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Wang D, Wei M, Zhao L, Song T, Li Q, Tan J, Tang J, Li Z, Zhu R. Development of a novel fluorescent protein-based probe for efficient detection of Pb 2+ in serum inspired by the metalloregulatory protein PbrR691. Anal Chim Acta 2024; 1305:342580. [PMID: 38677837 DOI: 10.1016/j.aca.2024.342580] [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: 12/15/2023] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND The accurate and rapid detection of blood lead concentration is of paramount importance for assessing human lead exposure levels. Fluorescent protein-based probes, known for their high detection capabilities and low toxicity, are extensively used in analytical sciences. However, there is currently a shortage of such probes designed for ultrasensitive detection of Pb2+, and no reported probes exist for the quantitative detection of Pb2+ in blood samples. This study aims to fill this critical void by developing and evaluating a novel fluorescent protein-based probe that promises accurate and rapid lead quantification in blood. RESULTS A simple and small-molecule fluorescent protein-based probe was successfully constructed herein using a peptide PbrBD designed for Pb2+ recognition coupled to a single fluorescent protein, sfGFP. The probe retains a three-coordinate configuration to identify Pb2+ and has a high affinity for it with a Kd' of 1.48 ± 0.05 × 10-17 M. It effectively transfers the conformational changes of the peptide to the chromophore upon Pb2+ binding, leading to fast fluorescence quenching and a sensitive response to Pb2+. The probe offers a broad dynamic response range of approximately 37-fold and a linear detection range from 0.25 nM to 3500 nM. More importantly, the probe can resist interference of metal ions in living organisms, enabling quantitative analysis of Pb2+ in the picomolar to millimolar range in serum samples with a recovery percentage of 96.64%-108.74 %. SIGNIFICANCE This innovative probe, the first to employ a single fluorescent protein-based probe for ultrasensitive and precise analysis of Pb2+ in animal and human serum, heralds a significant advancement in environmental monitoring and public health surveillance. Furthermore, as a genetically encoded fluorescent probe, this probe also holds potential for the in vivo localization and concentration monitoring of Pb2+.
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Affiliation(s)
- Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China; Nanning New Technology Entrepreneur Center, Nanning, 530006, China.
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Liu Zhao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Tianyu Song
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Qunfang Li
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Jiaxin Tan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Jing Tang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
| | - Rukui Zhu
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China.
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Hu Q, Wang J, Liu C, Feng Y, Chen H. Determinants of mer Promoter Activity from Pseudomonas aeruginosa. Genes (Basel) 2024; 15:490. [PMID: 38674424 PMCID: PMC11049809 DOI: 10.3390/genes15040490] [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: 03/18/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Since the MerR family is known for its special regulatory mechanism, we aimed to explore which factors determine the expression activity of the mer promoter. The Tn501/Tn21 mer promoter contains an abnormally long spacer (19 bp) between the -35 and -10 elements, which is essential for the unique DNA distortion mechanism. To further understand the role of base sequences in the mer promoter spacer, this study systematically engineered a series of mutant derivatives and used luminescent and fluorescent reporter genes to investigate the expression activity of these derivatives. The results reveal that the expression activity of the mer promoter is synergistically modulated by the spacer length (17 bp is optimal) and the region upstream of -10 (especially -13G). The spacing is regulated by MerR transcription factors through symmetrical sequences, and -13G presumably functions through interaction with the RNA polymerase sigma-70 subunit.
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Affiliation(s)
| | | | | | | | - Hao Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (Q.H.); (J.W.); (C.L.); (Y.F.)
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3
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Hui CY, Ma BC, Wang YQ, Yang XQ, Cai JM. Designed bacteria based on natural pbr operons for detecting and detoxifying environmental lead: A mini-review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115662. [PMID: 37939554 DOI: 10.1016/j.ecoenv.2023.115662] [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: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023]
Abstract
Lead (Pb), a naturally occurring element, is redistributed in the environment mainly due to anthropogenic activities. Pb pollution is a crucial public health problem worldwide due to its adverse effects. Environmental bacteria have evolved various protective mechanisms against high levels of Pb. The pbr operon, first identified in Cupriavidus metallidurans CH34, encodes a unique Pb(II) resistance mechanism involving transport, efflux, sequestration, biomineralization, and precipitation. Similar pbr operons are gradually found in diverse bacterial strains. This review focuses on the pbr-encoded Pb(II) resistance system. It summarizes various whole-cell biosensors harboring artificially designed pbr operons for Pb(II) biomonitoring with fluorescent, luminescent, and colorimetric signal output. Optimization of genetic circuits, employment of pigment-based reporters, and screening of host cells are promising in improving the sensitivity, selectivity, and response range of whole-cell biosensors. Engineered bacteria displaying Pb(II) binding and sequestration proteins, including PbrR and its derivatives, PbrR2 and PbrD, for adsorption are involved. Although synthetic bacteria show great potential in determining and removing Pb at the nanomolar level for environmental protection and food safety, some challenges must be addressed to meet demanding application requirements.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yong-Qiang Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Xue-Qin Yang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Jin-Min Cai
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
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Hess SS, Coppola F, Dang VT, Tran PN, Mickel PJ, Oktawiec J, Ren Z, Král P, Nguyen AI. Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. J Am Chem Soc 2023; 145:19588-19600. [PMID: 37639365 DOI: 10.1021/jacs.3c03645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Though thiols are exceptionally versatile, their high reactivity has also hindered the synthesis and characterization of well-defined thiol-containing porous materials. Leveraging the mild conditions of the noncovalent peptide assembly, we readily synthesized and characterized a number of frameworks with thiols displayed at many unique positions and in several permutations. Importantly, nearly all assemblies were structurally determined using single-crystal X-ray diffraction to reveal their rich sequence-structure landscape and the cooperative noncovalent interactions underlying their assembly. These observations and supporting molecular dynamics calculations enabled rational engineering by the positive and negative design of noncovalent interactions. Furthermore, the thiol-containing frameworks undergo diverse single-crystal-to-single-crystal reactions, including toxic metal ion coordination (e.g., Cd2+, Pb2+, and Hg2+), selective uptake of Hg2+ ions, and redox transformations. Notably, we find a framework that supports thiol-nitrosothiol interconversion, which is applicable for biocompatible nitric oxide delivery. The modularity, ease of synthesis, functionality, and well-defined nature of these peptide-based thiol frameworks are expected to accelerate the design of complex materials with reactive active sites.
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Affiliation(s)
- Selina S Hess
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Francesco Coppola
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Philip J Mickel
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Petr Král
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
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Wang D, Wei L, Tan J, Yan Y, Wei M, Song T, Li S, Zhao L, Wu W, Li Z, Liu Q. A novel strategy of engineering genetically encoded probe for ultrasensitive sensing Hg 2+ with unusual planar trigonometric coordination configuration. Anal Chim Acta 2023; 1252:341049. [PMID: 36935153 DOI: 10.1016/j.aca.2023.341049] [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: 01/07/2023] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
At present, few genetically encoded fluorescent probes are currently available for the analysis of toxic heavy metal ions, and most have poor performance that cannot meet the requirements of sensitive and dynamic detection in living cells. In this study, we designed a single fluorescent protein-based probe sfGFP-MerBD, which can specifically response to Hg2+ with high binding affinity and wide dynamic range. More importantly, the developing probe can timely and reversibly monitor changes of Hg2+ concentration in living mammalian cells. The excellent performance of this probe is largely due to the recognition element of the probe, MerBD, which adopts an unusual planar trigonometric coordination configuration with Hg2+, and the coordination can cause enough conformational change to influence the fluorescence of skeleton protein sfGFP coupled with it. The small peptide MerBD was delicately designed based on the three-dimensional structure of metalloprotein MerR. This novel design strategy solves the challenging problems that there are few natural functional proteins in the process of constructing fluorescent probes for toxic metal ions and some functional proteins cannot be directly used as recognition elements. Based on the new strategy, more genetically encoded fluorescent probes of toxic heavy metal ions can be efficiently constructed and applied in the future.
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Affiliation(s)
- Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China; Nanning New Technology Entrepreneur Center, Nanning, 530006, China.
| | - Liudan Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China; Guangxi Academy of Sciences, Nanning, 530007, China
| | - Jiaxin Tan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Yiyu Yan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Tianyu Song
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Sihang Li
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Liu Zhao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Weibo Wu
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
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Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes. J Bacteriol 2023; 205:e0034322. [PMID: 36892288 PMCID: PMC10127602 DOI: 10.1128/jb.00343-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.
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Shan B, Hao R, Zhang J, Li J, Ye Y, Lu A. Microbial remediation mechanisms and applications for lead-contaminated environments. World J Microbiol Biotechnol 2022; 39:38. [PMID: 36510114 DOI: 10.1007/s11274-022-03484-1] [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: 10/24/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
High concentrations of lead (Pb) in agricultural soil and wastewater represent a severe threat to the ecosystem and health of living organisms. Among available removal techniques, microbial remediation has attracted much attention due to its lower cost, higher efficiency, and less impact on the environment; hence, it is an effective alternative to conventional physical or chemical Pb-remediation technologies. In the present review, recent advances on the Pb-remediation mechanisms of bacteria, fungi and microalgae have been reported, as well as their detoxification pathways. Based on the previous researches, microorganisms have various remediation mechanisms to cope with Pb pollution, which are basically categorized into biosorption, bioprecipitation, biomineralization, and bioaccumulations. This paper summarizes microbial Pb-remediation mechanisms, factors affecting Pb removal, and examples of each case are described in detail. We emphatically discuss the mechanisms of microbial immobilization of Pb, which can resist toxicity by synthesizing nanoparticles to convert dissolved Pb(II) into less toxic forms. The tolerance mechanisms of microbes to Pb are discussed at the molecular level as well. Finally, we conclude the research challenges and development prospects regarding the microbial remediation of Pb-polluted environment. The current review provides insight of interaction between lead and microbes and their potential applications for Pb removal.
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Affiliation(s)
- Bing Shan
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Ruixia Hao
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
| | - Junman Zhang
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Jiani Li
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Yubo Ye
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China
| | - Anhuai Lu
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing, 100871, China
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Mendoza JI, Lescano J, Soncini FC, Checa SK. The protein scaffold calibrates metal specificity and activation in MerR sensors. Microb Biotechnol 2022; 15:2992-3002. [PMID: 36134649 PMCID: PMC9733647 DOI: 10.1111/1751-7915.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
MerR metalloregulators are the central components of many biosensor platforms designed to report metal contamination. However, most MerR proteins are non-specific. This makes it difficult to apply these biosensors in the analysis of real environmental samples. On-demand implementation of molecular engineering to modify the MerR metal preferences is innovative, although it does not always yield the expected results. As the metal binding loop region (MBL) of these sensors has been proposed to be the major modulator of their specificity, we surgically switched this region for that of well-characterized specific and non-specific homologues. We found that identical modifications in different MerR proteins result in synthetic sensors displaying particular metal-detection patterns that cannot be predicted from the nature of the assembled modules. For instance, the MBL from a native Hg(II) sensor provided non-specificity or specificity toward Hg(II) or Cd(II) depending on the MerR scaffold into which it was integrated. These and other evidences reveal that residues outside the MBL are required to modulate ion recognition and transduce the input signal to the target promoter. Revealing their identity and their interactions with other residues is a critical step toward the design of more efficient biosensor devices for environmental metal monitoring.
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Affiliation(s)
- Julián I. Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Julián Lescano
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Fernando C. Soncini
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Susana K. Checa
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
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Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans. Microbiol Spectr 2022; 10:e0012122. [PMID: 35311568 PMCID: PMC9045368 DOI: 10.1128/spectrum.00121-22] [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] [Indexed: 11/20/2022] Open
Abstract
The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans contains a large number of horizontally acquired plasmids and genomic islands that were integrated into its chromosome or chromid. For the C. metallidurans CH34 wild-type strain growing under nonchallenging conditions, 5,763 transcriptional starting sequences (TSSs) were determined. Using a custom-built motif discovery software based on hidden Markov models, patterns upstream of the TSSs were identified. The pattern TTGACA, −35.6 ± 1.6 bp upstream of the TSSs, in combination with a TATAAT sequence 15.8 ± 1.4 bp upstream occurred frequently, especially upstream of the TSSs for 48 housekeeping genes, and these were assigned to promoters used by RNA polymerase containing the main housekeeping sigma factor RpoD. From patterns upstream of the housekeeping genes, a score for RpoD-dependent promoters in C. metallidurans was derived and applied to all 5,763 TSSs. Among these, 2,572 TSSs could be associated with RpoD with high probability, 373 with low probability, and 2,818 with no probability. In a detailed analysis of horizontally acquired genes involved in metal resistance and not involved in this process, the TSSs responsible for the expression of these genes under nonchallenging conditions were assigned to RpoD- or non-RpoD-dependent promoters. RpoD-dependent promoters occurred frequently in horizontally acquired metal resistance and other determinants, which should allow their initial expression in a new host. However, other sigma factors and sense/antisense effects also contribute—maybe to mold in subsequent adaptation steps the assimilated gene into the regulatory network of the cell. IMPORTANCE In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed. We show here that the main housekeeping sigma factor RpoD plays an important role in the expression of horizontally acquired genes in the metal-resistant hydrogen-oxidizing bacterium C. metallidurans. By conservation of the RpoD recognition consensus sequence, a newly arriving gene has a high probability to be expressed in the new host cell. In addition to integrons and genes travelling together with that for their sigma factor, conservation of the RpoD consensus sequence may be an important contributor to the overall evolutionary success of horizontal gene transfer in bacteria. Using C. metallidurans as an example, this publication sheds some light on the fate and function of horizontally acquired genes in bacteria.
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Wei T, Huang S, Hu Q, Wang J, Huo Z, Zhu T, Wu C, Chen H. Thermoresponsive Metallo-protein-based Hybrid Hydro-gels for Reversible and Highly Selective Removal of Lead(II) from Water. Polym Chem 2022. [DOI: 10.1039/d1py01574e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is interesting to develop biomaterials for easily removing ultra-trace toxic metal ions from the environment. Herein, we have synthesized a thermoresponsive hybrid hydrogel PNIPAM-co-PbrRP by incorporating a reconstituted lead-binding...
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11
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Computational strategies to model the interaction and the reactivity of biologically-relevant transition metal complexes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Jiang C, Yang L, Li P, Liu Y, Li S, Fu Y, Ye F. A simple and rapid fluorescent approach for Pb 2+ determination and application in water samples and living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 263:120168. [PMID: 34273892 DOI: 10.1016/j.saa.2021.120168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/20/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
A novel selective fluorescent chemosensor, thiosemicarbazide-appended naphthalimide derivative (TND), has been designed and synthesized, which exhibited good selectivity and sensibility for Pb2+ in CH3CN:H2O (1:1) solution. The probe TND showed obvious color changes under UV light of 365 nm and displayed turn-on fluorescence response with Pb2+ added. The binding mode of TND with Pb2+ was found to be 1:1 based on the Job's plot analysis. The detection limit of Pb2+ was 4.7 nM, which is far below the allowable concentration determined by WHO in drinking water. Moreover, the fortified recoveries of Pb2+ were from 100.54% to 113.68% in water samples. TND is also applied for fluorescence imaging of Pb2+ in lysosomes of human stromal cell line (HSC). This study indicated that TND would be a potential sensor detecting Pb2+ in real sample.
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Affiliation(s)
- Chunyu Jiang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Liu Yang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ping Li
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yulong Liu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Shijie Li
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, 150030, PR China.
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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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Behind the shield of Czc: ZntR controls expression of the gene for the zinc-exporting P-type ATPase ZntA in Cupriavidus metallidurans. J Bacteriol 2021; 203:JB.00052-21. [PMID: 33685972 PMCID: PMC8117531 DOI: 10.1128/jb.00052-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the metallophilic beta-proteobacterium Cupriavidus metallidurans, the plasmid-encoded Czc metal homeostasis system adjusts the periplasmic zinc, cobalt and cadmium concentration, which influences subsequent uptake of these metals into the cytoplasm. Behind this shield, the PIB2-type APTase ZntA is responsible for removal of surplus cytoplasmic zinc ions, thereby providing a second level of defense against toxic zinc concentrations. ZntA is the counterpart to the Zur-regulated zinc uptake system ZupT and other import systems; however, the regulator of zntA expression was unknown. The chromid-encoded zntA gene is adjacent to the genes czcI2C2B2', which are located on the complementary DNA strand and transcribed from a common promoter region. These genes encode homologs of plasmid pMOL30-encoded Czc components. Candidates for possible regulators of zntA were identified and subsequently tested: CzcI, CzcI2, and the MerR-type gene products of the locus tags Rmet_2302, Rmet_0102, Rmet_3456. This led to the identification of Rmet_3456 as ZntR, the main regulator of zntA expression. Moreover, both CzcIs decreased Czc-mediated metal resistance, possibly to avoid "over-excretion" of periplasmic zinc ions, which could result in zinc starvation due to diminished zinc uptake into the cytoplasm. Rmet_2302 was identified as CadR, the regulator of the cadA gene for an important cadmium-exporting PIB2-type ATPase, which provides another system for removal of cytoplasmic zinc and cadmium. Rmet_0102 was not involved in regulation of the metal resistance systems examined here. Thus, ZntR forms a complex regulatory network with CadR, Zur and the CzcIs. Moreover, these discriminating regulatory proteins assign the efflux systems to their particular function.ImportanceZinc is an essential metal for numerous organisms from humans to bacteria. The transportome of zinc uptake and efflux systems controls the overall cellular composition and zinc content in a double feed-back loop. Zinc starvation mediates, via the Zur regulator, an up-regulation of the zinc import capacity via the ZIP-type zinc importer ZupT and an amplification of zinc storage capacity, which together raise the cellular zinc content again. On the other hand, an increasing zinc content leads to ZntR-mediated up-regulation of the zinc efflux system ZntA, which decreases the zinc content. Together, the Zur regulon components and ZntR/ZntA balance the cellular zinc content under both high external zinc concentrations and zinc starvation conditions.
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15
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Tolbatov I, Marrone A. Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02718-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractThe coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.
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16
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Kim H, Jang G, Kim BG, Yoon Y. Modulation of the Metal(loid) Specificity of Whole-Cell Bioreporters by Genetic Engineering of ZntR Metal-Binding Loops. J Microbiol Biotechnol 2020; 30:681-688. [PMID: 32482933 PMCID: PMC9728388 DOI: 10.4014/jmb.1911.11053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/09/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cell-based biosensors, or whole-cell bioreporters (WCBs), are an alternative tool for the quantification of hazardous materials. Most WCBs share similar working mechanisms. In brief, the recognition of a target by sensing domains induces a biological event, such as changes in protein conformation or gene expression, providing a basis for quantification. WCBs targeting heavy metal(loid)s employ metalloregulators as sensing domains and control the expression of genes in the presence of target metal(loid) ions, but the diversity of targets, specificity, and sensitivity of these WCBs are limited. In this study, we genetically engineered the metal-binding loop (MBL) of ZntR, which controls the znt-operon in Escherichia coli. In the MBL of ZntR, three Cys sites interact with metal ions. Based on the crystal structure of ZntR, MBL sequences were modified by sitedirected mutagenesis. As a result, the metal-sensing properties of WCBs differed depending on amino acid sequences and the new selectivity to Cr or Pb was observed. Although there is room for improvement, our results support the use of currently available WCBs as a platform to generate new WCBs to target other environmental pollutants including metal(loid)s.
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Affiliation(s)
- Hyojin Kim
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bong-Gyu Kim
- Department of Forest Resources, Gyeongnam National University of Science and Technology, Jinju 52725, Republic of Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea
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17
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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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18
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Tolbatov I, Re N, Coletti C, Marrone A. Determinants of the Lead(II) Affinity in pbrR Protein: A Computational Study. Inorg Chem 2019; 59:790-800. [DOI: 10.1021/acs.inorgchem.9b03059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iogann Tolbatov
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università“G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, Chieti, Italy
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19
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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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20
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Chen B, Fang L, Yan X, Zhang A, Chen P, Luan T, Hu L, Jiang G. A unique Pb-binding flagellin as an effective remediation tool for Pb contamination in aquatic environment. JOURNAL OF HAZARDOUS MATERIALS 2019; 363:34-40. [PMID: 30300776 DOI: 10.1016/j.jhazmat.2018.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/10/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Metal contaminants present persistent and deleterious threats to environmental ecosystems and human health. Microorganisms can rapidly develop protective mechanisms against metal toxicity, such as metallothionein production. The identification of biological factors related to these protective mechanisms is essential for effective metal remediation. This study presents a robust pathway to rapidly locate and characterize a Pb-binding flagellin in Serratia Se1998, which can bind Pb at a 16:1 Pb: protein ratio. A column gel electrophoresis system hyphenated with inductively coupled plasma mass spectrometry (ICP MS) was constructed to efficiently separate and identify Pb-binding proteins from the whole bacterial proteome. PCR and transgenic assays were used to elucidate the exact sequences and biological function of Pb-binding proteins and heterogeneous expression of Pb-binding flagellin in E. coli could significantly enhance Pb removal from aqueous solution by approximately 45%. This method provides a benchmark procedure to rapidly identify biological factors responsible for metal biosorption. Identification of this unique Pb-binding flagellin highlights that microorganisms can survive high metal stresses due to various complex biological pathways for metal detoxification and remediation.
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Affiliation(s)
- Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, PR China
| | - Xueting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing, 100085, PR China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing, 100085, PR China
| | - Ping Chen
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Tiangang Luan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing, 100085, PR China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing, 100085, PR China
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21
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Braga CP, Adamec J, de Magalhães Padilha P. Metallomics in Fish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1055:101-110. [PMID: 29884963 DOI: 10.1007/978-3-319-90143-5_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Metallomics allows the integration of traditionally analytical studies with inorganic and biochemical studies. The study of metallomics in living organisms allows us to obtain information about how the metal ion is distributed and coordinated with proteins, the essentiality and/or toxicity, and the individual concentrations of metal species, thus contributing to elucidation of the physiological and functional aspects of these biomolecules. In this context, several lines of research have appeared in the literature with different terms and approaches. For example, metallomic, which deals with the characterization of the total metal/metalloid species present in an organism; metalloprotein, which deals with the characterization of the total elements present in a specific site of an organism (cellular behavior, protein, metalloprotein); and metallomic, which deals with a more in-depth study of metallome. In this area, information is sought on the interactions and functional connections of metal/metalloid species with genes, proteins, metabolites and other biomolecules of the organism and, therefore, the elucidation of the biological role exerted by the metal ions bound to the biomolecules. In this chapter, we will describe techniques used in animal studies.
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Affiliation(s)
| | - Jiri Adamec
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Pedro de Magalhães Padilha
- Department of Chemistry and Biochemistry, Institute of Bioscience, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
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22
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Wei W, Sun P, Li Z, Song K, Su W, Wang B, Liu Y, Zhao J. A surface-display biohybrid approach to light-driven hydrogen production in air. SCIENCE ADVANCES 2018; 4:eaap9253. [PMID: 29492458 PMCID: PMC5821488 DOI: 10.1126/sciadv.aap9253] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/23/2018] [Indexed: 05/04/2023]
Abstract
Solar-to-chemical production by artificial and bioinspired photosynthetic systems is of tremendous interest to help solve current global energy and environmental problems. We developed a bioinorganic hybrid system for photocatalytic hydrogen production under aerobic conditions by combining light-harvesting semiconductors, hydrogenase catalysis, and self-aggregation of whole bacterial cells. We induced hydrogen production via self-photosynthesis in engineered Escherichia coli cells, which were originally designed for bioremediation, with in situ biosynthesis of biocompatible cadmium sulfide nanoparticles using a surface-display system. We also introduced a biomimetic silica encapsulation strategy into the engineered E. coli cells, enabling this hybrid system to continuously produce hydrogen for 96 hours, even under natural aerobic conditions. This biohybrid catalytic approach may serve as a general strategy for solar-to-chemical production.
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Affiliation(s)
- Wei Wei
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Peiqing Sun
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Zhen Li
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Kuisong Song
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Wenyin Su
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Bao Wang
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yangzhong Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Soft Matter Chemistry, CAS High Magnetic Field Laboratory, Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- Corresponding author.
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23
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Allocating dissipation across a molecular machine cycle to maximize flux. Proc Natl Acad Sci U S A 2017; 114:11057-11062. [PMID: 29073016 DOI: 10.1073/pnas.1707534114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapid-turnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that-in contrast to previous findings-the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both "irreversible" and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that, in evolved machines, different transitions differ significantly in their dissipation.
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24
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Saha RP, Samanta S, Patra S, Sarkar D, Saha A, Singh MK. Metal homeostasis in bacteria: the role of ArsR-SmtB family of transcriptional repressors in combating varying metal concentrations in the environment. Biometals 2017; 30:459-503. [PMID: 28512703 DOI: 10.1007/s10534-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023]
Abstract
Bacterial infections cause severe medical problems worldwide, resulting in considerable death and loss of capital. With the ever-increasing rise of antibiotic-resistant bacteria and the lack of development of new antibiotics, research on metal-based antimicrobial therapy has now gained pace. Metal ions are essential for survival, but can be highly toxic to organisms if their concentrations are not strictly controlled. Through evolution, bacteria have acquired complex metal-management systems that allow them to acquire metals that they need for survival in different challenging environments while evading metal toxicity. Metalloproteins that controls these elaborate systems in the cell, and linked to key virulence factors, are promising targets for the anti-bacterial drug development. Among several metal-sensory transcriptional regulators, the ArsR-SmtB family displays greatest diversity with several distinct metal-binding and nonmetal-binding motifs that have been characterized. These prokaryotic metolloregulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of metal ions by directly binding to the regulatory regions of DNA, while derepression results from direct binding of metal ions by these homodimeric proteins. Many bacteria, e.g., Mycobacterium tuberculosis, Bacillus anthracis, etc., have evolved to acquire multiple metal-sensory motifs which clearly demonstrate the importance of regulating concentrations of multiple metal ions. Here, we discussed the mechanisms of how ArsR-SmtB family regulates the intracellular bioavailability of metal ions both inside and outside of the host. Knowledge of the metal-challenges faced by bacterial pathogens and their survival strategies will enable us to develop the next generation drugs.
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Affiliation(s)
- Rudra P Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India.
| | - Saikat Samanta
- Department of Microbiology, School of Science, Adamas University, Kolkata, 700126, India
| | - Surajit Patra
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Diganta Sarkar
- Department of Biotechnology, Techno India University, Kolkata, 700091, India
| | - Abinit Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
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25
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Metallochaperones and metalloregulation in bacteria. Essays Biochem 2017; 61:177-200. [PMID: 28487396 DOI: 10.1042/ebc20160076] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Bacterial transition metal homoeostasis or simply 'metallostasis' describes the process by which cells control the intracellular availability of functionally required metal cofactors, from manganese (Mn) to zinc (Zn), avoiding both metal deprivation and toxicity. Metallostasis is an emerging aspect of the vertebrate host-pathogen interface that is defined by a 'tug-of-war' for biologically essential metals and provides the motivation for much recent work in this area. The host employs a number of strategies to starve the microbial pathogen of essential metals, while for others attempts to limit bacterial infections by leveraging highly competitive metals. Bacteria must be capable of adapting to these efforts to remodel the transition metal landscape and employ highly specialized metal sensing transcriptional regulators, termed metalloregulatory proteins,and metallochaperones, that allocate metals to specific destinations, to mediate this adaptive response. In this essay, we discuss recent progress in our understanding of the structural mechanisms and metal specificity of this adaptive response, focusing on energy-requiring metallochaperones that play roles in the metallocofactor active site assembly in metalloenzymes and metallosensors, which govern the systems-level response to metal limitation and intoxication.
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26
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Entropy redistribution controls allostery in a metalloregulatory protein. Proc Natl Acad Sci U S A 2017; 114:4424-4429. [PMID: 28348247 DOI: 10.1073/pnas.1620665114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond-nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast motions and concerted slower motions. Allosterically impaired CzrA mutants are characterized by distinct nonnative fast internal dynamics "fingerprints" upon Zn binding, and DNA binding is weakly regulated. We demonstrate the predictive power of the wild-type dynamics fingerprint to identify key residues in dynamics-driven allostery. We propose that driving forces arising from dynamics can be harnessed by nature to evolve new allosteric ligand specificities in a compact molecular scaffold.
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