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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024; 291:2980-2993. [PMID: 38555564 DOI: 10.1111/febs.17125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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Diep P, Leo Shen H, Wiesner JA, Mykytczuk N, Papangelakis V, Yakunin AF, Mahadevan R. Engineered nickel bioaccumulation in Escherichia coli by NikABCDE transporter and metallothionein overexpression. Eng Life Sci 2023; 23:2200133. [PMID: 37408871 PMCID: PMC10317975 DOI: 10.1002/elsc.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/24/2023] [Indexed: 07/07/2023] Open
Abstract
Mine wastewater often contains dissolved metals at concentrations too low to be economically extracted by existing technologies, yet too high for environmental discharge. The most common treatment is chemical precipitation of the dissolved metals using limestone and subsequent disposal of the sludge in tailing impoundments. While it is a cost-effective solution to meet regulatory standards, it represents a lost opportunity. In this study, we engineered Escherichia coli to overexpress its native NikABCDE transporter and a heterologous metallothionein to capture nickel at concentrations in local effluent streams. We found the engineered strain had a 7-fold improvement in the bioaccumulation performance for nickel compared to controls, but also observed a drastic decrease in cell viability due to metabolic burden or inducer (IPTG) toxicity. Growth kinetic analysis revealed the IPTG concentrations used based on past studies lead to growth inhibition, thus delineating future avenues for optimization of the engineered strain and its growth conditions to perform in more complex environments.
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Affiliation(s)
- Patrick Diep
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | - Heping Leo Shen
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | | | | | - Vladimiros Papangelakis
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | - Alexander F. Yakunin
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
- Centre for Environmental BiotechnologySchool of Natural SciencesUniversity of BangorWalesUK
| | - Radhakrishnan Mahadevan
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
- Institute of Biomedical EngineeringUniversity of TorontoTorontoCanada
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Santomartino R, Averesch NJH, Bhuiyan M, Cockell CS, Colangelo J, Gumulya Y, Lehner B, Lopez-Ayala I, McMahon S, Mohanty A, Santa Maria SR, Urbaniak C, Volger R, Yang J, Zea L. Toward sustainable space exploration: a roadmap for harnessing the power of microorganisms. Nat Commun 2023; 14:1391. [PMID: 36944638 PMCID: PMC10030976 DOI: 10.1038/s41467-023-37070-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Finding sustainable approaches to achieve independence from terrestrial resources is of pivotal importance for the future of space exploration. This is relevant not only to establish viable space exploration beyond low Earth-orbit, but also for ethical considerations associated with the generation of space waste and the preservation of extra-terrestrial environments. Here we propose and highlight a series of microbial biotechnologies uniquely suited to establish sustainable processes for in situ resource utilization and loop-closure. Microbial biotechnologies research and development for space sustainability will be translatable to Earth applications, tackling terrestrial environmental issues, thereby supporting the United Nations Sustainable Development Goals.
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Affiliation(s)
- Rosa Santomartino
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| | - Nils J H Averesch
- Department of Civil & Environmental Engineering, Stanford University, Stanford, CA, USA
- Center for Utilization of Biological Engineering in Space, Berkeley, CA, USA
| | | | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | | | - Yosephine Gumulya
- Centre for Microbiome Research, Queensland University of Technology, Brisbane, QLD, Australia
| | | | | | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Anurup Mohanty
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA, 98104, USA
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, India
| | - Sergio R Santa Maria
- Space Biosciences, NASA Ames Research Center, Mountain View, CA, USA
- KBR, Moffett Field, Mountain View, CA, USA
| | - Camilla Urbaniak
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
- ZIN Technologies Inc, Middleburg Heights, OH, USA
| | - Rik Volger
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luis Zea
- BioServe Space Technologies, University of Colorado Boulder, Boulder, CO, USA.
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Giachino A, Focarelli F, Marles-Wright J, Waldron KJ. Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling. FEMS Microbiol Ecol 2021; 97:6021318. [PMID: 33501489 DOI: 10.1093/femsec/fiaa249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022] Open
Abstract
One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.
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Affiliation(s)
- Andrea Giachino
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Francesca Focarelli
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Kevin J Waldron
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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Abdelbasir SM, McCourt KM, Lee CM, Vanegas DC. Waste-Derived Nanoparticles: Synthesis Approaches, Environmental Applications, and Sustainability Considerations. Front Chem 2020; 8:782. [PMID: 33110911 PMCID: PMC7488813 DOI: 10.3389/fchem.2020.00782] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/27/2020] [Indexed: 12/02/2022] Open
Abstract
For the past few decades, a plethora of nanoparticles have been produced through various methods and utilized to advance technologies for environmental applications, including water treatment, detection of persistent pollutants, and soil/water remediation, amongst many others. The field of materials science and engineering is increasingly interested in increasing the sustainability of the processes involved in the production of nanoparticles, which motivates the exploration of alternative inputs for nanoparticle production as well as the implementation of green synthesis techniques. Herein, we start by overviewing the general aspects of nanoparticle synthesis from industrial, electric/electronic, and plastic waste. We expand on critical aspects of waste identification as a viable input for the treatment and recovery of metal- and carbon-based nanoparticles. We follow-up by discussing different governing mechanisms involved in the production of nanoparticles, and point to potential inferences throughout the synthesis processes. Next, we provide some examples of waste-derived nanoparticles utilized in a proof-of-concept demonstration of technologies for applications in water quality and safety. We conclude by discussing current challenges from the toxicological and life-cycle perspectives that must be taken into consideration before scale-up manufacturing and implementation of waste-derived nanoparticles.
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Affiliation(s)
| | - Kelli M. McCourt
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Cindy M. Lee
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
- Department of Engineering and Science Education, Clemson University, Clemson, SC, United States
| | - Diana C. Vanegas
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
- Interdisciplinary Group for Biotechnological Innovation and Ecosocial Change-BioNovo, Universidad del Valle, Cali, Colombia
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Capeness MJ, Horsfall LE. Synthetic biology approaches towards the recycling of metals from the environment. Biochem Soc Trans 2020; 48:1367-1378. [PMID: 32627824 PMCID: PMC7458392 DOI: 10.1042/bst20190837] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/29/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Metals are a finite resource and their demand for use within existing and new technologies means metal scarcity is increasingly a global challenge. Conversely, there are areas containing such high levels of metal pollution that they are hazardous to life, and there is loss of material at every stage of the lifecycle of metals and their products. While traditional resource extraction methods are becoming less cost effective, due to a lowering quality of ore, industrial practices have begun turning to newer technologies to tap into metal resources currently locked up in contaminated land or lost in the extraction and manufacturing processes. One such technology uses biology for the remediation of metals, simultaneously extracting resources, decontaminating land, and reducing waste. Using biology for the identification and recovery of metals is considered a much 'greener' alternative to that of chemical methods, and this approach is about to undergo a renaissance thanks to synthetic biology. Synthetic biology couples molecular genetics with traditional engineering principles, incorporating a modular and standardised practice into the assembly of genetic parts. This has allowed the use of non-model organisms in place of the normal laboratory strains, as well as the adaption of environmentally sourced genetic material to standardised parts and practices. While synthetic biology is revolutionising the genetic capability of standard model organisms, there has been limited incursion into current practices for the biological recovery of metals from environmental sources. This mini-review will focus on some of the areas that have potential roles to play in these processes.
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Affiliation(s)
- Michael J. Capeness
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| | - Louise E. Horsfall
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
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