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Zhang J, Guo Y, Lin YR, Ma BC, Ge XR, Zhang WQ, Zhang NX, Yang SM, Hui CY. Detection of Cadmium in Human Biospecimens by a Cadmium-Selective Whole-Cell Biosensor Based on Deoxyviolacein. ACS Biomater Sci Eng 2024; 10:4046-4058. [PMID: 38722544 DOI: 10.1021/acsbiomaterials.3c01814] [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] [Indexed: 06/11/2024]
Abstract
Cadmium poses a severe health risk, impacting various bodily systems. Monitoring human exposure is vital. Urine and blood cadmium serve as critical biomarkers. However, current urine and blood cadmium detection methods are expensive and complex. Being cost-effective, user-friendly, and efficient, visual biosensing offers a promising complement to existing techniques. Therefore, we constructed a cadmium whole-cell biosensor using CadR10 and deoxyviolacein pigment in this study. We assessed the sensor for time-dose response, specific response to cadmium, sensitivity response to cadmium, and stability response to cadmium. The results showed that (1) the sensor had a preferred signal-to-noise ratio when the incubation time was 4 h; (2) the sensor showed excellent specificity for cadmium compared to the group 12 metals and lead; (3) the sensor was responsive to cadmium down to 1.53 nM under experimental conditions and had good linearity over a wide range from 1.53 nM to 100 μM with good linearity (R2 = 0.979); and (4) the sensor had good stability. Based on the excellent results of the performance tests, we developed a cost-effective, high-throughput method for detecting urinary and blood cadmium. Specifically, this was realized by adding the blood or urine samples into the culture system in a particular proportion. Then, the whole-cell biosensor was subjected to culture, n-butanol extraction, and microplate reading. The results showed that (1) at 20% urine addition ratio, the sensor had an excellent curvilinear relationship (R2 = 0.986) in the range of 3.05 nM to 100 μM, and the detection limit could reach 3.05 nM. (2) At a 10% blood addition ratio, the sensor had an excellent nonlinear relationship (R2 = 0.978) in the range of 0.097-50 μM, and the detection limit reached 0.195 μM. Overall, we developed a sensitive and wide-range method based on a whole-cell biosensor for the detection of cadmium in blood and urine, which has the advantages of being cost-effective, ease of operation, fast response, and low dependence on instrumentation and has the potential to be applied in the monitoring of cadmium exposure in humans as a complementary to the mainstream detection techniques.
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Affiliation(s)
- Juan Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Yi-Ran Lin
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Bing-Chan Ma
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Xue-Ru Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Wen-Qi Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Nai-Xing Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Shu-Man Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
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2
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Sharma M, Sharma S, Paavan, Gupta M, Goyal S, Talukder D, Akhtar MS, Kumar R, Umar A, Alkhanjaf AAM, Baskoutas S. Mechanisms of microbial resistance against cadmium - a review. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2024; 22:13-30. [PMID: 38887775 PMCID: PMC11180082 DOI: 10.1007/s40201-023-00887-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/15/2023] [Indexed: 06/20/2024]
Abstract
The escalating cadmium influx from industrial activities and anthropogenic sources has raised serious environmental concerns due to its toxic effects on ecosystems and human health. This review delves into the intricate mechanisms underlying microbial resistance to cadmium, shedding light on the multifaceted interplay between microorganisms and this hazardous heavy metal. Cadmium overexposure elicits severe health repercussions, including renal carcinoma, mucous membrane degradation, bone density loss, and kidney stone formation in humans. Moreover, its deleterious impact extends to animal and plant metabolism. While physico-chemical methods like reverse osmosis and ion exchange are employed to mitigate cadmium contamination, their costliness and incomplete efficacy necessitate alternative strategies. Microbes, particularly bacteria and fungi, exhibit remarkable resilience to elevated cadmium concentrations through intricate resistance mechanisms. This paper elucidates the ingenious strategies employed by these microorganisms to combat cadmium stress, encompassing metal ion sequestration, efflux pumps, and enzymatic detoxification pathways. Bioremediation emerges as a promising avenue for tackling cadmium pollution, leveraging microorganisms' ability to transform toxic cadmium forms into less hazardous derivatives. Unlike conventional methods, bioremediation offers a cost-effective, environmentally benign, and efficient approach. This review amalgamates the current understanding of microbial cadmium resistance mechanisms, highlighting their potential for sustainable remediation strategies. By unraveling the intricate interactions between microorganisms and cadmium, this study contributes to advancing our knowledge of bioremediation approaches, thereby paving the way for safer and more effective cadmium mitigation practices.
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Affiliation(s)
- Monu Sharma
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Sonu Sharma
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Paavan
- Department of Biotechnology, Ambala College of Engineering and Applied Research, Devsthali, Ambala, 133101 Haryana India
| | - Mahiti Gupta
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Soniya Goyal
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Daizee Talukder
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Mohd. Sayeed Akhtar
- Department of Botany, Gandhi Faiz-E-Aam College, Shahjahanpur, 242001 Uttar Pradesh India
| | - Raman Kumar
- Department of Biosciences and Technology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 Haryana India
| | - Ahmad Umar
- Department of Chemistry, Faculty of Science and ArtsPromising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001 Kingdom of Saudi Arabia
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Abdulrab Ahmed M. Alkhanjaf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 11001 Najran, Saudi Arabia
| | - Sotirios Baskoutas
- Department of Materials Science, University of Patras, 26500 Patras, Greece
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3
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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [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: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Zafar S, Ashraf A, Hayat S, Siddique MH, Waseem M, Hassan M, Qaisar H, Muzammil S. Isolation and characterization of novel cadmium-resistant Escherichia fergusonii ZSF-15 from industrial effluent for flocculant production and antioxidant enzyme activity. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:412. [PMID: 38565815 DOI: 10.1007/s10661-024-12545-x] [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: 09/19/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
Cadmium (Cd) is a highly toxic metal that frequently contaminates our environment. In this study, the bioflocculant-producing, cadmium-resistant Escherichia fergusonii ZSF-15 was characterized from Paharang drain, Bawa Chak, Faisalabad, Pakistan. The Cd-resistant E. fergusonii was used to determine the bioflocculant production using yeast-peptone-glycerol medium (pH 6.5) supplemented with 50 mg L-1 of Cd. The culture was incubated for 3 days at 37 °C in a rotary shaker at 120 rpm. The fermentation broth was centrifuged at 4000 g for 10 min after the incubation period. The maximum flocculating activity by isolate ZSF-15 was found to be 71.4% after 48 h of incubation. According to the Fourier transform infrared spectroscopy analysis, the bioflocculant produced by strain ZSF-15 was comprised of typical polysaccharide and protein, i.e. hydroxyl, carboxyl, and amino groups. The strain ZSF-15 exhibited bioflocculant activity at range of pH (6-8) and temperature (35-50℃). Maximum flocculation activity (i.e. 71%) was observed at 47℃, whereas 63% flocculation production was observed at pH 8. In the present study, antioxidant enzyme profile of ZSF-15 was also evaluated under cadmium stress. A significant increase in antioxidant enzymes including superoxide dismutase (118%) and ascorbate peroxidase (28%) was observed, whereas contents of catalase (86%), glutathione transferase (13%), and peroxidase (8%) were decreased as compared to control.
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Affiliation(s)
- Saima Zafar
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Asma Ashraf
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Sumreen Hayat
- Institute of Microbiology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Hussnain Siddique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Waseem
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Mudassir Hassan
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Hira Qaisar
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Saima Muzammil
- Institute of Microbiology, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
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5
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Tartilán-Choya B, Tejedor C, Conde-Álvarez R, Muñoz PM, Vizcaíno N. Characterization of three predicted zinc exporters in Brucella ovis identifies ZntR-ZntA as a powerful zinc and cadmium efflux system not required for virulence and unveils pathogenic Brucellae heterogeneity in zinc homeostasis. Front Vet Sci 2024; 10:1323500. [PMID: 38260206 PMCID: PMC10800456 DOI: 10.3389/fvets.2023.1323500] [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: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Brucella ovis causes non-zoonotic ovine brucellosis of worldwide distribution and is responsible for important economic losses mainly derived from male genital lesions and reproductive fails. Studies about the virulence mechanisms of this rough species (lacking lipopolysaccharide O-chains) are underrepresented when compared to the main zoonotic Brucella species that are smooth (with O-chains). Zinc intoxication constitutes a defense mechanism of the host against bacterial pathogens, which have developed efflux systems to counterbalance toxicity. In this study, we have characterized three potential B. ovis zinc exporters, including the ZntA ortholog previously studied in B. abortus. Despite an in-frame deletion removing 100 amino acids from B. ovis ZntA, the protein retained strong zinc efflux properties. Only indirect evidence suggested a higher exporter activity for B. abortus ZntA, which, together with differences in ZntR-mediated regulation of zntA expression between B. ovis and B. abortus, could contribute to explaining why the ΔzntR mutant of B. abortus is attenuated while that of B. ovis is virulent. Additionally, B. ovis ZntA was revealed as a powerful cadmium exporter contributing to cobalt, copper, and nickel detoxification, properties not previously described for the B. abortus ortholog. Deletion mutants for BOV_0501 and BOV_A1100, also identified as potential zinc exporters and pseudogenes in B. abortus, behaved as the B. ovis parental strain in all tests performed. However, their overexpression in the ΔzntA mutant allowed the detection of discrete zinc and cobalt efflux activity for BOV_0501 and BOV_A1100, respectively. Nevertheless, considering their low expression levels and the stronger activity of ZntA as a zinc and cobalt exporter, the biological role of BOV_0501 and BOV_A1100 is questionable. Results presented in this study evidence heterogeneity among pathogenic Brucellae regarding zinc export and, considering the virulence of B. ovis ΔzntA, suggest that host-mediated zinc intoxication is not a relevant mechanism to control B. ovis infection.
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Affiliation(s)
| | - Carmen Tejedor
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raquel Conde-Álvarez
- Instituto de Investigación Sanitaria de Navarra and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Pilar María Muñoz
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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6
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Herath HMLPB, de Silva WRM, Dassanayake RS, Gunawardene YINS, Jayasingha JRP, Gayashan MK, Afonso LOB, de Silva KMN. Validation and calibration of a novel GEM biosensor for specific detection of Cd 2+, Zn 2+, and Pb 2. BMC Biotechnol 2023; 23:52. [PMID: 38066557 PMCID: PMC10709830 DOI: 10.1186/s12896-023-00820-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In this study, we designed a novel genetic circuit sensitive to Cd2+, Zn2+ and Pb2+ by mimicking the CadA/CadR operon system mediated heavy metal homeostasis mechanism of Pseudomonas aeruginosa. The regular DNA motifs on natural operon were reconfigured and coupled with the enhanced Green Fluorescent Protein (eGFP) reporter to develop a novel basic NOT type logic gate CadA/CadR-eGFP to respond metal ions mentioned above. A Genetically Engineered Microbial (GEM)-based biosensor (E.coli-BL21:pJET1.2-CadA/CadR-eGFP) was developed by cloning the chemically synthesised CadA/CadR-eGFP gene circuit into pJET1.2-plasmid and transforming into Escherichia coli (E. coli)-BL21 bacterial cells. RESULTS The GEM-based biosensor cells indicated the reporter gene expression in the presence of Cd2+, Zn2+ and Pb2+ either singly or in combination. Further, the same biosensor cells calibrated for fluorescent intensity against heavy metal concentration generated linear graphs for Cd2+, Zn2+ and Pb2+ with the R2 values of 0.9809, 0.9761 and 0.9758, respectively as compared to non-specific metals, Fe3+ (0.0373), AsO43- (0.3825) and Ni2+ (0.8498) making our biosensor suitable for the detection of low concentration of the former metal ions in the range of 1-6 ppb. Furthermore, the GEM based biosensor cells were growing naturally within the concentration range of heavy metals, at 37 °C and optimum pH = 7.0 in the medium, resembling the characteristics of wildtype E.coli. CONCLUSION Finally, the novel GEM based biosensor cells developed in this study can be applied for detection of targeted heavy metals in low concentration ranges (1-6 ppb) at normal bacterial physiological conditions.
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Affiliation(s)
- H M L P B Herath
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - W R M de Silva
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - R S Dassanayake
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - Y I N S Gunawardene
- Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - J R P Jayasingha
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - M K Gayashan
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - L O B Afonso
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia.
| | - K M N de Silva
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka.
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7
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Hu S, Zhang G, Jia X. Improvement of a highly sensitive and specific whole-cell biosensor by adding a positive feedback amplifier. Synth Syst Biotechnol 2023; 8:292-299. [PMID: 37090062 PMCID: PMC10113786 DOI: 10.1016/j.synbio.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
In this study, we designed a Cd2+ whole-cell biosensor with both positive and negative feedback cascade amplifiers in Pseudomonas putida KT2440 (LTCM) based on our previous design with only a negative feedback amplifier (TCM). The results showed that the newly developed biosensor LTCM was greatly improved compared to TCM. Firstly, the linear response range of LTCM was expanded while the maximum linear response range was raised from 0.05 to 0.1 μM. Meanwhile, adding a positive feedback amplifier further increased the fluorescence output signal of LTCM 1.11-2.64 times under the same culture conditions. Moreover, the response time of LTCM for detection of practical samples was reduced from 6 to 4 h. At the same time, LTCM still retained very high sensitivity and specificity, while its lowest detection limit was 0.1 nM Cd2+ and the specificity was 23.29 (compared to 0.1 nM and 17.55 in TCM, respectively). In summary, the positive and negative feedback cascade amplifiers effectively improved the performance of the biosensor LTCM, resulting in a greater linear response range, higher output signal intensity, and shorter response time than TCM while retaining comparable sensitivity and specificity, indicating better potential for practical applications.
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8
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Chen Y, Liu X, Li Q, Cai X, Wu W, Wu Q, Yuan W, Deng X, Liu Z, Zhao S, Wang B. Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum. Int J Biol Macromol 2023; 229:388-400. [PMID: 36592848 DOI: 10.1016/j.ijbiomac.2022.12.298] [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: 09/06/2022] [Revised: 12/05/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.
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Affiliation(s)
- Yaping Chen
- College of Tea Science, Yunnan Agricultural University, Kunming, China; College of Plant Protection, Yunnan Agricultural University, Kunming, China; Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China
| | - Xiaohui Liu
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Qiang Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiaobo Cai
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China
| | - Wendou Wu
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China
| | - Qi Wu
- College of Science, Yunnan Agricultural University, Kunming, China
| | - Wenxia Yuan
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Xiujuan Deng
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Zhiwe Liu
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Shengnan Zhao
- College of Tea Science, Yunnan Agricultural University, Kunming, China
| | - Baijuan Wang
- College of Tea Science, Yunnan Agricultural University, Kunming, China; College of Big Data, Yunnan Agricultural University, Kunming, China; Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Kunming, China.
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9
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Sandoz A, Ducret V, Gottwald GA, Vilmart G, Perron K. SINDy for delay-differential equations: application to model bacterial zinc response. Proc Math Phys Eng Sci 2023. [DOI: 10.1098/rspa.2022.0556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We extend the data-driven method of sparse identification of nonlinear dynamics (SINDy) developed by Brunton
et al.
,
Proc. Natl Acad. Sci. USA
113
(2016) to the case of delay differential equations (DDEs). This is achieved in a bilevel optimization procedure by first applying SINDy for fixed delay and then subsequently optimizing the error of the reconstructed SINDy model over delay times. We test the SINDy-delay method on a noisy short dataset from a toy DDE and show excellent agreement. We then apply the method to experimental data of gene expressions in the bacterium
Pseudomonas aeruginosa
subject to the influence of zinc. The derived SINDy model suggests that the increase in zinc concentration mainly affects the time delay and not the strengths of the interactions between the different agents controlling the zinc export mechanism.
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Affiliation(s)
- Antoine Sandoz
- Department of Plant Sciences, Microbiology Unit, and Section of Mathematics, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Verena Ducret
- Department of Plant Sciences, Microbiology Unit, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Georg A. Gottwald
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Gilles Vilmart
- Section of Mathematics, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
| | - Karl Perron
- Department of Plant Sciences, Microbiology Unit, and Section of Pharmaceutical Sciences, University of Geneva, CP64, 1211 Geneva 4, Switzerland
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10
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Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods 2022; 11:foods11233777. [PMID: 36496584 PMCID: PMC9741282 DOI: 10.3390/foods11233777] [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: 09/17/2022] [Revised: 11/05/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
The waterborne Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. Pollution of heavy metals in aquatic environments is proposed to link high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution and heavy metal tolerance mechanism of V. parahaemolyticus in aquatic animals remain to be largely unveiled. Here, we overcome the limitation by characterizing an MDR V. parahaemolyticus N10-18 isolate with high cadmium (Cd) tolerance using genomic and transcriptomic techniques. The draft genome sequence (4,910,080 bp) of V. parahaemolyticus N10-18 recovered from Ostrea gigas Thunberg was determined, and 722 of 4653 predicted genes had unknown function. Comparative genomic analysis revealed mobile genetic elements (n = 11) and heavy metal and antibiotic-resistance genes (n = 38 and 7). The bacterium significantly changed cell membrane structure to resist the Cd2+ (50 μg/mL) stress (p < 0.05). Comparative transcriptomic analysis revealed seven significantly altered metabolic pathways elicited by the stress. The zinc/Cd/mercury/lead transportation and efflux and the zinc ATP-binding cassette (ABC) transportation were greatly enhanced; metal and iron ABC transportation and thiamine metabolism were also up-regulated; conversely, propanoate metabolism and ribose and maltose ABC transportation were inhibited (p < 0.05). The results of this study demonstrate multiple strategies for the Cd tolerance in V. parahaemolyticus.
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Khan Z, Elahi A, Bukhari DA, Rehman A. Cadmium sources, toxicity, resistance and removal by microorganisms-A potential strategy for cadmium eradication. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Xing S, Yan Z, Song C, Tian H, Wang S. Limited Role of Rhamnolipids on Cadmium Resistance for an Endogenous-Secretion Bacterium. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12555. [PMID: 36231857 PMCID: PMC9566264 DOI: 10.3390/ijerph191912555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Rhamnolipids, a type of biosurfactant, represent a potential strategy for both enhancing organismic resistance and in situ remediation of heavy metals contaminations. In-depth study of the mechanism of rhamnolipids synthesis in response to heavy metals stress, is indispensable for a wide use of biosurfactant-secreting microbes in bioremediation. In this study, we employed the wild-type and the rhlAB deficient strain (ΔrhlAB) of Pseudomonas aeruginosa, a prototypal rhamnolipids-producing soil microorganism, to investigate its responses to cadmium resistance based on its physicochemical, and physiological properties. Compared with the wild-type strain, the ΔrhlAB were more sensitive to Cd-stress at low Cd concentration (<50 mg/L), whereas there was little difference in sensitivity at higher Cd concentrations, as shown by spot titers and cell viability assays. Secreted rhamnolipids reduced intracellular Cd2+ accumulation to alleviate Cd2+ stress, whereas endogenous rhamnolipids played a limited role in alleviating Cd2+ stress. Synthesized rhamnolipids exhibited a higher critical micelle concentration (CMC) (674.1 mg/L) and lower emulsification index (4.7%) under high Cd-stress, while these parameters showed no obvious changes. High Cd-stress resulted in high hydrophilic wild-type bacterial surface and lower bioremediation ability. This study could advance a deeper understanding of the mechanism of cadmium resistance and provide a theoretical foundation for the application of biosurfactant and biosurfactant-secreted bacterium in contaminant bioremediation.
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Affiliation(s)
- Sufang Xing
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Zhen Yan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chao Song
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Huifang Tian
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Shuguang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- Sino-French Research Institute for Ecology and Environment (ISFREE), School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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13
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Pang B, Yu H, Zhang J, Ye F, Wu H, Shang C. Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium. PLoS One 2022; 17:e0272528. [PMID: 35930609 PMCID: PMC9355187 DOI: 10.1371/journal.pone.0272528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 07/20/2022] [Indexed: 12/02/2022] Open
Abstract
Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. Cr13.
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Affiliation(s)
- Bingbing Pang
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Hongling Yu
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Jin Zhang
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Fengcai Ye
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Haifeng Wu
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Changhua Shang
- College of Life Science, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
- * E-mail:
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Cai Y, Zhu K, Shen L, Ma J, Bao L, Chen D, Wei L, Wei N, Liu B, Wu Y, Chen S. Evolved Biosensor with High Sensitivity and Specificity for Measuring Cadmium in Actual Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10062-10071. [PMID: 35762704 DOI: 10.1021/acs.est.2c00627] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial biosensors have great potential in contaminant detection for sensitivity, specificity, cost-effectiveness, and easy operation. However, the existing cadmium-responsive bacterial biosensors cannot meet the real-world detection requirements due to lack of sensitivity, specificity, and anti-interference capability. This study aimed to develop a bacterial biosensor for detecting the total and extractable cadmium in actual environmental samples. We constructed the cadmium-responsive biosensor with the regulatory element (cadmium resistance transcriptional regulatory, CadR) and the reporting element (GFP) and improved its performance by directed evolution. The mutant libraries of biosensors were generated by error-prone PCR and screened by continuous five-round fluorescence-activated cell sorting (FACS), and a bacteria variant epCadR5 with higher performance was finally isolated. Biosensor fluorescence intensity was measured by a microplate reader, and results showed that the evolved cadmium-responsive bacterial biosensor was of high sensitivity and specificity in detecting trace cadmium, with a detection limit of 0.45 μg/L, which is 6.8 times more specific to cadmium than that of the wild-type. Furthermore, microscopic qualitative analysis results showed that the bacteria could produce fluorescence response in a cadmium-contaminated soil matrix, and quantitative analysis results showed that the values of cadmium from epCadR5 bacteria were close to that from inductively coupled plasma-mass spectrometry. These results suggest that the biosensor may have a broad application prospect in the detection of cadmium-contaminated soil and water.
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Affiliation(s)
- Yeshen Cai
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Kaili Zhu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Dongdong Chen
- Institute of Environmental Physics and Technology, Anhui University, Hefei 230039, China
| | - Liangchen Wei
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Nan Wei
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Binmei Liu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yuejin Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Shaopeng Chen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- School of Public Health, Wannan Medical College, Wuhu 241002, China
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15
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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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Hui CY, Guo Y, Li H, Chen YT, Yi J. Differential Detection of Bioavailable Mercury and Cadmium Based on a Robust Dual-Sensing Bacterial Biosensor. Front Microbiol 2022; 13:846524. [PMID: 35495723 PMCID: PMC9043898 DOI: 10.3389/fmicb.2022.846524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Genetically programmed biosensors have been widely used to monitor bioavailable heavy metal pollutions in terms of their toxicity to living organisms. Most bacterial biosensors were initially designed to detect specific heavy metals such as mercury and cadmium. However, most available biosensors failed to distinguish cadmium from various heavy metals, especially mercury. Integrating diverse sensing elements into a single genetic construct or a single host strain has been demonstrated to quantify several heavy metals simultaneously. In this study, a dual-sensing construct was assembled by employing mercury-responsive regulator (MerR) and cadmium-responsive regulator (CadR) as the separate sensory elements and enhanced fluorescent protein (eGFP) and mCherry red fluorescent protein (mCherry) as the separate reporters. Compared with two corresponding single-sensing bacterial sensors, the dual-sensing bacterial sensor emitted differential double-color fluorescence upon exposure to 0–40 μM toxic Hg(II) and red fluorescence upon exposure to toxic Cd(II) below 200 μM. Bioavailable Hg(II) could be quantitatively determined using double-color fluorescence within a narrow concentration range (0–5 μM). But bioavailable Cd(II) could be quantitatively measured using red fluorescence over a wide concentration range (0–200 μM). The dual-sensing biosensor was applied to detect bioavailable Hg(II) and Cd(II) simultaneously. Significant higher red fluorescence reflected the predominant pollution of Cd(II), and significant higher green fluorescence suggested the predominant pollution of Hg(II). Our findings show that the synergistic application of various sensory modules contributes to an efficient biological device that responds to concurrent heavy metal pollutants in the environment.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Han Li
- College of Lab Medicine, Hebei North University, Zhangjiakou, China
| | - Yu-Ting Chen
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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17
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Detection of environmental pollutant cadmium in water using a visual bacterial biosensor. Sci Rep 2022; 12:6898. [PMID: 35477977 PMCID: PMC9046199 DOI: 10.1038/s41598-022-11051-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
Cadmium (Cd) contamination in water and soil is considered an environmental pollutant. Food crops can absorb and accumulate bioavailable Cd. Continuous monitoring of Cd levels in the environment can minimize exposure and harm to humans. Visual pigments have been demonstrated to have great potential in the development of minimal-equipment biosensors. In the present study, a metabolically engineered bacterium was employed to produce blue-purple pigment violacein responsive to toxic Cd(II). The high stability of the bisindole pigment contributed to determining the violacein at wavelengths of 578 nm. Visual and quantifiable signals could be captured after a 1.5-h Cd(II) exposure. This novel biosensor showed significantly stronger responses to Cd(II) than to other heavy metals including Pb(II), Zn(II), and Hg(II). A significant increase in pigment signal was found to respond to as low as 0.049 μM Cd(II). The naked eye can detect the color change when violacein-based biosensor is exposed to 25 μM Cd(II). A high-throughput method for rapid determination of soluble Cd(II) in environmental water was developed using a colorimetric microplate.
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Hu S, Yang J, Liao A, Lin Y, Liang S. Fluorescent indicators for live-cell and in vitro detection of inorganic cadmium dynamics. J Fluoresc 2022; 32:1397-1404. [PMID: 35438371 DOI: 10.1007/s10895-022-02919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/01/2022] [Indexed: 11/29/2022]
Abstract
Cadmium contamination is a severe threat to the environment and food safety. Thus, there is an urgent need to develop highly sensitive and selective cadmium detection tools. The engineered fluorescent indicator is a powerful tool for the rapid detection of inorganic cadmium in the environment. In this study, the development of yellow fluorescent indicators of cadmium chloride by inserting a fluorescent protein at different positions of the high cadmium-specific repressor and optimizing the flexible linker between the connection points is reported. These indicators provide a fast, sensitive, specific, high dynamic range, and real-time readout of cadmium ion dynamics in solution. The excitation and emission wavelength of this indicator used in this work are 420/485 and 528 nm, respectively. Fluorescent indicators N0C0/N1C1 showed a linear response to cadmium concentration within the range from 10/30 to 50/100 nM and with a detection limit of 10/33 nM under optimal condition. Escherichia coli cells containing the indicator were used to further study the response of cadmium ion concentration in living cells. E. coli N1C1 could respond to different concentrations of cadmium ions. This study provides a rapid and straightforward method for cadmium ion detection in vitro and the potential for biological imaging.
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Affiliation(s)
- Shulin Hu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Jun Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Anqi Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China. .,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.
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Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use. Folia Microbiol (Praha) 2022; 67:707-719. [PMID: 35415828 DOI: 10.1007/s12223-022-00970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/05/2022] [Indexed: 11/04/2022]
Abstract
Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.
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Lunavat SK, Singh SS, Mohammed AQ, Nakka VP, Phanithi PB, Medisetty R, Gogada R. The MreA Metal-Binding Sites C40, H65, and C69 Play a Critical Role in the Metal Tolerance of Pseudomonas putida KT2440. Curr Microbiol 2022; 79:142. [PMID: 35322302 DOI: 10.1007/s00284-022-02804-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Metal-binding proteins occur in the cytosol of most eubacteria. The hypothetical metal responsive protein MreA (PP-2969 gene; NreA) seems responsible for zinc, chromium, cadmium accumulation, and metal ion homeostasis. However, there is a lack of definitive evidence regarding the specific metal-binding sites of MreA protein. The present study aimed to identify putative metal-binding regions for MreA. In silico analysis revealed that amino acids C40, H65, and C69 (CHC region) seem critical for metal-protein interactions. We created site-directed mutants (SDM's) of MreA for interacted amino acids to validate in silico results. The differential scanning fluorimetry (DSF) and atomic absorption spectroscopy (AAS) showed that SDM strains of MreA protein curtailed metal accumulation compared to the wild types indicating C40, H65, and C69 amino acids are critical for metal binding. Thus, we report potential implications for MreA-bioengineered strains of Pseudomonas putida KT2440 for metal ion homeostasis by alleviating metal toxicity in the biological environment.
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Affiliation(s)
- Shanti Kumari Lunavat
- Department of Biochemistry, Osmania University, Hyderabad, Telangana, 500 007, India
| | | | - Abdul Qadeer Mohammed
- Department of Biochemistry, Osmania University, Hyderabad, Telangana, 500 007, India
| | - Venkata Prasuja Nakka
- Department of Biochemistry, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522510, India
| | - Prakash-Babu Phanithi
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Rajesh Medisetty
- Department of Biochemistry, Osmania University, Hyderabad, Telangana, 500 007, India
| | - Raghu Gogada
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana, 500046, India.
- Department of Biochemistry, Osmania University, Hyderabad, Telangana, 500 007, India.
- Department of Biochemistry and Plant Physiology, MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, Odisha, 761211, India.
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21
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A Recombinase-Based Genetic Circuit for Heavy Metal Monitoring. BIOSENSORS 2022; 12:bios12020122. [PMID: 35200383 PMCID: PMC8870050 DOI: 10.3390/bios12020122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Rapid progress in the genetic circuit design enabled whole-cell biosensors (WCBs) to become prominent in detecting an extensive range of analytes with promise in many fields, from medical diagnostics to environmental toxicity assessment. However, several drawbacks, such as high background signal or low precision, limit WCBs to transfer from proof-of-concept studies to real-world applications, particularly for heavy metal toxicity monitoring. For an alternative WCB module design, we utilized Bxb1 recombinase that provides tight control as a switch to increase dose-response behavior concerning leakiness. The modularity of Bxb1 recombinase recognition elements allowed us to combine an engineered semi-specific heat shock response (HSR) promoter, sensitive to stress conditions including toxic ions such as cadmium, with cadmium resistance regulatory elements; a cadmium-responsive transcription factor and its cognitive promoter. We optimized the conditions for the recombinase-based cadmium biosensor to obtain increased fold change and shorter response time. This system can be expanded for various heavy metals to make an all-in-one type of WCB, even using semi-specific parts of a sensing system.
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22
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Chen J, Wang L, Li W, Zheng X, Li X. Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. Front Microbiol 2022; 12:784575. [PMID: 35154027 PMCID: PMC8832061 DOI: 10.3389/fmicb.2021.784575] [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: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Our current knowledge on bacterial cadmium (Cd) resistance is mainly based on the functional exploration of specific Cd-resistance genes. In this study, we carried out a genomic study on Cd resistance of a newly isolated Cellulomonas strain with a MIC of 5 mM Cd. Full genome of the strain, with a genome size of 4.47 M bp and GC-content of 75.35%, was obtained through high-quality sequencing. Genome-wide annotations identified 54 heavy metal-related genes. Four potential Cd-resistance genes, namely zntAY8, copAY8, HMTY8, and czcDY8, were subjected to functional exploration. Quantitative PCR determination of in vivo expression showed that zntAY8, copAY8, and HMTY8 were strongly Cd-inducible. Expression of the three inducible genes against time and Cd concentrations were further quantified. It is found that zntAY8 responded more strongly to higher Cd concentrations, while expression of copAY8 and HMTY8 increased over time at lower Cd concentrations. Heterologous expression of the four genes in Cd-sensitive Escherichia coli led to different impacts on hosts’ Cd sorption, with an 87% reduction by zntAY8 and a 3.7-fold increase by HMTY8. In conclusion, a Cd-resistant Cellulomonas sp. strain was isolated, whose genome harbors a diverse panel of metal-resistance genes. Cd resistance in the strain is not controlled by a dedicated gene alone, but by several gene systems collectively whose roles are probably time- and dose-dependent. The plasmid-free, high-GC strain Y8 may provide a platform for exploring heavy metal genomics of the Cellulomonas genus.
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Affiliation(s)
- Jinghao Chen
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Xiaofang Li,
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Gupta R, Kumari A, Sharma S, Alzahrani OM, Noureldeen A, Darwish H. Identification, characterization and optimization of phosphate solubilizing rhizobacteria (PSRB) from rice rhizosphere. Saudi J Biol Sci 2022; 29:35-42. [PMID: 35002393 PMCID: PMC8717154 DOI: 10.1016/j.sjbs.2021.09.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Two billion people worldwide take rice (Oryza sativa L.) as a staple food. Phosphorus (P) and Nitrogen (N) are the major requirements of rice; although these are available in limited concentrations within rice growing regions. Among different types of Plant growth-promoting rhizobacteria (PGPR), Phosphate solubilizing rhizobacteria (PSRB) constitute an important class. These are known for plant growth promotion by enhancing P and N uptake. PSRB are nowadays used as biofertilizers to restore the soil health. Under the present investigation identification, characterization and optimization of phosphate solubilizing activity of these microbes at different pH, temperature and salt concentrations was carried out. Thirty-seven isolates were recovered from different regions of rice rhizosphere on Pikovskaya (PVK) agar among which 15 isolates were recovered from R.S. Pura, 12 isolates from Bishnah and 10 isolates were recovered from Akhnoor sector of Jammu, India. A prominent halo zone of clearance was developed around the colonies of 12 different isolates, indicating phosphate solubilization activity. Four distinct isolates were amplified, cloned and sequenced for taxonomic identification using 16S primers. The results indicated that PS 1, PS 2, PS 3, PS 4 were related to Pseudomonas aeruginosa, Bacillus subtilis strain 1, B. subtilis strain 2, B. subtilis strain 3, respectively. These strains when grown at a wide range of ecological factors showed maximum growth at pH between 6.8 and 8.8, temperature between 28 °C and 37 °C and salinity between 1% and 2%. Screening for phosphate solubilization activity revealed that the halo zone diameter formed by these isolates extended from 2.1 to 3.2 mm. The phosphate solubilizing efficiency (SE) ranged from 35.4 to 50.9 with highest value of 50.9 by PS4 and maximum P solubilization of 10.22 µg/ml was recorded by PS4 at 7th day. Phosphate solubilization activity of these identified PSRB strains can be utilized and explored in the rice growing belts of Jammu region which are deficient in phosphorus. MIC value for zinc sulphate heptahydrate in 12 isolates varied from 1 mg/ml to 6 mg/ml. Phosphate solubilization activity and MIC of these identified PSRB strains can be utilized and explored in the rice growing belts of Jammu region which are deficient in phosphorus.
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Affiliation(s)
- Renu Gupta
- Division of Soil Science & Agriculture Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha 180009, Jammu, India
| | - Anshu Kumari
- Division of Soil Science & Agriculture Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha 180009, Jammu, India
| | - Shiwali Sharma
- Division of Soil Science & Agriculture Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha 180009, Jammu, India
| | - Othman M Alzahrani
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Noureldeen
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hadeer Darwish
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress. mSystems 2021; 6:e0118921. [PMID: 34874779 PMCID: PMC8651089 DOI: 10.1128/msystems.01189-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation. IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.
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Zhang G, Hu S, Jia X. Highly Sensitive Whole-Cell Biosensor for Cadmium Detection Based on a Negative Feedback Circuit. Front Bioeng Biotechnol 2021; 9:799781. [PMID: 34926437 PMCID: PMC8678453 DOI: 10.3389/fbioe.2021.799781] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
Although many whole-cell biosensors (WCBs) for the detection of Cd2+ have been developed over the years, most lack sensitivity and specificity. In this paper, we developed a Cd2+ WCB with a negative feedback amplifier in P. putida KT2440. Based on the slope of the linear detection curve as a measure of sensitivity, WCB with negative feedback amplifier greatly increased the output signal of the reporter mCherry, resulting in 33% greater sensitivity than in an equivalent WCB without the negative feedback circuit. Moreover, WCB with negative feedback amplifier exhibited increased Cd2+ tolerance and a lower detection limit of 0.1 nM, a remarkable 400-fold improvement compared to the WCB without the negative feedback circuit, which is significantly below the World Health Organization standard of 27 nM (0.003 mg/L) for cadmium in drinking water. Due to the superior amplification of the output signal, WCB with negative feedback amplifier can provide a detectable signal in a much shorter time, and a fast response is highly preferable for real field applications. In addition, the WCB with negative feedback amplifier showed an unusually high specificity for Cd2+ compared to other metal ions, giving signals with other metals that were between 17.6 and 41.4 times weaker than with Cd2+. In summary, the negative feedback amplifier WCB designed in this work meets the requirements of Cd2+ detection with very high sensitivity and specificity, which also demonstrates that genetic negative feedback amplifiers are excellent tools for improving the performance of WCBs.
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Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Shuting Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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26
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Fang C, Zhang Y. Bacterial MerR family transcription regulators: activationby distortion. Acta Biochim Biophys Sin (Shanghai) 2021; 54:25-36. [PMID: 35130613 PMCID: PMC9909328 DOI: 10.3724/abbs.2021003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factors (TFs) modulate gene expression by regulating the accessibility of promoter DNA to RNA polymerases (RNAPs) in bacteria. The MerR family TFs are a large class of bacterial proteins unique in their physiological functions and molecular action: they function as transcription repressors under normal circumstances, but rapidly transform to transcription activators under various cellular triggers, including oxidative stress, imbalance of cellular metal ions, and antibiotic challenge. The promoters regulated by MerR TFs typically contain an abnormal long spacer between the -35 and -10 elements, where MerR TFs bind and regulate transcription activity through unique mechanisms. In this review, we summarize the function, ligand reception, DNA recognition, and molecular mechanism of transcription regulation of MerR-family TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yu Zhang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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27
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Hui CY, Guo Y, Liu L, Yi J. Recent advances in bacterial biosensing and bioremediation of cadmium pollution: a mini-review. World J Microbiol Biotechnol 2021; 38:9. [PMID: 34850291 DOI: 10.1007/s11274-021-03198-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
Cadmium (Cd) pollution has become a global environmental issue because Cd gets easily accumulated and translocated in the food chain, threatening human health. Considering the detrimental effects and non-biodegradability of environmental Cd, this is an urgent issue that needs to be addressed through the development of robust, cost-effective, and eco-friendly green routes for monitoring and remediating toxic levels of Cd. This article attempts to review various bacterial approaches toward biosensing and bioremediation of Cd in the environment. This review focuses on the recent development of bacterial cell-based biosensors for the detection of bioavailable Cd and the bioremediation of toxic Cd by natural or genetically-engineered bacteria. The present limitations and future perspectives of these available bacterial approaches are outlined. New trends for integrating synthetic biology and metabolic engineering into the design of bacterial biosensors and bioadsorbers are additionally highlighted.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Pennsylvania, USA
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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28
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Ducret V, Abdou M, Goncalves Milho C, Leoni S, Martin-Pelaud O, Sandoz A, Segovia Campos I, Tercier-Waeber ML, Valentini M, Perron K. Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics. Front Microbiol 2021; 12:739988. [PMID: 34690984 PMCID: PMC8531726 DOI: 10.3389/fmicb.2021.739988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022] Open
Abstract
Zinc is one of the most important trace elements for life and its deficiency, like its excess, can be fatal. In the bacterial opportunistic pathogen Pseudomonas aeruginosa, Zn homeostasis is not only required for survival, but also for virulence and antibiotic resistance. Thus, the bacterium possesses multiple Zn import/export/storage systems. In this work, we determine the expression dynamics of the entire P. aeruginosa Zn homeostasis network at both transcript and protein levels. Precisely, we followed the switch from a Zn-deficient environment, mimicking the initial immune strategy to counteract bacterial infections, to a Zn-rich environment, representing the phagocyte metal boost used to eliminate an engulfed pathogen. Thanks to the use of the NanoString technology, we timed the global silencing of Zn import systems and the orchestrated induction of Zn export systems. We show that the induction of Zn export systems is hierarchically organized as a function of their impact on Zn homeostasis. Moreover, we identify PA2807 as a novel Zn resistance component in P. aeruginosa and highlight new regulatory links among Zn-homeostasis systems. Altogether, this work unveils a sophisticated and adaptive homeostasis network, which complexity is key in determining a pathogen spread in the environment and during host-colonization.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Melina Abdou
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Catarina Goncalves Milho
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Oriane Martin-Pelaud
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Antoine Sandoz
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Inés Segovia Campos
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | | | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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29
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Wang M, Wang L, Shi H, Liu Y, Chen S. Soil bacteria, genes, and metabolites stimulated during sulfur cycling and cadmium mobilization under sodium sulfate stress. ENVIRONMENTAL RESEARCH 2021; 201:111599. [PMID: 34214562 DOI: 10.1016/j.envres.2021.111599] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/27/2021] [Accepted: 06/22/2021] [Indexed: 05/12/2023]
Abstract
Sodium sulfate stress is known to improve cadmium (Cd) mobilization in soil and microbial sulfur oxidation, Cd resistance, and the accumulation of stress tolerance-associated metabolites has been correlated with increased soil Cd availability and toxicity. In this study, aerobic soil microcosms with Cd-contamination were stimulated with sodium sulfate to investigate its effects on soil microbial community structure, functional genes, and associated metabolite profiles. Metagenomic analysis revealed that sulfur oxidizing and Cd-resistant bacteria carried gene clusters encoding sox, dsr, and sqr genes, and znt, czc, and cad genes, respectively. Exposure to sodium sulfate resulted in the reprogram of soil metabolites. In particular, intensification of sulfur metabolism triggered an up-regulation in the tricarboxylic acid (TCA) cycle, which promoted the secretion of carboxylic acids and their precursors by soil bacteria. The accumulation of organic acids induced in response to high sodium sulfate dosages potentially drove an observed increase in Cd mobility. Pseudomonas and Erythrobacter spp. exhibited a high capacity for adaptation to heavy metal- or sulfur-induced stress, evident by an increased abundance of genes and metabolites for sulfur cycling and Cd resistance. These results provide valuable insights towards understanding the microbial mechanisms of sulfur transformation and Cd dissolution under saline stress.
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Affiliation(s)
- Meng Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Lifu Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Huading Shi
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing, 100012, PR China.
| | - Yongbing Liu
- National Research Center for Geoanalysis, Beijing, 100037, PR China
| | - Shibao Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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30
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Hui CY, Guo Y, Wu J, Liu L, Yang XQ, Guo X, Xie Y, Yi J. Detection of Bioavailable Cadmium by Double-Color Fluorescence Based on a Dual-Sensing Bioreporter System. Front Microbiol 2021; 12:696195. [PMID: 34603225 PMCID: PMC8481780 DOI: 10.3389/fmicb.2021.696195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Cadmium (Cd) is carcinogenic to humans and can accumulate in the liver, kidneys, and bones. There is widespread presence of cadmium in the environment as a consequence of anthropogenic activities. It is important to detect cadmium in the environment to prevent further exposure to humans. Previous whole-cell biosensor designs were focused on single-sensing constructs but have had difficulty in distinguishing cadmium from other metal ions such as lead (Pb) and mercury (Hg). We developed a dual-sensing bacterial bioreporter system to detect bioavailable cadmium by employing CadC and CadR as separate metal sensory elements and eGFP and mCherry as fluorescent reporters in one genetic construct. The capability of this dual-sensing biosensor was proved to simultaneously detect bioavailable cadmium and its toxic effects using two sets of sensing systems while still maintaining similar specificity and sensitivity of respective signal-sensing biosensors. The productions of double-color fluorescence were directly proportional to the exposure concentration of cadmium, thereby serving as an effective quantitative biosensor to detect bioavailable cadmium. This novel dual-sensing biosensor was then validated to respond to Cd(II) spiked in environmental water samples. This is the first report of the development of a novel dual-sensing, whole-cell biosensor for simultaneous detection of bioavailable cadmium. The application of two biosensing modules provides versatile biosensing signals and improved performance that can make a significant impact on monitoring high concentration of bioavailable Cd(II) in environmental water to reduce human exposure to the harmful effects of cadmium.
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Jian Wu
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Ambler, PA, United States
| | - Xue-qin Yang
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Xiang Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Ying Xie
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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Liu H, Zhang Y, Wang Y, Xie X, Shi Q. The Connection between Czc and Cad Systems Involved in Cadmium Resistance in Pseudomonas putida. Int J Mol Sci 2021; 22:ijms22189697. [PMID: 34575861 PMCID: PMC8469834 DOI: 10.3390/ijms22189697] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022] Open
Abstract
Heavy metal pollution is widespread and persistent, and causes serious harm to the environment. Pseudomonas putida, a representative environmental microorganism, has strong resistance to heavy metals due to its multiple efflux systems. Although the functions of many efflux systems have been well-studied, the relationship between them remains unclear. Here, the relationship between the Czc and Cad systems that are predominantly responsible for cadmium efflux in P. putida KT2440 is identified. The results demonstrated that CzcR3, the response regulator of two-component system CzcRS3 in the Czc system, activates the expression of efflux pump genes czcCBA1 and czcCBA2 by directly binding to their promoters, thereby helping the strain resist cadmium stress. CzcR3 can also bind to its own promoter, but it has only a weak regulatory effect. The high-level expression of czcRS3 needs to be induced by Cd2+, and this relies on the regulation of CadR, a key regulator in the Cad system, which showed affinity to czcRS3 promoter. Our study indicates that the Cad system is involved in the regulation of the Czc system, and this relationship is important for maintaining the considerable resistance to cadmium in P. putida.
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Pal A, Bhattacharjee S, Saha J, Sarkar M, Mandal P. Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview. Crit Rev Microbiol 2021; 48:327-355. [PMID: 34473592 DOI: 10.1080/1040841x.2021.1970512] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.
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Affiliation(s)
- Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Sukanya Bhattacharjee
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Sarkar
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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33
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Joshi G, Meena B, Verma P, Nayak J, Vinithkumar NV, Dharani G. Deep-sea mercury resistant bacteria from the Central Indian Ocean: A potential candidate for mercury bioremediation. MARINE POLLUTION BULLETIN 2021; 169:112549. [PMID: 34182201 DOI: 10.1016/j.marpolbul.2021.112549] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Deep-sea bacteria when grown in normal environmental conditions get morphologically and genetically adapted to resist the provided culture conditions for their survival, making them a possible aspirant in mercury bioremediation. In this study, seawater samples were collected from different depths of the Central Indian Ocean and seven mercury resistant bacteria (resistant to 100 mg L-1 concentration of inorganic Hg as HgCl2) were isolated. Based on 16S rRNA gene sequencing, the identified isolates belong to the genera Pseudomonas, Bacillus and Pseudoalteromonas. The presence of the merA gene in the isolates contributes to the effective volatilization of mercury. The Inductively Coupled Plasma Mass-Spectroscopy analysis revealed that the isolates can reduce up to >80% of inorganic mercury. Moreover, Fourier Transform Infrared spectrum analysis indicates that functional groups play a key role in the mechanism of adaptation towards Hg2+ reduction. Thus, the deep-sea bacteria expressed significant tolerance and reduction potential towards ionic mercury.
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Affiliation(s)
- Gajendra Joshi
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103, Andaman and Nicobar Islands, India.
| | - Balakrishnan Meena
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Pankaj Verma
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Chennai 600100, India
| | - Jibananand Nayak
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Nambali Valsalan Vinithkumar
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Gopal Dharani
- Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Chennai 600100, India
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Hui CY, Guo Y, Li LM, Liu L, Chen YT, Yi J, Zhang NX. Indigoidine biosynthesis triggered by the heavy metal-responsive transcription regulator: a visual whole-cell biosensor. Appl Microbiol Biotechnol 2021; 105:6087-6102. [PMID: 34291315 DOI: 10.1007/s00253-021-11441-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/22/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
During the last few decades, whole-cell biosensors have attracted increasing attention for their enormous potential in monitoring bioavailable heavy metal contaminations in the ecosystem. Visual and measurable output signals by employing natural pigments have been demonstrated to offer another potential choice to indicate the existence of bioavailable heavy metals in recent years. The biosynthesis of the blue pigment indigoidine has been achieved in E. coli following heterologous expression of both BpsA (a single-module non-ribosomal peptide synthetase) and PcpS (a PPTase to activate apo-BpsA). Moreover, we demonstrated herein the development of the indigoidine-based whole-cell biosensors to detect bioavailable Hg(II) and Pb(II) in water samples by employing metal-responsive transcriptional regulator MerR and PbrR as the sensory elements, and the indigoidine biosynthesis gene cluster as a reporter element. The resulting indigoidine-based biosensors presented a good selectivity and high sensitivity to target metal ions. High concentration of target metal exposure could be clearly recognized by the naked eye due to the color change by the secretion of indigoidine, and quantified by measuring the absorbance of the culture supernatants at 600 nm. Dose-response relationships existed between the exposure concentrations of target heavy metals and the production of indigoidine. Although fairly good linear relationships were obtained in a relatively limited concentration range of the concentrations of heavy metal ions, these findings suggest that genetically controlled indigoidine biosynthesis triggered by the MerR family transcriptional regulator can enable a sensitive, visual, and qualitative whole-cell biosensor for bioindicating the presence of bioaccessible heavy metal in environmental water samples. KEY POINTS: • Biosynthesis pathway of indigoidine reconstructed in a high copy number plasmid in E. coli. • Visual and colorimetric detection of Hg(II) and Pb(II) by manipulation of indigoidine biosynthesis through MerR family metalloregulator. •Enhanced detection sensitivity toward Hg(II) and Pb(II) achieved using novel pigment-based whole-cell biosensors.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Yu-Ting Chen
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
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He MY, Lin YJ, Kao YL, Kuo P, Grauffel C, Lim C, Cheng YS, Chou HHD. Sensitive and Specific Cadmium Biosensor Developed by Reconfiguring Metal Transport and Leveraging Natural Gene Repositories. ACS Sens 2021; 6:995-1002. [PMID: 33444502 DOI: 10.1021/acssensors.0c02204] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Whole-cell biosensors are useful for monitoring heavy metal toxicity in public health and ecosystems, but their development has been hindered by intrinsic trade-offs between sensitivity and specificity. Here, we demonstrated an effective engineering solution by building a sensitive, specific, and high-response biosensor for carcinogenic cadmium ions. We genetically programmed the metal transport system of Escherichia coli to enrich intracellular cadmium ions and deprive interfering metal species. We then selected 16 cadmium-sensing transcription factors from the GenBank database and tested their reactivity to 14 metal ions in the engineered E. coli using the expression of the green fluorescent protein as the readout. The resulting cadmium biosensor was highly specific and showed a detection limit of 3 nM, a linear increase in fluorescent intensities from 0 to 200 nM, and a maximal 777-fold signal change. Using this whole-cell biosensor, a smartphone, and low-tech equipment, we developed a simple assay capable of measuring cadmium ions at the same concentration range in irrigation water and human urine. This method is user-friendly and cost-effective, making it affordable to screen large amounts of samples for cadmium toxicity in agriculture and medicine. Moreover, our work highlights natural gene repositories as a treasure chest for bioengineering.
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Affiliation(s)
- Mei-Ying He
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Jen Lin
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Ling Kao
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Pu Kuo
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Sheng Cheng
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung David Chou
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
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Guo Y, Hui CY, Zhang NX, Liu L, Li H, Zheng HJ. Development of Cadmium Multiple-Signal Biosensing and Bioadsorption Systems Based on Artificial Cad Operons. Front Bioeng Biotechnol 2021; 9:585617. [PMID: 33644011 PMCID: PMC7902519 DOI: 10.3389/fbioe.2021.585617] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 01/22/2021] [Indexed: 02/04/2023] Open
Abstract
The development of genetic engineering, especially synthetic biology, greatly contributes to the development of novel metal biosensors. The cad operon encoding cadmium resistance was previously characterized from Pseudomonas putida. In this study, single-, dual-, and triple-signal output Cd(II) biosensors were successfully developed using artificial translationally coupled cad operons. Sensitivity, selectivity, and response toward Cd(II) and Hg(II), of three biosensors were all determined. Reporter signals of three biosensors all increased within the range 0.1-3.125 μM Cd(II). Three biosensors responded strongly to Cd(II), and weakly to Hg(II). However, the detection ranges of Cd(II) and Hg(II) do not overlap in all three biosensors. Next, novel Cd(II) biosensing coupled with bioadsorptive artificial cad operons were assembled for the first time. Cd(II)-induced fluorescence emission, enzymatic indication, and Cd(II) binding protein surface display can be achieved simultaneously. This study provides an example of one way to realize multiple signal outputs and bioadsorption based on the redesigned heavy metal resistance operons, which may be a potential strategy for biodetection and removal of toxic metal in the environment, facilitating the study of the mechanism and dynamics of bioremediation.
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Affiliation(s)
- Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Chang-ye Hui
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Nai-xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Institute of Translational Medicine, Shenzhen Second People's Hospital, Shenzhen, China
| | - Hui Li
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hong-ju Zheng
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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Fang C, Li L, Zhao Y, Wu X, Philips SJ, You L, Zhong M, Shi X, O'Halloran TV, Li Q, Zhang Y. The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription. Nat Commun 2020; 11:6284. [PMID: 33293519 PMCID: PMC7722741 DOI: 10.1038/s41467-020-20134-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ'ωε) RNA Polymerase (RNAP) core enzyme, σA, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the -35 element to the -10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal -35/-10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linyu Li
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yihan Zhao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Steven J Philips
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingkang Zhong
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xiaojin Shi
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Thomas V O'Halloran
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
- The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Qunyi Li
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
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Ji Y, Guan F, Zhou X, Liu X, Wu N, Liu D, Tian J. Construction of a mApple-D6A3-mediated biosensor for detection of heavy metal ions. AMB Express 2020; 10:213. [PMID: 33284386 PMCID: PMC7721944 DOI: 10.1186/s13568-020-01154-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
Pollution of heavy metals in agricultural environments is a growing problem to the health of the world’s human population. Green, low-cost, and efficient detection methods can help control such pollution. In this study, a protein biosensor, mApple-D6A3, was built from rice-derived Cd2+-binding protein D6A3 fused with the red fluorescent protein mApple at the N-terminus to detect the contents of heavy metals. Fluorescence intensity of mApple fused with D6A3 indicated the biosensor’s sensitivity to metal ions and its intensity was more stable under alkaline conditions. mApple-D6A3 was most sensitive to Cu2+, then Ni2+, then Cd2+. Isothermal titration calorimetry experiments demonstrated that mApple-D6A3 successfully bound to each of these three metal ions, and its ability to bind the ions was, from strongest to weakest, Cu2+ > Cd2+ > Ni2+. There were strong linear relationships between the fluorescence intensity of mApple-D6A3 and concentrations of Cd2+ (0–100 μM), Cu2+ (0–60 μM) and Ni2+ (0–120 μM), and their respective R2 values were 0.994, 0.973 and 0.973. When mApple-D6A3 was applied to detect concentrations of heavy metal ions in water (0–0.1 mM) or culture medium (0–1 mM), its accuracy for detection attained more than 80%. This study demonstrates the potential of this biosensor as a tool for detection of heavy metal ions.
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39
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Ducret V, Gonzalez MR, Leoni S, Valentini M, Perron K. The CzcCBA Efflux System Requires the CadA P-Type ATPase for Timely Expression Upon Zinc Excess in Pseudomonas aeruginosa. Front Microbiol 2020; 11:911. [PMID: 32477311 PMCID: PMC7242495 DOI: 10.3389/fmicb.2020.00911] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/17/2020] [Indexed: 11/13/2022] Open
Abstract
Zinc (Zn) is a trace element essential for life but can be toxic if present in excess. While cells have import systems to guarantee a vital Zn intracellular concentration, they also rely on export systems to avoid lethal Zn overload. In particular, the opportunistic pathogen Pseudomonas aeruginosa possesses four Zn export systems: CadA, CzcCBA, CzcD, and YiiP. In this work, we compare the importance for bacterial survival of each export system at high Zn concentrations. We show that the P-type ATPase CadA, and the efflux pump CzcCBA are the main efflux systems affecting the bacterium tolerance to Zn. In addition, cadA and czcCBA genes expression kinetics revealed a hierarchical organization and interdependence. In the presence of high Zn concentrations, cadA expression is very rapidly induced (<1 min), while czcCBA expression occurs subsequently (>15 min). Our present data show that the fast responsiveness of cadA to Zn excess is due to its transcriptional activator, CadR, which is constitutively present on its promoter and promptly activating cadA gene expression upon Zn binding. Moreover, we showed that CadA is essential for a timely induction of the CzcCBA efflux system. Finally, we observed an induction of cadA and czcCBA efflux systems upon phagocytosis of P. aeruginosa by macrophages, in which a toxic metal boost is discharged into the phagolysosome to intoxicate microbes. Importantly, we demonstrated that the regulatory link between induction of the CzcCBA system and the repression of the OprD porin responsible for carbapenem antibiotic resistance, is maintained in the macrophage environment.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Manuel R Gonzalez
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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40
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Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00314-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThe effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P < 0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.
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Elcin E, Öktem HA. Inorganic Cadmium Detection Using a Fluorescent Whole-Cell Bacterial Bioreporter. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1755867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Evrim Elcin
- Department of Agricultural Biotechnology, Adnan Menderes University, Aydın, Turkey
| | - Huseyin Avni Öktem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Nanobiz Technology Inc, Ankara, Turkey
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Huang S, Liu X, Hu Q, Wei T, Wang J, Chen H, Wu C. Temperature-Driven Metalloprotein-Based Hybrid Hydrogels for Selective and Reversible Removal of Cadmium(II) from Water. ACS APPLIED MATERIALS & INTERFACES 2020; 12:2991-2998. [PMID: 31860264 DOI: 10.1021/acsami.9b19306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To develop biomaterials that easily and reversibly remove trace amounts of metal ions, we synthesized PNIPAM-co-CadRP, a thermally sensitive hybrid hydrogel by immobilizing a reconstituted cadmium binding peptide (CadRP) derived from the metalloregulatory protein CadR in a poly(N-isopropylacrylamide) (PNIPAM) gel network. The hybrid hydrogel retains the properties of the immobilized peptide and highly sensitively and selectively binds Cd(II) ions. The thermally sensitive properties of the hybrid hydrogel, which swells at low temperatures (<34 °C) and shrinks at high temperatures, provides a driving force sufficient to alternate the conformation of the immobilized CadRP such that the peptide captures and releases metal ions at high and low temperatures, respectively. Using this novel hybrid gel, we captured nanomolar Cd(II) from samples of environmental water in a highly efficient manner, leading to a practical and repeatedly reusable material to remediate our environment.
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Affiliation(s)
- Shanqing Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Xichun Liu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Qingyuan Hu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Tianbiao Wei
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Jue Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Hao Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences , Nanjing University , Nanjing , China
| | - Chi Wu
- Department of Chemistry , The Chinese University of Hong Kong , Hong Kong , China
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Elizabeth George S, Wan Y. Advances in characterizing microbial community change and resistance upon exposure to lead contamination: Implications for ecological risk assessment. CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY 2019; 50:2223-2270. [PMID: 34326626 PMCID: PMC8318135 DOI: 10.1080/10643389.2019.1698260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent advancement in molecular techniques has spurred waves of studies on responses of microorganisms to lead contamination exposure, leveraging detailed phylogenetic analyses and functional gene identification to discern the effects of lead toxicity on microbial communities. This work provides a comprehensive review of recent research on (1) microbial community changes in contaminated aquatic sediments and terrestrial soils; (2) lead resistance mechanisms; and (3) using lead resistance genes for lead biosensor development. Sufficient evidence in the literature, including both in vitro and in situ studies, indicates that exposure to lead contamination inhibits microbial activity resulting in reduced respiration, suppressed metabolism, and reduced biomass as well as altered microbial community structure. Even at sites where microbial communities do not vary compositionally with contamination levels due to extremely long periods of exposure, functional differences between microbial communities are evident, indicating that some microorganisms are susceptible to lead toxicity as others develop resistance mechanisms to survive in lead contaminated environments. The main mechanisms of lead resistance involve extracellular and intracellular biosorption, precipitation, complexation, and/or efflux pumps. These lead resistance mechanisms are associated with suites of genes responsible for specific lead resistance mechanisms and may serving as indicators of lead contamination in association with dominance of certain phyla. This allows for development of several lead biosensors in environmental biotechnology. To promote applications of these advanced understandings, molecular techniques, and lead biosensor technology, perspectives of future work on using microbial indicators for site ecological assessment is presented.
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Affiliation(s)
- S. Elizabeth George
- US EPA Office of Research and Development, National Health and Environmental Effects Laboratory, Gulf Ecology Division, Sabine Island Drive, Gulf Breeze, FL 32561
| | - Yongshan Wan
- US EPA Office of Research and Development, National Health and Environmental Effects Laboratory, Gulf Ecology Division, Sabine Island Drive, Gulf Breeze, FL 32561
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Original sequence divergence among Pseudomonas putida CadRs drive specificity. Res Microbiol 2019; 171:21-27. [PMID: 31730797 DOI: 10.1016/j.resmic.2019.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 11/23/2022]
Abstract
Bacteria, especially those living in soils, are in constant contact with metals. Transition metals like Fe or Zn, are required for proper growth. Some other metals like Cd or Hg are only toxic. Several systems exist to detoxify cells when these metals are present in concentrations harmful to biological systems. The expression of these systems is under control of specialized regulatory proteins able to detect metals and to regulate cognate detoxifying systems. In this work we report on the characterisation of the metallo-regulator CadR from Pseudomonas putida KT2440. By using gene reporter assays, we investigated the repertoire of metals detected by CadR. We show that CadR is much more responsive to Hg than to Cd, as compared to CadR from P. putida 06909. CadR from P. putida KT2440 differs in only 3 amino-acids in its metal-binding domain with respect to CadR from P. putida 06909. We show that these residues are important determinants of metal selectivity by engineering a modified CadR.
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Abstract
The highly toxic cadmium ion can cause destructive hazards to living systems by nonspecific and tight binding on functional macromolecules. However, most of the developed cadmium detoxification systems are not sufficient to recognize or detoxify cadmium ions, specifically due to the similar coordination behavior of heavy metal ions in thiolate-rich sites. Here we report that the ultraspecific cadmium regulator CadR has evolved 2 distinct types of functional recognition sites rather than a mono-type thiolate-rich site to achieve outstanding selectivity. The thiolate-rich site I and the adjacent histidine-rich recognition site II are highly associated with transcription activation. This cooperative binding mechanism could improve our understanding of the relationship between the structural dynamics and biological function of metalloregulators. Detoxification of the highly toxic cadmium element is essential for the survival of living organisms. Pseudomonas putida CadR, a MerR family transcriptional regulator, has been reported to exhibit an ultraspecific response to the cadmium ion. Our crystallographic and spectroscopic studies reveal that the extra cadmium selectivity of CadR is mediated by the unexpected cooperation of thiolate-rich site I and histidine-rich site II. Cadmium binding in site I mediates the reorientation of protein domains and facilitates the assembly of site II. Subsequently, site II bridge-links 2 DNA binding domains through ligands His140/His145 in the C-terminal histidine-rich tail. With dynamic transit between 2 conformational states, this bridge could stabilize the regulator into an optimal conformation that is critical for enhancing the transcriptional activity of the cadmium detoxification system. Our results provide dynamic insight into how nature utilizes the unique cooperative binding mechanism in multisite proteins to recognize cadmium ions specifically.
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Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol 2019; 10:1154. [PMID: 31178851 PMCID: PMC6543543 DOI: 10.3389/fmicb.2019.01154] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.
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Affiliation(s)
- Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolas Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - José I Costa
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Computational Genomics Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Andrés E Marcoleta
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
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Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients. mSystems 2019; 4:mSystems00312-18. [PMID: 31086830 PMCID: PMC6506614 DOI: 10.1128/msystems.00312-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/07/2019] [Indexed: 01/09/2023] Open
Abstract
While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia. Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mechanism has not been previously described. To examine the effect of trauma-induced changes in blood on the expression of P. aeruginosa genes, we grew strain UCBPP-PA14 (PA14) in blood samples from eight TPs and seven healthy volunteers (HVs). Compared with its growth in blood from HVs, the growth of PA14 in blood from TPs significantly altered the expression of 285 genes. Genes whose expression was significantly increased were related to carbon metabolism, especially malonate utilization and mannitol uptake, and efflux of heavy metals. Genes whose expression was significantly reduced included genes of the type VI secretion system, genes related to uptake and metabolism of amino acids, and genes related to biosynthesis and transport of the siderophores pyoverdine and pyochelin. These results suggest that during systemic infection in trauma patients, and to adapt to the trauma-induced changes in blood, P. aeruginosa adjusts positively and negatively the expression of numerous genes related to carbon metabolism and virulence, respectively. IMPORTANCE While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P. aeruginosa in whole blood from either healthy volunteers or trauma patients. The specific changes in the P. aeruginosa transcriptome in response to growth in blood from trauma patients reflect the adaptation of this organism to the bloodstream environment. This knowledge is vital for understanding the strategies this pathogen uses to adapt and survive within the host during systemic infection. Such information will help researchers and clinicians to develop new approaches for treatment of sepsis caused by P. aeruginosa in trauma patients, especially in terms of recognizing the effects of specific therapies (e.g., iron, zinc, or mannitol) on the organism. Further, this information can most likely be extrapolated to all patients with P. aeruginosa septicemia. Author Video: An author video summary of this article is available.
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Manzoor M, Abid R, Rathinasabapathi B, De Oliveira LM, da Silva E, Deng F, Rensing C, Arshad M, Gul I, Xiang P, Ma LQ. Metal tolerance of arsenic-resistant bacteria and their ability to promote plant growth of Pteris vittata in Pb-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:18-24. [PMID: 30639714 DOI: 10.1016/j.scitotenv.2019.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Soils contaminated with Pb and As are difficult to remediate. In this study, the utility of coupling As-hyperaccumulator Pteris vittata with metal-resistant rhizobacteria was explored. Siderophore-producing and P-solubilizing As-resistant bacteria from the P. vittata rhizosphere were screened for resistance to multiple metals. Results indicated Pseudomonas spp. strain PG-12 was most efficient in resisting multiple metals, i.e., up to 0.6 mM Cd and 10 mM Pb. Amplification of gene fragments encoding various metal efflux transporters (PbrA and CadA2) from genomic DNA of PG-12 suggested that metal efflux might play a role in its metal resistance and detoxification. In addition, PG-12 produced significant levels of plant growth hormones including 17.4 μg mL-1 indole acetic acid and 3.54 μg mL-1 gibberellin. P. vittata sporophytes inoculated with PG-12 were grown in Pb-contaminated medium and exhibited improved growth, increased P uptake, and reduced Pb uptake into plant tissue compared to the control. Results demonstrated that viable PG-12 cells were responsible for Pb immobilization and plant growth enhancement in P. vittata. The ability of PG-12 cells to solubilize P and display resistance to multiple metals combined with the production of plant hormones indole acetic acid and gibberellin make PG-12 a suitable candidate for plant growth promotion in metal-contaminated soil.
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Affiliation(s)
- Maria Manzoor
- Research Center for Soil Contamination and Environmental Remediation, Southwest Forestry University, Kunming 650224, China; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA; Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Rafia Abid
- Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA; Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Letuzia M De Oliveira
- Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA
| | - Evandro da Silva
- Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA
| | - Fenglin Deng
- Research Center for Soil Contamination and Environmental Remediation, Southwest Forestry University, Kunming 650224, China
| | - Christopher Rensing
- Research Center for Soil Contamination and Environmental Remediation, Southwest Forestry University, Kunming 650224, China; Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Iram Gul
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Ping Xiang
- Research Center for Soil Contamination and Environmental Remediation, Southwest Forestry University, Kunming 650224, China.
| | - Lena Q Ma
- Research Center for Soil Contamination and Environmental Remediation, Southwest Forestry University, Kunming 650224, China; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA.
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Prabhakaran R, Rajkumar SN, Ramprasath T, Selvam GS. Identification of promoter P cadR, in silico characterization of cadmium resistant gene cadR and molecular cloning of promoter P cadR from Pseudomonas aeruginosa BC15. Toxicol Ind Health 2018; 34:819-833. [PMID: 30407121 DOI: 10.1177/0748233718795934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cadmium (Cd) remediation in Pseudomonas aeruginosa is achieved through the function of two vital genes, cadA and cadR, that code for P-type ATPase (CadA) and transcription regulatory protein (CadR), respectively. Although numerous studies are available on these metal-sensing and regulatory proteins, the promoter of these genes, metal sensing and binding ability, are poorly understood. The present work is aimed at the characterization of the CadR protein, identification of the PcadR promoter and protein-promoter-metal binding affinity using bioinformatics and to validate the results by cloning the PcadR promoter in Escherichia coli DH5α. The promoter regions and its curvature were identified and analysed using PePPER software (University of Groningen, The Netherland) and the Bendit program (Version: v.1.0), respectively. Using Phyre, the three-dimensional structure of CadR was modelled, and the structure was validated by Ramachandran plots. The DNA-binding domain was present in the N-terminal region of CadR. A dimeric interface was observed in helix-turn-helix and metal ion-binding sites at the C-terminal. Docking studies showed higher affinity of Cd to both CadR (Atomic contact energy = -15.04 kcal/Mol) and PcadR (Atomic contact energy = -40.18 kcal/Mol) when compared to other metal ions. CadR with PcadR showed the highest binding affinity (Atomic contact energy= -250.40 kcal/Mol) when compared with PcadA. In vitro studies using green fluorescent protein tagged with PcadR (gfp-PcadR) cloned in E. coli-expressed gfp protein in a concentration-dependent manner upon Cd exposure. Based on our in silico studies and in vitro molecular cloning analysis, we conclude that PcadR and CadR are active only in the presence of Cd. The CadR protein has the highest binding affinity with PcadR. As it became apparent that the cadR gene regulates the PcadR activity in the presence of Cd with high specificity, and the cadR and PcadR can be used as a biological tool for development of a microbial biosensor.
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Affiliation(s)
- Rajkumar Prabhakaran
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | | | - Tharmarajan Ramprasath
- Center for Molecular and Translational Medicine, Petit Science Center, Georgia State University, Atlanta, GA, USA
| | - Govindan Sadasivam Selvam
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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Rodríguez Hernáez J, Cerón Cucchi ME, Cravero S, Martinez MC, Gonzalez S, Puebla A, Dopazo J, Farber M, Paniego N, Rivarola M. The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid. Microb Genom 2018; 4. [PMID: 30216146 PMCID: PMC6249431 DOI: 10.1099/mgen.0.000216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.
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Affiliation(s)
- Javier Rodríguez Hernáez
- 3Skoklab - Department of Pathology, NYU Langone Health, New York, USA.,1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,2Fundación Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Maria Esperanza Cerón Cucchi
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Silvio Cravero
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Maria Carolina Martinez
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Sergio Gonzalez
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Andrea Puebla
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Joaquin Dopazo
- 4Clinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, Sevilla, Spain
| | - Marisa Farber
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
| | - Norma Paniego
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
| | - Máximo Rivarola
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,2Fundación Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
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