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Ma Y, Liu Y, Sun J, Min P, Liu W, Li L, Yi P, Guo R, Chen J. Ecological risks of high-ammonia environment with inhibited growth of Daphnia magna: Disturbed energy metabolism and oxidative stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174959. [PMID: 39059654 DOI: 10.1016/j.scitotenv.2024.174959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024]
Abstract
High ammonia pollution is a common problem in water bodies. However, research on the mechanisms underlying the toxic effects on organisms at different nutritional levels is still insufficient. Herein, based on the environmental concentration, the toxic effects of high ammonia pollution on Daphnia magna were investigated. Overall, the feeding and filtration rates of D. magna were significantly decreased by ammonia. Growth inhibition of D. magna by ammonia was confirmed by the decreased body length. After ammonia exposure, the metabolic status of D. magna changed, the correlation network weakened, and the correlations between metabolites were disrupted. Changes occurred in metabolites primarily involved in oxidative stress, fatty acid oxidation, tricarboxylic acid cycle, and protein digestion, absorption, and synthesis, which were validated through alterations in multiple biomarkers. In addition, mitochondrial function was evaluated and was found to inhibit mitochondrial activity, which was accompanied by a decreased marker of mitochondrial activity contents and ATPase activity. Thus, the results suggested that energy metabolism and oxidative stress were involved in ammonia-induced growth toxicity. This study provides new insights into the impact of ammonia on aquatic ecological health.
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Affiliation(s)
- Yunfeng Ma
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Yanhua Liu
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Jiawei Sun
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Min
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Wei Liu
- State Key Laboratory for Environmental Protection of Water Ecological Health in the Middle and Lower Reaches of the Yangtze River, Jiangsu Provincial Academy of Environmental Science, Nanjing 210036, China
| | - Lei Li
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Pan Yi
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Ruixin Guo
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Jianqiu Chen
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China.
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2
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Tang GQ, Hu H, Douglas J, Carter C. Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA. Nucleic Acids Res 2024; 52:7096-7111. [PMID: 38783009 PMCID: PMC11229368 DOI: 10.1093/nar/gkae417] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) and tRNAs translate the genetic code in all living cells. Little is known about how their molecular ancestors began to enforce the coding rules for the expression of their own genes. Schimmel et al. proposed in 1993 that AARS catalytic domains began by reading an 'operational' code in the acceptor stems of tRNA minihelices. We show here that the enzymology of an AARS urzyme•TΨC-minihelix cognate pair is a rich in vitro realization of that idea. The TΨC-minihelixLeu is a very poor substrate for full-length Leucyl-tRNA synthetase. It is a superior RNA substrate for the corresponding urzyme, LeuAC. LeuAC active-site mutations shift the choice of both amino acid and RNA substrates. AARS urzyme•minihelix cognate pairs are thus small, pliant models for the ancestral decoding hardware. They are thus an ideal platform for detailed experimental study of the operational RNA code.
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Affiliation(s)
- Guo Qing Tang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Hao Hu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, New Zealand
- Department of Computer Science, The University of Auckland, New Zealand
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA
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Wu W, Ma X, Chen R, Fan J, Ye W, Chen Z, Huang Q, Qian L. Effects of Phytosterol Ester Supplementation on Egg Characteristics, Eggshell Ultrastructure, Antioxidant Capacity, Liver Function and Hepatic Metabolites of Laying Hens during Peak Laying Period. Antioxidants (Basel) 2024; 13:458. [PMID: 38671906 PMCID: PMC11047565 DOI: 10.3390/antiox13040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this experiment was to investigate the effects of dietary Phytosterol Ester (PSE) supplementation on egg characteristics, eggshell ultrastructure, antioxidant capacity, liver function, hepatic metabolites, and its mechanism of action in Hy-Line Brown laying hens during peak laying period. A total of 256 healthy Hy-Line Brown laying hens were randomly allocated into four groups. The hens in the control group were fed a basal diet, while those in the experimental groups were fed a basal diet further supplemented with 10, 20, and 40 mg/kg PSE, respectively. It was found that the addition of 20 mg/kg and 40 mg/kg PSE to the diets increased egg weight, but decreased egg breaking strength (p < 0.05). The addition of PSEs to the diets increased albumen height and Haugh unit in all experimental groups (p < 0.05). Electron microscopic observation revealed that the mammillary thickness increased significantly at doses of 20 and 40 mg/kg, but the total thickness decreased, and the effective thickness also thinned (p < 0.05). The mammillary width narrowed in all experimental groups (p < 0.001). Dietary supplementation with 40 mg/kg PSE significantly increased egg yolk Phenylalanine, Leucine, and Isoleucine levels (p < 0.05). In untargeted liver metabolomic analyses, L-Phenylalanine increased significantly in all experimental groups. Leucyl-Lysine, Glutamyl-Leucyl-Arginine, and L-Tryptophan increased significantly at doses of 10 and 20 mg/kg (p < 0.05), and L-Tyrosine increased significantly at doses of 10 and 40 mg/kg (p = 0.033). Aspartyl-Isoleucine also increased significantly at a dose of 10 mg/kg (p = 0.044). The concentration of total protein in the liver was significantly higher at doses of 20 and 40 mg/kg than that of the control group, and the concentrations of total cholesterol and low-density lipoprotein cholesterol were significantly reduced (p < 0.05). The concentration of triglyceride and alkaline phosphatase were significantly reduced in all experimental groups (p < 0.05). Steatosis and hemorrhage in the liver were also improved by observing the H&E-stained sections of the liver. Concerning the antioxidant capacity in the liver, malondialdehyde concentration was significantly reduced (p < 0.05) at a dose of 40 mg/kg. In the ovary, malondialdehyde and nitric oxide concentrations were significantly reduced (p < 0.001). In all the experimental groups, plasma nitric oxide concentration was significantly decreased while superoxide dismutase was significantly increased, and total antioxidant capacity concentration was significantly increased (p < 0.05) in the 10 mg/kg and 40 mg/kg doses. Metabolomics analyses revealed that PSEs play a role in promoting protein synthesis by promoting Aminoacyl-tRNA biosynthesis and amino acid metabolism, among other pathways. This study showed that the dietary addition of PSEs improved egg characteristics, antioxidant capacity, liver function, and symptoms of fatty liver hemorrhagic syndrome in Hy-Line Brown laying hens at peak laying stage. The changes in liver metabolism suggest that the mechanism of action may be related to pathways such as Aminoacyl-tRNA biosynthesis and amino acid metabolism. In conclusion, the present study demonstrated that PSEs are safe and effective dietary additives as an alternative to antibiotics.
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Affiliation(s)
- Wenzi Wu
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (W.W.); (X.M.); (Q.H.)
| | - Xin Ma
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (W.W.); (X.M.); (Q.H.)
| | - Rui Chen
- Hainan Institute of Zhejiang University, Sanya 572025, China; (R.C.); (W.Y.); (Z.C.)
| | - Jinghui Fan
- Hangzhou Academy of Agricultural Sciences, Hangzhou 310004, China;
| | - Wenxin Ye
- Hainan Institute of Zhejiang University, Sanya 572025, China; (R.C.); (W.Y.); (Z.C.)
| | - Zhuo Chen
- Hainan Institute of Zhejiang University, Sanya 572025, China; (R.C.); (W.Y.); (Z.C.)
| | - Qixin Huang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (W.W.); (X.M.); (Q.H.)
| | - Lichun Qian
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (W.W.); (X.M.); (Q.H.)
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Geng R, Zhang B, Cheng H, Wang M, Dang Z. Pyrrhotite-dependent microbial reduction and magnetic separation for efficient vanadium detoxification and recovery in contaminated aquifer. WATER RESEARCH 2024; 251:121143. [PMID: 38277824 DOI: 10.1016/j.watres.2024.121143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Microbial reduction under anaerobic condition is a promising method for remediating vanadate [V(V)] contamination in aquifers, while V(V) may be re-generated with redox fluctuations. The inability to remove vanadium after remediation has become a key issue limiting bioremediation. In this study, we proposed the use of pyrrhotite, a natural mineral with magnetic properties, to immobilize V(V) to insoluble V(IV) under microbial action and remove vanadium from the aquifer using a magnetic field, which could avoid the problem of V(V) recontamination under redox fluctuating conditions. Up to 49.0 ± 4.7 % of vanadium could be removed from the aquifer by the applied magnetic field, and the vanadium in the aquifer after the reaction was mainly in the acid-extractable and reducible states. pH had a strong effect on the magnetic recovery of V(V), while the influence of initial V(V) concentration was weak. Microbial community structure analysis showed that Thiobacillus, Proteiniphilum, Fermentimonas, and Desulfurivibrio played key roles for V(V) reduction and pyrrhotite oxidation. Structural equation model indicated the positive correlation between these genera with the magnetic recovery of vanadium. Real time-qPCR confirmed the roles of functional genes of V(V) reduction (napA and nirK) and SO42- reduction (dsrA) in such biological processes. This study provides a novel route to sustainable V(V) remediation in aquifers, with synchronous recovery of vanadium resources without rebound.
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Affiliation(s)
- Rongyue Geng
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China
| | - Baogang Zhang
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China.
| | - Haoyi Cheng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Mengnan Wang
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, PR China
| | - Zhi Dang
- School of Environment and Energy, MOE Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, South China University of Technology, Guangzhou 510006, PR China
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5
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Douglas J, Bouckaert R, Carter CW, Wills P. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Res 2024; 52:558-571. [PMID: 38048305 PMCID: PMC10810186 DOI: 10.1093/nar/gkad1160] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
How genetic information gained its exquisite control over chemical processes needed to build living cells remains an enigma. Today, the aminoacyl-tRNA synthetases (AARS) execute the genetic codes in all living systems. But how did the AARS that emerged over three billion years ago as low-specificity, protozymic forms then spawn the full range of highly-specific enzymes that distinguish between 22 diverse amino acids? A phylogenetic reconstruction of extant AARS genes, enhanced by analysing modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades, resulting in a total of 36 families of AARS catalytic domains. Small structural modules that differentiate one AARS family from another played pivotal roles in discriminating between amino acid side chains, thereby expanding the genetic code and refining its precision. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that were not synthesised until later in the evolution of the code. The most probable evolutionary route for an emergent amino acid type to establish a place in the code was by recruiting older, less specific AARS, rather than adapting contemporary lineages. This process, retrofunctionalisation, differs from previously described mechanisms through which amino acids would enter the code.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
- School of Computer Science, The University of Auckland, New Zealand
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA
| | - Peter R Wills
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
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6
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Patra SK, Douglas J, Wills PR, Bouckeart R, Betts L, Qing TG, Carter CW. Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575260. [PMID: 38260702 PMCID: PMC10802616 DOI: 10.1101/2024.01.11.575260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The chief barrier to studies of how genetic coding emerged is the lack of experimental models for ancestral aminoacyl-tRNA synthetases (AARS). We hypothesized that conserved core catalytic sites could represent such ancestors. That hypothesis enabled engineering functional "urzymes" from TrpRS, LeuRS, and HisRS. We describe here a fourth urzyme, GlyCA, detected in an open reading frame from the genomic record of the arctic fox, Vulpes lagopus. GlyCA is homologous to a bacterial heterotetrameric Class II GlyRS-B. Alphafold2 predicted that the N-terminal 81 amino acids would adopt a 3D structure nearly identical to the HisRS urzyme (HisCA1). We expressed and purified that N-terminal segment. Enzymatic characterization revealed a robust single-turnover burst size and a catalytic rate for ATP consumption well in excess of that previously published for HisCA1. Time-dependent aminoacylation of tRNAGly proceeds at a rate consistent with that observed for amino acid activation. In fact, GlyCA is actually 35 times more active in glycine activation by ATP than the full-length GlyRS-B α-subunit dimer. ATP-dependent activation of the 20 canonical amino acids favors Class II amino acids that complement those favored by HisCA and LeuAC. These properties reinforce the notion that urzymes represent the requisite ancestral catalytic activities to implement a reduced genetic coding alphabet.
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Affiliation(s)
- Sourav Kumar Patra
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
| | - Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, New Zealand
| | - Peter R. Wills
- Department of Physics, The University of Auckland, New Zealand
| | - Remco Bouckeart
- Centre for Computational Evolution, University of Auckland, New Zealand
- Department of Computer Science, The University of Auckland, New Zealand
| | - Laurie Betts
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
| | | | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
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Labine LM, Pereira EAO, Kleywegt S, Jobst KJ, Simpson AJ, Simpson MJ. Environmental metabolomics uncovers oxidative stress, amino acid dysregulation, and energy impairment in Daphnia magna with exposure to industrial effluents. ENVIRONMENTAL RESEARCH 2023; 234:116512. [PMID: 37394164 DOI: 10.1016/j.envres.2023.116512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/24/2023] [Indexed: 07/04/2023]
Abstract
Anthropogenic activities are regarded as point sources of pollution entering freshwater bodies worldwide. With over 350,000 chemicals used in manufacturing, wastewater treatment and industrial effluents are comprised of complex mixtures of organic and inorganic pollutants of known and unknown origins. Consequently, their combined toxicity and mode of action are not well understood in aquatic organisms such as Daphnia magna. In this study, effluent samples from wastewater treatment and industrial sectors were used to examine molecular-level perturbations to the polar metabolic profile of D. magna. To determine if the industrial sector and/or the effluent chemistries played a role in the observed biochemical responses, Daphnia were acutely (48 h) exposed to undiluted (100%) and diluted (10, 25, and 50%) effluent samples. Endogenous metabolites were extracted from single daphnids and analyzed using targeted mass spectrometry-based metabolomics. The metabolic profile of Daphnia exposed to effluent samples resulted in significant separation compared to the unexposed controls. Linear regression analysis determined that no single pollutant detected in the effluents was significantly correlated with the responses of metabolites. Significant perturbations were uncovered across many classes of metabolites (amino acids, nucleosides, nucleotides, polyamines, and their derivatives) which serve as intermediates in keystone biochemical processes. The combined metabolic responses are consistent with oxidative stress, disruptions to energy metabolism, and protein dysregulation which were identified through biochemical pathway analysis. These results provide insight into the molecular processes driving stress responses in D. magna. Overall, we determined that the metabolic profile of Daphnia could not be predicted by the chemical composition of environmentally relevant mixtures. The findings of this study demonstrate the advantage of metabolomics in conjunction with chemical analyses to assess the interactions of industrial effluents. This work further demonstrates the ability of environmental metabolomics to characterize molecular-level perturbations in aquatic organisms exposed to complex chemical mixtures directly.
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Affiliation(s)
- L M Labine
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - E A Oliveira Pereira
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - S Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, M4V 1M2, Canada
| | - K J Jobst
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - A J Simpson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - M J Simpson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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Chen B, Mansour B, Zheng E, Liu Y, Gauld JW, Wang Q. Fundamentals behind the specificity of Cysteinyl-tRNA synthetase: MD and QM/MM joint investigations. Proteins 2023; 91:354-362. [PMID: 36196751 DOI: 10.1002/prot.26433] [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: 04/20/2022] [Revised: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Cysteinyl-tRNA synthetase (CysRS) catalyzes the aminoacylation reaction of cysteine to its cognate tRNACys in the first step of protein translation. It is found that CysRS is different from other aaRSs as it transfers cysteine without the need for an editing reaction, which is not applicable in the case of serine despite the similarity in their structures. Surprisingly, the reasons why CysRS has high amino acid specificity are not clear yet. In this research, the binding configurations of Cys-AMP and its near-cognate amino acid Ser-AMP with CysRS are compared by Molecular Dynamics (MD). The results reveal that CysRS screens the substrate Cys-AMP to a certain extent in the process of combination and recognition, thus providing a guarantee for the high selectivity of the next reaction. While Ser-AMP is in a folded state in CysRS. In the meanwhile, the interaction between Cys-AMP and Zn963 in CysRS is much stronger than Ser-AMP. The substrate-assisted aminoacylation mechanism in CysRS is also explored by Quantum Mechanics/Molecular Mechanics (QM/MM) modeling. According to the QM/MM potential energies, the energy barrier of TSCys-AMP is 91.75 kJ/mol, while that of TSSer-AMP is close to 150 kJ/mol. Based on thermochemistry calculations, it is found that the product of Cys-AMP is more stable than the reactant. In contrast, Ser-AMP has a reactant that is more stable than its product. As a result, it reflects that the specificity of CysRS originates from both the kinetic and thermodynamical perspectives of the reaction. Our investigations demonstrate comprehensively on how CysRS recognizes and catalyzes the substrate Cys-AMP, hoping to provide some guidance for researchers in this area.
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Affiliation(s)
- Binbin Chen
- Department of Chemistry, Zhejiang University, Hangzhou, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Basel Mansour
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - En Zheng
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Yingchun Liu
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou, China
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Labine LM, Oliveira Pereira EA, Kleywegt S, Jobst KJ, Simpson AJ, Simpson MJ. Sublethal Exposure of Per- and Polyfluoroalkyl Substances of Varying Chain Length and Polar Functionality Results in Distinct Metabolic Responses in Daphnia magna. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:242-256. [PMID: 36345965 DOI: 10.1002/etc.5517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/11/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a class of persistent organic pollutants used in industrial applications because of their physicochemical properties, which results in their ubiquitous presence across environmental matrices. To date, legacy PFAS have been well studied; however, the concentration of alternative PFAS may exceed the concentration of legacy pollutants, and more information is needed regarding the sublethal toxicity at the molecular level of aquatic model organisms, such as Daphnia magna. Perfluorobutanoic acid (PFBA), perfluorohexanoic acid (PFHxA), perfluorohexanesulfonic acid (PFHxS), and perfluorononanoic acid (PFNA) are four widely detected PFAS alternatives of varying chain length and polar functionality that are quantified in aquatic environments. The present study examines the metabolic perturbations of PFAS with varying chemistries to D. magna using targeted mass spectrometry-based metabolomics. Daphnia were acutely exposed to sublethal concentrations of PFBA, PFHxA, PFHxS, and PFNA before the polar metabolite profile was extracted from single organisms. Multivariate analysis demonstrated significant separation between the sublethal concentrations of PFHxA, PFHxS, and PFNA relative to the controls; in sum, longer chain lengths demonstrated greater overall perturbations to the extracted metabolic profiles. Univariate statistics revealed significant perturbations in the concentrations of several amino acids, nucleotides/nucleosides, and neurotransmitters with exposure to PFAS. These metabolic perturbations are consistent with disruptions in energy metabolism (pantothenate and coenzyme A metabolism, histidine metabolism) and protein synthesis (aminoacyl-transfer RNA biosynthesis and amino acid metabolism), which were identified through biochemical pathway analysis. These results provide evidence that although PFAS chemistry (chain length and polar functional group) invokes unique metabolic responses, there is also an underlying toxic mode of action that is common with select PFAS exposure. Overall, the present study highlights the capabilities of environmental metabolomics to elucidate the molecular-level perturbations of pollutants within the same chemical class to model aquatic organisms, which can be used to prioritize risk assessment of substituted PFAS alternatives. Environ Toxicol Chem 2023;42:242-256. © 2022 SETAC.
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Affiliation(s)
- Lisa M Labine
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Erico A Oliveira Pereira
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Sonya Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, Ontario, Canada
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - André J Simpson
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Myrna J Simpson
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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10
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Labine LM, Oliveira Pereira EA, Kleywegt S, Jobst KJ, Simpson AJ, Simpson MJ. Comparison of sub-lethal metabolic perturbations of select legacy and novel perfluorinated alkyl substances (PFAS) in Daphnia magna. ENVIRONMENTAL RESEARCH 2022; 212:113582. [PMID: 35661729 DOI: 10.1016/j.envres.2022.113582] [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: 04/11/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a class of pollutants of concern due to their ubiquitous presence, persistence, and toxicity in aquatic environments. Legacy PFAS pollutants such as perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) have been more widely studied in aquatic environments. However, replacement PFAS, such as ammonium perfluoro (2-methyl-3-oxahexanoate; GenX) are increasingly being detected with little known information surrounding their toxicity. Here, Daphnia magna, a model organism for freshwater ecotoxicology was used to compare the acute sub-lethal toxicity of PFOS, PFOA, GenX, and PFAS mixtures. Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), the targeted polar metabolic profile extracted from single Daphnia was quantified to investigate perturbations in the exposure groups versus the unexposed organisms. Multivariate statistical analyses demonstrated significant non-monotonic separation in PFOA, GenX, and PFAS mixture exposures. Sub-lethal exposure to concentrations of PFOS did not lead to significant separation in multivariate analyses. Univariate statistics and pathway analyses were used to elucidate the mode of action of PFAS exposure. Exposure to all individual PFAS led to significant perturbations in many amino acids including cysteine, histidine, tryptophan, glycine, and serine. These perturbations are consistent with biochemical pathway disruptions in the pantothenate and Coenzyme A (CoA) biosynthesis, thiamine metabolism, histidine metabolism, and aminoacyl-tRNA biosynthesis pathways. Overall, the collected metabolomic data is consistent with disruptions in energy metabolism and protein synthesis as the primary mode of action of sub-lethal PFAS exposure. Secondary modes of action among individual pollutant exposures demonstrated that the structural properties (carboxylic acid vs. sulfonic acid group) may play a role in the metabolic perturbations observed. Sub-lethal exposure to PFAS mixtures highlighted a mixed response when compared to the individual pollutants (PFOS, PFOA, and GenX). Overall, this study emphasizes the niche capability of environmental metabolomics to differentiate secondary modes of action from metabolic perturbations in both single pollutant and pollutant mixtures within the same chemical class.
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Affiliation(s)
- Lisa M Labine
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Erico A Oliveira Pereira
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Sonya Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, Canada, M4V 1M2
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X7
| | - Andre J Simpson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Myrna J Simpson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada; Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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11
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Characterization of metabolite, genome and volatile organic compound changes provides insights into the spoilage and cold adaptive markers of Acinetobacter johnsonii XY27. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Abstract
Codon-dependent translation underlies genetics and phylogenetic inferences, but its origins pose two challenges. Prevailing narratives cannot account for the fact that aminoacyl-tRNA synthetases (aaRSs), which translate the genetic code, must collectively enforce the rules used to assemble themselves. Nor can they explain how specific assignments arose from rudimentary differentiation between ancestral aaRSs and corresponding transfer RNAs (tRNAs). Experimental deconstruction of the two aaRS superfamilies created new experimental tools with which to analyze the emergence of the code. Amino acid and tRNA substrate recognition are linked to phase transfer free energies of amino acids and arise largely from aaRS class-specific differences in secondary structure. Sensitivity to protein folding rules endowed ancestral aaRS-tRNA pairs with the feedback necessary to rapidly compare alternative genetic codes and coding sequences. These and other experimental data suggest that the aaRS bidirectional genetic ancestry stabilized the differentiation and interdependence required to initiate and elaborate the genetic coding table.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA;
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland 1142, New Zealand
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13
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Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution? Genes (Basel) 2021; 12:genes12030409. [PMID: 33809136 PMCID: PMC8001834 DOI: 10.3390/genes12030409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.
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14
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Demongeot J, Moreira A, Seligmann H. Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings. Bioessays 2020; 43:e2000071. [PMID: 33319381 DOI: 10.1002/bies.202000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023]
Abstract
Theoretical minimal RNA rings are candidate primordial genes evolved for non-redundant coding of the genetic code's 22 coding signals (one codon per biogenic amino acid, a start and a stop codon) over the shortest possible length: 29520 22-nucleotide-long RNA rings solve this min-max constraint. Numerous RNA ring properties are reminiscent of natural genes. Here we present analyses showing that all RNA rings lack dinucleotide CG (a mutable, chemically instable dinucleotide coding for Arginine), bearing a resemblance to known CG-depleted genomes. CG in "incomplete" RNA rings (not coding for all coding signals, with only 3-12 nucleotides) gradually decreases towards CG absence in complete, 22-nucleotide-long RNA rings. Presumably, feedback loops during RNA ring growth during evolution (when amino acid assignment fixed the genetic code) assigned Arg to codons lacking CG (AGR) to avoid CG. Hence, as a chemical property of base pairs, CG mutability restructured the genetic code, thereby establishing itself as genetically encoded biological information.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, France
| | - Andrés Moreira
- Departamento de Informática, Universidad Técnica Federico Santa María, Santiago, Chile
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, France.,The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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15
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Wills PR, Carter CW. Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding. Int J Mol Sci 2020; 21:E7392. [PMID: 33036401 PMCID: PMC7582391 DOI: 10.3390/ijms21197392] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 01/07/2023] Open
Abstract
We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, Iσ; an impedance parameter, Z; and an effective alphabet size, neff; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small.
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Affiliation(s)
- Peter R. Wills
- Department of Physics and Te Ao Marama Centre for Fundamental Inquiry, University of Auckland, PB 92019, Auckland 1142, New Zealand
| | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA
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The evolution of aminoacyl-tRNA synthetases: From dawn to LUCA. BIOLOGY OF AMINOACYL-TRNA SYNTHETASES 2020; 48:11-37. [DOI: 10.1016/bs.enz.2020.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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