1.
Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance.
Li, X, Islam, MM, Chen, L, Wang, L, Zheng, X
Applied and environmental microbiology. 2020;(9)
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Abstract
Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.
2.
Highly sensitive colorimetric detection of glucose through glucose oxidase and Cu2+-catalyzed 3,3',5,5'-tetramethylbenzidine oxidation.
Li, X, Gao, L, Chen, Z
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy. 2019;:37-41
Abstract
We develop a glucose oxidase (GOx)-mediated strategy for detecting glucose based on oxidized 3,3',5,5'-tetramethylbenzidine (oxTMB), which is generated from Cu2+-catalyzed 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 reaction, as colorimetric readout. The sensing system involves two processes: generation of H2O2 from GOx-catalyzed oxidation of glucose, and H2O2-induced the oxidization of TMB via the catalysis of Cu2+. The H2O2 formed by GOx-catalyzed oxidation of glucose oxidizes colorless TMB to blue oxTMB, thus enhancing the absorbance intensity at 670 nm. Therefore, we draw a conclusion that the enhancement in colorimetric signal relies directly on H2O2 concentration, which, in turn, depends on glucose concentration. This color change can be used not only for visual detection of glucose by naked eyes but for reliable glucose quantification in the range from 1 to 100 nM with a detection limit of 0.21 nM. The method possesses the following advantages: simple design, low experimental cost, and no any additional experimental equipment for heating, illuminating, or bubbling.
3.
Trypsin Binding with Copper Ions Scavenges Superoxide: Molecular Dynamics-Based Mechanism Investigation.
Li, X, Zhong, Y, Zhao, C
International journal of environmental research and public health. 2018;(1)
Abstract
Trypsin is a serine protease, which has been proved to be a novel superoxide scavenger. The burst of superoxide induced by polychlorinated biphenyls can be impeded by trypsin in both wild type and sod knockout mutants of Escherichia coli. The experimental results demonstrated that the activities of superoxide scavenging of trypsin were significantly accelerated by Cu ions. Also, with the addition of Cu ions, a new β-sheet (β7) transited from a random coil in the Cu(II)-trypsin (TP) system, which was favorable for the formation of more contacts with other sheets of trypsin. Residue-residue network analysis and the porcupine plots proved that the Cu ion in trypsin strengthened some native interactions among residues, which ultimately resulted in much greater stability of the Cu(II)-TP system. Moreover, compact and stable trypsin structures with Cu ions might be responsible for significantly provoking the activity of superoxide scavenging.
4.
Serum Levels of Copper and Zinc in Patients with Rheumatoid Arthritis: a Meta-analysis.
Xin, L, Yang, X, Cai, G, Fan, D, Xia, Q, Liu, L, Hu, Y, Ding, N, Xu, S, Wang, L, et al
Biological trace element research. 2015;(1):1-10
Abstract
Many publications with conflicting results have evaluated serum levels of copper (Cu) and zinc (Zn) in patients with rheumatoid arthritis (RA). To derive a more precise estimation of the relationship, a meta-analysis was conducted. Relevant published data were retrieved through PubMed, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biomedical Database (CBM) before September 20, 2014. Weighted mean difference (WMD) with a 95 % confidence interval (95 % CI) was calculated using STATA 11.0. A total of 26 studies, including 1444 RA cases and 1241 healthy controls, were collected in this meta-analysis. Pooled analysis found that patients with RA had a higher serum level of Cu and a lower serum Zn level than the healthy controls (Cu (μg/dl), WMD = 31.824, 95 % CI = 20.334, 43.314; Zn (μg/dl), WMD = -12.683, 95 % CI = -19.783, -5.584). Subgroup analysis showed that ethnicity had influence on the serum level of Cu (μg/dl) (Caucasian, WMD = 43.907, 95 % CI = 35.090, 52.723, P < 0.001; Asian, WMD = 14.545, 95 % CI = -12.365, 41.455, P = 0.289) and Zn (μg/dl) (Caucasian, WMD = -11.038, 95 % CI = -23.420, 1.344, P = 0.081; Asian, WMD = -14.179, 95 % CI = -18.963, -9.394, P < 0.001) in RA and healthy controls. No evidence of publication bias was observed. This meta-analysis suggests that increased serum level of Cu and decreased serum level of Zn are generally present in RA patients.