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Bales MK, Vergara MM, Eckert CA. Application of functional genomics for domestication of novel non-model microbes. J Ind Microbiol Biotechnol 2024; 51:kuae022. [PMID: 38925657 PMCID: PMC11247347 DOI: 10.1093/jimb/kuae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications. ONE-SENTENCE SUMMARY The development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.
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Affiliation(s)
- Margaret K Bales
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael Melesse Vergara
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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3
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Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy. Biotechnol Bioeng 2021; 118:4360-4374. [PMID: 34309016 DOI: 10.1002/bit.27904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 11/09/2022]
Abstract
Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.
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Affiliation(s)
- Jae-Yoon Sung
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Jik Lee
- Department of Bio-Cosmetics, Seowon University, Chung-Ju, South Korea
| | - Yong-Joon Cho
- Department of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Myeong-Na Shin
- Department of Central Area Crop Science, NICS, RDA, Suwon, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Han-Seung Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Hong Koh
- Department of Pediatrics, Yonsei University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
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Krüger A, Schäfers C, Busch P, Antranikian G. Digitalization in microbiology - Paving the path to sustainable circular bioeconomy. N Biotechnol 2020; 59:88-96. [PMID: 32750680 DOI: 10.1016/j.nbt.2020.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022]
Abstract
The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.
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Affiliation(s)
- Anna Krüger
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Christian Schäfers
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Philip Busch
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
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Mongui A, Lozano GL, Handelsman J, Restrepo S, Junca H. Design and validation of a transposon that promotes expression of genes in episomal DNA. J Biotechnol 2020; 310:1-5. [PMID: 31954761 DOI: 10.1016/j.jbiotec.2020.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/15/2020] [Indexed: 01/20/2023]
Abstract
Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.
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Affiliation(s)
- Alvaro Mongui
- Molecular Biotechnology, Corporación CorpoGen, Bogotá, Colombia; Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
| | - Gabriel L Lozano
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Diseases, Universidad de los Andes, Bogotá, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Microbiomas Foundation, Chía, Colombia
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Calderon D, Peña L, Suarez A, Villamil C, Ramirez-Rojas A, Anzola JM, García-Betancur JC, Cepeda ML, Uribe D, Del Portillo P, Mongui A. Recovery and functional validation of hidden soil enzymes in metagenomic libraries. Microbiologyopen 2019; 8:e00572. [PMID: 30851083 PMCID: PMC6460280 DOI: 10.1002/mbo3.572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/01/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
Abstract
The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated the analysis of DNA from multiple environments and has expanded the limits of known microbial diversity. However, the functional characterization of enzymes, metabolites, and products encoded by diverse microbial genomes is limited by the inefficient heterologous expression of foreign genes. We have implemented a pipeline that combines NGS and Sanger sequencing as a way to identify fosmids within metagenomic libraries. This strategy facilitated the identification of putative proteins, subcloning of targeted genes and preliminary characterization of selected proteins. Overall, the in silico approach followed by the experimental validation allowed us to efficiently recover the activity of previously hidden enzymes derived from agricultural soil samples. Therefore, the methodology workflow described herein can be applied to recover activities encoded by environmental DNA from multiple sources.
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Affiliation(s)
- Dayana Calderon
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Luis Peña
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich-Schiller Universität, Jena, Germany
| | - Angélica Suarez
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Carolina Villamil
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Adan Ramirez-Rojas
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Juan M Anzola
- Computational Biology, Corporación CorpoGen, Bogotá, Colombia
| | | | - Martha L Cepeda
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Daniel Uribe
- Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Alvaro Mongui
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Araújo FVDE, Netto MCM, Azevedo GP, Jayme MMA, Nunes-Carvalho MC, Silva MM, Carmo FLDO. Ecology and biotechnological potential of bacterial community from three marine sponges of the coast of Rio de Janeiro, Brazil. AN ACAD BRAS CIENC 2017; 89:2785-2792. [PMID: 29236862 DOI: 10.1590/0001-3765201720170462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2017] [Indexed: 11/22/2022] Open
Abstract
Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil. The profile of the bacterial community present in sponges and water was obtained by PCR-DGGE technique and the biotechnological potential of the strains isolated by producing amylase, cellulase, protease and biosurfactants. The results showed that despite the influence of the environment in the composition of the microbial community, studied marine sponges shown to have specific bacterial populations, with some, showing potential in the production of substances of biotechnological applications.
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Affiliation(s)
- Fábio V DE Araújo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelle C M Netto
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Gustavo P Azevedo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelly M A Jayme
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524, 3° andar , Maracanã, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Monica C Nunes-Carvalho
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Av. Athos da Silveira Ramos, 149, 21044-020 Rio de Janeiro, RJ, Brazil
| | - Mariana M Silva
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Flávia L DO Carmo
- Departamento de Microbiologia Geral, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil
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Hvidsten I, Mjøs SA, Bødtker G, Barth T. Lipids of Dietzia sp. A14101. Part II: A study of the dynamics of the release of surface active compounds by Dietzia sp. A14101 into the medium. Chem Phys Lipids 2017; 208:31-42. [PMID: 28837792 DOI: 10.1016/j.chemphyslip.2017.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Abstract
Dietzia sp. A14101 isolated from an oil reservoir model column was found to induce a strong decrease of the interfacial tension (IFT) in hydrocarbon-water mixtures in the presence of the intact bacterial cells (Kowalewski et al., 2005). The strain was shown to be able to degrade a wide range of hydrocarbon substrates (Bødtker et al., 2009). Further studies showed that the surface-active compounds tentatively identified as glycolipids were produced by Dietzia sp. A14101 on non- and water-immiscible -hydrocarbon substrates, Part I (Hvidsten et al., 2017). The results suggested that biosurfactant (BS) was a mixture of several isomers. The study presented here is aimed to investigate whether BS are secreted into the aqueous medium, and if so, then at which phase of the culture growth and in which amounts - the dynamics of the BS release in incubations on water-immiscible hydrocarbons. Two methods of BS extraction from the medium were attempted and compared: a liquid-liquid extraction (LLE) and precipitation by acid. For qualitative and semi-quantitative assessment, gas chromatography-mass spectrometry (GC/MS), thin-layer chromatography (TLC), liquid chromatography-mass spectrometry (LC-MS), surface tension measurements (SFT), emulsification (E24) and oil-spreading tests were employed. The results indicated that BS only partially were secreted into the medium. Detectable amounts of glycolipids in media were first identified during the exponential growth phase. However, only a slight decrease of SFT was observed in the cell-free medium. The emulsification index values of the sampled material were lower than those reported for related strains. The results suggested that most of the BS produced by Dietzia sp. A14101 remains cell-bound during the culture development in a batch mode and only a narrow range of the BS isomers can be detected in small amounts in media.
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Affiliation(s)
- Ina Hvidsten
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway.
| | - Svein Are Mjøs
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Gunhild Bødtker
- Uni Research CIPR, Uni Research, P.O. Box 7810, 5020 Bergen, Norway
| | - Tanja Barth
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
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Purification and characterization of lipase by Bacillus methylotrophicus PS3 under submerged fermentation and its application in detergent industry. J Genet Eng Biotechnol 2017; 15:369-377. [PMID: 30647675 PMCID: PMC6296573 DOI: 10.1016/j.jgeb.2017.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/07/2017] [Accepted: 06/10/2017] [Indexed: 11/20/2022]
Abstract
Lipase production bacterial isolate was isolated from soil of service station and identified as Bacillus methylotrophicus PS3 by 16SrRNA with accession number |LN999829.1|. Lipase enzyme was purified by sequential methods of ammonium sulfate precipitation and Sephadex G-100 gel column chromatography. The molecular weight of purified enzyme was 31.40 kDa on SDS-PAGE. This purification procedure resulted in 2.90-fold purification of lipase with a 24.10% final yield. The purified lipase presented maximal hydrolytic activity at a temperature of 55 °C, and pH of 7.0. Lipase activity was stimulated by Triton X-100 and SDS with Mg2+ and Ca2+ metals employ a positive effect and outlast its stable in organic solvent i.e. methanol and ethanol.
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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Tobalina L, Bargiela R, Pey J, Herbst FA, Lores I, Rojo D, Barbas C, Peláez AI, Sánchez J, von Bergen M, Seifert J, Ferrer M, Planes FJ. Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. ACTA ACUST UNITED AC 2015; 31:1771-9. [PMID: 25618865 DOI: 10.1093/bioinformatics/btv036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 01/18/2015] [Indexed: 12/21/2022]
Abstract
MOTIVATION With the advent of meta-'omics' data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited. RESULTS Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data.
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Affiliation(s)
- Luis Tobalina
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Rafael Bargiela
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jon Pey
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Florian-Alexander Herbst
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Iván Lores
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - David Rojo
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Coral Barbas
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ana I Peláez
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jesús Sánchez
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Martin von Bergen
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jana Seifert
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Manuel Ferrer
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Francisco J Planes
- CEIT and Tecnun (University of Navarra), San Sebastián, Spain, CSIC, Institute of Catalysis, Madrid, Spain, Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany, Área de Microbiología, IUBA, Universidad de Oviedo, Oviedo, Spain, Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain, Department of Metabolomics, UFZ-Helmholtz-Zentrum für Umweltforschung GmbH, Leipzig, Germany and Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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12
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Fondi M, Liò P. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res 2015; 171:52-64. [PMID: 25644953 DOI: 10.1016/j.micres.2015.01.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/02/2015] [Accepted: 01/03/2015] [Indexed: 12/27/2022]
Abstract
Integrated -omics approaches are quickly spreading across microbiology research labs, leading to (i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organization and (ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi -omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.
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Affiliation(s)
- Marco Fondi
- Florence Computational Biology Group (ComBo), University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence 50019, Italy; Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence 50019, Italy.
| | - Pietro Liò
- University of Cambridge, Computer Laboratory, 15 JJ Thomson Avenue, CB3 0FD Cambridge, UK
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13
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Abstract
Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process.
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Affiliation(s)
- Marco Fondi
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence, Italy,
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14
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Goers L, Freemont P, Polizzi KM. Co-culture systems and technologies: taking synthetic biology to the next level. J R Soc Interface 2014; 11:rsif.2014.0065. [PMID: 24829281 DOI: 10.1098/rsif.2014.0065] [Citation(s) in RCA: 343] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.
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Affiliation(s)
- Lisa Goers
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Paul Freemont
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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15
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Yang G, Ding Y. Recent advances in biocatalyst discovery, development and applications. Bioorg Med Chem 2014; 22:5604-12. [DOI: 10.1016/j.bmc.2014.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
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16
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Ortiz-Marquez JCF, Do Nascimento M, Zehr JP, Curatti L. Genetic engineering of multispecies microbial cell factories as an alternative for bioenergy production. Trends Biotechnol 2013; 31:521-9. [PMID: 23791304 DOI: 10.1016/j.tibtech.2013.05.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 01/01/2023]
Abstract
There is currently much interest in developing technology to use microlgae or cyanobacteria for the production of bioenergy and biomaterials. Here, we summarize some remarkable achievements in strains improvement by traditional genetic engineering and discuss common drawbacks for further progress. We present general knowledge on natural microalgal-bacterial mutualistic interactions and discuss the potential of recent developments in genetic engineering of multispecies microbial cell factories. This synthetic biology approach would rely on the assembly of complex metabolic networks from optimized metabolic modules such as photosynthetic or nitrogen-fixing parts.
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Affiliation(s)
- Juan Cesar Federico Ortiz-Marquez
- Instituto de Investigaciones en Biodiversidad y Biotecnología - Consejo Nacional de Investigaciones Científicas y Técnicas. Mar del Plata, Buenos Aires, Argentina
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17
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Enzymatic Catalysis at Interfaces—Heterophase Systems as Substrates for Enzymatic Action. Catalysts 2013. [DOI: 10.3390/catal3020401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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18
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Shainsky J, Bernath-Levin K, Isaschar-Ovdat S, Glaser F, Fishman A. Protein engineering of nirobenzene dioxygenase for enantioselective synthesis of chiral sulfoxides. Protein Eng Des Sel 2013; 26:335-45. [PMID: 23442445 DOI: 10.1093/protein/gzt005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nitrobenzene dioxygenase (NBDO) from Comamonas sp. is shown here to perform enantioselective oxidation of aromatic sulfides. Several para-substituted alkyl aryl sulfides were examined and it was found that the activity of the enzyme is dependent on the size of the substrate. Saturation mutagenesis was performed on different residues in the active site in order to improve activity and selectivity. Mutagenesis at position 258 in the α-hydroxylase subunit of NBDO improved both activity and enantioselectivity. Substitutions in position 293 improved the activity on all substrates and had diverse influence on enantioselectivity. Mutagenesis in position 207 provided two interesting variants, V207I and V207A, with opposite enantioselectivities. Furthermore, combining two favorable mutations, N258A and F293H, provided an improved variant with both higher activity (5.20 ± 0.01, 2.12 ± 0.21, 2.64 ± 0.14 and 4.01 ± 0.34 nmol min(-1) mg protein(-1) on thioanisole, ptolyl, Cl-thioanisole and Br-thioanisole, respectively, which is 1.7, 4.6, 7.1 and 26.7-fold compared with wild type) and improved enantioselectivity (e.g. 67% enantiomeric excess for Cl-thioanisole vs. 5% for wild type). Molecular docking and active site volume calculations were used to correlate between the structure of the substrates and the function of the enzymes. The results from this work suggest that the location of pro-chiral sulfides in the active site is coordinated by hydrophobic interactions and by steric considerations, which in turn influences the activity and enantioselectivity of NBDO.
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Affiliation(s)
- Janna Shainsky
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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19
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Kuriata-Adamusiak R, Strub D, Lochyński S. Application of microorganisms towards synthesis of chiral terpenoid derivatives. Appl Microbiol Biotechnol 2012; 95:1427-36. [PMID: 22846902 PMCID: PMC3427490 DOI: 10.1007/s00253-012-4304-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 11/27/2022]
Abstract
Biotransformations are a standard tool of green chemistry and thus are following the rules of sustainable development. In this article, we describe the most common types of reactions conducted by microorganisms applied towards synthesis of chiral terpenoid derivatives. Potential applications of obtained products in various areas of industry and agriculture are shown. We also describe biological activity of presented compounds. Stereoselective hydroxylation, epoxidation, Baeyer-Villiger oxidation, stereo- and enantioselective reduction of ketones, and various kinetic resolutions carried out by bacteria and fungi have been reviewed. Mechanistic considerations regarding chemical and enzymatic reactions are presented. We also briefly describe modern approaches towards enhancing desired enzymatic activity in order to apply modified biocatalysts as an efficient tool and green alternative to chemical catalysts used in industry.
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Affiliation(s)
- Renata Kuriata-Adamusiak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50–370 Wrocław, Poland
| | - Daniel Strub
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50–370 Wrocław, Poland
| | - Stanisław Lochyński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50–370 Wrocław, Poland
- Institute of Cosmetology, Wrocław College of Physiotherapy, Kościuszki 4, 50–038 Wrocław, Poland
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20
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Ekkers DM, Cretoiu MS, Kielak AM, van Elsas JD. The great screen anomaly--a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 2011; 93:1005-20. [PMID: 22189864 PMCID: PMC3264863 DOI: 10.1007/s00253-011-3804-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/27/2011] [Accepted: 11/29/2011] [Indexed: 11/25/2022]
Abstract
Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product.
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Affiliation(s)
- David Matthias Ekkers
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mariana Silvia Cretoiu
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna Maria Kielak
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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21
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Domínguez de María P. Recent developments in the biotechnological production of hydrocarbons: paving the way for bio-based platform chemicals. CHEMSUSCHEM 2011; 4:327-329. [PMID: 21394920 DOI: 10.1002/cssc.201000306] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 10/12/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Pablo Domínguez de María
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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22
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Ni Y, Li CX, Wang LJ, Zhang J, Xu JH. Highly stereoselective reduction of prochiral ketones by a bacterial reductase coupled with cofactor regeneration. Org Biomol Chem 2011; 9:5463-8. [DOI: 10.1039/c1ob05285c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Fernández-Arrojo L, Guazzaroni ME, López-Cortés N, Beloqui A, Ferrer M. Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 2010; 21:725-33. [PMID: 20934867 DOI: 10.1016/j.copbio.2010.09.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 09/09/2010] [Accepted: 09/09/2010] [Indexed: 02/01/2023]
Abstract
Microbial enzymes have many known applications as biocatalysts. However, only a few of them are currently employed for biocatalysis even though an annotated collection of more than 190 billion bases is available in metagenome sequence databases from uncultured and highly diverse microbial populations. This review aims at providing conceptual and technical bases for the translation of metagenome data into both experimental and computational frameworks that facilitates a comprehensive analysis of the biocatalysts diversity space. We will also briefly present the status of the current capabilities that assess and predict catalytic potential of environmental sites and track its diversity and evolution in large-scale biocatalysis process resulting from studies applying metagenomics in association with gene fingerprinting, catabolic arrays and complementary '-omics'.
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24
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Kuhn D, Blank LM, Schmid A, Bühler B. Systems biotechnology - Rational whole-cell biocatalyst and bioprocess design. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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25
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Jiang C, Hao ZY, Jin K, Li SX, Che ZQ, Ma GF, Wu B. Identification of a metagenome-derived β-glucosidase from bioreactor contents. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Molecular methods to study complex microbial communities. Methods Mol Biol 2010; 668:1-37. [PMID: 20830553 DOI: 10.1007/978-1-60761-823-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Microbes, which constitute a major fraction of the total biomass, are the main source of biodiversity on our Planet and play an essential role in maintaining global processes, which ultimately regulate the functioning of the Biosphere. Recent emergence of "metagenomics" allows for the analysis of microbial communities without tedious cultivation efforts. Metagenomics approach is analogous to the genomics with the difference that it does not deal with the single genome from a clone or microbe cultured or characterized in laboratory, but rather with that from the entire microbial community present in an environmental sample; it is the community genome. Global understanding by metagenomics depends essentially on the possibility of isolating the entire bulk DNA and identifying the genomes, genes, and proteins more relevant to each of the environmental sample under investigation. Following on this, in this chapter, we provide an analysis of methods available to isolate environmental DNA and to establish metagenomic libraries that can further be used for extensive activity screens.
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27
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Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 2009; 20:616-22. [DOI: 10.1016/j.copbio.2009.09.010] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/18/2009] [Accepted: 09/25/2009] [Indexed: 11/17/2022]
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28
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Croyle MA. Long-term virus-induced alterations of CYP3A-mediated drug metabolism: a look at the virology, immunology and molecular biology of a multi-faceted problem. Expert Opin Drug Metab Toxicol 2009; 5:1189-211. [PMID: 19732028 DOI: 10.1517/17425250903136748] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Virus infections are on the rise. Although the first description of CYP expression during virus infection was recorded 50 years ago, mechanistic studies of this phenomenon only began to appear in the last decade due to breakthroughs in molecular biology, genomic and transgenic technology. This review describes the relationship(s) among CYP-mediated drug metabolism, virus infection and the immune response and evaluates in vitro and in vivo models for mechanistic studies. The first studies that assessed CYP expression during infection focused on inflammatory mediators and the innate immune response at early time points. Recent studies assessing virus infection and its effect on hepatic CYP expression noted more long-term effects. An obvious approach toward understanding how viruses affect hepatic CYP3A expression and function would be to assess key regulators of CYP during infection. Improvements in techniques to identify post-translational modifications of CYP and systems that focus on virus-receptor interactions which allow subtraction and addition of immunological and regulatory elements that drive CYP will demonstrate that long-term changes in drug metabolism start from the time the virus enters the circulation, are reinforced by virus binding to cellular targets and further solidified by changes in cellular processes long after the virus is cleared.
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Affiliation(s)
- Maria A Croyle
- The University of Texas at Austin, College of Pharmacy, Division of Pharmaceutics and Institute of Cellular and Molecular Biology, PHR 4.214D, 2409 W University Avenue, Austin, TX 78712-1074, USA.
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29
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Carballeira J, Quezada M, Hoyos P, Simeó Y, Hernaiz M, Alcantara A, Sinisterra J. Microbial cells as catalysts for stereoselective red–ox reactions. Biotechnol Adv 2009; 27:686-714. [DOI: 10.1016/j.biotechadv.2009.05.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 04/26/2009] [Accepted: 05/04/2009] [Indexed: 01/31/2023]
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30
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Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Metagenomics as a new technological tool to gain scientific knowledge. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-9971-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Gamenara D, Domínguez de María P. Candida spp. redox machineries: an ample biocatalytic platform for practical applications and academic insights. Biotechnol Adv 2009; 27:278-85. [PMID: 19500548 DOI: 10.1016/j.biotechadv.2009.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Revised: 12/31/2008] [Accepted: 01/12/2009] [Indexed: 10/21/2022]
Abstract
The use of oxidoreductases as biocatalysts for the production of a wide number of chiral building blocks is presently a mature (bio-)technology. In this context some industrial applications are currently performed by means of those enzymatic approaches, and new examples are expected to be realized. Moreover, oxidoreductases provide an interesting academic platform to undertake fundamental research in enzymology, to acquire a better understanding on catalytic mechanisms, and to facilitate the development of new biocatalytic applications. Within this area, a wide number of oxidoreductases from genus Candida spp. have been characterized and used as biocatalysts. These enzymes are rather diverse, and are able to carry out many useful reactions, like highly (enantio)selective keto-reductions, (de)racemizations and stereoinversions, and promiscuous catalytic imine reductions. In addition, some Candida spp. dehydrogenases are very useful for regenerating the cofactors, with the aid of sacrificial substrates. Addressing those features, the present paper aims to give an overview of these enzymes, by focusing on practical applications that these biocatalysts can provide. Furthermore, when possible, academic insights on the enzymatic performances will be discussed as well.
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Affiliation(s)
- Daniela Gamenara
- Organic Chemistry Department, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
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32
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Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 2009; 33:236-55. [DOI: 10.1111/j.1574-6976.2008.00152.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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33
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Ferrer M, Beloqui A, Vieites JM, Guazzaroni ME, Berger I, Aharoni A. Interplay of metagenomics and in vitro compartmentalization. Microb Biotechnol 2008; 2:31-9. [PMID: 21261880 PMCID: PMC3815420 DOI: 10.1111/j.1751-7915.2008.00057.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In recent years, the application of approaches for harvesting DNA from the environment, the so-called, 'metagenomic approaches' has proven to be highly successful for the identification, isolation and generation of novel enzymes. Functional screening for the desired catalytic activity is one of the key steps in mining metagenomic libraries, as it does not rely on sequence homology. In this mini-review, we survey high-throughput screening tools, originally developed for directed evolution experiments, which can be readily adapted for the screening of large libraries. In particular, we focus on the use of in vitro compartmentalization (IVC) approaches to address potential advantages and problems the merger of culture-independent and IVC techniques might bring on the mining of enzyme activities in microbial communities.
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Affiliation(s)
- Manuel Ferrer
- CSIC, Institute of Catalysis, Department of Applied Biocatalysis, Madrid, Spain.
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