysteresis (TH) activity. Ice recrystallization inhibition (IRI) activity was observed in most cultures at low protein concentration. Bacterial AFPs produced rounded shape of ice crystals that did not change their size and morphology within the TH window. Cry-g (P. ficuserectae) failed to inhibit ice recrystallization, indicating that the IRI activity of the AFPs does not relate to the strength of TH activity. SDS-PAGE analysis of the AFPs suggests their apparent molecular weights to be around 23 kDa. This study is significant as it screens several species of Arctic bacterial strains for AFP activity. So far, only one species of bacteria, Pseudomonas putida, was reported from the Arctic to produce AFPs. N-terminal amino acid sequence analysis shows that the bacterial AFPs isolated belong to the AFP family IBP-1, which is known to have an important physiological role in the cold environment. AFPs of glacier cryoconite habitat have been discussed.
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Affiliation(s)
- Purnima Singh
- Birla Institute of Technology and Science (BITS), Goa campus, Zuarinagar, Goa, India
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45
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Tarkowski P, Vereecke D. Threats and opportunities of plant pathogenic bacteria. Biotechnol Adv 2013; 32:215-29. [PMID: 24216222 DOI: 10.1016/j.biotechadv.2013.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/22/2013] [Accepted: 11/03/2013] [Indexed: 02/08/2023]
Abstract
Plant pathogenic bacteria can have devastating effects on plant productivity and yield. Nevertheless, because these often soil-dwelling bacteria have evolved to interact with eukaryotes, they generally exhibit a strong adaptivity, a versatile metabolism, and ingenious mechanisms tailored to modify the development of their hosts. Consequently, besides being a threat for agricultural practices, phytopathogens may also represent opportunities for plant production or be useful for specific biotechnological applications. Here, we illustrate this idea by reviewing the pathogenic strategies and the (potential) uses of five very different (hemi)biotrophic plant pathogenic bacteria: Agrobacterium tumefaciens, A. rhizogenes, Rhodococcus fascians, scab-inducing Streptomyces spp., and Pseudomonas syringae.
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Affiliation(s)
- Petr Tarkowski
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic.
| | - Danny Vereecke
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000 Ghent, Belgium.
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Yu F, Liu X, Tao Y, Zhu K. High saturated fatty acids proportion in Escherichia coli enhances the activity of ice-nucleation protein from Pantoea ananatis. FEMS Microbiol Lett 2013; 345:141-6. [PMID: 23763336 DOI: 10.1111/1574-6968.12197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/06/2013] [Accepted: 06/10/2013] [Indexed: 11/29/2022] Open
Abstract
The ice-nucleation protein (INP) from Pantoea ananatis was expressed in Escherichia coli. INP expression increased the freezing point of the E. coli culture by a few degrees. Deletion of FabH, an important enzyme in fatty acid biosynthesis, significantly inhibited the ice-nucleation activity. Increased unsaturated fatty acids in the fabH mutant cells decreased the ice-nucleation activity. Adding exogenous saturated fatty acids increased both E. coli fatty acid saturation and the ice-nucleation activity. In contrast, adding unsaturated fatty acids exhibited the opposite effects. Furthermore, an E. coli MG1655-fadR strain with high saturated fatty acids content was constructed, in which the INP activity was enhanced by about 17% compared with its activity in the wild-type MG1655 strain.
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Affiliation(s)
- Feifei Yu
- Institute of Microbiology Chinese Academy of Sciences, Beijing, China
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Polysaccharide hydrolysis with engineered Escherichia coli for the production of biocommodities. ACTA ACUST UNITED AC 2013; 40:401-10. [DOI: 10.1007/s10295-013-1245-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/13/2013] [Indexed: 02/06/2023]
Abstract
Abstract
Escherichia coli can ferment a broad range of sugars, including pentoses, hexoses, uronic acids, and polyols. These features make E. coli a suitable microorganism for the development of biocatalysts to be used in the production of biocommodities and biofuels by metabolic engineering. E. coli cannot directly ferment polysaccharides because it does not produce and secrete the necessary saccharolytic enzymes; however, there are many genetic tools that can be used to confer this ability on this prokaryote. The construction of saccharolytic E. coli strains will reduce costs and simplify the production process because the saccharification and fermentation can be conducted in a single reactor with a reduced concentration or absence of additional external saccharolytic enzymes. Recent advances in metabolic engineering, surface display, and excretion of hydrolytic enzymes provide a framework for developing E. coli strains for the so-called consolidated bioprocessing. This review presents the different strategies toward the development of E. coli strains that have the ability to display and secrete saccharolytic enzymes to hydrolyze different sugar-polymeric substrates and reduce the loading of saccharolytic enzymes.
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Brödel A, Raymond J, Duman J, Bier F, Kubick S. Functional evaluation of candidate ice structuring proteins using cell-free expression systems. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Optimization of the pilot-scale production of an ice-binding protein by fed-batch culture of Pichia pastoris. Appl Microbiol Biotechnol 2012. [PMID: 23203635 DOI: 10.1007/s00253-012-4594-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ice-binding proteins (IBPs) can bind to the ice crystal and inhibit its growth. Because this property of IBPs can increase the freeze-thaw survival of cells, IBPs have attracted the attention from industries for their potential use in biotechnological applications. However, their use was largely hampered by the lack of the large-scale recombinant production system. In this study, the codon-optimized IBP from Leucosporidium sp. (LeIBP) was constructed and subjected to high-level expression in methylotrophic Pichia pastoris system. In a laboratory-scale fermentation (7 L), the optimal induction temperature and pH were determined to be 25 °C and 6.0, respectively. Further, employing glycerol fed-batch phase prior to methanol induction phase enhanced the production of recombinant LelBP (rLeIBP) by ∼100 mg/l. The total amount of secreted proteins at these conditions (25 °C, pH 6.0, and glycerol fed-batch phase) was ∼443 mg/l, 60 % of which was rLeIBP, yielding ∼272 mg/l. In the pilot-scale fermentation (700 L) under the same conditions, the yield of rLeIBP was 300 mg/l. To our best knowledge, this result reports the highest production yield of the recombinant IBP. More importantly, the rLeIBP secreted into culture media was stable and active for 6 days of fermentation. The thermal hysteresis (TH) activity of rLeIBP was about 0.42 °C, which is almost the same to those reported previously. The availability of large quantities of rLeIBP may accelerate further application studies.
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50
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Wu JY, Chen CI, Chen CM, Lin CC, Kan SC, Shieh CJ, Liu YC. Cell disruption enhanced the pure EGFP recovery from an EGFP-intein-surface protein production system in recombinant E. coli. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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