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Sun S, Chen W, Peng K, Chen X, Chen J. Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20970-20982. [PMID: 38383926 PMCID: PMC10948491 DOI: 10.1007/s11356-024-32362-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.
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Affiliation(s)
- Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Wanqi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kailin Peng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xueyingzi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Materials, Loughborough University, Loughborough, LE11 3TU, UK.
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2
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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3
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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4
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Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability. ENVIRONMENTAL RESEARCH 2022; 211:113102. [PMID: 35300964 DOI: 10.1016/j.envres.2022.113102] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023]
Abstract
Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur-208001, India.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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Wu G, Huang A, Wen Y, Wang H, Wang J, Luo F, Wu M. Euendolithic Cyanobacteria and Proteobacteria Together Contribute to Trigger Bioerosion in Aquatic Environments. Front Microbiol 2022; 13:938359. [PMID: 35875561 PMCID: PMC9298513 DOI: 10.3389/fmicb.2022.938359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Shellfish, mussels, snails, and other aquatic animals, which assimilate limestone (calcium carbonate, CaCO3) to build shells and skeletons, are effective carbon sinks that help mitigate the greenhouse effect. However, bioerosion, the dissolution of calcium carbonate and the release of carbon dioxide, hinders carbon sequestration process. The bioerosion of aquatic environments remains to be elucidated. In this study, the bioerosion of Bellamya spp. shells from the aquatic environment was taken as the research object. In situ microbial community structure analysis of the bioerosion shell from different geographical locations, laboratory-level infected culture, and validated experiments were conducted by coupling traditional observation and 16S rRNA sequencing analysis method. Results showed that bioeroders can implant into the CaCO3 layer of the snail shell, resulting in the formation of many small holes in the shell, which reduced the shell’s density and made the shell fragile. Results also showed that bioeroders were distributed in two major phyla, namely, Cyanobacteria and Proteobacteria. Cluster analysis showed that Cyanobacteria sp. and two unidentified genera (Burkholderiaceae and Raistonia) were the key bioeroders. Moreover, results suggested that the interaction of Cyanobacteria and other bacteria promoted the biological function of “shell bioerosion.” This study identified the causes of “shell bioerosion” in aquatic environments and provided some theoretical basis for preventing and controlling it in the aquatic industry. Results also provided new insights of cyanobacterial bioerosion of shells and microalgae carbon sequestration.
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Affiliation(s)
- Guimei Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Aiyou Huang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Yanhong Wen
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
| | - Hongxia Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiangxin Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Fuguang Luo
- Liuzhou Aquaculture Technology Extending Station, Liuzhou, China
- *Correspondence: Fuguang Luo,
| | - Mingcan Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, China
- Mingcan Wu,
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6
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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7
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Vuong P, Wise MJ, Whiteley AS, Kaur P. Small investments with big returns: environmental genomic bioprospecting of microbial life. Crit Rev Microbiol 2022; 48:641-655. [PMID: 35100064 DOI: 10.1080/1040841x.2021.2011833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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8
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Basit A, Shah ST, Ullah I, Muntha ST, Mohamed HI. Microbe-assisted phytoremediation of environmental pollutants and energy recycling in sustainable agriculture. Arch Microbiol 2021; 203:5859-5885. [PMID: 34545411 DOI: 10.1007/s00203-021-02576-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 01/17/2023]
Abstract
The perception of phytoremediation is efficiently utilized as an eco-friendly practice of green plants combating and cleaning up the stressed environment without harming it. The industrial revolution was followed by the green revolution which fulfilled the food demands of the growing population caused an increase in yield per unit area in crop production, but it also increased the use of synthetic fertilizers in agriculture. Globally, the intensive use of inorganic fertilizers in agriculture has led to serious health problems and irreversible environmental damage. Biofertilizers improve the growth of the plant and can be applied as an alternative to chemical/synthetic fertilizers. Cyanobacteria, bacteria, and fungi are known as some of the principal microbe groups used to produce biofertilizers that form symbiotic associations with plants. Microorganisms perform a key role in phosphate solubilization and mobilization, nitrogen fixation, nutrient management, biotic elicitors and probiotics, and pollution management (biodegradation agents), specifically bacteria which also help in atmospheric nitrogen fixation and are thus available for the growth of the plant. Management or biodegradation of hazardous chemical residues and heavy metals produced by a huge number of large-scale industries should be given primary importance to be transformed by various bacterial strains, fungi, algae. Currently, modern omics technologies such as metagenomic, transcriptomic, and proteomic are being used to develop strategies for studying the ecology of microorganisms, as well as their use in environmental monitoring and bioremediation. This review briefly discusses some of the major groups of microorganisms that can perform different functions responsible for plant health, crop production, phytoremediation and also focus on the omics techniques reportedly used in environmental monitoring to tackle the pollution load.
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Affiliation(s)
- Abdul Basit
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Syed Tanveer Shah
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Izhar Ullah
- Department of Horticulture, Faculty of Crop Production, The University of Agriculture Peshawar, Peshawar, 25120, Pakistan
| | - Sidra Tul Muntha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
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Tyagi I, Tyagi K, Bhutiani R, Chandra K, Kumar V. Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42372-42386. [PMID: 33813698 DOI: 10.1007/s11356-021-13756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Rakesh Bhutiani
- Department of Environmental Sciences, Gurukul Kangri Vishwavidyalaya, Haridwar, 249404, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India.
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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11
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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12
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Hsiao CC, Sieber S, Georgiou A, Bailly A, Emmanouilidou D, Carlier A, Eberl L, Gademann K. Synthesis and Biological Evaluation of the Novel Growth Inhibitor Streptol Glucoside, Isolated from an Obligate Plant Symbiont. Chemistry 2019; 25:1722-1726. [PMID: 30508325 DOI: 10.1002/chem.201805693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/29/2018] [Indexed: 12/23/2022]
Abstract
The plant Psychotria kirkii hosts an obligatory bacterial symbiont, Candidatus Burkholderia kirkii, in nodules on their leaves. Recently, a glucosylated derivative of (+)-streptol, (+)-streptol glucoside, was isolated from the nodulated leaves and was found to possess a plant growth inhibitory activity. To establish a structure-activity relationship study, a convergent strategy was developed to obtain several pseudosugars from a single synthetic precursor. Furthermore, the glucosylation of streptol was investigated in detail and conditions affording specifically the α or β glucosidic anomer were identified. Although (+)-streptol was the most active compound, its concentration in P. kirkii plant leaves extract was approximately ten-fold lower than that of (+)-streptol glucoside. These results provide compelling evidence that the glucosylation of (+)-streptol protects the plant host against the growth inhibitory effect of the compound, which might constitute a molecular cornerstone for this successful plant-bacteria symbiosis.
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Affiliation(s)
- Chien-Chi Hsiao
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Antri Georgiou
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Aurélien Bailly
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Despina Emmanouilidou
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Aurélien Carlier
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Leo Eberl
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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13
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Akal AL, Karan R, Hohl A, Alam I, Vogler M, Grötzinger SW, Eppinger J, Rueping M. A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. FEBS Open Bio 2018; 9:194-205. [PMID: 30761247 PMCID: PMC6356862 DOI: 10.1002/2211-5463.12557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/06/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single-cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 m KCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl-methyl-ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo- and thermoadaptation.
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Affiliation(s)
- Anastassja L Akal
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Adrian Hohl
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Intikhab Alam
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Malvina Vogler
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Stefan W Grötzinger
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Biochemical Engineering Technical University of Munich (TUM) Garching Germany
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Magnus Rueping
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Organic Chemistry RWTH Aachen Aachen Germany
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14
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Duque E, Daddaoua A, Cordero BF, Udaondo Z, Molina‐Santiago C, Roca A, Solano J, Molina‐Alcaide E, Segura A, Ramos J. Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. Microb Biotechnol 2018; 11:781-787. [PMID: 29663699 PMCID: PMC6011990 DOI: 10.1111/1751-7915.13269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/01/2022] Open
Abstract
The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.
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Affiliation(s)
- Estrella Duque
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Abdelali Daddaoua
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Faculty of PharmacyDepartment of PharmacologyUniversity of Granada18071GranadaSpain
| | - Baldo F. Cordero
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Zulema Udaondo
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Carlos Molina‐Santiago
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Amalia Roca
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | - Jennifer Solano
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | | | - Ana Segura
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
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15
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Plewniak F, Crognale S, Rossetti S, Bertin PN. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. Front Microbiol 2018; 9:820. [PMID: 29755441 PMCID: PMC5932151 DOI: 10.3389/fmicb.2018.00820] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simona Rossetti
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
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16
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Razzaghi M, Homaei A, Mosaddegh E. Penaeus vannamei protease stabilizing process of ZnS nanoparticles. Int J Biol Macromol 2018; 112:509-515. [PMID: 29382577 DOI: 10.1016/j.ijbiomac.2018.01.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/24/2022]
Abstract
The protease enzyme purified from the Penaeus vannamei shrimp has unique properties, so improving the stability of this enzyme can improve their practical applications. In this study, ZnS nanoparticles, which have special properties for enzyme immobilization, were synthesized using a chemical precipitation method, and Penaeus vannamei protease was successfully immobilized on them. The size, structure, and morphology of the ZnS nanoparticles, and the immobilization of the protease were studied, using Transmission Electron Microscopy (TEM), Fourier Transform Infrared (FT-IR) spectroscopy, UV-Vis spectroscopy and Dynamic Light Scattering (DLS) analysis. We show that the immobilized enzyme has improved functionality at high temperatures, extreme pH conditions (pH3 and 12), and during storage. Immobilization increased the optimum temperature range of the enzyme, but did not change the pH optimum, which remained at pH7. Immobilization of P. vannamei protease enzyme increased the Km and decreased kcat/Km. These results indicate that P. vannamei protease immobilized on ZnS nanoparticles, has improved properties due to its high stability and unique properties, can be used for biotechnology applications.
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Affiliation(s)
- Mozhgan Razzaghi
- Department of Marine Biology, Faculty of Science, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Biochemistry, Faculty of Science, University of Hormozgan, Bandar Abbas, Iran.
| | - Elaheh Mosaddegh
- Department of New Materials, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, PO Box 76315-117, Kerman, Iran
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17
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D'Auria G, Artacho A, Rojas RA, Bautista JS, Méndez R, Gamboa MT, Gamboa JR, Gómez-Cruz R. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs. Genes (Basel) 2018; 9:E55. [PMID: 29361802 PMCID: PMC5793206 DOI: 10.3390/genes9010055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 01/22/2023] Open
Abstract
New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.
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Affiliation(s)
- Giuseppe D'Auria
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Alejandro Artacho
- Center for Advanced Research in Public Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Rafael A Rojas
- Chemical Engineering Faculty, Exact Sciences and Engineering Campus, Autonomous University of Yucatán (UADY), Mérida, Yucatán 97050..
| | - José S Bautista
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Roberto Méndez
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - María T Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Jesús R Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Rodolfo Gómez-Cruz
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
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18
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Grötzinger SW, Karan R, Strillinger E, Bader S, Frank A, Al Rowaihi IS, Akal A, Wackerow W, Archer JA, Rueping M, Weuster-Botz D, Groll M, Eppinger J, Arold ST. Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes. ACS Chem Biol 2018; 13:161-170. [PMID: 29188989 DOI: 10.1021/acschembio.7b00792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because only 0.01% of prokaryotic genospecies can be cultured and in situ observations are often impracticable, culture-independent methods are required to understand microbial life and harness potential applications of microbes. Here, we report a methodology for the production of proteins with desired functions based on single amplified genomes (SAGs) from unculturable species. We use this method to resurrect an alcohol dehydrogenase (ADH/D1) from an uncharacterized halo-thermophilic archaeon collected from a brine pool at the bottom of the Red Sea. Our crystal structure of 5,6-dihydroxy NADPH-bound ADH/D1 combined with biochemical analyses reveal the molecular features of its halo-thermophily, its unique habitat adaptations, and its possible reaction mechanism for atypical oxygen activation. Our strategy offers a general guide for using SAGs as a source for scientific and industrial investigations of "microbial dark matter."
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Affiliation(s)
- Stefan W. Grötzinger
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
| | - Ram Karan
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Eva Strillinger
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Stefan Bader
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Annika Frank
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Israa S. Al Rowaihi
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Anastassja Akal
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Wiebke Wackerow
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - John A. Archer
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Magnus Rueping
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Dirk Weuster-Botz
- Technical University of Munich, Department of Mechanical
Engineering, Institute of Biochemical Engineering, Garching, Germany
| | - Michael Groll
- Technical University of Munich, Center for Integrated
Protein Science Munich in the Department Chemistry, Garching, Germany
| | - Jörg Eppinger
- King Abdullah University of Science and Technology, Physical Science and Engineering Division, KAUST Catalysis Center, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering
Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
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19
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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20
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Sukul P, Schäkermann S, Bandow JE, Kusnezowa A, Nowrousian M, Leichert LI. Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics. MICROBIOME 2017; 5:28. [PMID: 28253936 PMCID: PMC5335836 DOI: 10.1186/s40168-017-0247-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/25/2017] [Indexed: 06/06/2023]
Abstract
Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information and our capacity of functionally screening for desired activities. Here, we present a simple workflow that combines functional metaproteomics and metagenomics, which facilitates the unmediated and direct discovery of biocatalysts in environmental samples. To identify the entirety of lipolytic biocatalysts in a soil sample contaminated with used cooking oil, we detected all proteins active against a fluorogenic substrate in sample's metaproteome using a 2D-gel zymogram. Enzymes' primary structures were then deduced by tryptic in-gel digest and mass spectrometry of the active protein spots, searching against a metagenome database created from the same contaminated soil sample. We then expressed one of the novel biocatalysts heterologously in Escherichia coli and obtained proof of lipolytic activity.
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Affiliation(s)
- Premankur Sukul
- Ruhr-Universität Bochum, Institute for Biochemistry and Pathobiochemistry – Microbial Biochemistry, Universitätsstr. 150, 44780 Bochum, Germany
| | - Sina Schäkermann
- Ruhr-Universität Bochum, Applied Microbiology, Universitätsstr. 150, 44780 Bochum, Germany
| | - Julia E. Bandow
- Ruhr-Universität Bochum, Applied Microbiology, Universitätsstr. 150, 44780 Bochum, Germany
| | - Anna Kusnezowa
- Ruhr-Universität Bochum, Institute for Biochemistry and Pathobiochemistry – Microbial Biochemistry, Universitätsstr. 150, 44780 Bochum, Germany
| | - Minou Nowrousian
- Ruhr-Universität Bochum, Lehrstuhl für Allgemeine und Molekulare Botanik, Universitätsstr. 150, 44780 Bochum, Germany
| | - Lars I. Leichert
- Ruhr-Universität Bochum, Institute for Biochemistry and Pathobiochemistry – Microbial Biochemistry, Universitätsstr. 150, 44780 Bochum, Germany
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