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Journal articles on the topic 'Bioinformatics; Bioremediation'
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Pazos, F. "MetaRouter: bioinformatics for bioremediation." Nucleic Acids Research 33, Database issue (2004): D588—D592. http://dx.doi.org/10.1093/nar/gki068.
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Kumar, S. Senthil, S. Shantkriti, T. Muruganandham, E. Murugesh, Niraj Rane, and S. P. Govindwar. "Bioinformatics aided microbial approach for bioremediation of wastewater containing textile dyes." Ecological Informatics 31 (January 2016): 112–21. http://dx.doi.org/10.1016/j.ecoinf.2015.12.001.
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Trifi, Houda, Afef Najjari, Wafa Achouak, et al. "Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation." Genomics 112, no. 1 (2020): 981–89. http://dx.doi.org/10.1016/j.ygeno.2019.06.014.
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Biggs, Matthew B., and Jason A. Papin. "Metabolic network-guided binning of metagenomic sequence fragments." Bioinformatics 32, no. 6 (2015): 867–74. http://dx.doi.org/10.1093/bioinformatics/btv671.
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Abstract Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks. Availability and implementation: The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/. Contact: papin@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Miralles-Robledillo, Jose María, Javier Torregrosa-Crespo, Rosa María Martínez-Espinosa, and Carmen Pire. "DMSO Reductase Family: Phylogenetics and Applications of Extremophiles." International Journal of Molecular Sciences 20, no. 13 (2019): 3349. http://dx.doi.org/10.3390/ijms20133349.
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Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.
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Miller, Ryan K., Robert M. Kirkham, and Adam J. Kleinschmit. "Bioinformatics Analysis of Microbial Abundance and Diversity in Acid Mine Drainage from the Solomon Mine Near Creede, Colorado." Fine Focus 4, no. 1 (2018): 41–65. http://dx.doi.org/10.33043/ff.4.1.41-65.
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This study focused on characterizing the phylotypic composition of acid mine drainage (AMD) communities associated with the Solomon Mine near Creede, Colorado, and its relative diversity compared to microbial communities found in the East Willow Creek (EWC) watershed. AMD from the Solomon Mine adit flows into an existing passive bioremediation wetland system located next to the Solomon Mine adit that currently is ineffective and is under consideration for renovation. We are interested in gaining an understanding of the baseline microbial communities present in AMD/EWC and to monitor them during future wetland renovation. Prokaryotic community profiling was approached using SSU 16S rRNA marker gene amplification coupled with next generation sequencing. Bioinformatics analysis included raw read preprocessing, data visualization, and statistical testing using a combination of USEARCH and QIIME-based scripts. A pH and conductivity gradient were observed for water moving through the currently inefficient wetland system at the Solomon Mine. The EWC microbiomes had statistically significant higher alpha diversity compared to the AMD microbiomes. Beta diversity analysis parsed the sample locations into statistically significant groups including core AMD microbiomes, the wetland Cell 3 microbiome, and EWC microbiomes using multidimensional scaling. Taxa driving beta diversity included the phylum Proteobacteria for the core AMD microbiomes, the phyla Firmicutes and Chloroflexi for the constructed wetland Cell 3, and the phyla Bacteroidetes and Verrucomicrobia for EWC. Our data suggests that the microbial community in constructed wetland Cell 3 is likely where limited sulfate reduction activity is operating at low capacity, which will be further investigated via shotgun metagenomic analysis.
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Setlhare, Boitumelo, Ajit Kumar, Mduduzi Mokoena, and Ademola Olaniran. "Catechol 1,2-Dioxygenase is an Analogue of Homogentisate 1,2-Dioxygenase in Pseudomonas chlororaphis Strain UFB2." International Journal of Molecular Sciences 20, no. 1 (2018): 61. http://dx.doi.org/10.3390/ijms20010061.
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Catechol dioxygenases in microorganisms cleave catechol into cis-cis-muconic acid or 2-hydroxymuconic semialdehyde via the ortho- or meta-pathways, respectively. The aim of this study was to purify, characterize, and predict the template-based three-dimensional structure of catechol 1,2-dioxygenase (C12O) from indigenous Pseudomonas chlororaphis strain UFB2 (PcUFB2). Preliminary studies showed that PcUFB2 could degrade 40 ppm of 2,4-dichlorophenol (2,4-DCP). The crude cell extract showed 10.34 U/mL of C12O activity with a specific activity of 2.23 U/mg of protein. A 35 kDa protein was purified to 1.5-fold with total yield of 13.02% by applying anion exchange and gel filtration chromatography. The enzyme was optimally active at pH 7.5 and a temperature of 30 °C. The Lineweaver–Burk plot showed the vmax and Km values of 16.67 µM/min and 35.76 µM, respectively. ES-MS spectra of tryptic digested SDS-PAGE band and bioinformatics studies revealed that C12O shared 81% homology with homogentisate 1,2-dioxygenase reported in other Pseudomonas chlororaphis strains. The characterization and optimization of C12O activity can assist in understanding the 2,4-DCP metabolic pathway in PcUFB2 and its possible application in bioremediation strategies.
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Peng, Tao, An Luo, Jie Kan, Lei Liang, Tongwang Huang, and Zhong Hu. "Identification of A Ring-Hydroxylating Dioxygenases Capable of Anthracene and Benz[a]anthracene Oxidization from Rhodococcus sp. P14." Journal of Molecular Microbiology and Biotechnology 28, no. 4 (2018): 183–89. http://dx.doi.org/10.1159/000494384.
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Nowadays, contamination of soil and marine sediments by polycyclic aromatic hydrocarbons (PAHs) has become a serious problem all over the world. <i>Rhodococcus</i> sp. P14 was isolated from sediments with crude oil contaminate and showed degradation ability on various PAHs. The genome of <i>Rhodococcus</i> sp. P14 was sequenced. A gene cluster encoding a ring-hydroxylating dioxygenase Baa related to PAH degradation was identified by bioinformatics. The expression level of gene <i>baaA</i> was increased when P14 was cultured with anthracene, pyrene, phenanthrene, or benz[a]anthracene as the single carbon source. The recombinant protein Baa was overexpressed in <i>E. coli</i> BL21 (DE3). Further investigations on the recombinant protein Baa in <i>E. coli</i> demonstrated that it was able to oxidize anthracene and benz [a]anthracene, resulting in 9,10-dihydroxyanthracene and 7, 12-dihydroxybenz[a]anthracene as metabolites, respectively. These results indicate that Baa plays an important role in PAH degradation in <i>Rhodococcus</i> sp. P14 and Baa has potential application in the bioremediation of PAHs in the contaminated environment.
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Li, Jiangwei, Anyi Hu, Shijie Bai, et al. "Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene." Microorganisms 9, no. 4 (2021): 751. http://dx.doi.org/10.3390/microorganisms9040751.
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Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.
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Bernabeu, Eric, Jose María Miralles-Robledillo, Micaela Giani, Elena Valdés, Rosa María Martínez-Espinosa, and Carmen Pire. "In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification." Biomolecules 11, no. 7 (2021): 1043. http://dx.doi.org/10.3390/biom11071043.
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During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Retamal-Morales, Gerardo, Marika Mehnert, Rïngo Schwabe, Dirk Tischler, Michael Schlömann, and Gloria J. Levicán. "Genomic Characterization of the Arsenic-Tolerant Actinobacterium, Rhodococcus erythropolis S43." Solid State Phenomena 262 (August 2017): 660–63. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.660.
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Rhodococcus erythropolis S43 is an actinobacterium isolated from an arsenic-contaminated soil sample, collected from an old smelter site, including an arsenic smelter, in Germany. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of arsenic. Here, we present the microbiological features and genomic properties of this biotechnologically relevant strain. The 6,812,940 bp draft genome is arranged into 264 scaffolds of 848 contigs. It possesses 62.5% of CG content and comprises 6,040 coding sequences and 49 tRNA genes. Bioinformatic genome analysis showed the presence of arsenic-resistance genes. A complete ars operon was found containing the arsACDR cluster coding for ArsA (efflux pump ATPase), ArsC (arsenate reductase), ArsD (chaperone) and ArsR (ars operon regulator). Our results show that the arsC mRNA level significantly increased in response to arsenite and arsenate exposure, suggesting its involvement in the arsenic resistance phenotype of strain S43. In addition, this strain showed to have a plethora of genes coding for proteins involved in oxidative-stress response, including catalase, super-oxide dismutase, glutathione peroxidase-related genes, thioredoxin and thioredoxin reductase, suggesting it is highly tolerant to oxidative conditions. Finally, genes for radiation resistance, biodesulfurization, and oil and phenol degrading pathways were also detected. Altogether this data make R. erythropolis S43 a good candidate microorganism for bioremediation of highly contaminated environments and other industrial applications.
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Jaswal, Rajneesh, Ashish Pathak, and Ashvini Chauhan. "Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils." Microorganisms 7, no. 9 (2019): 324. http://dx.doi.org/10.3390/microorganisms7090324.
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Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.
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Borg, Yanika, Aurelija Marija Grigonyte, Philipp Boeing, et al. "Open source approaches to establishingRoseobacterclade bacteria as synthetic biology chassis for biogeoengineering." PeerJ 4 (July 7, 2016): e2031. http://dx.doi.org/10.7717/peerj.2031.
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Aim.The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods.Roseobacterclade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from theRoseobacterclade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTMstandard and finally, (iii) that identifying and subcloning genes from aRoseobacterclade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools.Method.We cultivated threeRoseobacterspecies,Roseobacter denitrificans,Oceanobulbus indolifexandDinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistanceanf1gene fromOceanobulbus indolifexcells and subcloning it into a BioBrickTMformatted plasmid.Results.All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, ‘UCLHack-12’ was assembled and used to cultivate sufficient quantity ofOceanobulbus indolifexcells to enable isolation of theanf1gene and its subcloning into a plasmid to generate the BioBrickTMBBa_K729016.Conclusion.The process of ‘de-skilling’ biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change.
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Khan, Nida Tabassum. "Integration of Bioinformatics in Bioremediation." International Journal of Biomedical Data Mining 07, no. 01 (2018). http://dx.doi.org/10.4172/2090-4924.1000130.
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Rana, Shashank, Preeti P, Vartika Singh, and Nikunj Bhardwaj. "Bioinformatics in Microbial Biotechnology: A Genomics and Proteomics Perspective." Innovations in Information and Communication Technology Series, February 28, 2021, 54–69. http://dx.doi.org/10.46532/978-81-950008-7-6_005.
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Biological data is a new era with new growth in numerical and memory retention capacity, many microbial and eukaryotic genomes encapsulate the human genome's pure structure, followed by raising the prospect of higher viral control. The goal is as high as the development of drug development based on the study of the structures and functions of target molecules (rational drug) and antimicrobial agents, the growth is simple to manage drugs, protein biomarkers that develop different bacterial infections and healthier considerate of protein(host)-protein(bacteria) interactions to avert bacterial disease. In addition to many bioinformatics processes and cross-reference, databases have made easy the understanding of these goals. The current study is divided into (I) genomics - sequencing and gene-related studies to determine the genetic function and genetic engineering, (II) proteomics - classification of associated properties of protein and rebuilding of the metabolic and regulatory pathway, (III) growth of drug and antimicrobial agents' application. Our center of attention on genomics and proteomics strategies and their restrictions in the current chapter. Bioinformatics study can be grouped under several main criteria: (1) research-based on existing wet-lab testing data, (2) new data obtained from the use of mathematical modelling and (3) an incorporated method that combines exploration procedure with a mathematical model. The main implications of bioinformatics examined area have automated genetic sequence, robotic expansion of integrated data of genomics and proteomics, computer-assisted comparison to find genome utility, the automatic origin of a metabolic pathway, gene expression analysis which was derived from the regulatory pathway, clustering techniques and strategies of data mining to identify the interaction of protein-protein and protein-DNA and silico modelling of three-dimensional protein arrangement and docking between proteins and biological chemicals for rational drug design, investigation of differences among infectious and non-infectious species to recognise genes drugs and antimicrobial agents and all genome comparisons to be aware of the development of microorganisms. Advanced bioinformatics has the potential to help (i) cause disease detection, (ii) develop new drugs and (iii) improve cost-effective bioremediation agents. Recent research is a part of the lack of genetic functionality found in wet laboratories information, the absence of computer algorithms to test large amounts of information on unidentified function and the continuous discovery of protein-to-protein, protein-to-DNA and Protein to RNA interaction.
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Chen, Angela, Mark W. Sherman, Cynthia Chu, Natalia Gonzalez, Tulshi Patel, and Lydia M. Contreras. "Discovery and Characterization of Native Deinococcus radiodurans Promoters for Tunable Gene Expression." Applied and Environmental Microbiology 85, no. 21 (2019). http://dx.doi.org/10.1128/aem.01356-19.
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ABSTRACT The potential utilization of extremophiles as a robust chassis for metabolic engineering applications has prompted interest in the use of Deinococcus radiodurans for bioremediation efforts, but current applications are limited by the lack of availability of genetic tools, such as promoters. In this study, we used a combined computational and experimental approach to identify and screen 30 predicted promoters for expression in D. radiodurans using a fluorescent reporter assay. The top eight candidates were further characterized, compared to currently available promoters, and optimized for engineering through minimization for use in D. radiodurans. Of these top eight, two promoter regions, PDR_1261 and PrpmB, were stronger and more consistent than the most widely used promoter sequence in D. radiodurans, PgroES. Furthermore, half of the top eight promoters could be minimized by at least 20% (to obtain final sequences that are approximately 24 to 177 bp), and several of the putative promoters either showed activity in Escherichia coli or were D. radiodurans specific, broadening the use of the promoters for various applications. Overall, this work introduces a suite of novel, well-characterized promoters for protein production and metabolic engineering in D. radiodurans. IMPORTANCE The tolerance of the extremophile, Deinococcus radiodurans, to numerous oxidative stresses makes it ideal for bioremediation applications, but many of the tools necessary for metabolic engineering are lacking in this organism compared to model bacteria. Although native and engineered promoters have been used to drive gene expression for protein production in D. radiodurans, very few have been well characterized. Informed by bioinformatics, this study expands the repertoire of well-characterized promoters for D. radiodurans via thorough characterization of eight putative promoters with various strengths. These results will help facilitate tunable gene expression, since these promoters demonstrate strong and consistent performance compared to the current standard, PgroES. This study also provides a methodology for high-throughput promoter identification and characterization using fluorescence in D. radiodurans. The promoters identified in this study will facilitate metabolic engineering of D. radiodurans and enable its use in biotechnological applications ranging from bioremediation to synthesis of commodity chemicals.
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Wei, Yahong, Jing Fu, Jianying Wu, et al. "Bioinformatics Analysis and Characterization of Highly Efficient Polyvinyl Alcohol (PVA)-Degrading Enzymes from the Novel PVA Degrader Stenotrophomonas rhizophila QL-P4." Applied and Environmental Microbiology 84, no. 1 (2017). http://dx.doi.org/10.1128/aem.01898-17.
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ABSTRACTPolyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader,Stenotrophomonas rhizophilaQL-P4, isolated from fallen leaves from a virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/vinyl alcohol oligomer (OVA)-degrading genes. Of these, seven genes were predicted to be involved in the classic intracellular PVA/OVA degradation pathway, and one (BAY15_3292) was identified as a novel PVA oxidase. Five PVA/OVA-degrading enzymes were purified and characterized. One of these, BAY15_1712, a PVA dehydrogenase (PVADH), displayed high catalytic efficiency toward PVA and OVA substrate. All reported PVADHs only have PVA-degrading ability. Most importantly, we discovered a novel PVA oxidase (BAY15_3292) that exhibited higher PVA-degrading efficiency than the reported PVADHs. Further investigation indicated that BAY15_3292 plays a crucial role in PVA degradation inS. rhizophilaQL-P4. Knocking out BAY15_3292 resulted in a significant decline in PVA-degrading activity inS. rhizophilaQL-P4. Interestingly, we found that BAY15_3292 possesses exocrine activity, which distinguishes it from classic PVADHs. Transparent circle experiments further proved that BAY15_3292 greatly affects extracellular PVA degradation inS. rhizophilaQL-P4. The exocrine characteristics of BAY15_3292 facilitate its potential application to PVA bioremediation. In addition, we report three new efficient secondary alcohol dehydrogenases (SADHs) with OVA-degrading ability inS. rhizophilaQL-P4; in contrast, only one OVA-degrading SADH was reported previously.IMPORTANCEWith the widespread application of PVA in industry, PVA-related environmental pollution is an increasingly serious issue. Because PVA is difficult to degrade, it accumulates in aquatic environments and causes chronic toxicity to aquatic organisms. Biodegradation of PVA, as an economical and environment-friendly method, has attracted much interest. To date, effective and applicable PVA-degrading bacteria/enzymes have not been reported. Herein, we report a new efficient PVA degrader (S. rhizophilaQL-P4) that has five PVA/OVA-degrading enzymes with high catalytic efficiency, among which BAY15_1712 is the only reported PVADH with both PVA- and OVA-degrading abilities. Importantly, we discovered a novel PVA oxidase (BAY15_3292) that is not only more efficient than other reported PVA-degrading PVADHs but also has exocrine activity. Overall, our findings provide new insight into PVA-degrading pathways in microorganisms and suggestS. rhizophilaQL-P4 and its enzymes have the potential for application to PVA bioremediation to reduce or eliminate PVA-related environmental pollution.
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Bamanga, Raji, Yusuf Y. Deeni, Andrew Spiers, and Scott Cameron. "Characterisation of surfactant-expressing bacteria and their potential bioremediation properties from hydrocarbon-contaminated and uncontaminated soils." Access Microbiology 2, no. 7A (2020). http://dx.doi.org/10.1099/acmi.ac2020.po0506.
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We are investigating characteristics associated with oil degradation amongst bacteria isolated from clean and hydrocarbon contaminated soils from Nigeria and the UK.Our focus has been to identify bacteria expressing surfactants following isolation on Pseudomonas selective (PSA-CFC) and non-selective nutrient media and investigate the nature of surfactants, heavy metal resistance and hydrocarbon-degrading enzymes expressed by the bacteria. Of five sites sampled, a total of 1460 colonies were tested using the drop collapse assay, and 110 were found to express surfactants reducing liquid surface tensions as assessed by quantitative tensiometry to between 24.7 and 26.7 mN.m-1 (Tukey-Kramer HSD, α=0.05). We undertook a range of growth and behaviour-based assays on 60 selected strain which, when investigated by Hierarchical cluster analysis (HCA) demonstrated that this collection showed considerable phenotypic diversity. Eight out of the 60 strains could grow at a high temperature (50 °C), 35 of the 60 strains utilized diesel as a sole carbon source, and most of the strains could tolerate high concentrations (up to 20 mM) of heavy metals. Identification by 16S rDNA sequencing revealed that some of the strains belong to Pseudomonas, Bacillus, and Stenotrophomonas genera. We found using bioinformatics analysis of eight-selected draft genome sequences (AntiSMASH and RAST) NRPS-like (probable surfactants), cytochrome P450, catechol-1,2/2,3-dioxygenase, lipase, and heavy metal resistance gene sequences. We intend to use the information provided in this research to select strains for potential applications in in-situor ex-situ bioremediation of hydrocarbon-contaminated soils.
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Pal, Siddhartha, and Kriti Sengupta. "In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil." Journal of Genetic Engineering and Biotechnology 19, no. 1 (2021). http://dx.doi.org/10.1186/s43141-021-00146-x.
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Abstract Background Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters. Results The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein. Conclusions Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites.
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Sidhu, Chandni, Vipul Solanki, Anil Kumar Pinnaka, and Krishan Gopal Thakur. "Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach." mSystems 4, no. 6 (2019). http://dx.doi.org/10.1128/msystems.00316-19.
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ABSTRACT The release of synthetic chemical pollutants in the environment is posing serious health risks. Enzymes, including oxygenases, play a crucial role in xenobiotic degradation. In the present study, we employed a functional metagenomics approach to overcome the limitation of cultivability of microbes under standard laboratory conditions in order to isolate novel dioxygenases capable of degrading recalcitrant pollutants. Fosmid clones possessing dioxygenase activity were further sequenced, and their genes were identified using bioinformatics tools. Two positive fosmid clones, SD3 and RW1, suggested the presence of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC-SD3) and catechol 2,3-dioxygenase (C23O-RW1), respectively. Recombinant versions of these enzymes were purified to examine their pollutant-degrading abilities. The crystal structure of BphC-SD3 was determined at 2.6-Å resolution, revealing a two-domain architecture, i.e., N-terminal and C-terminal domains, with the sequential arrangement of βαβββ in each domain, characteristic of Fe-dependent class II type I extradiol dioxygenases. The structure also reveals the presence of conserved amino acids lining the catalytic pocket and Fe3+ metal ion in the large funnel-shaped active site in the C-terminal domain. Further studies suggest that Fe3+ bound in the BphC-SD3 active site probably imparts aerobic stability. We further demonstrate the potential application of BphC-SD3 in biosensing of catecholic compounds. The halotolerant and oxygen-resistant properties of these enzymes reported in this study make them potential candidates for bioremediation and biosensing applications. IMPORTANCE The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is currently not practical due to their aerobically unstable nature. The significance of our research lies in the discovery of aerobically stable and halotolerant catechol dioxygenases that are efficient in degrading the targeted environmental pollutants and, hence, could be used as cost-effective alternatives for the treatment of hypersaline industrial effluents. Moreover, the structural determination of novel catechol dioxygenases would greatly enhance our knowledge of the function of these enzymes and facilitate directed evolution to further enhance or engineer desired properties.
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Taleski, Vaso, Ivica Dimkić, Blazo Boev, Ivan Boev, Sanja Živković, and Slaviša Stanković. "Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia." FEMS Microbiology Ecology 96, no. 9 (2020). http://dx.doi.org/10.1093/femsec/fiaa155.
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ABSTRACT The Allchar mineral mine is one of the oldest arsenic–antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.
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Sturm, Gunnar, Stefanie Brunner, Elena Suvorova, et al. "Chromate Resistance Mechanisms inLeucobacter chromiiresistens." Applied and Environmental Microbiology 84, no. 23 (2018). http://dx.doi.org/10.1128/aem.02208-18.
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ABSTRACTChromate is one of the major anthropogenic contaminants on Earth.Leucobacter chromiiresistensis a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress,L. chromiiresistensforms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of theL. chromiiresistensgenome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use ofL. chromiiresistensas a new model organism to study microbial chromate resistance.IMPORTANCEChromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies ofL. chromiiresistensto establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.
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Gunasekera, Thusitha S., Loryn L. Bowen, Carol E. Zhou, et al. "Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel." Applied and Environmental Microbiology 83, no. 10 (2017). http://dx.doi.org/10.1128/aem.03249-16.
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ABSTRACT Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have various degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons, while P. aeruginosa strain PAO1, a human pathogen, is less adapted and degrades jet fuel at a lower rate than does ATCC 33988. We investigated fuel-specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat shock response, membrane proteins, efflux pumps, and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but it was not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved Yx(FWY)xxD motif, which is shared among bacterial adhesins. Overexpression of the putative resistance-nodulation-division (RND) efflux pump PA3521 to PA3523 increased the growth of the ATCC 33988 strain, suggesting a possible role in fuel tolerance. Interestingly, the PAO1 strain cannot utilize n-C8 and n-C10. The expression of green fluorescent protein (GFP) under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that the regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation. IMPORTANCE These results support that specific signal transduction, gene regulation, and coordination of multiple biological responses are required to improve the survival, growth, and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic differences between strains and helpful information that may be applied in the improvement of bacterial strains for resistance to biotic and abiotic factors encountered during bioremediation and industrial biotechnological processes.