1
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Cao W, Huang C, Zhou X, Zhou S, Deng Y. Engineering two-component systems for advanced biosensing: From architecture to applications in biotechnology. Biotechnol Adv 2024; 75:108404. [PMID: 39002783 DOI: 10.1016/j.biotechadv.2024.108404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
Two-component systems (TCSs) are prevalent signaling pathways in bacteria. These systems mediate phosphotransfer between histidine kinase and a response regulator, facilitating responses to diverse physical, chemical, and biological stimuli. Advancements in synthetic and structural biology have repurposed TCSs for applications in monitoring heavy metals, disease-associated biomarkers, and the production of bioproducts. However, the utility of many TCS biosensors is hindered by undesired performance due to the lack of effective engineering methods. Here, we briefly discuss the architectures and regulatory mechanisms of TCSs. We also summarize the recent advancements in TCS engineering by experimental or computational-based methods to fine-tune the biosensor functional parameters, such as response curve and specificity. Engineered TCSs have great potential in the medical, environmental, and biorefinery fields, demonstrating a crucial role in a wide area of biotechnology.
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Affiliation(s)
- Wenyan Cao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chao Huang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xuan Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shenghu Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Yu Deng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
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2
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MacGregor H, Fukai I, Ash K, Arkin AP, Hazen TC. Potential applications of microbial genomics in nuclear non-proliferation. Front Microbiol 2024; 15:1410820. [PMID: 39360321 PMCID: PMC11445143 DOI: 10.3389/fmicb.2024.1410820] [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: 04/01/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024] Open
Abstract
As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.
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Affiliation(s)
| | - Isis Fukai
- Bredesen Center, University of Tennessee, Knoxville, TN, United States
| | - Kurt Ash
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
| | - Adam Paul Arkin
- University of California, Berkeley, Berkeley, CA, United States
| | - Terry C. Hazen
- Bredesen Center, University of Tennessee, Knoxville, TN, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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3
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Xu J, Wang S, Yi Z, Wu X, Wang M, Liu Y, Wu Y, Chen D, Lai J, Sun H. Novel biocompatible N-rich AIE fluorescent probe for live cell imaging and visual onsite detection of uranium. Mikrochim Acta 2024; 191:302. [PMID: 38709346 DOI: 10.1007/s00604-024-06390-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
A sensitive and biocompatible N-rich probe for rapid visual uranium detection was constructed by grafting two trianiline groups to 2,6-bis(aminomethyl)pyridine. Possessing excellent aggregation-induced emission (AIE) property and the advantages to form multidentate chelate with U selectively, the probe has been applied successfully to visualize uranium in complex environmental water samples and living cells, demonstrating outstanding anti-interference ability against large equivalent of different ions over a wide effective pH range. A large linear range (1.0 × 10-7-9.0 × 10-7 mol/L) and low detection limit (72.6 nmol/L, 17.28 ppb) were achieved for the visual determination of uranium. The recognition mechanism, photophysical properties, analytical performance and cytotoxicity were systematically investigated, demonstrating high potential for fast risk assessment of uranium pollution in field and in vivo.
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Affiliation(s)
- Jie Xu
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shenneng Wang
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Zhenni Yi
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoyi Wu
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Menghao Wang
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yu Liu
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yuexi Wu
- School of Chemistry, South China Normal University, Guangzhou, 510006, China
| | - Diyun Chen
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiaping Lai
- School of Chemistry, South China Normal University, Guangzhou, 510006, China.
| | - Hui Sun
- College of Environmental Science & Engineering, Guangzhou University, Guangzhou, 510006, China.
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou, 510006, China.
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4
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Sauge-Merle S, Recuerda M, Beccia MR, Lemaire D, Cherif R, Bremond N, Merola F, Bousmah Y, Berthomieu C. Development of an Efficient FRET-Based Ratiometric Uranium Biosensor. BIOSENSORS 2023; 13:bios13050561. [PMID: 37232922 DOI: 10.3390/bios13050561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
The dispersion of uranium in the environment can pose a problem for the health of humans and other living organisms. It is therefore important to monitor the bioavailable and hence toxic fraction of uranium in the environment, but no efficient measurement methods exist for this. Our study aims to fill this gap by developing a genetically encoded FRET-based ratiometric uranium biosensor. This biosensor was constructed by grafting two fluorescent proteins to both ends of calmodulin, a protein that binds four calcium ions. By modifying the metal-binding sites and the fluorescent proteins, several versions of the biosensor were generated and characterized in vitro. The best combination results in a biosensor that is affine and selective for uranium compared to metals such as calcium or other environmental compounds (sodium, magnesium, chlorine). It has a good dynamic range and should be robust to environmental conditions. In addition, its detection limit is below the uranium limit concentration in drinking water defined by the World Health Organization. This genetically encoded biosensor is a promising tool to develop a uranium whole-cell biosensor. This would make it possible to monitor the bioavailable fraction of uranium in the environment, even in calcium-rich waters.
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Affiliation(s)
- Sandrine Sauge-Merle
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
| | - Morgane Recuerda
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
| | - Maria Rosa Beccia
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
| | - David Lemaire
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
| | - Rym Cherif
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
| | - Nicolas Bremond
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
| | - Fabienne Merola
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Yasmina Bousmah
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Catherine Berthomieu
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, 13108 Saint Paul-Lez-Durance, France
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5
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Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol 2023; 11:1178680. [PMID: 37122866 PMCID: PMC10133563 DOI: 10.3389/fbioe.2023.1178680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.
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Affiliation(s)
| | | | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
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6
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Pardoux R, Sauge-Merle S, Bremond N, Beccia MR, Lemaire D, Battesti C, Delangle P, Solari PL, Guilbaud P, Berthomieu C. Optimized Coordination of Uranyl in Engineered Calmodulin Site 1 Provides a Subnanomolar Affinity for Uranyl and a Strong Uranyl versus Calcium Selectivity. Inorg Chem 2022; 61:20480-20492. [DOI: 10.1021/acs.inorgchem.2c03185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Romain Pardoux
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Sandrine Sauge-Merle
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Nicolas Bremond
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Maria Rosa Beccia
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - David Lemaire
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Christine Battesti
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000Grenoble, France
| | - Pier Lorenzo Solari
- MARS beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192Gif-sur-Yvette Cedex, France
| | | | - Catherine Berthomieu
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
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7
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The role of sensory kinase proteins in two-component signal transduction. Biochem Soc Trans 2022; 50:1859-1873. [DOI: 10.1042/bst20220848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Two-component systems (TCSs) are modular signaling circuits that regulate diverse aspects of microbial physiology in response to environmental cues. These molecular circuits comprise a sensor histidine kinase (HK) protein that contains a conserved histidine residue, and an effector response regulator (RR) protein with a conserved aspartate residue. HKs play a major role in bacterial signaling, since they perceive specific stimuli, transmit the message across the cytoplasmic membrane, and catalyze their own phosphorylation, and the trans-phosphorylation and dephosphorylation of their cognate response regulator. The molecular mechanisms by which HKs co-ordinate these functions have been extensively analyzed by genetic, biochemical, and structural approaches. Here, we describe the most common modular architectures found in bacterial HKs, and address the operation mode of the individual functional domains. Finally, we discuss the use of these signaling proteins as drug targets or as sensing devices in whole-cell biosensors with medical and biotechnological applications.
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8
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Ze Y, Wang R, Deng H, Zhou Z, Chen X, Huang L, Yao Y. Three-dimensional bioprinting: A cutting-edge tool for designing and fabricating engineered living materials. BIOMATERIALS ADVANCES 2022; 140:213053. [PMID: 35964390 DOI: 10.1016/j.bioadv.2022.213053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The design of engineered living materials (ELMs) is an emerging field developed from synthetic biology and materials science principles. ELMs are multi-scale bulk materials that combine the properties of self-healing and organism adaptability with the designed physicochemical or mechanical properties for functional applications in various fields, including therapy, electronics, and architecture. Among the many ELM design and manufacturing methods, three-dimensional (3D) bioprinting stands out for its precise control over the structure of the fabricated constructs and the spatial distribution of cells. In this review, we summarize the progress in the field, cell type and material selection, and the latest applications of 3D bioprinting to manufacture ELMs, as well as their advantages and limitations, hoping to deepen our understanding and provide new insights into ELM design. We believe that 3D bioprinting will become an important development direction and provide more contributions to this field.
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Affiliation(s)
- Yiting Ze
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ruixin Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanzhi Deng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zheqing Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoju Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Linyang Huang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
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9
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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10
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Rogiers T, Van Houdt R, Williamson A, Leys N, Boon N, Mijnendonckx K. Molecular Mechanisms Underlying Bacterial Uranium Resistance. Front Microbiol 2022; 13:822197. [PMID: 35359714 PMCID: PMC8963506 DOI: 10.3389/fmicb.2022.822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.
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Affiliation(s)
- Tom Rogiers
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Adam Williamson
- Centre Etudes Nucléaires de Bordeaux Gradignan (CENBG), Bordeaux, France
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Kristel Mijnendonckx
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- *Correspondence: Kristel Mijnendonckx,
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11
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. THE ISME JOURNAL 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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12
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Tsai ST, Cheng WJ, Zhang QX, Yeh YC. Gold-Specific Biosensor for Monitoring Wastewater Using Genetically Engineered Cupriavidus metallidurans CH34. ACS Synth Biol 2021; 10:3576-3582. [PMID: 34860511 DOI: 10.1021/acssynbio.1c00520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Transcription factor-based whole-cell biosensors have recently become promising alternatives to conventional analytical methods due to their advantage of simplicity, cost-effectiveness, and environmental friendliness. In this study, we used genetic engineering to develop a whole-cell biosensor based on the activation of promoters by CupR via interactions with gold ions, leading to the expression of reporter genes that yield output signals. Altering the promoter sequences was shown to significantly improve the performance of the biosensor strain in terms of gold-specificity. The detection sensitivity of our engineered strains was 42-fold higher than that of wild-type strains. The linear range of the purposed sensor was 125-1000 nM with a limit of detection at 46.5 nM. The effectiveness of the sensor strain was verified in wastewater samples.
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Affiliation(s)
- Ssu-Tzu Tsai
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Wen-Jui Cheng
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Qian-Xian Zhang
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
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13
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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14
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Kannappan S, Ramisetty BCM. Engineered Whole-Cell-Based Biosensors: Sensing Environmental Heavy Metal Pollutants in Water-a Review. Appl Biochem Biotechnol 2021; 194:1814-1840. [PMID: 34783990 DOI: 10.1007/s12010-021-03734-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
The frequent exposure and accumulation of heavy metals in organisms cause serious health issues affecting a range of organs such as the brain, liver, and reproductive organs in adults, infants, and children. Several parts of the world have high levels of heavy metals affecting millions of people, costing millions of dollars for improving the potability of water and medical treatment of the affected. Hence, water quality assessment is required to monitor the degree of heavy metal contamination in potable water. In nature, organisms respond to various environmental pollutants such as heavy metals, allowing their survival in a diverse environmental niche. With the advent of recombinant DNA technology, it is now possible to manipulate these natural bioreporters into controlled systems which either turn on or off gene expression or activity of enzymes in the presence of specific heavy metals (compound-specific biosensors) otherwise termed as whole-cell biosensors (WCBs). WCBs provide an upper hand compared to other immunosensors, enzyme-based sensors, and DNA-based sensors since microbes can be relatively easily manipulated, scaled up with relative ease, and can detect only the bioavailable heavy metals. In this review, we summarize the current knowledge of the various mechanisms of toxicity elicited by various heavy metals, thence emphasizing the need to develop heavy metal sensing platforms. Following this, the biosensor-based platforms including WCBs for detecting heavy metals developed thus far have been briefly elaborated upon, emphasizing the challenges and solutions associated with WCBs.
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Affiliation(s)
- Shrute Kannappan
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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15
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Herdman M, von Kügelgen A, Kureisaite-Ciziene D, Duman R, El Omari K, Garman EF, Kjaer A, Kolokouris D, Löwe J, Wagner A, Stansfeld PJ, Bharat TAM. High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure 2021; 30:215-228.e5. [PMID: 34800371 PMCID: PMC8828063 DOI: 10.1016/j.str.2021.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
Abstract
Surface layers (S-layers) are proteinaceous crystalline coats that constitute the outermost component of most prokaryotic cell envelopes. In this study, we have investigated the role of metal ions in the formation of the Caulobacter crescentus S-layer using high-resolution structural and cell biology techniques, as well as molecular simulations. Utilizing optical microscopy of fluorescently tagged S-layers, we show that calcium ions facilitate S-layer lattice formation and cell-surface binding. We report all-atom molecular dynamics simulations of the S-layer lattice, revealing the importance of bound metal ions. Finally, using electron cryomicroscopy and long-wavelength X-ray diffraction experiments, we mapped the positions of metal ions in the S-layer at near-atomic resolution, supporting our insights from the cellular and simulations data. Our findings contribute to the understanding of how C. crescentus cells form a regularly arranged S-layer on their surface, with implications on fundamental S-layer biology and the synthetic biology of self-assembling biomaterials. Live imaging shows Ca2+-dependent expansion of the C. crescentus S-layer Molecular simulations reveal Ca2+-binding properties of the S-layer Ca2+ ion mapping in three-dimensional crystals using in-vacuum X-ray anomalous diffraction Ca2+ replacement by Ho3+ allows cryo-EM mapping of heavy metals
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Ramona Duman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Kjaer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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16
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Abstract
Microbially produced indole metabolites serve as a diverse family of interspecies and interkingdom signaling molecules in the context of human health, crop production, and antibiotic resistance. We mined the protein database for sensors of indole metabolites and developed a biosensor for indole-3-aldehyde (I3A). Microbially produced I3A has been associated with reducing inflammation in diseases such as ulcerative colitis by stimulating the aryl hydrocarbon receptor pathway. We engineered an E. coli strain embedded with a single plasmid carrying a chimeric two-component system that detects I3A. Our I3A receptor characterization confirmed binding site residues that contribute to the sensor's I3A detection range of 0.1-10 μM. This new I3A biosensor opens the door to sensing indole metabolites produced at various host-microbe interfaces and provides new parts for synthetic biology applications.
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Affiliation(s)
- Jiefei Wang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Chao Zhang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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17
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Ali SA, Mittal D, Kaur G. In-situ monitoring of xenobiotics using genetically engineered whole-cell-based microbial biosensors: recent advances and outlook. World J Microbiol Biotechnol 2021; 37:81. [PMID: 33843020 DOI: 10.1007/s11274-021-03024-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Industrialisation, directly or indirectly, exposes humans to various xenobiotics. The increased magnitude of chemical pesticides and toxic heavy metals in the environment, as well as their intrusion into the food chain, seriously threatens human health. Therefore, the surveillance of xenobiotics is crucial for social safety and security. Online investigation by traditional methods is not sufficient for the detection and identification of such compounds because of the high costs and their complexity. Advancement in the field of genetic engineering provides a potential opportunity to use genetically modified microorganisms. In this regard, whole-cell-based microbial biosensors (WCBMB) represent an essential tool that couples genetically engineered organisms with an operator/promoter derived from a heavy metal-resistant operon combined with a regulatory protein in the gene circuit. The plasmid controls the expression of the reporter gene, such as gfp, luc, lux and lacZ, to an inducible gene promoter and has been widely applied to assay toxicity and bioavailability. This review summarises the recent trends in the development and application of microbial biosensors and the use of mobile genes for biomedical and environmental safety concerns.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India. .,Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, 132001, Karnal, Haryana, India.
| | - Deepti Mittal
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052, Sydney, NSW, Australia
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18
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Dubbin K, Dong Z, Park DM, Alvarado J, Su J, Wasson E, Robertson C, Jackson J, Bose A, Moya ML, Jiao Y, Hynes WF. Projection Microstereolithographic Microbial Bioprinting for Engineered Biofilms. NANO LETTERS 2021; 21:1352-1359. [PMID: 33508203 DOI: 10.1021/acs.nanolett.0c04100] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbes are critical drivers of all ecosystems and many biogeochemical processes, yet little is known about how the three-dimensional (3D) organization of these dynamic organisms contributes to their overall function. To probe how biofilm structure affects microbial activity, we developed a technique for patterning microbes in 3D geometries using projection stereolithography to bioprint microbes within hydrogel architectures. Bacteria were printed and monitored for biomass accumulation, demonstrating postprint viability of cells using this technique. We verified our ability to integrate biological and geometric complexity by fabricating a printed biofilm with two E. coli strains expressing different fluorescence. Finally, we examined the target application of microbial absorption of metal ions to investigate geometric effects on both the metal sequestration efficiency and the uranium sensing capability of patterned engineered Caulobacter crescentus strains. This work represents the first demonstration of the stereolithographic printing of microbials and presents opportunities for future work of engineered biofilms and other complex 3D structured cultures.
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Affiliation(s)
- Karen Dubbin
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ziye Dong
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Dan M Park
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Javier Alvarado
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jimmy Su
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Elisa Wasson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Claire Robertson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Julie Jackson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Arpita Bose
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Monica L Moya
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Yongqin Jiao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - William F Hynes
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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19
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Mattocks JA, Cotruvo JA. Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides. Chem Soc Rev 2020; 49:8315-8334. [PMID: 33057507 DOI: 10.1039/d0cs00653j] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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20
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Pathak A, Jaswal R, Xu X, White JR, Edwards B, Hunt J, Brooks S, Rathore RS, Agarwal M, Chauhan A. Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps. Front Microbiol 2020; 11:1024. [PMID: 32655505 PMCID: PMC7325934 DOI: 10.3389/fmicb.2020.01024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Rajneesh Jaswal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Xiaoyu Xu
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - John R White
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Bobby Edwards
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Jaden Hunt
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Scott Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Rajesh Singh Rathore
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Meenakshi Agarwal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
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21
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Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
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Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
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