1
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Pizzi A, Dhaka A, Beccaria R, Resnati G. Anion⋯anion self-assembly under the control of σ- and π-hole bonds. Chem Soc Rev 2024; 53:6654-6674. [PMID: 38867604 DOI: 10.1039/d3cs00479a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The electrostatic attraction between charges of opposite signs and the repulsion between charges of the same sign are ubiquitous and influential phenomena in recognition and self-assembly processes. However, it has been recently revealed that specific attractive forces between ions with the same sign are relatively common. These forces can be strong enough to overcome the Coulomb repulsion between ions with the same sign, leading to the formation of stable anion⋯anion and cation⋯cation adducts. Hydroden bonds (HBs) are probably the best-known interaction that can effectively direct these counterintuitive assembly processes. In this review we discuss how σ-hole and π-hole bonds can break the paradigm of electrostatic repulsion between like-charges and effectively drive the self-assembly of anions into discrete as well as one-, two-, or three-dimensional adducts. σ-Hole and π-hole bonds are the attractive forces between regions of excess electron density in molecular entities (e.g., lone pairs or π bond orbitals) and regions of depleted electron density that are localized at the outer surface of bonded atoms opposite to the σ covalent bonds formed by atoms (σ-holes) and above and below the planar portions of molecular entities (π-holes). σ- and π-holes can be present on many different elements of the p and d block of the periodic table and the self-assembly processes driven by their presence can thus involve a wide diversity of mono- and di-anions. The formed homomeric and heteromeric adducts are typically stable in the solid phase and in polar solvents but metastable or unstable in the gas phase. The pivotal role of σ- and π-hole bonds in controlling anion⋯anion self-assembly is described in key biopharmacological systems and in molecular materials endowed with useful functional properties.
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Affiliation(s)
- Andrea Pizzi
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Arun Dhaka
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Roberta Beccaria
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Giuseppe Resnati
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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2
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Saura MLP, Cajachagua CL, Balan A, General IJ. Phosphate uptake in PhoX: Molecular mechanisms. Int J Biol Macromol 2024; 269:131993. [PMID: 38705335 DOI: 10.1016/j.ijbiomac.2024.131993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
PhoX is a high-affinity phosphate binding protein, present in Xanthomonas citri, a phytopathogen responsible for the citrus canker disease. Performing molecular dynamics simulations and different types of computational analyses, we study the molecular mechanisms at play in relation to phosphate binding, revealing the global functioning of the protein: PhoX naturally oscillates along its global normal modes, which allow it to explore both bound and unbound conformations, eventually attracting a nearby negative phosphate ion to the highly positive electrostatic potential on its surface, particularly close to the binding pocket. There, several hydrogen bonds are formed with the two main domains of the structure. Phosphate creates, in this way, a strong bridge that connects the domains, keeping itself between them, in a tight closed conformation, explaining its high binding affinity.
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Affiliation(s)
- María Luz Perez Saura
- School of Science and Technology, Universidad Nacional de San Martin, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina
| | - Cindy Lee Cajachagua
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Andrea Balan
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Ignacio J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina.
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3
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Fowler W, Deng C, Teodoro OT, de Pablo JJ, Tirrell MV. Synthetic and Computational Design Insights toward Mimicking Protein Binding of Phosphate. Bioconjug Chem 2024; 35:300-311. [PMID: 38377539 PMCID: PMC10962344 DOI: 10.1021/acs.bioconjchem.3c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
The unique and precise capabilities of proteins are renowned for their specificity and range of application. Effective mimicking of protein-binding offers enticing potential to direct their abilities toward useful applications, but it is nevertheless quite difficult to realize this characteristic of protein behavior in a synthetic material. Here, we design, synthesize, and evaluate experimentally and computationally a series of multicomponent phosphate-binding peptide amphiphile micelles to derive design insights into how protein binding behavior translates to synthetic materials. By inserting the Walker A P-loop binding motif into this peptide synthetic material, we successfully implemented the protein-binding design parameters of hydrogen-bonding and electrostatic interaction to bind phosphate completely and selectively in this highly tunable synthetic platform. Moreover, in this densely arrayed peptide environment, we use molecular dynamics simulations to identify an intriguing mechanistic shift of binding that is inaccessible in traditional proteins, introducing two corresponding new design elements─flexibility and minimization of the loss of entropy due to ion binding, in protein-analogous synthetic materials. We then translate these new design factors to de novo peptide sequences that bind phosphate independent of protein-extracted sequence or conformation. Overall, this work reveals that traditional complex conformational restrictions of binding by proteins can be replaced and repurposed in a multicomponent peptide amphiphile synthetic material, opening up opportunities for future enhanced protein-inspired design.
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Affiliation(s)
- Whitney
C. Fowler
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Chuting Deng
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - O. Therese Teodoro
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Juan J. de Pablo
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Matthew V. Tirrell
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Argonne
National Laboratory, Lemont, Illinois 60439, United States
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4
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Jing L, Deplazes E, Clegg JK, Wu X. A charge-neutral organic cage selectively binds strongly hydrated sulfate anions in water. Nat Chem 2024; 16:335-342. [PMID: 38351381 DOI: 10.1038/s41557-024-01457-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
In biological systems, enzymes and transport proteins can bind anions in aqueous media solely by forming hydrogen bonds with charge-neutral motifs. Reproducing this functionality in synthetic systems presents challenges and incurs high costs, particularly when targeting strongly hydrated anions such as sulfate. Here we report a [2.2.2]urea cryptand (cage), synthesized in one pot, that selectively binds sulfate in a mixture of dimethyl sulfoxide and water and in water with affinities in the micromolar to millimolar range. The neutral cage bearing six urea groups donates 12 strong hydrogen bonds to encapsulate a sulfate anion, showing favourable enthalpy even in pure water. Sulfate binding can be further enhanced by using micelles to provide a low-polarity microenvironment. The cage finds utility in analysing divalent anions in water and beverage samples or in removing sulfate. The work demonstrates the achievability of robust and selective anion binding in water with minimal synthetic efforts, by using neutral NH hydrogen bonds akin to those found in biology.
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Affiliation(s)
- Liuyang Jing
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Xin Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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5
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Ranjit P, Varkey D, Shah BS, Paulsen IT. Substrate specificity and ecological significance of PstS homologs in phosphorus uptake in marine Synechococcus sp. WH8102. Microbiol Spectr 2024; 12:e0278623. [PMID: 38179917 PMCID: PMC10846223 DOI: 10.1128/spectrum.02786-23] [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: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Phosphorus, a vital macronutrient, often limits primary productivity in marine environments. Marine Synechococcus strains, including WH8102, rely on high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate in oligotrophic oceans. However, WH8102 possesses three distinct PstS homologs whose substrate specificity and ecological roles are unclear. The three PstS homologs were heterologously expressed and purified to investigate their substrate specificity and binding kinetics. Our study revealed that all three PstS homologs exhibited a high degree of specificity for phosphate but differed in phosphate binding affinities. Notably, PstS1b displayed nearly 10-fold higher binding affinity (KD = 0.44 µM) compared to PstS1a (KD = 3.3 μM) and PstS2 (KD = 4.3 μM). Structural modeling suggested a single amino acid variation in the binding pocket of PstS1b (threonine instead of serine in PstS1a and PstS2) likely contributed to its higher Pi affinity. Genome context data, together with the protein biophysical data, suggest distinct ecological roles for the three PstS homologs. We propose that PstS1b may be involved in scavenging inorganic phosphorus in oligotrophic conditions and that PstS1a may be involved in transporting recycled phosphate derived from organic phosphate cleavage. The role of PstS2 is less clear, but it may be involved in phosphate uptake when environmental phosphate concentrations are transiently higher. The conservation of three distinct PstS homologs in Synechococcus clade III strains likely reflects distinct adaptations for P acquisition under varying oligotrophic conditions.IMPORTANCEPhosphorus is an essential macronutrient that plays a key role in marine primary productivity and biogeochemistry. However, intense competition for bioavailable phosphorus in the marine environment limits growth and productivity of ecologically important cyanobacteria. In oligotrophic oceans, marine Synechococcus strains, like WH8102, utilize high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate. However, WH8102 possesses three distinct PstS homologs, with unclear substrate specificity and ecological roles, creating a knowledge gap in understanding phosphorus acquisition mechanisms in picocyanobacteria. Through genomic, functional, biophysical, and structural analysis, our study unravels the ecological functions of these homologs. Our findings enhance our understanding of cyanobacterial nutritional uptake strategies and shed light on the crucial role of these conserved nutrient uptake systems in adaptation to specific niches, which ultimately underpins the success of marine Synechococcus across a diverse array of marine ecosystems.
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Affiliation(s)
- Pramita Ranjit
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Bhumika S. Shah
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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6
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Hutchison JM, Hussein FB, Mayer BK. Evaluating Sustainable Development Pathways for Protein- and Peptide-Based Bioadsorbents for Phosphorus Recovery from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16317-16326. [PMID: 37856833 PMCID: PMC10620995 DOI: 10.1021/acs.est.3c04016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023]
Abstract
Recovering phosphate (P) from point sources such as wastewater effluent is a priority in order to alleviate the impacts of eutrophication and implement a circular economy for an increasingly limited resource. Bioadsorbents featuring P-binding proteins and peptides offer exquisite P specificity and sensitivity for achieving ultralow P concentrations, i.e., <100 μg P L-1, a discharge limit that has been implemented in at least one treatment facility in nine U.S. states. To prioritize research objectives for P recovery in wastewater treatment, we compared the financial and environmental sustainability of protein/peptide bioadsorbents to those of LayneRT anion exchange resin. The baseline scenario (reflecting lab-demonstrated performance at a full-scale implementation) had costs that were 3 orders of magnitude higher than those for typical wastewater treatment. However, scenarios exploring bioadsorbent improvements, including increasing the P-binding capacity per unit volume by using smaller P-selective peptides and nanoparticle base materials and implementing reuse, dramatically decreased median impacts to $1.06 m-3 and 0.001 kg CO2 equiv m-3; these values are in line with current wastewater treatment impacts and lower than the median LayneRT impacts of $4.04 m-3 and 0.19 kg CO2 equiv m-3. While the financial viability of capturing low P concentrations is a challenge, incorporating the externalities of environmental impacts may provide a feasible path forward to motivate ultralow P capture.
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Affiliation(s)
- Justin M. Hutchison
- Department
of Civil, Environmental and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, Kansas 66045, United States
| | - Faten B. Hussein
- Department
of Civil, Construction and Environmental Engineering, Marquette University, 1637 W Wisconsin Ave, Milwaukee, Wisconsin 53233, United States
| | - Brooke K. Mayer
- Department
of Civil, Construction and Environmental Engineering, Marquette University, 1637 W Wisconsin Ave, Milwaukee, Wisconsin 53233, United States
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7
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Sun ZY, Chen SQ, Liang L, Zhao W, Yang XJ, Wu B. pH-Dependent phosphate separation using a tripodal hexaurea receptor. Chem Commun (Camb) 2023; 59:12923-12926. [PMID: 37823279 DOI: 10.1039/d3cc04122k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
We demonstrate that a tripodal hexaurea receptor can selectively bind PO43- anions via 12 hydrogen bonds with up to 3.8 × 106 M-1 binding affinity in DMSO, which is 38-fold stronger than SO42-. This receptor facilitates the extraction of PO43- from strongly basic aqueous solutions into chloroform using liquid-liquid extraction, followed by its release as the H2PO4- anion into an acidic solution. This pH-dependent phosphate extraction successfully enables selective separation of phosphate and sulfate anions.
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Affiliation(s)
- Zhong-Yu Sun
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
| | - Si-Qi Chen
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
| | - Lin Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
| | - Xiao-Juan Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
| | - Biao Wu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China.
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8
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Bains RK, Nasseri SA, Liu F, Wardman JF, Rahfeld P, Withers SG. Characterization of a new family of 6-sulfo-N-acetylglucosaminidases. J Biol Chem 2023; 299:105214. [PMID: 37660924 PMCID: PMC10570127 DOI: 10.1016/j.jbc.2023.105214] [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: 06/15/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Sulfation is widespread in nature and plays an important role in modulating biological function. Among the strategies developed by microbes to access sulfated oligosaccharides as a nutrient source is the production of 6-sulfoGlcNAcases to selectively release 6-sulfoGlcNAc from target oligosaccharides. Thus far, all 6-sulfoGlcNAcases identified have belonged to the large GH20 family of β-hexosaminidases. Ηere, we identify and characterize a new, highly specific non-GH20 6-sulfoGlcNAcase from Streptococcus pneumoniae TIGR4, Sp_0475 with a greater than 110,000-fold preference toward N-acetyl-β-D-glucosamine-6-sulfate substrates over the nonsulfated version. Sp_0475 shares distant sequence homology with enzymes of GH20 and with the newly formed GH163 family. However, the sequence similarity between them is sufficiently low that Sp_0475 has been assigned as the founding member of a new glycoside hydrolase family, GH185. By combining results from site-directed mutagenesis with mechanistic studies and bioinformatics we provide insight into the substrate specificity, mechanism, and key active site residues of Sp_0475. Enzymes of the GH185 family follow a substrate-assisted mechanism, consistent with their distant homology to the GH20 family, but the catalytic residues involved are quite different. Taken together, our results highlight in more detail how microbes can degrade sulfated oligosaccharides for nutrients.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seyed A Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob F Wardman
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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9
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Shah BS, Ford BA, Varkey D, Mikolajek H, Orr C, Mykhaylyk V, Owens RJ, Paulsen IT. Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter. THE ISME JOURNAL 2023:10.1038/s41396-023-01417-w. [PMID: 37087502 DOI: 10.1038/s41396-023-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Despite being fundamental to multiple biological processes, phosphorus (P) availability in marine environments is often growth-limiting, with generally low surface concentrations. Picocyanobacteria strains encode a putative ABC-type phosphite/phosphate/phosphonate transporter, phnDCE, thought to provide access to an alternative phosphorus pool. This, however, is paradoxical given most picocyanobacterial strains lack known phosphite degradation or carbon-phosphate lyase pathway to utilise alternate phosphorus pools. To understand the function of the PhnDCE transport system and its ecological consequences, we characterised the PhnD1 binding proteins from four distinct marine Synechococcus isolates (CC9311, CC9605, MITS9220, and WH8102). We show the Synechococcus PhnD1 proteins selectively bind phosphorus compounds with a stronger affinity for phosphite than for phosphate or methyl phosphonate. However, based on our comprehensive ligand screening and growth experiments showing Synechococcus strains WH8102 and MITS9220 cannot utilise phosphite or methylphosphonate as a sole phosphorus source, we hypothesise that the picocyanobacterial PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter, and the measured affinity of PhnD1 to phosphite or methyl phosphonate is fortuitous. Our MITS9220_PhnD1 structure explains the comparatively lower affinity of picocyanobacterial PhnD1 for phosphate, resulting from a more limited H-bond network. We propose two possible physiological roles for PhnD1. First, it could function in phospholipid recycling, working together with the predicted phospholipase, TesA, and alkaline phosphatase. Second, by having multiple transporters for P (PhnDCE and Pst), picocyanobacteria could balance the need for rapid transport during transient episodes of higher P availability in the environment, with the need for efficient P utilisation in typical phosphate-deplete conditions.
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Affiliation(s)
- Bhumika S Shah
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
| | - Benjamin A Ford
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Halina Mikolajek
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Christian Orr
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Structural Biology, Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
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10
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Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
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Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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11
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Yu J, Zhang Y, Zhao Y, Zhang X, Ren H. Highly Sensitive and Selective Detection of Inorganic Phosphates in the Water Environment by Biosensors Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2023; 95:4904-4913. [PMID: 36942460 DOI: 10.1021/acs.analchem.2c04748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The accurate detection of phosphate in water is very important to prevent water eutrophication and ensure the health of water quality. However, traditional phosphomolybdenum blue spectrophotometry is not sensitive, is time-consuming, and demands large amounts of chemical reagents. Therefore, highly sensitive, rapid, and environmentally friendly Pi detection methods are urgently needed. Here, we developed a bioluminescence resonance energy transfer (BRET)-based biosensor, which can detect Pi in water quickly, highly sensitively, and highly selectively. The NanoLuc and the Venus fluorescent protein were selected as the bioluminescence donor and energy acceptor, respectively. The best-performing BRET sensor variant, VenusΔC10-PΔC12-ΔN4Nluc, was identified by Pi-specific binding protein (PiBP) screening and systematic truncation. Single-factor experiments optimized the key parameters affecting the detection performance of the sensor. Under the optimal detection conditions, the detection limit of this method was 1.3 μg·L-1, the detection range was 3.3-434 μg·L-1, and it had excellent selectivity, repeatability, and stability. This low-cost and environment-friendly BRET sensor showed a good application prospect in real water quality detection.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yanping Zhao
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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12
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Alexander C, Thom JA, Kenwright AM, Christensen KE, Sørensen TJ, Faulkner S. Chelating chloride using binuclear lanthanide complexes in water. Chem Sci 2023; 14:1194-1204. [PMID: 36756316 PMCID: PMC9891377 DOI: 10.1039/d2sc05417e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/27/2022] [Indexed: 12/28/2022] Open
Abstract
Halide recognition by supramolecular receptors and coordination complexes in water is a long-standing challenge. In this work, we report chloride binding in water and in competing media by pre-organised binuclear kinetically inert lanthanide complexes, bridged by flexible -(CH2)2- and -(CH2)3- spacers, forming [Ln2(DO3A)2C-2] and [Ln2(DO3A)2C-3], respectively. These hydrophilic, neutral lanthanide coordination complexes are shown to bind chloride with apparent association constants of up to 105 M-1 in water and in buffered systems. Hydroxide bridging was observed in these complexes at basic pH, which was proven to be overcome by chloride. Thus, these lanthanide complexes show promise towards chloride recognition in biology and beyond. The results described here have clearly identified a new area of anion coordination chemistry that is ripe for detailed exploration.
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Affiliation(s)
- Carlson Alexander
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - James A Thom
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Alan M Kenwright
- Department of Chemistry, University of Durham South Road Durham DH1 3LE UK
| | - Kirsten E Christensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Thomas Just Sørensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
- Nano-Science Centre and Department of Chemistry, University of Copenhagen 2100 København Ø Denmark
| | - Stephen Faulkner
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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13
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Mallick SP, Hussein FB, Husted S, Mayer BK. Adsorption of recalcitrant phosphorus compounds using the phosphate-selective binding-protein PstS. CHEMOSPHERE 2022; 304:135311. [PMID: 35709849 DOI: 10.1016/j.chemosphere.2022.135311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Currently available wastewater phosphorus (P) treatment technologies target removal of reactive forms of P. Selective adsorption of more recalcitrant soluble non-reactive phosphorus (sNRP) can improve P removal and recovery. A phosphate-selective phosphate-binding protein (PBP), PstS, was immobilized onto NHS-activated beads to assess the ability of this novel bioadsorbent to remove (adsorb) and subsequently recover (desorb) a range of sNRP compounds. Four sNRP compounds representative of wastewater sNRP were selected for use in this study: phytic acid (PA), sodium triphosphate (TrP), beta-glycerol phosphate (BGP), and sodium hexametaphosphate (HMP). Using PBP, adsorption of all sNRP compounds was thermodynamically favorable. The PBP had nearly equivalent binding affinity for PA compared to PBP's typical target, orthophosphate, although it had less affinity for the other sNRP compounds. Adsorption followed pseudo-second order reaction kinetics, with 95% of maximum adsorption occurring within 4 min. This was substantially faster sNRP adsorption compared to other adsorbents in the literature. Adsorption was modeled using the Langmuir isotherm, reflecting that one phosphate molecule attached to one PBP binding site. Notably, this selective 1:1 attachment resulted in higher total P removal for sNRP molecules with high P content. The binding site lost activity with increasing pH, and as such, highest desorption was achieved at pH 12, making the system amenable to sNRP removal as well as controlled recovery.
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Affiliation(s)
- Synthia P Mallick
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI, 53233, USA.
| | - Faten B Hussein
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI, 53233, USA.
| | - Shayla Husted
- Department of Biological Sciences, Marquette University, 1428 W. Clybourn St., Milwaukee, WI, 53233, USA.
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI, 53233, USA.
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14
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Zheng Y, Wan Y, Zhang Y, Huang J, Yang Y, Tsang DCW, Wang H, Chen H, Gao B. Recovery of phosphorus from wastewater: A review based on current phosphorous removal technologies. CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY 2022; 53:1148-1172. [PMID: 37090929 PMCID: PMC10116781 DOI: 10.1080/10643389.2022.2128194] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phosphorus (P) as an essential nutrient for life sustains the productivity of food systems; yet misdirected P often accumulates in wastewater and triggers water eutrophication if not properly treated. Although technologies have been developed to remove P, little attention has been paid to the recovery of P from wastewater. This work provides a comprehensive review of the state-of-the-art P removal technologies in the science of wastewater treatment. Our analyses focus on the mechanisms, removal efficiencies, and recovery potential of four typical water and wastewater treatment processes including precipitation, biological treatment, membrane separation, and adsorption. The design principles, feasibility, operation parameters, and pros & cons of these technologies are analyzed and compared. Perspectives and future research of P removal and recovery are also proposed in the context of paradigm shift to sustainable water treatment technology.
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Affiliation(s)
- Yulin Zheng
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
| | - Yongshan Wan
- National Health and Environmental Effects Research Laboratory, US EPA, Gulf Breeze, Florida, USA
| | - Yue Zhang
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
| | - Jinsheng Huang
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
| | - Yicheng Yang
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Hailong Wang
- School of Environmental and Chemical Engineering, Foshan University, Foshan, China
| | - Hao Chen
- Department of Agriculture, University of Arkansas at Pine Bluff, Pine Bluff, Arkansas, USA
| | - Bin Gao
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
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15
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Bio-Inspired phosphate adsorption by Copper-Decorated weak base anion exchanger. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Zeng J, Tu Q, Yu X, Qian L, Wang C, Shu L, Liu F, Liu S, Huang Z, He J, Yan Q, He Z. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. MICROBIOME 2022; 10:101. [PMID: 35787295 PMCID: PMC9252087 DOI: 10.1186/s40168-022-01292-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. RESULTS In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. CONCLUSIONS We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.
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Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Jianguo He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
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17
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Towards Anion Recognition and Precipitation with Water-Soluble 1,2,4-Selenodiazolium Salts: Combined Structural and Theoretical Study. Int J Mol Sci 2022; 23:ijms23126372. [PMID: 35742815 PMCID: PMC9224156 DOI: 10.3390/ijms23126372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
The synthesis and structural characterization of a series of supramolecular complexes of bicyclic cationic pyridine-fused 1,2,4-selenodiazoles with various anions is reported. The binding of trifluoroacetate, tetrachloroaurate, tetraphenylborate, perrhenate, and pertechnetate anions in the solid state is regarded. All the anions interact with selenodiazolium cations exclusively via a pair of “chelating” Se⋯O and H⋯O non-covalent interactions, which make them an attractive, novel, non-classical supramolecular recognition unit or a synthon. Trifluoroacetate salts were conveniently generated via novel oxidation reaction of 2,2′-dipyridyl diselenide with bis(trifluoroacetoxy)iodo)benzene in the presence of corresponding nitriles. Isolation and structural characterization of transient 2-pyridylselenyl trifluoroacetate was achieved. X-ray analysis has demonstrated that the latter forms dimers in the solid state featuring very short and strong Se⋯O and Se⋯N ChB contacts. 1,2,4-Selenodiazolium trifluoroacetates or halides show good solubility in water. In contrast, (AuCl4)−, (ReO4)−, or (TcO4)− derivatives immediately precipitate from aqueous solutions. Structural features of these supramolecular complexes in the solid state are discussed. The nature and energies of the non-covalent interactions in novel assembles were studied by the theoretical methods. To the best of our knowledge, this is the first study that regards perrhenate and pertechnetate as acceptors in ChB interactions. The results presented here will be useful for further developments in anion recognition and precipitation involving cationic 1,2,4-selenodiazoles.
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18
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Zhao F, Lin X, Cai K, Jiang Y, Ni T, Chen Y, Feng J, Dang S, Zhou CZ, Zeng Q. Biochemical and structural characterization of the cyanophage-encoded phosphate binding protein: implications for enhanced phosphate uptake of infected cyanobacteria. Environ Microbiol 2022; 24:3037-3050. [PMID: 35590460 DOI: 10.1111/1462-2920.16043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 12/01/2022]
Abstract
To acquire phosphorus, cyanobacteria use the typical bacterial ABC-type phosphate transporter, which is composed of a periplasmic high-affinity phosphate-binding protein PstS and a channel formed by two transmembrane proteins PstC and PstA. A putative pstS gene was identified in the genomes of cyanophages that infect the unicellular marine cyanobacteria Prochlorococcus and Synechococcus. However, it has not been determined whether the cyanophage PstS protein is functional during infection to enhance the phosphate uptake rate of host cells. Here we showed that the cyanophage P-SSM2 PstS protein was abundant in the infected Prochlorococcus NATL2A cells and the host phosphate uptake rate was enhanced after infection. This is consistent with our biochemical and structural analyses showing that the phage PstS protein is indeed a high-affinity phosphate-binding protein. We further modeled the complex structure of phage PstS with host PstCA and revealed three putative interfaces that may facilitate the formation of a chimeric ABC transporter. Our results provide insights into the molecular mechanism by which cyanophages enhance the phosphate uptake rate of cyanobacteria. Phosphate acquisition by infected bacteria can increase the phosphorus contents of released cellular debris and virus particles, which together constitute a significant proportion of the marine dissolved organic phosphorus pool. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fangxin Zhao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xingqin Lin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Kun Cai
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - YongLiang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Tianchi Ni
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yue Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianrong Feng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shangyu Dang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China
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19
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Hussein FB, Mayer BK. Fixed-bed column study of phosphate adsorption using immobilized phosphate-binding protein. CHEMOSPHERE 2022; 295:133908. [PMID: 35143858 DOI: 10.1016/j.chemosphere.2022.133908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Bio-adsorption using high-affinity phosphate-binding proteins (PBP) has demonstrated effective phosphorus removal and recovery in batch-scale tests. Subsequent optimization of design and performance of fixed-bed column systems is essential for scaling up and implementation. Here, continuous-flow fixed-bed column tests were used to investigate the adsorption of inorganic phosphate (orthophosphate, Pi) using phosphate-binding proteins immobilized on resin (PBP-NHS) targeting Pi removal to ultra-low levels followed by recovery. Time to breakthrough decreased with higher influent Pi concentration, smaller bed volume, and higher influent flow rates. The Thomas and Yoon-Nelson breakthrough models adequately described PBP-NHS resin performance with a correlation coefficient of R2 > 0.95. The sharp S-shape of the breakthrough curves for both Pi-only solution and multi-ion solution indicated highly favorable and selective separation of Pi using PBP-NHS resin, beyond that achieved using LayneRT™, a commercial ion exchange resin. The Pi adsorption capacity of the PBP-NHS column was unaffected by competing anions, whereas capacity of the LayneRT™ column dropped by 20%. Tertiary wastewater effluent was also successfully treated in PBP-NHS column tests with a typical S-shaped breakthrough curve. Operating the fixed-bed column in multi-cycle mode evidenced the reusability of PBP-NHS resin with no significant decline in column performance. The results of this study contribute to efforts to scale up designs of PBP-NHS adsorption systems.
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Affiliation(s)
- Faten B Hussein
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W Wisconsin Ave, Milwaukee, WI, 53233, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W Wisconsin Ave, Milwaukee, WI, 53233, USA.
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20
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Niedbała P, Ceborska M, Mehmet M, Ignacak W, Jurczak J, Dąbrowa K. Anion Recognition by a Pincer-Type Host Constructed from Two Polyamide Macrocyclic Frameworks Jointed by a Photo-Addressable Azobenzene Switch. MATERIALS (BASEL, SWITZERLAND) 2022; 15:692. [PMID: 35057408 PMCID: PMC8777895 DOI: 10.3390/ma15020692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/10/2022]
Abstract
A sterically crowded light-responsive host 1 was synthetized with a 93% yield by applying a post-functionalization protocol utilizing the double amidation of 4,4'-azodibenzoyl dichloride with a readily available 26-membered macrocyclic amine. X-ray structures of two hydrates of trans-1 demonstrate a very different alignment of the azobenzene linkage, which is involved in T-shape or parallel-displaced π⋯π stacking interactions with the pyridine-2,6-dicarboxamide moieties from the macrocyclic backbone. Despite the rigidity of the macrocyclic framework, which generates a large steric hindrance around the azobenzene chromophore, the host 1 retains the ability to undergo a reversible cis⟷trans isomerization upon irradiation with UVA (368 nm) and blue (410 nm) light. Moreover, thermal cis→trans back-isomerization (ΔG0 = 106.5 kJ∙mol-1, t½ = 141 h) is markedly slowed down as compared to the non-macrocyclic analog. 1H NMR titration experiments in DMSO-d6/0.5% water solution reveal that trans-1 exhibits a strong preference for dihydrogenphosphate (H2PO4-) over other anions (Cl-, MeCO2-, and PhCO2-), whereas the photogenerated metastable cis-1 shows lower affinity for the H2PO4- anion.
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Affiliation(s)
- Patryk Niedbała
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Magdalena Ceborska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Mart Mehmet
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Wiktor Ignacak
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Janusz Jurczak
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Kajetan Dąbrowa
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
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21
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Isophthalamide bearing 1-pyrenylethynyl group as a highly fluorescent hydrogen bond motif for anion receptors. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Venkiteshwaran K, Wells E, Mayer BK. Immobilized phosphate-binding protein can effectively discriminate against arsenate during phosphate adsorption and recovery. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1173-1178. [PMID: 33316118 DOI: 10.1002/wer.1498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/23/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
There is a strong impetus to establish a circular phosphorus economy by securing internally renewable phosphate (Pi ) resources for use as agricultural fertilizers. Reversible Pi adsorption technologies such as ion exchange can remove and recover Pi from water/wastewater for reuse. However, existing reversible adsorbents cannot effectively discriminate against arsenate (As(V)) due to the similarity between As(V) and Pi chemical structure. If As(V) is co-recovered with Pi , the value of the recovered products for agricultural reuse is low. The objective of this study was to construct an immobilized phosphate-binding protein (PBP)-based Pi removal and recovery system and analyze its selectivity for Pi adsorption in the presence of As(V). A range of conditions was tested, including independent, sequential, and simultaneous exposure of the two oxyanions to immobilized PBP (PBP resin). The purity of the recovered Pi product was assessed after inducing controlled desorption of the adsorbed oxyanions at high pH (pH 12.5). Pi constituted more than 97% of the adsorbed oxyanions in the recovered product, even when As(V) was initially present at twofold higher concentrations than Pi . Therefore, PBP resin has potential to selectively remove Pi , as well as release high-purity Pi free of As(V) contamination suitable for subsequent agricultural reuse. PRACTITIONER POINTS: Existing reversible phosphate (Pi ) adsorbents cannot effectively discriminate against arsenate (As(V)) due to the similarity in their chemical structure. Co-recovery of As(V) with Pi can reduce the recovered product's reuse as a fertilizer. An immobilized phosphate-binding protein (PBP)-based system can be highly selective for Pi even in the presence of As(V). Pi constituted more than 97% of the recovered product, even when As(V) was present at 2-fold higher concentrations than Pi . Immobilized PBP offers advantages over existing Pi adsorbents by providing high-purity Pi products free of As(V) contamination for reuse.
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Affiliation(s)
- Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | - Erin Wells
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
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24
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Liu Y, Parks FC, Sheetz EG, Chen CH, Flood AH. Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion. J Am Chem Soc 2021; 143:3191-3204. [PMID: 33596052 DOI: 10.1021/jacs.0c12562] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Persistent anion binding in a wide range of solution environments is a key challenge that continues to motivate and demand new strategies in synthetic receptor design. Though strong binding in low-polarity solvents has become routine, our ability to maintain high affinities in high-polarity solvents has not yet reached the standard set by nature. Anions are bound and transported regularly in aqueous environments by proteins that use secondary and tertiary structure to isolate anion binding sites from water. Inspired by this principle of solvent exclusion, we created a sequence-defined foldameric capsule whose global minimum conformation displays a helical folded state and is preorganized for 1:1 anion complexation. The high stability of the folded geometry and its ability to exclude solvent were supported by solid-state and solution phase studies. This capsule then withstood a 4-fold increase in solvent dielectric constant (εr) from dichloromethane (9) to acetonitrile (36) while maintaining a high and solvent-independent affinity of 105 M-1; ΔG ∼ 28 kJ mol-1. This behavior is unusual. More typical of solvent-dependent behavior, Cl- affinities were seen to plummet in control compounds, such as aryl-triazole macrocycles and pentads, with their solvent-exposed binding cavities susceptible to dielectric screening. Finally, dimethyl sulfoxide denatures the foldamer by putative solvent binding, which then lowers the foldamer's Cl- affinity to normal levels. The design of this capsule demonstrates a new prototype for the development of potent receptors that can operate in polar solvents and has the potential to help manage hydrophilic anions present in the hydrosphere and biosphere.
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Affiliation(s)
- Yun Liu
- Department of Chemistry, Indiana University 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Fred C Parks
- Department of Chemistry, Indiana University 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Edward G Sheetz
- Department of Chemistry, Indiana University 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Chun-Hsing Chen
- Department of Chemistry, Indiana University 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Amar H Flood
- Department of Chemistry, Indiana University 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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25
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Tobolska A, Wezynfeld NE, Wawrzyniak UE, Bal W, Wróblewski W. Copper(ii) complex of N-truncated amyloid-β peptide bearing a His-2 motif as a potential receptor for phosphate anions. Dalton Trans 2021; 50:2726-2730. [PMID: 33576751 DOI: 10.1039/d0dt03898a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electrochemical and spectroscopic studies demonstrated that the N-truncated amyloid β peptide Aβ5-9 (Arg-His-Asp-Ser-Gly-NH2) possessing histidine at position 2 (His-2) formed ternary complexes with copper(ii) and phosphate anions or phosphate groups of biomolecules. The recognition ability of Cu(ii)-Aβ5-9 toward phosphate species provided a new perspective on designing phosphate-selective molecular receptors.
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Affiliation(s)
- Aleksandra Tobolska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
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Porzio E, Faraone Mennella MR, Manco G. DING Proteins Extend to the Extremophilic World. Int J Mol Sci 2021; 22:2035. [PMID: 33670786 PMCID: PMC7922408 DOI: 10.3390/ijms22042035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/16/2022] Open
Abstract
The DING proteins are ubiquitous in the three domains of life, from mesophiles to thermo- and hyperthermophiles. They belong to a family of more than sixty members and have a characteristic N-terminus, DINGGG, which is considered a "signature" of these proteins. Structurally, they share a highly conserved phosphate binding site, and a three dimensional organization resembling the "Venus Flytrap", both reminding the ones of PstS proteins. They have unusually high sequence conservation, even between distantly related species. Nevertheless despite that the genomes of most of these species have been sequenced, the DING gene has not been reported for all the relative characterized DING proteins. Identity of known DING proteins has been confirmed immunologically and, in some cases, by N-terminal sequence analysis. Only a few of the DING proteins have been purified and biochemically characterized. DING proteins are heterogeneous for their wide range of biological activities and some show different activities not always correlated with each other. Most of them have been originally identified for different biological properties, or rather for binding to phosphate and also to other ligands. Their involvement in pathologies is described. This review is an update of the most recent findings on old and new DING proteins.
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Affiliation(s)
- Elena Porzio
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy;
| | | | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy;
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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Shi H, Hou J, Jiang P, Yang Q, Lin Q, Wei T, Yao H, Zhang Y, Wu S. A Novel Imidazophenazine-Based Stimuli Responsive Chemosensor for Highly Selective and Sensitive Fluorescence Detection of CN–. Aust J Chem 2021. [DOI: 10.1071/ch20299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A fluorescent imidazophenazine-based derivative (S) has been successfully synthesised, and can be used as a chemsensor for relay recognition of CN– in DMSO/H2O (7:3, v/v) solution, which exhibited external stimuli-responsiveness. The sensor immediately responded with obvious colour changes (from red to purple) and fluorescent quenching when CN– was added to the S solution. Its detection limit for CN– is 2.16×10−7 M. In addition, NMR spectroscopy and density function theory calculations were also used to confirm the recognition mechanism. In particular, the fluorescence responding circle could be repeated three times by the sequential addition of CN– and CH3COO– or CN– and HSO4–. Moreover, a CN– detection test paper was prepared using S, providing a convenient method for CN– identification.
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Nord E, Zhou H, Rayat S. Interaction of aryl tetrazolones with anions: proton transfer vs. hydrogen bonding. NEW J CHEM 2021. [DOI: 10.1039/d1nj02647j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tetrazolones 1a,b interact with HSO4−, Br−, NO3−, NCS− and Cl− through H-bonding, but undergo deprotonation with a more basic AcO− anion.
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Affiliation(s)
- Erika Nord
- Department of Chemistry
- Foundational Sciences Building
- Ball State University
- Muncie
- USA
| | - Hanyang Zhou
- Department of Chemistry
- Foundational Sciences Building
- Ball State University
- Muncie
- USA
| | - Sundeep Rayat
- Department of Chemistry
- Foundational Sciences Building
- Ball State University
- Muncie
- USA
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Dąbrowa K, Niedbała P, Pawlak M, Lindner M, Ignacak W, Jurczak J. Tuning Anion-Binding Properties of 22-Membered Unclosed Cryptands by Structural Modification of the Lariat Arm. ACS OMEGA 2020; 5:29601-29608. [PMID: 33225192 PMCID: PMC7676298 DOI: 10.1021/acsomega.0c04660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/21/2020] [Indexed: 05/03/2023]
Abstract
A series of 22-membered unclosed cryptands end-capped with intra-annular methyl (1), phenyl (2), p-tert-butylphenyl (3), and p-nitrophenyl (4) amide substituents (lariat arm) were synthesized to elucidate the effect of steric and electronic factors on their anion recognition behavior. The 1H NMR titrations in DMSO-d 6 with 0.5% water reveal enhanced selectivity for H2PO4 - vs Cl- and PhCO2 -. The para-attachment of the electron-withdrawing nitro group (-NO2 vs -H and -t-Bu) was found to increase anion-binding affinity, whereas the steric bulkiness of lariat arm (methyl vs aryl) has a marginal effect. DFT calculations reveal that binding of H2PO4 - is associated with minimal conformational change in the lariat arm moiety and involve four hydrogen bond acceptor and one donor sites of host.
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Wang H, Fang S, Wu G, Lei Y, Chen Q, Wang H, Wu Y, Lin C, Hong X, Kim SK, Sessler JL, Li H. Constraining Homo- and Heteroanion Dimers in Ultraclose Proximity within a Self-Assembled Hexacationic Cage. J Am Chem Soc 2020; 142:20182-20190. [DOI: 10.1021/jacs.0c10253] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hongye Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Shuai Fang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Guangcheng Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Ye Lei
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Qiong Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Hongliang Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yating Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Chuhao Lin
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Xin Hong
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Sung Kuk Kim
- Department of Chemistry, Research Institute of Natural Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Jonathan L. Sessler
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street-A5300, Austin, Texas 78712-1224 United States
| | - Hao Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO. Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships. mSystems 2020; 5:e00980-20. [PMID: 33172971 PMCID: PMC7657598 DOI: 10.1128/msystems.00980-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/20/2020] [Indexed: 11/27/2022] Open
Abstract
Escherichia coli uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli's global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded.IMPORTANCE E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli's two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in E. coli and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.
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Affiliation(s)
- Kumari Sonal Choudhary
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Julia A Kleinmanns
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Katherine Decker
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Ye Gao
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Venkiteshwaran K, Wells E, Mayer BK. Kinetics, Affinity, Thermodynamics, and Selectivity of Phosphate Removal Using Immobilized Phosphate-Binding Proteins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10885-10894. [PMID: 32786572 DOI: 10.1021/acs.est.0c02272] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A phosphate (Pi)-selective adsorption system featuring immobilized Pi-binding proteins (PBP) has recently attracted attention for ultralow Pi removal followed by recovery. This study investigated the adsorption kinetics, affinity, thermodynamics, and selectivity, as well as the effect of pH and temperature on Pi adsorption using immobilized PBP (PBP resin). Immobilizing PBP did not affect its Pi affinity. Kinetic studies at 22 °C and pH 7.1 showed that the PBP resin achieved 95% of its equilibrium capacity within 0.64 ± 0.2 min. The estimated Langmuir affinity constant (KL) was 21 ± 5 μM-1 Pi (220 ± 52 L/mg-Pi), which is higher than Pi adsorbents recently reported in literature. The ideal operating ranges for high-affinity Pi adsorption using PBP resin were pH 4.5 to 9 and temperature 14 to 37 °C. The Pi-PBP resin adsorption process was not affected by the presence of common anions (Cl-, Br-, NO2-, NO3-, SO42-, and HCO3-). Adsorption using the Pi-PBP resin was exothermic (ΔH = -6.3 ± 1.3 kJ/mol) and spontaneous (ΔG = -39.7 ± 0.1 to -43.2 ± 0.2 kJ/mol) between 14 and 43 °C. These results indicate that PBP resin's Pi adsorption rate and affinity surpass those of existing adsorbents. Future work to increase the PBP resin's adsorption capacity is important to its application as a viable Pi adsorbent.
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Affiliation(s)
- Kaushik Venkiteshwaran
- 1637 W. Wisconsin Ave. Department of Civil, Construction and Environmental Engineering Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Erin Wells
- 1637 W. Wisconsin Ave. Department of Civil, Construction and Environmental Engineering Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Brooke K Mayer
- 1637 W. Wisconsin Ave. Department of Civil, Construction and Environmental Engineering Marquette University, Milwaukee, Wisconsin 53233, United States
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34
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Zhao W, Flood AH, White NG. Recognition and applications of anion-anion dimers based on anti-electrostatic hydrogen bonds (AEHBs). Chem Soc Rev 2020; 49:7893-7906. [PMID: 32677649 DOI: 10.1039/d0cs00486c] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Based on Coulomb's Law alone, electrostatic repulsion between two anions is expected to prevent their dimerization. Contrary to that idea, this Tutorial Review will present evidence showing that anion-anion dimers of protic hydroxyanions can form readily, and describe conditions that facilitate their formation. From X-ray crystal structures, we learn that hydroxyanions dimerize and oligomerize by overcoming long-range electrostatic opposition. Common examples are hydroxyanions of phosphate, sulfate, and carbonate, often in partnership with charged and neutral receptors. Short-range hydrogen bonds between anionic donors and acceptors are defined as anti-electrostatic hydrogen bonds (AEHBs) with insight from theoretical studies. While anion dimers are difficult to identify unequivocally in solution, these solution dimers have recently been definitively identified. The development of the supramolecular chemistry of anion-anion dimers has led to applications in hierarchical assemblies, such as supramolecular polymers and hydrogen bonded organic frameworks.
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Affiliation(s)
- Wei Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA.
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35
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Hussein FB, Venkiteshwaran K, Mayer BK. Cell surface-expression of the phosphate-binding protein PstS: System development, characterization, and evaluation for phosphorus removal and recovery. J Environ Sci (China) 2020; 92:129-140. [PMID: 32430116 DOI: 10.1016/j.jes.2020.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
Simultaneous overabundance and scarcity of inorganic phosphate (Pi) is a critical issue driving the development of innovative water/wastewater treatment technologies that not only facilitate Pi removal to prevent eutrophication, but also recover Pi for agricultural reuse. Here, a cell-surface expressed high-affinity phosphate binding protein (PstS) system was developed, and its Pi capture and release potential was evaluated. E. coli was genetically modified to express PstS on its outer membrane using the ice nucleation protein (INP) as an anchoring motif. Verification of protein expression and localization were performed utilizing SDS-polyacrylamide gel electrophoresis (SDS-PAGE), western blot, and outer membrane separation analyses. Cell surface characterization was investigated through acid-base titration, X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FTIR). These tests provided information on the macromolecular structure and composition of the bacteria surface as well as the proton-exchange properties of the surface functional groups (i.e., pKa values). Phosphate desorption and adsorption batch experiments were conducted to evaluate the effects of temperature, pH, and ionic strength on phosphate capture and release. The PstS surface-displayed cells demonstrated greater potential to release and capture phosphate compared to non-modified cells. Higher temperatures up to 40°C, basic pH conditions (pH = 10.5), and higher ionic strength up to 1.0 mol/L KCl promoted 20%-50% higher phosphate release.
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Affiliation(s)
- Faten B Hussein
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, 53233, USA
| | - Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, 53233, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, 53233, USA.
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36
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Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent. Nat Commun 2020; 11:2642. [PMID: 32457313 PMCID: PMC7250820 DOI: 10.1038/s41467-020-16428-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria. The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.
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37
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Bąk KM, van Kolck B, Maslowska-Jarzyna K, Papadopoulou P, Kros A, Chmielewski MJ. Oxyanion transport across lipid bilayers: direct measurements in large and giant unilamellar vesicles. Chem Commun (Camb) 2020; 56:4910-4913. [PMID: 32238998 DOI: 10.1039/c9cc09888g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A simple di(thioamido)carbazole 1 serves as a potent multispecific transporter for various biologically relevant oxyanions, such as drugs, metabolites and model organic phosphate. The transport kinetics of a wide range of oxyanions can be easily quantified by a modified lucigenin assay in both large and giant unilamellar vesicles.
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Affiliation(s)
- Krzysztof M Bąk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Bartjan van Kolck
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Krystyna Maslowska-Jarzyna
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Panagiota Papadopoulou
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Alexander Kros
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Michał J Chmielewski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
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Mishra SK, Gao YG, Zou X, Stephenson DJ, Malinina L, Hinchcliffe EH, Chalfant CE, Brown RE. Emerging roles for human glycolipid transfer protein superfamily members in the regulation of autophagy, inflammation, and cell death. Prog Lipid Res 2020; 78:101031. [PMID: 32339554 DOI: 10.1016/j.plipres.2020.101031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
Glycolipid transfer proteins (GLTPs) were first identified over three decades ago as ~24kDa, soluble, amphitropic proteins that specifically accelerate the intermembrane transfer of glycolipids. Upon discovery that GLTPs use a unique, all-α-helical, two-layer 'sandwich' architecture (GLTP-fold) to bind glycosphingolipids (GSLs), a new protein superfamily was born. Structure/function studies have provided exquisite insights defining features responsible for lipid headgroup selectivity and hydrophobic 'pocket' adaptability for accommodating hydrocarbon chains of differing length and unsaturation. In humans, evolutionarily-modified GLTP-folds have been identified with altered sphingolipid specificity, e. g. ceramide-1-phosphate transfer protein (CPTP), phosphatidylinositol 4-phosphate adaptor protein-2 (FAPP2) which harbors a GLTP-domain and GLTPD2. Despite the wealth of structural data (>40 Protein Data Bank deposits), insights into the in vivo functional roles of GLTP superfamily members have emerged slowly. In this review, recent advances are presented and discussed implicating human GLTP superfamily members as important regulators of: i) pro-inflammatory eicosanoid production associated with Group-IV cytoplasmic phospholipase A2; ii) autophagy and inflammasome assembly that drive surveillance cell release of interleukin-1β and interleukin-18 inflammatory cytokines; iii) cell cycle arrest and necroptosis induction in certain colon cancer cell lines. The effects exerted by GLTP superfamily members appear linked to their ability to regulate sphingolipid homeostasis by acting in either transporter and/or sensor capacities. These timely findings are opening new avenues for future cross-disciplinary, translational medical research involving GLTP-fold proteins in human health and disease. Such avenues include targeted regulation of specific GLTP superfamily members to alter sphingolipid levels as a therapeutic means for combating viral infection, neurodegenerative conditions and circumventing chemo-resistance during cancer treatment.
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Affiliation(s)
- Shrawan K Mishra
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yong-Guang Gao
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Xianqiong Zou
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Daniel J Stephenson
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0614, USA; Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lucy Malinina
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | | | - Charles E Chalfant
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; Research Service, James A. Haley Veterans Hospital, Tampa, FL 33612, USA; The Moffitt Cancer Center, Tampa, FL 33620, USA
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39
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Abstract
Phosphorus is required for many biological molecules and essential functions, including DNA replication, transcription of RNA, protein translation, posttranslational modifications, and numerous facets of metabolism. In order to maintain the proper level of phosphate for these processes, many bacteria adapt to changes in environmental phosphate levels. The mechanisms for sensing phosphate levels and adapting to changes have been extensively studied for multiple organisms. The phosphate response of Escherichia coli alters the expression of numerous genes, many of which are involved in the acquisition and scavenging of phosphate more efficiently. This review shares findings on the mechanisms by which E. coli cells sense and respond to changes in environmental inorganic phosphate concentrations by reviewing the genes and proteins that regulate this response. The PhoR/PhoB two-component signal transduction system is central to this process and works in association with the high-affinity phosphate transporter encoded by the pstSCAB genes and the PhoU protein. Multiple models to explain how this process is regulated are discussed.
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Wu B, Wan J, Zhang Y, Pan B, Lo IMC. Selective Phosphate Removal from Water and Wastewater using Sorption: Process Fundamentals and Removal Mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:50-66. [PMID: 31804806 DOI: 10.1021/acs.est.9b05569] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Eutrophication of water bodies is a serious and widespread environmental problem. Achieving low levels of phosphate concentration to prevent eutrophication is one of the important goals of the wastewater engineering and surface water management. Meeting the increasingly stringent standards is feasible in using a phosphate-selective sorption system. This critical review discusses the most fundamental aspects of selective phosphate removal processes and highlights gains from the latest developments of phosphate-selective sorbents. Selective sorption of phosphate over other competing anions can be achieved based on their differences in acid-base properties, geometric shapes, and metal complexing abilities. Correspondingly, interaction mechanisms between the phosphate and sorbent are categorized as hydrogen bonding, shape complementarity, and inner-sphere complexation, and their representative sorbents are organic-functionalized materials, molecularly imprinted polymers, and metal-based materials, respectively. Dominating factors affecting the phosphate sorption performance of these sorbents are critically examined, along with a discussion of some overlooked facts regarding the development of high-performance sorbents for selective phosphate removal from water and wastewater.
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Affiliation(s)
- Baile Wu
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jun Wan
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanyang Zhang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Bingcai Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Irene M C Lo
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
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41
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Cho J, Verwilst P, Kang M, Pan JL, Sharma A, Hong CS, Kim JS, Kim S. Crown ether-appended calix[2]triazolium[2]arene as a macrocyclic receptor for the recognition of the H2PO4−anion. Chem Commun (Camb) 2020; 56:1038-1041. [DOI: 10.1039/c9cc08906c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the synthesis of a crown ether-appended calix[2]triazolium[2]arene receptor that shows excellent selectivity for H2PO4−and the binding ability and mode of the receptor to H2PO4−were demonstrated by1H NMR studies and DFT calculation.
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Affiliation(s)
- Jihee Cho
- College of Pharmacy
- Seoul National University
- Gwanak-gu
- Korea
| | | | | | - Jia-Lin Pan
- Department of Chemistry
- Korea University
- Korea
| | - Amit Sharma
- Department of Chemistry
- Korea University
- Korea
| | | | | | - Sanghee Kim
- College of Pharmacy
- Seoul National University
- Gwanak-gu
- Korea
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Huang SY, Qian M, Pierre VC. A Combination of Factors: Tuning the Affinity of Europium Receptors for Phosphate in Water. Inorg Chem 2019; 58:16087-16099. [PMID: 31738520 DOI: 10.1021/acs.inorgchem.9b02650] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although recognition of hard anions by hard metal ions is primarily achieved via direct coordination, electrostatic and hydrogen-bonding interactions also play essential roles in tuning the affinity of such supramolecular receptors for their target. In the case of EuIII hydroxypyridinone-based complexes, the addition of a single charged group (-NH3+, -CO2-, or -SO3-) or neutral hydrogen-bonding moiety (-OH) peripheral to the open coordination site substantially affects the affinity of the metal receptor for phosphate in water at neutral pH. A single primary ammonium increases the first association constant for phosphate in neutral water by 2 orders of magnitude over its neutral analogue. The addition of a peripheral alcohol group also increases the affinity of the receptor but to a lesser degree (21-fold). On the other hand, negatively charged complexes bearing either a carboxylate or sulfate moiety have negligible affinity for phosphate. Interestingly, the peripheral group also influences the stoichiometry of the lanthanide receptor for phosphate. While the complex bearing a -NH3+ group binds phosphate in a 1:2 ratio, those with -OH and H (control) both form 1:3 complexes. Although the positively charged EuIII-Lys-HOPO has the highest Ka1 for phosphate, a greater increase in luminescence intensity (36-fold) is observed with the neutral EuIII-Ser-HOPO complex. Notably, whereas the affinity of the EuIII complexes for phosphate is substantially influenced by the presence of a single charged group or hydrogen-bond donor, their selectivity for phosphate over competing anions remains unaffected by the addition of the peripheral groups.
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Affiliation(s)
- Sheng-Yin Huang
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
| | - Michelle Qian
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
| | - Valerie C Pierre
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
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Li W, Gong X, Fan X, Yin S, Su D, Zhang X, Yuan L. Recent advances in molecular fluorescent probes for organic phosphate biomolecules recognition. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.07.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Boer SA, Foyle EM, Thomas CM, White NG. Anion coordination chemistry using O-H groups. Chem Soc Rev 2019; 48:2596-2614. [PMID: 30860210 DOI: 10.1039/c8cs00828k] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review covers significant advances in the use of O-H groups in anion coordination chemistry. The review focuses on the use of these groups in synthetic anion receptors, as well as more recent developments in transport, self-assembly and catalysis.
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Affiliation(s)
- Stephanie A Boer
- Research School of Chemistry, The Australian National University, Canberra, Australia.
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Neal JF, Zhao W, Grooms AJ, Smeltzer MA, Shook BM, Flood AH, Allen HC. Interfacial Supramolecular Structures of Amphiphilic Receptors Drive Aqueous Phosphate Recognition. J Am Chem Soc 2019; 141:7876-7886. [DOI: 10.1021/jacs.9b02148] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jennifer F. Neal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander J. Grooms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Morgan A. Smeltzer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brittany M. Shook
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amar H. Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Heather C. Allen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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46
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Heeley DH, White HD, Taylor EW. Investigation into the mechanism of thin filament regulation by transient kinetics and equilibrium binding: Is there a conflict? J Gen Physiol 2019; 151:628-634. [PMID: 30824574 PMCID: PMC6504287 DOI: 10.1085/jgp.201812198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/23/2018] [Accepted: 02/07/2019] [Indexed: 11/22/2022] Open
Abstract
The authors examine the apparent discrepancies from studies aimed at understanding the mechanism of thin filament regulation. Striated muscle contraction occurs when myosin undergoes a lever-type structural change. This process (the power stroke) requires ATP and is governed by the thin filament, a complex of actin, tropomyosin, and troponin. The authors have used a fast-mixing instrument to investigate the mechanism of regulation. Such (pre–steady-state kinetic) experiments allow biochemical intermediates in a working actomyosin cycle to be monitored. The regulatory focal point is demonstrated to be the step that involves the departure of inorganic phosphate (i.e., AM-ADP-Pi → AM-ADP). This part of the cycle, which lies on the main kinetic pathway and coincides with the drive stroke, is maximally accelerated ∼100-fold by the combined association of ligands (Ca[II] and rigor myosin heads) with the thin filament. However, the observed ligand dependencies of the rates of Pi dissociation that are reported herein are at variance with predictions of models derived from experiments where ATP hydrolysis is not taking place (and myosin exists in a nonphysiological form). It is concluded that the principal influence of the thin filament is in setting the rate of Pi dissociation and that physiological levels of regulation are dependent upon the liganded state of the thin filament as well as the conformation of myosin.
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Affiliation(s)
- David H Heeley
- Department of Biochemistry, Memorial University, St. John's, Canada
| | - Howard D White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA
| | - Edwin W Taylor
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
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47
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Murota C, Fujiwara S, Tsujishita M, Urabe K, Takayanagi S, Aoki M, Umemura T, Eaton-Rye JJ, Pitt FD, Tsuzuki M. Hyper-resistance to arsenate in the cyanobacterium Synechocystis sp. PCC 6803 is influenced by the differential kinetics of its pst-ABC transporters and external phosphate concentration exposure. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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48
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Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI, Luthey-Schulten Z. Essential metabolism for a minimal cell. eLife 2019; 8:36842. [PMID: 30657448 PMCID: PMC6609329 DOI: 10.7554/elife.36842] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/17/2019] [Indexed: 11/29/2022] Open
Abstract
JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life. Using the vast amount of experimental information available on its precursor, Mycoplasma mycoides capri, we assembled a near-complete metabolic network with 98% of enzymatic reactions supported by annotation or experiment. The model agrees well with genome-scale in vivo transposon mutagenesis experiments, showing a Matthews correlation coefficient of 0.59. The genes in the reconstruction have a high in vivo essentiality or quasi-essentiality of 92% (68% essential), compared to 79% in silico essentiality. This coherent model of the minimal metabolism in JCVI-syn3A at the same time also points toward specific open questions regarding the minimal genome of JCVI-syn3A, which still contains many genes of generic or completely unclear function. In particular, the model, its comparison to in vivo essentiality and proteomics data yield specific hypotheses on gene functions and metabolic capabilities; and provide suggestions for several further gene removals. In this way, the model and its accompanying data guide future investigations of the minimal cell. Finally, the identification of 30 essential genes with unclear function will motivate the search for new biological mechanisms beyond metabolism. One way that researchers can test whether they understand a biological system is to see if they can accurately recreate it as a computer model. The more they learn about living things, the more the researchers can improve their models and the closer the models become to simulating the original. In this approach, it is best to start by trying to model a simple system. Biologists have previously succeeded in creating ‘minimal bacterial cells’. These synthetic cells contain fewer genes than almost all other living things and they are believed to be among the simplest possible forms of life that can grow on their own. The minimal cells can produce all the chemicals that they need to survive – in other words, they have a metabolism. Accurately recreating one of these cells in a computer is a key first step towards simulating a complete living system. Breuer et al. have developed a computer model to simulate the network of the biochemical reactions going on inside a minimal cell with just 493 genes. By altering the parameters of their model and comparing the results to experimental data, Breuer et al. explored the accuracy of their model. Overall, the model reproduces experimental results, but it is not yet perfect. The differences between the model and the experiments suggest new questions and tests that could advance our understanding of biology. In particular, Breuer et al. identified 30 genes that are essential for life in these cells but that currently have no known purpose. Continuing to develop and expand models like these to reproduce more complex living systems provides a tool to test current knowledge of biology. These models may become so advanced that they could predict how living things will respond to changing situations. This would allow scientists to test ideas sooner and make much faster progress in understanding life on Earth. Ultimately, these models could one day help to accelerate medical and industrial processes to save lives and enhance productivity.
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Affiliation(s)
- Marian Breuer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Tyler M Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | | | - Kim S Wise
- J Craig Venter Institute, La Jolla, United States
| | - Lijie Sun
- J Craig Venter Institute, La Jolla, United States
| | | | | | | | - John D Lapek
- Department of Pharmacology and School of Pharmacy, University of California at San Diego, La Jolla, United States
| | - David J Gonzalez
- Department of Pharmacology and School of Pharmacy, University of California at San Diego, La Jolla, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, United States
| | - Piyush Labhsetwar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
| | - John I Glass
- J Craig Venter Institute, La Jolla, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States
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Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions. Molecules 2019; 24:molecules24020227. [PMID: 30634503 PMCID: PMC6358819 DOI: 10.3390/molecules24020227] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/05/2019] [Accepted: 01/05/2019] [Indexed: 11/22/2022] Open
Abstract
Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl− was thus compared to that of HCOO−, HSO4−, and H2PO4− with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO2− > Cl− > H2PO4− > HSO4− general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor.
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Jin J, Wang H, Jing Y, Liu M, Wang D, Li Y, Bao M. An efficient and environmental-friendly dispersant based on the synergy of amphiphilic surfactants for oil spill remediation. CHEMOSPHERE 2019; 215:241-247. [PMID: 30317095 DOI: 10.1016/j.chemosphere.2018.09.159] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
Eliminating the adverse environmental impact of chemical dispersants for oil spill has been a significant challenge since decades ago. Here, we prepared an effective and environmentally-friend dispersant with stable emulsifying capacity by the soybean lecithin and Tween 80. The mean droplet diameters of emulsions prepared by decane decreased from 11.3 to 4.1 μm, the emulsification index of emulsion climbed from 0 to 22.0% by 0.5 wt% dispersant. This dispersant exhibits favorable emulsifying capacity when the temperature ranges from 10 to 40 °C, pH within 5-7, and the concentration of inorganic cation is 30000 mg/L. Fluorescence microscopy analysis, FTIR, and the interfacial tension meter were employed to investigate the interaction between the soybean lecithin and Tween 80, a clear redshift of the hydroxyl group on the lecithin/Tween 80 dispersant and the detected surfactants over the oil-water interface confirm that there exists a synergy between the lecithin and Tween 80 due to the electrostatic attractions, which tremendously contribute to the reduction in the interfacial tension between water and oil. To further understand the influence of the dispersant on the oil hydrocarbon concentration in the water column, visualization simulation with the varying depths were performed. The results showed that the oil hydrocarbon concentration in the water column bottom was proportional to the addition of the dispersant, which facilitates spilled oil dispersing into smaller droplets, accelerates the biodegradation process. Hence, the lecithin/Tween 80 dispersant can be perceived as a promising alternative for oil spill remediation.
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Affiliation(s)
- Jiafeng Jin
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China
| | - Haoyu Wang
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China
| | - Yannan Jing
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China
| | - Min Liu
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China
| | - Daigang Wang
- Beijing International Center for Gas Hydrate, Peking University, Beijing, PR China.
| | - Yiming Li
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, 238 Song-Ling Road, Qingdao 266100, PR China.
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