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Chuzel L, Sinha A, Cunningham CV, Taron CH. High-throughput nanopore DNA sequencing of large insert fosmid clones directly from bacterial colonies. Appl Environ Microbiol 2024; 90:e0024324. [PMID: 38767355 PMCID: PMC11218629 DOI: 10.1128/aem.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/21/2024] [Indexed: 05/22/2024] Open
Abstract
Fosmids and cosmids are vectors frequently used in functional metagenomic studies. With a large insert capacity (around 30 kb) they can encode dozens of cloned genes or in some cases, entire biochemical pathways. Fosmids with cloned inserts can be transferred to heterologous hosts and propagated to enable screening for new enzymes and metabolites. After screening, fosmids from clones with an activity of interest must be de novo sequenced, a critical step toward the identification of the gene(s) of interest. In this work, we present a new approach for rapid and high-throughput fosmid sequencing directly from Escherichia coli colonies without liquid culturing or fosmid purification. Our sample preparation involves fosmid amplification with phi29 polymerase and then direct nanopore sequencing using the Oxford Nanopore Technologies system. We also present a bioinformatics pipeline termed "phiXXer" that facilitates both de novo read assembly and vector trimming to generate a linear sequence of the fosmid insert. Finally, we demonstrate the accurate sequencing of 96 fosmids in a single run and validate the method using two fosmid libraries that contain cloned large insert (~30-40 kb) genomic or metagenomic DNA.IMPORTANCELarge-insert clone (fosmids or cosmids) sequencing is challenging and arguably the most limiting step of functional metagenomic screening workflows. Our study establishes a new method for high-throughput nanopore sequencing of fosmid clones directly from lysed Escherichia coli cells. It also describes a companion bioinformatic pipeline that enables de novo assembly of fosmid DNA insert sequences. The devised method widens the potential of functional metagenomic screening by providing a simple, high-throughput approach to fosmid clone sequencing that dramatically speeds the pace of discovery.
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Affiliation(s)
- Léa Chuzel
- New England Biolabs, Ipswich, Massachusetts, USA
| | - Amit Sinha
- New England Biolabs, Ipswich, Massachusetts, USA
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2
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Sumida T, Hiraoka S, Usui K, Ishiwata A, Sengoku T, Stubbs KA, Tanaka K, Deguchi S, Fushinobu S, Nunoura T. Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun 2024; 15:3543. [PMID: 38730244 PMCID: PMC11087588 DOI: 10.1038/s41467-024-47653-2] [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: 08/23/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Keiko Usui
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Saburi W, Ota T, Kato K, Tagami T, Yamashita K, Yao M, Mori H. Function and Structure of Lacticaseibacillus casei GH35 β-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N-biose I and Galacto- N-biose. J Appl Glycosci (1999) 2023; 70:43-52. [PMID: 37599861 PMCID: PMC10432377 DOI: 10.5458/jag.jag.jag-2022_0014] [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: 12/02/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
β-Galactosidase (EC 3.2.1.23) hydrolyzes β-D-galactosidic linkages at the non-reducing end of substrates to produce β-D-galactose. Lacticaseibacillus casei is one of the most widely utilized probiotic species of lactobacilli. It possesses a putative β-galactosidase belonging to glycoside hydrolase family 35 (GH35). This enzyme is encoded by the gene included in the gene cluster for utilization of lacto-N-biose I (LNB; Galβ1-3GlcNAc) and galacto-N-biose (GNB; Galβ1-3GalNAc) via the phosphoenolpyruvate: sugar phosphotransferase system. The GH35 protein (GnbG) from L. casei BL23 is predicted to be 6-phospho-β-galactosidase (EC 3.2.1.85). However, its 6-phospho-β-galactosidase activity has not yet been examined, whereas its hydrolytic activity against LNB and GNB has been demonstrated. In this study, L. casei JCM1134 LBCZ_0230, homologous to GnbG, was characterized enzymatically and structurally. A recombinant LBCZ_0230, produced in Escherichia coli, exhibited high hydrolytic activity toward o-nitrophenyl β-D-galactopyranoside, p-nitrophenyl β-D-galactopyranoside, LNB, and GNB, but not toward o-nitrophenyl 6-phospho-β-D-galactopyranoside. Crystal structure analysis indicates that the structure of subsite -1 of LBCZ_0230 is very similar to that of Streptococcus pneumoniae β-galactosidase BgaC and not suitable for binding to 6-phospho-β-D-galactopyranoside. These biochemical and structural analyses indicate that LBCZ_0230 is a β-galactosidase. According to the prediction of LNB's binding mode, aromatic residues, Trp190, Trp240, Trp243, Phe244, and Tyr458, form hydrophobic interactions with N-acetyl-D-glucosamine residue of LNB at subsite +1.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University
| | - Tomoya Ota
- Research Faculty of Agriculture, Hokkaido University
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University
| | | | | | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University
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4
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Thakor A, Cheng J, Charles TC. Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities. Methods Mol Biol 2023; 2555:115-123. [PMID: 36306082 DOI: 10.1007/978-1-0716-2795-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The ability to produce high-value products using bacteria will increasingly rely on continued research to make large-scale bacterial fermentation cost-efficient. Engineering bacteria to use alternate carbon sources as feedstock provides an opportunity to reduce production costs. Using inexpensive carbon sources from various forms of waste provides an opportunity to substantially reduce feedstock costs. Functional carbon metabolism pathways can be identified by the introduction of metagenomic libraries into the organism of interest followed by screening for the desired phenotype. We present here a method to transfer metagenomic libraries from E. coli to Pseudomonas alloputida, followed by screening for use of galactose as a sole carbon source.
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Affiliation(s)
- Aranksha Thakor
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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5
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Du M, Yang S, Jiang T, Liang T, Li Y, Cai S, Wu Q, Zhang J, Chen W, Xie X. Cloning, Expression, Purification, and Characterization of β-Galactosidase from Bifidobacterium longum and Bifidobacterium pseudocatenulatum. Molecules 2022; 27:molecules27144497. [PMID: 35889370 PMCID: PMC9323360 DOI: 10.3390/molecules27144497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023] Open
Abstract
Expression and purification of β-galactosidases derived from Bifidobacterium provide a new resource for efficient lactose hydrolysis and lactose intolerance alleviation. Here, we cloned and expressed two β-galactosidases derived from Bifidobacterium. The optimal pH for BLGLB1 was 5.5, and the optimal temperature was 45 °C, at which the enzyme activity of BLGLB1 was higher than that of commercial enzyme E (300 ± 3.6 U/mg) under its optimal conditions, reaching 2200 ± 15 U/mg. The optimal pH and temperature for BPGLB1 were 6.0 and 45 °C, respectively, and the enzyme activity (0.58 ± 0.03 U/mg) under optimum conditions was significantly lower than that of BLGLB1. The structures of the two β-galactosidase were similar, with all known key sites conserved. When o-nitrophenyl-β-D-galactoside (oNPG) was used as an enzyme reaction substrate, the maximum reaction velocity (Vmax) for BLGLB1 and BPGLB1 was 3700 ± 100 U/mg and 1.1 ± 0.1 U/mg, respectively. The kinetic constant (Km) of BLGLB1 and BPGLB1 was 1.9 ± 0.1 and 1.3 ± 0.3 mmol/L, respectively. The respective catalytic constant (kcat) of BLGLB1 and BPGLB1 was 1700 ± 40 s−1 and 0.5 ± 0.02 s−1, respectively; the respective kcat/Km value of BLGLB1 and BPGLB1 was 870 L/(mmol∙s) and 0.36 L/(mmol∙s), respectively. The Km, kcat and Vmax values of BLGLB1 were superior to those of earlier reported β-galactosidase derived from Bifidobacterium. Overall, BLGLB1 has potential application in the food industry.
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Affiliation(s)
- Mingzhu Du
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (M.D.); (S.Y.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Shuanghong Yang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (M.D.); (S.Y.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Tong Jiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Tingting Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Shuzhen Cai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
- Correspondence: (J.Z.); (W.C.); (X.X.)
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (M.D.); (S.Y.)
- Correspondence: (J.Z.); (W.C.); (X.X.)
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (T.J.); (T.L.); (Y.L.); (S.C.); (Q.W.)
- Correspondence: (J.Z.); (W.C.); (X.X.)
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6
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Neun S, Brear P, Campbell E, Tryfona T, El Omari K, Wagner A, Dupree P, Hyvönen M, Hollfelder F. Functional metagenomic screening identifies an unexpected β-glucuronidase. Nat Chem Biol 2022; 18:1096-1103. [PMID: 35799064 DOI: 10.1038/s41589-022-01071-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently 'unpredictable' by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >107 library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.
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Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Eleanor Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Australian Synchrotron, Clayton, VIC, Australia
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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A novel salt-tolerant GH42 β-galactosidase with transglycosylation activity from deep-sea metagenome. World J Microbiol Biotechnol 2022; 38:154. [PMID: 35796808 DOI: 10.1007/s11274-022-03348-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
Abstract
β-Galactosidase is a widely adopted enzyme in the food and pharmaceutical industries. Metagenome techniques have the advantage of discovering novel functional genes, particularly potential genes from uncultivated microbes. In this study, a novel GH42 β-galactosidase isolated from a deep-sea metagenome was overexpressed in Escherichia coli BL21 (DE3) and purified by affinity chromatography. The optimal temperatures and pH of the enzyme for o-nitrophenyl-β-D-galactopyranoside (oNPG) and lactose were 40 ℃, 6.5 and 50 ℃, 7, respectively. The enzyme was stable at temperatures between 4 and 30 ℃ and within the pH range of 6-9. Moreover, it was highly tolerant to salt and inhibited by Zn2+ and Cu2+. The kinetic values of Km and kcat of the enzyme against oNPG were 1.1 mM and 57.8 s-1, respectively. Furthermore, it showed hydrolysis and transglycosylation activity to lactose and the extra monosaccharides could improve the productivity of oligosaccharides. Overall, this recombinant β-galactosidase is a potential biocatalyst for the hydrolysis of milk lactose and synthesis of functional oligosaccharides.
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8
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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9
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Tatta ER, Imchen M, Moopantakath J, Kumavath R. Bioprospecting of microbial enzymes: current trends in industry and healthcare. Appl Microbiol Biotechnol 2022; 106:1813-1835. [PMID: 35254498 DOI: 10.1007/s00253-022-11859-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022]
Abstract
Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.
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Affiliation(s)
- Eswar Rao Tatta
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India.
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10
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Zhang L, Chen F, Zeng Z, Xu M, Sun F, Yang L, Bi X, Lin Y, Gao Y, Hao H, Yi W, Li M, Xie Y. Advances in Metagenomics and Its Application in Environmental Microorganisms. Front Microbiol 2022; 12:766364. [PMID: 34975791 PMCID: PMC8719654 DOI: 10.3389/fmicb.2021.766364] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/04/2023] Open
Abstract
Metagenomics is a new approach to study microorganisms obtained from a specific environment by functional gene screening or sequencing analysis. Metagenomics studies focus on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, and interactions and relationships with the environment. Sequencing technologies have evolved from shotgun sequencing to high-throughput, next-generation sequencing (NGS), and third-generation sequencing (TGS). NGS and TGS have shown the advantage of rapid detection of pathogenic microorganisms. With the help of new algorithms, we can better perform the taxonomic profiling and gene prediction of microbial species. Functional metagenomics is helpful to screen new bioactive substances and new functional genes from microorganisms and microbial metabolites. In this article, basic steps, classification, and applications of metagenomics are reviewed.
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Affiliation(s)
- Lu Zhang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - FengXin Chen
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhan Zeng
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Mengjiao Xu
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Sun
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Liu Yang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaoyue Bi
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yanjie Lin
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - YuanJiao Gao
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - HongXiao Hao
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Wei Yi
- Department of Gynecology and Obstetrics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
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11
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Metagenomic identification, purification and characterisation of the Bifidobacterium adolescentis BgaC β-galactosidase. Appl Microbiol Biotechnol 2021; 105:1063-1078. [PMID: 33427933 PMCID: PMC7843569 DOI: 10.1007/s00253-020-11084-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/19/2020] [Accepted: 12/27/2020] [Indexed: 11/27/2022]
Abstract
Members of the human gut microbiota use glycoside hydrolase (GH) enzymes, such as β-galactosidases, to forage on host mucin glycans and dietary fibres. A human faecal metagenomic fosmid library was constructed and functionally screened to identify novel β-galactosidases. Out of the 16,000 clones screened, 30 β-galactosidase-positive clones were identified. The β-galactosidase gene found in the majority of the clones was BAD_1582 from Bifidobacterium adolescentis, subsequently named bgaC. This gene was cloned with a hexahistidine tag, expressed in Escherichia coli and His-tagged-BgaC was purified using Ni2+-NTA affinity chromatography and size filtration. The enzyme had optimal activity at pH 7.0 and 37 °C, with a wide range of pH (4–10) and temperature (0–40 °C) stability. It required a divalent metal ion co-factor; maximum activity was detected with Mg2+, while Cu2+ and Mn2+ were inhibitory. Kinetic parameters were determined using ortho-nitrophenyl-β-d-galactopyranoside (ONPG) and lactose substrates. BgaC had a Vmax of 107 μmol/min/mg and a Km of 2.5 mM for ONPG and a Vmax of 22 μmol/min/mg and a Km of 3.7 mM for lactose. It exhibited low product inhibition by galactose with a Ki of 116 mM and high tolerance for glucose (66% activity retained in presence of 700 mM glucose). In addition, BgaC possessed transglycosylation activity to produce galactooligosaccharides (GOS) from lactose, as determined by TLC and HPLC analysis. The enzymatic characteristics of B. adolescentis BgaC make it an ideal candidate for dairy industry applications and prebiotic manufacture. Key points • Bifidobacterium adolescentis BgaC β-galactosidase was selected from human faecal metagenome. • BgaC possesses sought-after properties for biotechnology, e.g. low product inhibition. • BgaC has transglycosylation activity producing prebiotic oligosaccharides. Graphical Abstract ![]()
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12
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Eberhardt MF, Irazoqui JM, Amadio AF. β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization. Microorganisms 2020; 9:microorganisms9010055. [PMID: 33379234 PMCID: PMC7823827 DOI: 10.3390/microorganisms9010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds' metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries' by-products.
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Santana-Pereira ALR, Sandoval-Powers M, Monsma S, Zhou J, Santos SR, Mead DA, Liles MR. Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library. Front Microbiol 2020; 11:585398. [PMID: 33365020 PMCID: PMC7750434 DOI: 10.3389/fmicb.2020.585398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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Affiliation(s)
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | - Jinglie Zhou
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Scott R. Santos
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Varigen Biosciences Corporation, Madison, WI, United States
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Verma D, Satyanarayana T. Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications. Front Microbiol 2020; 11:551109. [PMID: 33042057 PMCID: PMC7527525 DOI: 10.3389/fmicb.2020.551109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/21/2020] [Indexed: 01/29/2023] Open
Abstract
Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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Alexa Oniciuc EA, Walsh CJ, Coughlan LM, Awad A, Simon CA, Ruiz L, Crispie F, Cotter PD, Alvarez-Ordóñez A. Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics. mSystems 2020; 5:e00723-19. [PMID: 32071160 PMCID: PMC7029220 DOI: 10.1128/msystems.00723-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/22/2020] [Indexed: 12/16/2022] Open
Abstract
Here, the role of the dairy-processing chain as a reservoir of antimicrobial resistance (AR) determinants and a source of novel biocontrol quorum-sensing inhibitors is assessed through a functional metagenomics approach. A metagenomic library comprising ∼22,000 recombinant clones was built from DNA isolated from raw milk, raw milk cheeses, and cheese-processing environment swab samples. The high-throughput sequencing of 9,216 recombinant clones showed that lactic acid bacteria (LAB) dominated the microbial communities of raw milk cheese, while Gram-negative microorganisms of animal or soil origin dominated the microbiota of raw milk and cheese-processing environments. Although functional screening of the metagenomic library did not recover potential quorum-sensing inhibitors, in silico analysis using an in-house database built specifically for this study identified homologues to several genes encoding proteins with predicted quorum-quenching activity, among which, the QsdH hydrolase was the most abundant. In silico screening of the library identified LAB, and especially Lactococcus lactis, as a relevant reservoir of AR determinants in cheese. Functional screening of the library allowed the isolation of 13 recombinant clones showing an increased resistance toward ampicillin, which in all cases was accompanied by a reduced susceptibility to a wide range of β-lactam antibiotics. This study shows that the dairy-processing environment is a rich reservoir of AR determinants, which vary by sample source, and suggests that combining next-generation sequencing with functional metagenomics can be of use in overcoming the limitations of both approaches.IMPORTANCE The study shows the potential of functional metagenomics analyses to uncover the diversity of functions in microbial communities prevailing in dairy products and their processing environments, evidencing that lactic acid bacteria (LAB) dominate the cheese microbiota, whereas Gram-negative microorganisms of animal or soil origin dominate the microbiota of milk and cheese-processing environments. The functional and in silico screening of the library allowed the identification of LAB, and especially Lactococcus lactis, as a relevant reservoir of antimicrobial resistance (AR) determinants in cheese. Quorum-quenching (QQ) determinants were not recovered through the execution of wet-lab function-based screenings but were detected through in silico sequencing-based analyses.
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Affiliation(s)
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Amal Awad
- Bacteriology, Mycology and Immunology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Cezara A Simon
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
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Kulichevskaya IS, Naumoff DG, Miroshnikov KK, Ivanova AA, Philippov DA, Hakobyan A, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN. Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. Int J Syst Evol Microbiol 2020; 70:1240-1249. [PMID: 31800383 PMCID: PMC7397252 DOI: 10.1099/ijsem.0.003904] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/16/2019] [Indexed: 11/18/2022] Open
Abstract
The family Gemmataceae accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52T, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52T was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were C18 : 1ɷ7c, C18 : 0 and βOH-C16:0; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52T was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52T displayed only 86.0-89.8 % 16S rRNA gene sequence similarity to taxonomically described Gemmataceae planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, Limnoglobus roseus gen. nov., sp. nov. The type strain is strain PX52T (=KCTC 72397T=VKM B-3275T).
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Affiliation(s)
- Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G. Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Anna Hakobyan
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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18
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A new β-galactosidase extracted from the infant feces with high hydrolytic and transgalactosylation activity. Appl Microbiol Biotechnol 2019; 103:8439-8448. [DOI: 10.1007/s00253-019-10092-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 02/05/2023]
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Willms IM, Kamran A, Aßmann NF, Krone D, Bolz SH, Fiedler F, Nacke H. Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes. Front Microbiol 2019; 10:460. [PMID: 30899254 PMCID: PMC6416219 DOI: 10.3389/fmicb.2019.00460] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/21/2019] [Indexed: 01/06/2023] Open
Abstract
Soil represents a significant reservoir of antibiotic resistance genes (ARGs), which can potentially spread across distinct ecosystems and be acquired by pathogens threatening human as well as animal health. Currently, information on the identity and diversity of these genes, enabling anticipation of possible future resistance development in clinical environments and the livestock sector, is lacking. In this study, we applied functional metagenomics to discover novel sulfonamide as well as tetracycline resistance genes in soils derived from forest and grassland. Screening of soil metagenomic libraries revealed a total of eight so far unknown ARGs. The recovered genes originate from phylogenetically diverse soil bacteria (e.g., Actinobacteria, Chloroflexi, or Proteobacteria) and encode proteins with a minimum identity of 46% to other antibiotic resistance determinants. In particular forest soil ecosystems have so far been neglected in studies focusing on antibiotic resistance. Here, we detected for the first time non-mobile dihydropteroate synthase (DHPS) genes conferring resistance to sulfonamides in forest soil with no history of exposure to these synthetic drugs. In total, three sulfonamide resistant DHPSs, differing in taxonomic origin, were discovered in beech or pine forest soil. This indicates that sulfonamide resistance naturally occurs in forest-resident soil bacterial communities. Besides forest soil-derived sulfonamide resistance proteins, we also identified a DHPS affiliated to Chloroflexi in grassland soil. This enzyme and the other recovered DHPSs confer reduced susceptibility toward sulfamethazine, which is widely used in food animal production. With respect to tetracycline resistance, four efflux proteins affiliated to the major facilitator superfamily (MFS) were identified. Noteworthy, one of these proteins also conferred reduced susceptibility toward lincomycin.
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Affiliation(s)
- Inka Marie Willms
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Aysha Kamran
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Nils Frederik Aßmann
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Denis Krone
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Simon Henning Bolz
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Fabian Fiedler
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
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Brahami A, Castonguay A, Déziel É. Novel 'Bacteriospray' Method Facilitates the Functional Screening of Metagenomic Libraries for Antimicrobial Activity. Methods Protoc 2019; 2:mps2010004. [PMID: 31164589 PMCID: PMC6481063 DOI: 10.3390/mps2010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/29/2018] [Accepted: 01/01/2019] [Indexed: 01/14/2023] Open
Abstract
Metagenomic techniques, notably the cloning of environmental DNA (eDNA) into surrogate hosts, have given access to the genome of uncultured bacteria. However, the determination of gene functions based on DNA sequences alone remains a significant challenge. The functional screening of metagenomic libraries represents an interesting approach in the discovery of microbial metabolites. We describe here an optimized screening approach that facilitates the identification of new antimicrobials among large metagenomic libraries. Notably, we report a detailed genomic library construction protocol using Escherichia coli DH10B as a surrogate host, and demonstrate how vector/genomic DNA dephosphorylation, ligase inactivation, dialysis of the ligation product and vector/genomic DNA ratio greatly influence clone recovery. Furthermore, we describe the use of an airbrush device to screen E. coli metagenomic libraries for their antibacterial activity against Staphylococcus aureus, a method we called bacteriospray. This bacterial spraying tool greatly facilitates and improves the functional screening of large genomic libraries, as it conveniently allows the production of a thinner and more uniform layer of target bacteria compared to the commonly used overlay method, resulting in the screening of 5–10 times more clones per agar plate. Using the Burkholderia thailandensis E264 genomic DNA as a proof of concept, four clones out of 70,000 inhibited the growth of S. aureus and were found to each contain a DNA insert. Analysis of these chromosomic fragments revealed genomic regions never previously reported to be responsible for the production of antimicrobials, nor predicted by bioinformatics tools.
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Affiliation(s)
- Anissa Brahami
- INRS-Institut Armand-Frappier, Laval, QC H7V 1B7, Canada.
| | | | - Éric Déziel
- INRS-Institut Armand-Frappier, Laval, QC H7V 1B7, Canada.
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Thornbury M, Sicheri J, Slaine P, Getz LJ, Finlayson-Trick E, Cook J, Guinard C, Boudreau N, Jakeman D, Rohde J, McCormick C. Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics. PLoS One 2019; 14:e0209221. [PMID: 30601862 PMCID: PMC6314593 DOI: 10.1371/journal.pone.0209221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5–7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.
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Affiliation(s)
- Mackenzie Thornbury
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jacob Sicheri
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick Slaine
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Landon J. Getz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emma Finlayson-Trick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Caroline Guinard
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nicholas Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Jakeman
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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Naumoff DG, Dedysh SN. Bacteria from Poorly Studied Phyla as a Potential Source of New Enzymes: β-Galactosidases from Planctomycetes and Verrucomicrobia. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718060127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Chuzel L, Ganatra MB, Rapp E, Henrissat B, Taron CH. Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156). J Biol Chem 2018; 293:18138-18150. [PMID: 30249617 PMCID: PMC6254351 DOI: 10.1074/jbc.ra118.003302] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.
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Affiliation(s)
- Léa Chuzel
- From New England Biolabs, Ipswich, Massachusetts 01938,; the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | | | - Erdmann Rapp
- the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany,; glyXera GmbH, 39120 Magdeburg, Germany
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France,; the Institut National de la Recherche Agronomique (INRA), Unité Sous Contrat (USC) 1408, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France, and; the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Sato M, Suda M, Okuma J, Kato T, Hirose Y, Nishimura A, Kondo Y, Shibata D. Isolation of highly thermostable β-xylosidases from a hot spring soil microbial community using a metagenomic approach. DNA Res 2018; 24:649-656. [PMID: 29106502 PMCID: PMC5726482 DOI: 10.1093/dnares/dsx032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022] Open
Abstract
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene. Individual genes were amplified by PCR using sequence-specific primers. The resultant DNA fragments were cloned and introduced into Escherichia coli BL21 Star(DE3). Consequently, 269 proteins were successfully expressed in the E. coli cells and then examined for β-xylosidase activity. A total of 82 proteins exhibited β-xylosidase activity at 50°C, six of which retained the activity even at 90°C. Out of the six, three proteins were originated from a single candidate sequence, AR19M-311. An amino acid sequence comparison suggested the amino acid residues that appeared to be crucial for thermal stability of the enzymes.
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Affiliation(s)
- Masaru Sato
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Migiwa Suda
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Jiro Okuma
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Tomohiko Kato
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshitsugu Hirose
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Asuka Nishimura
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Yasuhiko Kondo
- Honda Research Institute Japan Co., Ltd., Wako, Saitama 351-0188, Japan
| | - Daisuke Shibata
- Department of Biotechnology Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Castilla IA, Woods DF, Reen FJ, O'Gara F. Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies. Mar Drugs 2018; 16:E227. [PMID: 29973493 PMCID: PMC6071119 DOI: 10.3390/md16070227] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023] Open
Abstract
In a demanding commercial world, large-scale chemical processes have been widely utilised to satisfy consumer related needs. Chemical industries are key to promoting economic growth and meeting the requirements of a sustainable industrialised society. The market need for diverse commodities produced by the chemical industry is rapidly expanding globally. Accompanying this demand is an increased threat to the environment and to human health, due to waste produced by increased industrial production. This increased demand has underscored the necessity to increase reaction efficiencies, in order to reduce costs and increase profits. The discovery of novel biocatalysts is a key method aimed at combating these difficulties. Metagenomic technology, as a tool for uncovering novel biocatalysts, has great potential and applicability and has already delivered many successful achievements. In this review we discuss, recent developments and achievements in the field of biocatalysis. We highlight how green chemistry principles through the application of biocatalysis, can be successfully promoted and implemented in various industrial sectors. In addition, we demonstrate how two novel lipases/esterases were mined from the marine environment by metagenomic analysis. Collectively these improvements can result in increased efficiency, decreased energy consumption, reduced waste and cost savings for the chemical industry.
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Affiliation(s)
- Ignacio Abreu Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
- Telethon Kids Institute, Perth, WA 6008, Australia.
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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