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Yan ZX, Li Y, Peng SY, Wei L, Zhang B, Deng XY, Zhong M, Cheng X. Cadmium biosorption and mechanism investigation using two cadmium-tolerant microorganisms isolated from rhizosphere soil of rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134134. [PMID: 38554514 DOI: 10.1016/j.jhazmat.2024.134134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/17/2024] [Accepted: 03/24/2024] [Indexed: 04/01/2024]
Abstract
Microbial remediation of cadmium-contaminated soil offers advantages like environmental friendliness, cost-effectiveness, and simple operation. However, the efficacy of this remediation process relies on obtaining dominant strains and a comprehensive understanding of their Cd adsorption mechanisms. This study identified two Cd-resistant bacteria, Burkholderia sp. 1-22 and Bacillus sp. 6-6, with significant growth-promoting effects from rice rhizosphere soil. The strains showed remarkable Cd resistance up to ∼200 mg/L and alleviated Cd toxicity by regulating pH and facilitating bacterial adsorption of Cd. FTIR analysis showed crucial surface functional groups, like carboxyl and amino groups, on bacteria played significant roles in Cd adsorption. The strains could induce CdCO3 formation via a microbially induced calcium precipitation (MICP) mechanism, confirmed by SEM-EDS, X-ray analysis, and elemental mapping. Pot experiments showed these strains significantly increased organic matter and enzyme activity (e.g., urease, sucrase, peroxidase) in the rhizosphere soil versus the control group. These changes are crucial for restricting Cd mobility. Furthermore, strains 6-6 and 1-22 significantly enhance plant root detoxification of Cd, alleviating toxicity. Notably, increased pH likely plays a vital role in enhancing Cd precipitation and adsorption by strains, converting free Cd into non-bioavailable forms.
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Affiliation(s)
- Zu-Xuan Yan
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yi Li
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shuai-Ying Peng
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lei Wei
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bao Zhang
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xin-Yao Deng
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Min Zhong
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xin Cheng
- Institute of Applied Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
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2
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Kim B, Madukoma CS, Shrout JD, Nerenberg R. Effect of EPS production on the performance of membrane-based biofilm reactors. WATER RESEARCH 2023; 240:120101. [PMID: 37224668 DOI: 10.1016/j.watres.2023.120101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
This study explored the effect of extracellular polymeric substance (EPS) production on the performance of membrane-based biofilm reactors. Changing EPS production was induced by eliminating one of the main EPS polysaccharides, i.e., Pel. The studies were carried out using a pure culture of either Pseudomonas aeruginosa or an isogenic P. aeruginosa mutant that was unable to produce the Pel polysaccharide. The biofilm cell density for both strains was compared to confirm the Pel deletion mutant decreased overall EPS production in a bioreactor system. When the Pel-deficient mutant was grown as a biofilm, its cell density, i.e., ratio of cells/(cells + EPS), was 74 % higher than the wild type, showing EPS production was reduced by eliminating pel production. The growth kinetics were determined for both strains. The Pel-deficient mutant had a maximum specific growth rate (μ^) that was 14% higher than the wild type. Next, the effects of EPS reduction on reactor performance were assessed for a membrane aerated biofilm reactor (MABR) and a membrane bioreactor (MBR). For the MABR, the organic removal with the Pel-deficient mutant was around 8% higher than for the wild type. For the MBR, the time to reach the fouling threshold was 65 % greater for the Pel-deficient mutant than for the wild type. These results suggest that amount of EPS production can have significant effects on bacterial growth kinetics and bacterial cell density, which in turn can affect the performance of the membrane-based biofilm reactors. In both cases, lower EPS production correlated with more efficient treatment processes.
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Affiliation(s)
- B Kim
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA; University of Wisconsin-Madison, Great Lakes Bioenergy Research Center (GLBRC), Madison, Wisconsin, USA
| | - C S Madukoma
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - J D Shrout
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - R Nerenberg
- University of Notre Dame, Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA.
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3
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Ozdemir S, Turkan Z, Kilinc E, Bayat R, Sen F. The removal of heavy metal pollution from wastewaters using thermophilic B. cereus SO-16 bacteria. CHEMOSPHERE 2023; 311:136986. [PMID: 36330980 DOI: 10.1016/j.chemosphere.2022.136986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
In this study, bioaccumulation, remediation, tolerance, and effects of manganese ions (Mn(II)) and copper ions (Cu(II)) on antioxidant enzymes of thermophilic Bacillus cereus (B. cereus) SO-16 were investigated in detail. The findings of the study showed that Mn(II) was less toxic than Cu(II) to B. cereus SO-16. Moreover, B. cereus SO-16 was exhibited less tolerance to Mn(II) and Cu(II) ions in the liquid medium compared to the solid medium. The growth of bacteria was expressively effective for Mn(II) and Cu(II) concentrations of 2.5 mg/L at 24th h. The highest Mn(II) and Cu(II) bioaccumulation values after 48 h incubation of thermophilic B. cereus SO-16 were measured as 102.04 (24th h) and 87.96 (36th h) metal/dry bacteria weight. The change in morphology and functionality of B. cereus SO-16 after interaction with Mn(II) and Cu(II) was tested using various methods. The results indicated that B. cereus SO-16, a thermophilic bacterium, can be utilized in industrial wastewaters to recover and remediation of toxic metals.
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Affiliation(s)
- Sadin Ozdemir
- Food Processing Programme, Technical Science Vocational School, Mersin University, TR-33343 Yenisehir, Mersin, Turkiye
| | | | - Ersin Kilinc
- Department of Chemistry and Chemical Processing Technologies, Vocational School of Technical Sciences, Dicle University, Diyarbakir, TR-21200, Turkiye.
| | - Ramazan Bayat
- Sen Research Group, Department of Biochemistry, Faculty of Art and Science, Kutahya Dumlupinar University, 43000, Kutahya, Turkiye
| | - Fatih Sen
- Sen Research Group, Department of Biochemistry, Faculty of Art and Science, Kutahya Dumlupinar University, 43000, Kutahya, Turkiye.
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4
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Zhao J, Ma Y, Steinmetz NF, Bae J. Toward Plant Cyborgs: Hydrogels Incorporated onto Plant Tissues Enable Programmable Shape Control. ACS Macro Lett 2022; 11:961-966. [PMID: 35819363 DOI: 10.1021/acsmacrolett.2c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered living materials (ELMs) that incorporate living organisms and synthetic materials enable advanced functional properties. Here, we seek to create plant cyborgs by combining plants or plant tissues with stimuli-responsive polymeric materials. Plant tissues with integrated shape control may find applications in regenerative medicine, and the shape control of living plants enables another dimension of adaptability and response to environmental threats, which can be applied to next-generation precision farming. In this work, we develop chemistry to integrate stimuli-responsive poly(N-isopropylacrylamide) (PNIPAM) hydrogels with decellularized plant tissues assisted by 3D printing. We demonstrate programmable shape morphing in response to thermal cues and ultraviolet (UV) light. Specifically, by taking advantage of the extrusion-based 3D printing method, we deposit nanocomposite PNIPAM precursors onto silane-treated decellularized leaf surface with prescribed shapes and spatial control. When subjected to external stimuli, the strain mismatch generated between the swellable nanocomposite PNIPAM and nonswellable decellularized leaf enables folding and bending to occur. This strategy to integrate the plant tissues with stimuli-responsive hydrogels allows the control of leaf morphology, opening avenues for plant-based biosensors and soft actuators to enhance food security; such materials also may find applications in biomedicine as tissue-engineering scaffolds.
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Affiliation(s)
- Jiayu Zhao
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Yifeng Ma
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States.,Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, California 92093, United States.,Institute for Materials Discovery and Design, University of California San Diego, La Jolla, California 92093, United States.,Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States.,Department of Radiology, University of California San Diego, La Jolla, California 92093, United States.,Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Jinhye Bae
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States.,Chemical Engineering Program, University of California San Diego, La Jolla, California 92093, United States.,Material Science and Engineering Program, University of California San Diego, La Jolla, California 92093, United States.,Sustainable Power and Energy Center (SPEC), University of California San Diego, La Jolla, California 92093, United States
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5
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Ozdemir S, Turkan Z, Kilinc E, Bayat R, Soylak M, Sen F. Preconcentrations of Cu (II) and Mn (II) by magnetic solid-phase extraction on Bacillus cereus loaded γ-Fe 2O 3 nanomaterials. ENVIRONMENTAL RESEARCH 2022; 209:112766. [PMID: 35085567 DOI: 10.1016/j.envres.2022.112766] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
For the simultaneous preconcentrations of Cu(II) and Mn(II), a novel preconcentration technique was developed and described. Bacillus cereus loaded magnetic ɣ-Fe2O3 nanoparticles were prepared and used as support materials on solid-phase extraction procedure. Important experimental parameters were investigated in details and pH 6.0, 3 mL min-1 of flow rate, 5 mL of 1 mol L-1 of HCl as eluent, 200 mg of biomass, and 200 mg of magnetic ɣ-Fe2O3 nanoparticles as support material was found as the best conditions. The preconcentrations factor were found to be 80 for Cu (II) and Mn(II). It was confirmed by the results that SPE columns could be used in 32 cycles. The LOD values calculated for Cu (II) and Mn (II) were 0.09 and 0.08 ng mL-1, respectively. The RSD values found were less than 3.4%. The extraction recoveries were achieved as higher than 98%. The biosorption capacities of Cu (II), and Mn (II) were 26.0 mg g-1, 30.3 mg g-1 respectively. The approach devised for analyzing analyte concentrations in food samples proved to be successful.
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Affiliation(s)
- Sadin Ozdemir
- Food Processing Programme, Technical Science Vocational School, Mersin University, 33343, Yenisehir, Mersin, Turkey
| | | | - Ersin Kilinc
- Department of Chemistry and Chemical Processing Technologies, Vocational School of Technical Sciences, Dicle University, Diyarbakir, 21200, Turkey.
| | - Ramazan Bayat
- Sen Research Group, Department of Biochemistry, Faculty of Art and Science, 43000, Dumlupınar University, Turkey; Department of Materials Science & Engineering, Faculty of Engineering, Dumlupinar University, Evliya Celebi Campus, 43100, Kutahya, Turkey
| | - Mustafa Soylak
- Department of Chemistry, Science Faculty, Erciyes University, 38039, Kayseri, Turkey
| | - Fatih Sen
- Sen Research Group, Department of Biochemistry, Faculty of Art and Science, 43000, Dumlupınar University, Turkey.
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Jiang M, Wang K, Wang Y, Zhao Q, Wang W. Technologies for the cobalt-contaminated soil remediation: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151908. [PMID: 34838917 DOI: 10.1016/j.scitotenv.2021.151908] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/14/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
The cobalt-contaminated soil has exposed potential toxicity to humans, plants, and animals. Industrial activities like ore smelting, alloy manufacture, and electric and electronic devices production have induced the increased cobalt content in soil resulting in higher ecosystem risk in diverse environmental media. However, knowledge gaps in cobalt transfer in soil and the limited understanding of remediation techniques make it challenging to estimate their potential application scenarios. Thus, keeping in view the above facts, this paper summarizes the natural and anthropogenic sources arousing the increase of cobalt in soil and reviews the cobalt species in soil and factors that influence the mobilization of cobalt. Moreover, the status of the remediation technologies is critically evaluated, including phytoremediation, immobilization, and separation technologies (soil washing and electroremediation) with a focus on the application and mechanism of phytoremediation and immobilization. Based on the actual application, further improvements and prospects of all techniques are proposed. This comprehensive review might serve to guide technique selection and inspire more scientific exploration on the remediation of cobalt-contaminated soil.
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Affiliation(s)
- Miao Jiang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kun Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yipeng Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Weiye Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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7
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Pachaiappan R, Cornejo-Ponce L, Rajendran R, Manavalan K, Femilaa Rajan V, Awad F. A review on biofiltration techniques: Recent advancements in the removal of volatile organic compounds and heavy metals in the treatment of polluted water. Bioengineered 2022; 13:8432-8477. [PMID: 35260028 PMCID: PMC9161908 DOI: 10.1080/21655979.2022.2050538] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Good quality of water determines the healthy life of living beings on this earth. The cleanliness of water was interrupted by the pollutants emerging out of several human activities. Industrialization, urbanization, heavy population, and improper disposal of wastes are found to be the major reasons for the contamination of water. Globally, the inclusion of volatile organic compounds (VOCs) and heavy metals released by manufacturing industries, pharmaceuticals, and petrochemical processes have created environmental issues. The toxic nature of these pollutants has led researchers, scientists, and industries to exhibit concern towards the complete eradication of them. In this scenario, the development of wastewater treatment methodologies at low cost and in an eco-friendly way had gained importance at the international level. Recently, bio-based technologies were considered for environmental remedies. Biofiltration based works have shown a significant result for the removal of volatile organic compounds and heavy metals in the treatment of wastewater. This was done with several biological sources such as bacteria, fungi, algae, plants, yeasts, etc. The biofiltration technique is cost-effective, simple, biocompatible, sustainable, and eco-friendly compared to conventional techniques. This review article provides deep insight into biofiltration technologies engaged in the removal of volatile organic compounds and heavy metals in the wastewater treatment process.
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Affiliation(s)
- Rekha Pachaiappan
- Departamento de Ingeniería Mecánica, Facultad de Ingeniería, Universidad de Tarapacá, Avda.General Velasquez, 1775, Arica, Chile
| | - Lorena Cornejo-Ponce
- Departamento de Ingeniería Mecánica, Facultad de Ingeniería, Universidad de Tarapacá, Avda.General Velasquez, 1775, Arica, Chile
| | - Rathika Rajendran
- Department of Physics, A.D.M. College for Women (Autonomous), Nagapattinam, Tamil Nadu - 611001, India
| | - Kovendhan Manavalan
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu - 603203, India
| | - Vincent Femilaa Rajan
- Department of Sustainable Energy Management, Stella Maris College (Autonomous), Chennai - 600086, Tamil Nadu, India
| | - Fathi Awad
- Department of Allied Health Professionals, Faculty of Medical and Health Sciences, Liwa College of Technology, Abu Dhabi, UAE
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8
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Hemdan B, Garlapati VK, Sharma S, Bhadra S, Maddirala S, K M V, Motru V, Goswami P, Sevda S, Aminabhavi TM. Bioelectrochemical systems-based metal recovery: Resource, conservation and recycling of metallic industrial effluents. ENVIRONMENTAL RESEARCH 2022; 204:112346. [PMID: 34742708 DOI: 10.1016/j.envres.2021.112346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Metals represent a large proportion of industrial effluents, which due to their high hazardous nature and toxicity are responsible to create environmental pollution that can pose significant threat to the global flora and fauna. Strict ecological rules compromise sustainable recovery of metals from industrial effluents by replacing unsustainable and energy-consuming physical and chemical techniques. Innovative technologies based on the bioelectrochemical systems (BES) are a rapidly developing research field with proven encouraging outcomes for many industrial commodities, considering the worthy options for recovering metals from industrial effluents. BES technology platform has redox capabilities with small energy-intensive processes. The positive stigma of BES in metals recovery is addressed in this review by demonstrating the significance of BES over the current physical and chemical techniques. The mechanisms of action of BES towards metal recovery have been postulated with the schematic representation. Operational limitations in BES-based metal recovery such as biocathode and metal toxicity are deeply discussed based on the available literature results. Eventually, a progressive inspection towards a BES-based metal recovery platform with possibilities of integration with other modern technologies is foreseen to meet the real-time challenges of viable industrial commercialization.
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Affiliation(s)
- Bahaa Hemdan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India; Water Pollution Research Department, Environmental Research Division, National Research Centre, 33 El-Bohouth St., Dokki, Giza, 12622, Egypt
| | - Vijay Kumar Garlapati
- Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, 173234, India
| | - Swati Sharma
- Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Himachal Pradesh, 173234, India
| | - Sudipa Bhadra
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, India
| | - Shivani Maddirala
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, India
| | - Varsha K M
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, India
| | - Vineela Motru
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, India
| | - Pranab Goswami
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Surajbhan Sevda
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, India.
| | - Tejraj M Aminabhavi
- School of Advanced Sciences, KLE Technological University, Hubballi, Karnataka, 580 031, India.
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9
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Han P, Teo WZ, Yew WS. Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. ENGINEERING BIOLOGY 2022; 6:23-34. [PMID: 36968558 PMCID: PMC9995160 DOI: 10.1049/enb2.12020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.
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Affiliation(s)
- Ping Han
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wei Zhe Teo
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
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10
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Wu X, Huang P, Dong C, Deng X. Nickel bioaccumulation by a marine bacterium Brevibacterium sp. (X6) isolated from Shenzhen Bay, China. MARINE POLLUTION BULLETIN 2021; 170:112656. [PMID: 34186449 DOI: 10.1016/j.marpolbul.2021.112656] [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] [Received: 04/01/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Nickel bioaccumulation capacity of a marine Brevibacterium sp., designated as X6, was evaluated to explore its potential application in the bioremediation of Ni2+ pollutants in marine environments. The minimum Ni2+ inhibitory concentration and maximum Ni2+ bioaccumulation of X6 were 1000 mg/L and 100.95 mg/g, respectively, higher than most reported strains. Among the co-existing metal ions in seawater, K+ caused a slight adverse impact on Ni2+ uptake, followed by Na+ and Ca2+, whereas Mg2+ drastically inhibited Ni2+ bioaccumulation. Other heavy metals such as Co2+, Zn2+ and Cd2+ moderately affected Ni2+ binding, but the adverse effect of Cu2+ was severe. The investigation of the mechanism of Ni2+ bioaccumulation revealed that 66.34% of the accumulated Ni2+ was bound to the cell surface. Carboxylic, hydroxyl, amino and thiol groups participated in Ni2+ binding, while carboxylic group contributed the most, while thiol group may be more involved in Ni2+ binding at low Ni2+ concentrations.
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Affiliation(s)
- Xujia Wu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Pei Huang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Chenyang Dong
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xu Deng
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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11
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Sengupta S, Sahasrabuddhe D, Wangikar PP. Transporter engineering for the development of cyanobacteria as cell factories: A text analytics guided survey. Biotechnol Adv 2021; 54:107816. [PMID: 34411662 DOI: 10.1016/j.biotechadv.2021.107816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are attractive candidates for photoautotrophic production of platform chemicals due to their inherent ability to utilize carbon dioxide as the sole carbon source. Metabolic pathways can be engineered more readily in cyanobacteria compared to higher photosynthetic organisms. Although significant progress has been made in pathway engineering, intracellular accumulation of the product is a potential bottleneck in large-scale production. Likewise, substrate uptake is known to limit growth and product formation. These limitations can potentially be addressed by targeted and controlled expression of transporter proteins in the metabolically engineered strains. This review focuses on the transporters that have been explored in cyanobacteria. To highlight the progress on characterization and application of cyanobacterial transporters, we applied text analytics to extract relevant information from over 1000 publications. We have categorized the transporters based on their source, their function and the solute they transport. Further, the review provides insights into the potential of transporters in the metabolic engineering of cyanobacteria for improved product titer.
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Affiliation(s)
- Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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12
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Wang X, Wei W, Zhao J. Using a Riboswitch Sensor to Detect Co 2+/Ni 2+ Transport in E. coli. Front Chem 2021; 9:631909. [PMID: 33659237 PMCID: PMC7917058 DOI: 10.3389/fchem.2021.631909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Intracellular concentrations of essential mental ions must be tightly maintained to avoid metal deprivation and toxicity. However, their levels in cells are still difficult to monitor. In this report, the combination of a Co2+Ni2+-specific riboswitch and an engineered downstream mCherry fluorescent protein allowed a highly sensitive and selective whole-cell Co2+/Ni2+ detection process. The sensors were applied to examine the resistance system of Co2+/Ni2+ in E. coli, and the sensors were able to monitor the effects of genetic deletions. These results indicate that riboswitch-based sensors can be employed in the study of related cellular processes.
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Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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13
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Complexation properties of water-soluble poly(vinyl alcohol) (PVA)-based acidic chelating polymers. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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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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Han L, Cui W, Lin Q, Chen Q, Suo F, Ma K, Wang Y, Hao W, Cheng Z, Zhou Z. Efficient Overproduction of Active Nitrile Hydratase by Coupling Expression Induction and Enzyme Maturation via Programming a Controllable Cobalt-Responsive Gene Circuit. Front Bioeng Biotechnol 2020; 8:193. [PMID: 32266230 PMCID: PMC7105576 DOI: 10.3389/fbioe.2020.00193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/27/2020] [Indexed: 11/13/2022] Open
Abstract
A robust and portable expression system is of great importance in enzyme production, metabolic engineering, and synthetic biology, which maximizes the performance of the engineered system. In this study, a tailor-made cobalt-induced expression system (CIES) was developed for low-cost and eco-friendly nitrile hydratase (NHase) production. First, the strong promoter Pveg from Bacillus subtilis, the Ni(II)/Co(II) responsive repressor RcnR, and its operator were reorganized to construct a CIES. In this system, the expression of reporter green fluorescent protein (GFP) was specifically triggered by Co(II) over a broad range of concentration. The performance of the cobalt-induced system was evolved to version 2.0 (CIES 2.0) for adaptation to different concentrations of Co(II) through programming a homeostasis system that rebalances cobalt efflux and influx with RcnA and NiCoT, respectively. Harnessing these synthetic platforms, the induced expression of NHase was coupled with enzyme maturation by Co(II) in a synchronizable manner without requiring additional inducers, which is a unique feature relative to other induced systems for production of NHase. The yield of NHase was 111.2 ± 17.9 U/ml using CIES and 114.9 ± 1.4 U/ml using CIES 2.0, which has a producing capability equivalent to that of commonly used isopropyl thiogalactoside (IPTG)-induced systems. In a scale-up system using a 5-L fermenter, the yielded enzymatic activity reached 542.2 ± 42.8 U/ml, suggesting that the designer platform for NHase is readily applied to the industry. The design of CIES in this study not only provided a low-cost and eco-friendly platform to overproduce NHase but also proposed a promising pipeline for development of synthetic platforms for expression of metalloenzymes.
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Affiliation(s)
- Laichuang Han
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiaoqing Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Feiya Suo
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Ke Ma
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Yang Wang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenliang Hao
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
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16
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Zhu B, Chen Y, Wei N. Engineering Biocatalytic and Biosorptive Materials for Environmental Applications. Trends Biotechnol 2019; 37:661-676. [DOI: 10.1016/j.tibtech.2018.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
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17
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Diep P, Mahadevan R, Yakunin AF. Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. Front Bioeng Biotechnol 2018; 6:157. [PMID: 30420950 PMCID: PMC6215804 DOI: 10.3389/fbioe.2018.00157] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Wastewater effluents from mines and metal refineries are often contaminated with heavy metal ions, so they pose hazards to human and environmental health. Conventional technologies to remove heavy metal ions are well-established, but the most popular methods have drawbacks: chemical precipitation generates sludge waste, and activated carbon and ion exchange resins are made from unsustainable non-renewable resources. Using microbial biomass as the platform for heavy metal ion removal is an alternative method. Specifically, bioaccumulation is a natural biological phenomenon where microorganisms use proteins to uptake and sequester metal ions in the intracellular space to utilize in cellular processes (e.g., enzyme catalysis, signaling, stabilizing charges on biomolecules). Recombinant expression of these import-storage systems in genetically engineered microorganisms allows for enhanced uptake and sequestration of heavy metal ions. This has been studied for over two decades for bioremediative applications, but successful translation to industrial-scale processes is virtually non-existent. Meanwhile, demands for metal resources are increasing while discovery rates to supply primary grade ores are not. This review re-thinks how bioaccumulation can be used and proposes that it can be developed for bioextractive applications-the removal and recovery of heavy metal ions for downstream purification and refining, rather than disposal. This review consolidates previously tested import-storage systems into a biochemical framework and highlights efforts to overcome obstacles that limit industrial feasibility, thereby identifying gaps in knowledge and potential avenues of research in bioaccumulation.
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Affiliation(s)
| | | | - Alexander F. Yakunin
- BioZone - Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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18
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Nguyen PQ, Courchesne NMD, Duraj-Thatte A, Praveschotinunt P, Joshi NS. Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704847. [PMID: 29430725 PMCID: PMC6309613 DOI: 10.1002/adma.201704847] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/25/2017] [Indexed: 05/20/2023]
Abstract
Vast potential exists for the development of novel, engineered platforms that manipulate biology for the production of programmed advanced materials. Such systems would possess the autonomous, adaptive, and self-healing characteristics of living organisms, but would be engineered with the goal of assembling bulk materials with designer physicochemical or mechanical properties, across multiple length scales. Early efforts toward such engineered living materials (ELMs) are reviewed here, with an emphasis on engineered bacterial systems, living composite materials which integrate inorganic components, successful examples of large-scale implementation, and production methods. In addition, a conceptual exploration of the fundamental criteria of ELM technology and its future challenges is presented. Cradled within the rich intersection of synthetic biology and self-assembling materials, the development of ELM technologies allows the power of biology to be leveraged to grow complex structures and objects using a palette of bio-nanomaterials.
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Affiliation(s)
- Peter Q. Nguyen
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Noémie-Manuelle Dorval Courchesne
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Anna Duraj-Thatte
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Pichet Praveschotinunt
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Neel S. Joshi
- School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
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Maruthamuthu MK, Selvamani V, Nadarajan SP, Yun H, Oh YK, Eom GT, Hong SH. Manganese and cobalt recovery by surface display of metal binding peptide on various loops of OmpC in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:31-41. [DOI: 10.1007/s10295-017-1989-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/14/2017] [Indexed: 12/24/2022]
Abstract
Abstract
In a cell-surface display (CSD) system, successful display of a protein or peptide is highly dependent on the anchoring motif and the position of the display in that anchoring motif. In this study, a recombinant bacterial CSD system for manganese (Mn) and cobalt (Co) recovery was developed by employing OmpC as an anchoring motif on three different external loops. A portion of Cap43 protein (TRSRSHTSEG)3 was employed as a manganese and cobalt binding peptide (MCBP), which was fused with OmpC at three different external loops. The fusions were made at the loop 2 [fusion protein-2 (FP2)], loop 6 (FP6), and loop 8 (FP8) of OmpC, respectively. The efficacy of the three recombinant strains in the recovery of Mn and Co was evaluated by varying the concentration of the respective metal. Molecular modeling studies showed that the short trimeric repeats of peptide probably form a secondary structure with OmpC, thereby giving rise to a difference in metal recovery among the three recombinant strains. Among the three recombinant strains, FP6 showed increased metal recovery with both Mn and Co, at 1235.14 (1 mM) and 379.68 (0.2 mM) µmol/g dry cell weight (DCW), respectively.
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Affiliation(s)
- Murali kannan Maruthamuthu
- 0000 0004 0533 4667 grid.267370.7 Department of Chemical Engineering University of Ulsan 44610 Ulsan Republic of Korea
| | - Vidhya Selvamani
- 0000 0004 0533 4667 grid.267370.7 Department of Chemical Engineering University of Ulsan 44610 Ulsan Republic of Korea
| | - Saravanan Prabhu Nadarajan
- 0000 0004 0532 8339 grid.258676.8 Department of Bioscience and Biotechnology Konkuk University 05029 Seoul Republic of Korea
| | - Hyungdon Yun
- 0000 0004 0532 8339 grid.258676.8 Department of Bioscience and Biotechnology Konkuk University 05029 Seoul Republic of Korea
| | - You-Kwan Oh
- 0000 0001 0691 7707 grid.418979.a Biomass and Waste Energy Laboratory Korea Institute of Energy Research 34129 Daejeon Republic of Korea
| | - Gyeong Tae Eom
- 0000 0001 2296 8192 grid.29869.3c Research Center for Bio-based Chemistry Korea Research Institute of Chemical Technology (KRICT) 44429 Ulsan Republic of Korea
- 0000 0004 1791 8264 grid.412786.e Department of Green Chemistry and Environmental Biotechnology Korea University of Science and Technology (UST) 34144 Daejeon Republic of Korea
| | - Soon Ho Hong
- 0000 0004 0533 4667 grid.267370.7 Department of Chemical Engineering University of Ulsan 44610 Ulsan Republic of Korea
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20
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Cayron J, Prudent E, Escoffier C, Gueguen E, Mandrand-Berthelot MA, Pignol D, Garcia D, Rodrigue A. Pushing the limits of nickel detection to nanomolar range using a set of engineered bioluminescent Escherichia coli. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:4-14. [PMID: 26498802 DOI: 10.1007/s11356-015-5580-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
The detection of nickel in water is of great importance due to its harmfulness for living organism. A way to detect Ni is the use of whole-cell biosensors. The aim of the present work was to build a light-emitting bacterial biosensor for the detection of Ni with high specificity and low detection limit properties. For that purpose, the regulatory circuit implemented relied on the RcnR Ni/Co metallo-regulator and its rcnA natural target promoter fused to the lux reporter genes. To convert RcnR to specifically detect Ni, several mutations were tested and the C35A retained. Deleting the Ni efflux pump rcnA and introducing genes encoding several Ni-uptake systems lowered the detection thresholds. When these constructs were assayed in several Escherichia coli strains, it appeared that the detection thresholds were highly variable. The TD2158 wild-type E. coli gave rise to a biosensor ten times more active and sensitive than its W3110 E. coli K12 equivalent. This biosensor was able to confidently detect Ni concentrations as little as 80 nM (4.7 μg l-1), which makes its use compatible with the norms governing the drinking water quality.
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Affiliation(s)
- Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Camille Escoffier
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Erwan Gueguen
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Marie-Andrée Mandrand-Berthelot
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - David Pignol
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France.
- INSA de Lyon, Villeurbanne, 69621, France.
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France.
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21
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Seppälä S, Solomon KV, Gilmore SP, Henske JK, O'Malley MA. Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. Microb Cell Fact 2016; 15:212. [PMID: 27998268 PMCID: PMC5168858 DOI: 10.1186/s12934-016-0611-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/02/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms. Here, we mined the transcriptome of three recently isolated strains of anaerobic fungi to identify membrane proteins responsible for sensing and transporting biomass hydrolysates within a competitive and rather extreme environment. RESULTS Using sequence analyses and homology, we identified membrane protein-coding sequences from assembled transcriptomes from three strains of anaerobic gut fungi: Neocallimastix californiae, Anaeromyces robustus, and Piromyces finnis. We identified nearly 2000 transporter components: about half of these are involved in the general secretory pathway and intracellular sorting of proteins; the rest are predicted to be small-solute transporters. Unexpectedly, we found a number of putative sugar binding proteins that are associated with prokaryotic uptake systems; and approximately 100 class C G-protein coupled receptors (GPCRs) with non-canonical putative sugar binding domains. CONCLUSIONS We report the first comprehensive characterization of the membrane protein machinery of biotechnologically relevant anaerobic gut fungi. Apart from identifying conserved machinery for protein sorting and secretion, we identify a large number of putative solute transporters that are of interest for biotechnological applications. Notably, our data suggests that the fungi display a plethora of carbohydrate binding domains at their surface, perhaps as a means to sense and sequester some of the sugars that their biomass degrading, extracellular enzymes produce.
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Affiliation(s)
- Susanna Seppälä
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800, Kgs. Lyngby, Denmark.,Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.,Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
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Duprey A, Muskhelishvili G, Reverchon S, Nasser W. Temporal control of Dickeya dadantii main virulence gene expression by growth phase-dependent alteration of regulatory nucleoprotein complexes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1470-1480. [PMID: 27498372 DOI: 10.1016/j.bbagrm.2016.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/29/2016] [Accepted: 08/04/2016] [Indexed: 01/08/2023]
Abstract
In bacteria, important genes are often controlled at the transcriptional level by several factors, forming a complex and intertwined web of interactions. Yet, transcriptional regulators are often studied separately and little information is available concerning their interactions. In this work, we dissect the regulation of the major virulence gene pelD in D. dadantii by taking into account the effects of individual binding sites for regulatory proteins FIS and CRP, and the impact of a newly discovered divergent promoter div. Using a combination of biochemistry and genetics approaches we provide an unprecedented level of detail on the multifactorial regulation of bacterial transcription. We show that the growth phase dependent regulation of pelD is under the control of changing composition of higher-order nucleoprotein complexes between FIS, CRP, div and pelD during the growth cycle that allow sequential expression of div and pelD in the early and late exponential growth phases, respectively. This work highlights the importance of "orphan" promoters in gene regulation and that the individual binding sites for a regulator can serve several purposes and have different effects on transcription, adding a new level of complexity to bacterial transcriptional regulation.
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Affiliation(s)
- Alexandre Duprey
- Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France; INSA-Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Georgi Muskhelishvili
- Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France; INSA-Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Sylvie Reverchon
- Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France; INSA-Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - William Nasser
- Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France; INSA-Lyon, F-69621 Villeurbanne, France; CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France.
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Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants. Appl Microbiol Biotechnol 2016; 100:2967-84. [PMID: 26860944 DOI: 10.1007/s00253-016-7364-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
Abstract
Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.
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IscR Regulates Synthesis of Colonization Factor Antigen I Fimbriae in Response to Iron Starvation in Enterotoxigenic Escherichia coli. J Bacteriol 2015; 197:2896-907. [PMID: 26124243 DOI: 10.1128/jb.00214-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Iron availability functions as an environmental cue for enteropathogenic bacteria, signaling arrival within the human host. As enterotoxigenic Escherichia coli (ETEC) is a major cause of human diarrhea, the effect of iron on ETEC virulence factors was evaluated here. ETEC pathogenicity is directly linked to production of fimbrial colonization factors and secretion of heat-labile enterotoxin (LT) and/or heat-stable enterotoxin (ST). Efficient colonization of the small intestine further requires at least the flagellin binding adhesin EtpA. Under iron starvation, production of the CFA/I fimbriae was increased in the ETEC H10407 prototype strain. In contrast, LT secretion was inhibited. Furthermore, under iron starvation, gene expression of the cfa (CFA/I) and etp (EtpBAC) operons was induced, whereas transcription of toxin genes was either unchanged or repressed. Transcriptional reporter fusion experiments focusing on the cfa operon further showed that iron starvation stimulated cfaA promoter activity in ETEC, indicating that the impact of iron on CFA/I production was mediated by transcriptional regulation. Evaluation of cfaA promoter activity in heterologous E. coli single mutant knockout strains identified IscR as the regulator responsible for inducing cfa fimbrial gene expression in response to iron starvation, and this was confirmed in an ETEC ΔiscR strain. The global iron response regulator, Fur, was not implicated. IscR binding sites were identified in silico within the cfaA promoter and fixation confirmed by DNase I footprinting, indicating that IscR directly binds the promoter region to induce CFA/I. IMPORTANCE Pathogenic enterobacteria modulate expression of virulence genes in response to iron availability. Although the Fur transcription factor represents the global regulator of iron homeostasis in Escherichia coli, we show that several ETEC virulence factors are modulated by iron, with expression of the major fimbriae under the control of the iron-sulfur cluster regulator, IscR. Furthermore, we demonstrate that the apo form of IscR, lacking an Fe-S cluster, is able to directly fix the corresponding promoter region. These results provide further evidence implicating IscR in bacterial virulence and suggest that IscR may represent a more general regulator mediating the iron response in enteropathogens.
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25
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Gogada R, Singh SS, Lunavat SK, Pamarthi MM, Rodrigue A, Vadivelu B, Phanithi PB, Gopala V, Apte SK. Engineered Deinococcus radiodurans R1 with NiCoT genes for bioremoval of trace cobalt from spent decontamination solutions of nuclear power reactors. Appl Microbiol Biotechnol 2015; 99:9203-13. [DOI: 10.1007/s00253-015-6761-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/12/2015] [Accepted: 06/08/2015] [Indexed: 11/30/2022]
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