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Wang S, Li X, Yang W, Huang R. Exploring the secrets of marine microorganisms: Unveiling secondary metabolites through metagenomics. Microb Biotechnol 2024; 17:e14533. [PMID: 39075735 PMCID: PMC11286668 DOI: 10.1111/1751-7915.14533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024] Open
Abstract
Marine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many of these organisms are unculturable, posing challenges for study. Metagenomic techniques enable research on these unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to marine microbial secondary metabolites, thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering marine microbial secondary metabolites, highlighting tools commonly employed in BGC identification, and discussing the potential and challenges in this field. It emphasizes the key role of metagenomics in unveiling secondary metabolites, particularly in marine sponges and tunicates. The review also explores current limitations in studying these metabolites through metagenomics, noting how long-read sequencing technologies and the evolution of computational biology tools offer more possibilities for BGC discovery. Furthermore, the development of synthetic biology allows experimental validation of computationally identified BGCs, showcasing the vast potential of metagenomics in mining marine microbial secondary metabolites.
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Affiliation(s)
- Shaoyu Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
| | - Xinyan Li
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
| | - Weiqin Yang
- School of Computer Science and TechnologyShandong UniversityQingdaoShandongChina
| | - Ranran Huang
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
- Global Ocean Negative Carbon Emissions (ONCE) Program AllianceQingdaoChina
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Maldonado-Ruiz K, Pedroza-Islas R, Pedraza-Segura L. Blue Biotechnology: Marine Bacteria Bioproducts. Microorganisms 2024; 12:697. [PMID: 38674641 PMCID: PMC11051736 DOI: 10.3390/microorganisms12040697] [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: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.
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Affiliation(s)
| | - Ruth Pedroza-Islas
- Department of Chemical, Industrial and Food Engineering, Universidad Iberoamericana, Prol. Paseo de la Reforma 880, Lomas de Santa Fe, Mexico City 01210, Mexico; (K.M.-R.); (L.P.-S.)
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3
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Lavecchia A, Fosso B, Engelen AH, Borin S, Manzari C, Picardi E, Pesole G, Placido A. Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism. MICROBIOME 2024; 12:47. [PMID: 38454513 PMCID: PMC10919026 DOI: 10.1186/s40168-023-01740-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules. RESULTS To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites. CONCLUSION The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.
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Affiliation(s)
- Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Aschwin H Engelen
- Center of Marine Sciences (CCMar), University of Algarve, Campus Gambelas, Faro, 8005-139, Portugal
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Antonio Placido
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy.
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Peters MK, Astafyeva Y, Han Y, Macdonald JFH, Indenbirken D, Nakel J, Virdi S, Westhoff G, Streit WR, Krohn I. Novel marine metalloprotease-new approaches for inhibition of biofilm formation of Stenotrophomonas maltophilia. Appl Microbiol Biotechnol 2023; 107:7119-7134. [PMID: 37755512 PMCID: PMC10638167 DOI: 10.1007/s00253-023-12781-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Many marine organisms produce bioactive molecules with unique characteristics to survive in their ecological niches. These enzymes can be applied in biotechnological processes and in the medical sector to replace aggressive chemicals that are harmful to the environment. Especially in the human health sector, there is a need for new approaches to fight against pathogens like Stenotrophomonas maltophilia which forms thick biofilms on artificial joints or catheters and causes serious diseases. Our approach was to use enrichment cultures of five marine resources that underwent sequence-based screenings in combination with deep omics analyses in order to identify enzymes with antibiofilm characteristics. Especially the supernatant of the enrichment culture of a stony coral caused a 40% reduction of S. maltophilia biofilm formation. In the presence of the supernatant, our transcriptome dataset showed a clear stress response (upregulation of transcripts for metal resistance, antitoxins, transporter, and iron acquisition) to the treatment. Further investigation of the enrichment culture metagenome and proteome indicated a series of potential antimicrobial enzymes. We found an impressive group of metalloproteases in the proteome of the supernatant that is responsible for the detected anti-biofilm effect against S. maltophilia. KEY POINTS: • Omics-based discovery of novel marine-derived antimicrobials for human health management by inhibition of S. maltophilia • Up to 40% reduction of S. maltophilia biofilm formation by the use of marine-derived samples • Metalloprotease candidates prevent biofilm formation of S. maltophilia K279a by up to 20.
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Affiliation(s)
- Marie Kristin Peters
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Jacqueline Nakel
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Sanamjeet Virdi
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Guido Westhoff
- Tierpark Hagenbeck, Gemeinnützige Gesellschaft mbH, Lokstedter Grenzstraße 2, 22527, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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5
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Lou D, Zhang X, Cao Y, Zhou Z, Liu C, Kuang G, Tan J, Zhu L. A novel NADP(H)-dependent 3α-HSDH from the intestinal microbiome of Ursus thibetanus. Int J Biol Macromol 2022; 219:159-165. [PMID: 35934074 DOI: 10.1016/j.ijbiomac.2022.07.252] [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: 06/13/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/05/2022]
Abstract
3α-HSDHs have a crucial role in the bioconversion of steroids, and have been widely applied in the detection of total bile acid (TBA). In this study, we report a novel NADP(H)-dependent 3α-HSDH (named Sc 3α-HSDH) cloned from the intestinal microbiome of Ursus thibetanus. Sc 3α-HSDH was solubly expressed in E. coli (BL21) as a recombinant glutathione-S-transferase (GST)-tagged protein and freed from its GST-fusion by cleavage using the PreScission protease. Sc 3α-HSDH is a new member of the short-chain dehydrogenases/reductase superfamily (SDRs) with a typical α/β folding pattern, based on protein three-dimensional models predicted by AlphaFold. The best activity of Sc 3α-HSDH occurred at pH 8.5 and the temperature optima was 55 °C, indicating that Sc 3α-HSDH is not an extremozyme. The catalytic efficiencies (kcat/Km) of Sc 3α-HSDH catalyzing the oxidation reaction with the substrates, glycochenodeoxycholic acid (GCDCA) and glycoursodeoxycholic acid (GUDCA), were 183.617 and 34.458 s-1 mM-1, respectively. In addition, multiple metal ions can enhance the activity of Sc 3α-HSDH when used at concentrations ranging from 2 % to 42 %. The results also suggest that the metagenomic approach is an efficient method for identifying novel enzymes.
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Affiliation(s)
- Deshuai Lou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China.
| | - Xiaoli Zhang
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Yangyang Cao
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Zixin Zhou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Cheng Liu
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Gang Kuang
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China.
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Alma'abadi A, Behzad H, Alarawi M, Conchouso D, Saito Y, Hosokawa M, Nishikawa Y, Kogawa M, Takeyama H, Mineta K, Gojobori T. Identification of Lipolytic Enzymes Using High-Throughput Single-cell Screening and Sorting of a Metagenomic Library. N Biotechnol 2022; 70:102-108. [PMID: 35636700 DOI: 10.1016/j.nbt.2022.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
Abstract
The demand for novel, robust microbial biocatalysts for use in industrial and pharmaceutical applications continues to increase rapidly. As a result, there is a need to develop advanced tools and technologies to exploit the vast metabolic potential of unculturable microorganisms found in various environments. Single-cell and functional metagenomics studies can explore the enzymatic potential of entire microbial communities in a given environment without the need to culture the microorganisms. This approach has contributed substantially to the discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples, constructing expression libraries comprising the entire microbial genome, and screening of the libraries for the presence of desired phenotypes. In this study, lipolytic enzymes from the Red Sea were targeted. A high-throughput single-cell microfluidic platform combined with a laser-based fluorescent screening bioassay was employed to discover new genes encoding lipolytic enzymes. Analysis of the metagenomic library led to the identification of three microbial genes encoding lipases based on their functional similarity and sequence homology to known lipases. The results demonstrated that microfluidics is a robust technology that can be used for screening in functional metagenomics. The results also indicate that the Red Sea is a promising, under-investigated source of new genes and gene products.
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Affiliation(s)
- Amani Alma'abadi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, National Center of Biotechnology, P.O Box 6086, Riyadh 11442, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - David Conchouso
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Puebla 72453, Mexico
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Marine Open Innovation (MaOI) Institute, 9-25, Hinodecho, Shimizu-ku, Shizuoka 424-0922, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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7
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Zhang Y, Guan F, Xu G, Liu X, Zhang Y, Sun J, Yao B, Huang H, Wu N, Tian J. A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem. BIORESOUR BIOPROCESS 2022; 9:54. [PMID: 38647756 PMCID: PMC10991277 DOI: 10.1186/s40643-022-00543-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/27/2022] [Indexed: 12/27/2022] Open
Abstract
Chitin is abundant in nature and its degradation products are highly valuable for numerous applications. Thermophilic chitinases are increasingly appreciated for their capacity to biodegrade chitin at high temperatures and prolonged enzyme stability. Here, using deep learning approaches, we developed a prediction tool, Preoptem, to screen thermophilic proteins. A novel thermophilic chitinase, Chi304, was mined directly from the marine metagenome. Chi304 showed maximum activity at 85 ℃, its Tm reached 89.65 ± 0.22℃, and exhibited excellent thermal stability at 80 and 90 °C. Chi304 had both endo- and exo-chitinase activities, and the (GlcNAc)2 was the main hydrolysis product of chitin-related substrates. The product yields of colloidal chitin degradation reached 97% within 80 min, and 20% over 4 days of reaction with crude chitin powder. This study thus provides a method to mine the novel thermophilic chitinase for efficient chitin biodegradation.
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Affiliation(s)
- Yan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jilu Sun
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Bin Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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8
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Polyextremophilic Chitinolytic Activity by a Marine Strain (IG119) of Clonostachys rosea. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030688. [PMID: 35163952 PMCID: PMC8838608 DOI: 10.3390/molecules27030688] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022]
Abstract
The investigation for novel unique extremozymes is a valuable business for which the marine environment has been overlooked. The marine fungus Clonostachys rosea IG119 was tested for growth and chitinolytic enzyme production at different combinations of salinity and pH using response surface methodology. RSM modelling predicted best growth in-between pH 3.0 and 9.0 and at salinity of 0-40‱, and maximum enzyme activity (411.137 IU/L) at pH 6.4 and salinity 0‱; however, quite high production (>390 IU/L) was still predicted at pH 4.5-8.5. The highest growth and activity were obtained, respectively, at pH 4.0 and 8.0, in absence of salt. The crude enzyme was tested at different salinities (0-120‱) and pHs (2.0-13.0). The best activity was achieved at pH 4.0, but it was still high (in-between 3.0 and 12.0) at pH 2.0 and 13.0. Salinity did not affect the activity in all tested conditions. Overall, C. rosea IG119 was able to grow and produce chitinolytic enzymes under polyextremophilic conditions, and its crude enzyme solution showed more evident polyextremophilic features. The promising chitinolytic activity of IG119 and the peculiar characteristics of its chitinolytic enzymes could be suitable for several biotechnological applications (i.e., degradation of salty chitin-rich materials and biocontrol of spoiling organisms, possibly solving some relevant environmental issues).
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Hou Q, Pucci F, Pan F, Xue F, Rooman M, Feng Q. Using metagenomic data to boost protein structure prediction and discovery. Comput Struct Biotechnol J 2022; 20:434-442. [PMID: 35070166 PMCID: PMC8760478 DOI: 10.1016/j.csbj.2021.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, metagenomic sequencing approaches have been providing an ever-increasing amount of protein sequence data at an astonishing rate. These constitute an invaluable source of information which has been exploited in various research fields such as the study of the role of the gut microbiota in human diseases and aging. However, only a small fraction of all metagenomic sequences collected have been functionally or structurally characterized, leaving much of them completely unexplored. Here, we review how this information has been used in protein structure prediction and protein discovery. We begin by presenting some widely used metagenomic databases and analyze in detail how metagenomic data has contributed to the impressive improvement in the accuracy of structure prediction methods in recent years. We then examine how metagenomic information can be exploited to annotate protein sequences. More specifically, we focus on the role of metagenomes in the discovery of enzymes and new CRISPR-Cas systems, and in the identification of antibiotic resistance genes. With this review, we provide an overview of how metagenomic data is currently revolutionizing our understanding of protein science.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fengming Pan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Qiang Feng
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Department of Human Microbiome, School of Stomatology, Shandong University, Jinan, Shandong Province 250012, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province 266237, China
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Mining marine metagenomes revealed a quorum-quenching lactonase with improved biochemical properties that inhibits the food spoilage bacteria Pseudomonas fluorescens. Appl Environ Microbiol 2021; 88:e0168021. [PMID: 34910563 DOI: 10.1128/aem.01680-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine environment presents great potential as a source of microorganisms that possess novel enzymes with unique activities and biochemical properties. Examples of such are the quorum-quenching (QQ) enzymes that hydrolyze bacterial quorum-sensing (QS) signaling molecules, such as N-acyl-homoserine lactones (AHLs). QS is a form of cell-to-cell communication that enables bacteria to synchronize gene expression in correlation with population density. Searching marine metagenomes for sequences homologous to an AHL lactonase from the phosphotriesterase-like lactonase (PLL) family, we identified new putative AHL lactonases (sharing 30-40% amino acid identity to a thermostable PLL member). Phylogenetic analysis indicated that these putative AHL lactonases comprise a new clade of marine enzymes in the PLL family. Following recombinant expression and purification, we verified the AHL lactonase activity for one of these proteins, named marine originated Lactonase Related Protein (moLRP). This enzyme presented greater activity and stability at a broad range of temperatures and pH, and tolerance to high salinity levels (up to 5M NaCl), as well as higher durability in bacterial culture, compared to another PLL member. The addition of purified moLRP to cultures of Pseudomonas fluorescens inhibited its extracellular protease activity, expression of the protease encoding gene, biofilm formation, and the sedimentation process in milk-based medium. These findings suggest that moLRP is adapted to the marine environment, and can potentially serve as an effective QQ enzyme, inhibiting the QS process in gram-negative bacteria involved in food spoilage. Importance Our results emphasize the potential of sequence and structure-based identification of new quorum-quenching (QQ) enzymes from environmental metagenomes, such as from the ocean, with improved stability or activity. The findings also suggest that purified QQ enzymes can present new strategies against food spoilage, in addition to their recognized involvement in inhibiting bacterial pathogen virulence factors. Future studies on the delivery and safety of enzymatic QQ strategy against bacterial food spoilage should be performed.
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Abstract
Proteases are ubiquitous enzymes, having significant physiological roles in both synthesis and degradation. The use of microbial proteases in food fermentation is an age-old process, which is today being successfully employed in other industries with the advent of ‘omics’ era and innovations in genetic and protein engineering approaches. Proteases have found application in industries besides food, like leather, textiles, detergent, waste management, agriculture, animal husbandry, cosmetics, and pharmaceutics. With the rising demands and applications, researchers are exploring various approaches to discover, redesign, or artificially synthesize enzymes with better applicability in the industrial processes. These enzymes offer a sustainable and environmentally safer option, besides possessing economic and commercial value. Various bacterial and fungal proteases are already holding a commercially pivotal role in the industry. The current review summarizes the characteristics and types of proteases, microbial source, their current and prospective applications in various industries, and future challenges. Promoting these biocatalysts will prove significant in betterment of the modern world.
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Conchouso D, Al-Ma'abadi A, Behzad H, Alarawi M, Hosokawa M, Nishikawa Y, Takeyama H, Mineta K, Gojobori T. Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:504-518. [PMID: 34952209 PMCID: PMC8864243 DOI: 10.1016/j.gpb.2021.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/09/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022]
Abstract
Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant due to the complex and multidisciplinary nature of the field. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (>50,000 cells/day) for mining and bioprospecting metagenomic data
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Affiliation(s)
- David Conchouso
- Department of Industrial and Mechanical Engineering, Universidad de las Américas Puebla, Puebla 72810, Mexico; Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Amani Al-Ma'abadi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:958-972. [PMID: 33631428 PMCID: PMC9402790 DOI: 10.1016/j.gpb.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/23/2019] [Accepted: 06/06/2019] [Indexed: 12/01/2022]
Abstract
Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.
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Liguori L, Monticelli M, Allocca M, Cubellis MV, Hay Mele B. Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach. BMC Bioinformatics 2020; 21:348. [PMID: 32838733 PMCID: PMC7447578 DOI: 10.1186/s12859-020-03560-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. RESULTS We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. CONCLUSION Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.
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Affiliation(s)
- Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy.
- Biology and Evolution of Marine Organisms Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Bruno Hay Mele
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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Sarkar J, Dutta A, Pal Chowdhury P, Chakraborty J, Dutta TK. Characterization of a novel family VIII esterase EstM2 from soil metagenome capable of hydrolyzing estrogenic phthalates. Microb Cell Fact 2020; 19:77. [PMID: 32209105 PMCID: PMC7092541 DOI: 10.1186/s12934-020-01336-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbes are rich sources of enzymes and esterases are one of the most important classes of enzymes because of their potential for application in the field of food, agriculture, pharmaceuticals and bioremediation. Due to limitations in their cultivation, only a small fraction of the complex microbial communities can be cultured from natural habitats. Thus to explore the catalytic potential of uncultured organisms, the metagenomic approach has turned out to be an effective alternative method for direct mining of enzymes of interest. Based on activity-based screening method, an esterase-positive clone was obtained from metagenomic libraries. RESULTS Functional screening of a soil metagenomic fosmid library, followed by transposon mutagenesis led to the identification of a 1179 bp esterase gene, estM2, that encodes a 392 amino acids long protein (EstM2) with a translated molecular weight of 43.12 kDa. Overproduction, purification and biochemical characterization of the recombinant protein demonstrated carboxylesterase activity towards short-chain fatty acyl esters with optimal activity for p-nitrophenyl butyrate at pH 8.0 and 37 °C. Amino acid sequence analysis and subsequent phylogenetic analysis suggested that EstM2 belongs to the family VIII esterases that bear modest similarities to class C β-lactamases. EstM2 possessed the conserved S-x-x-K motif of class C β-lactamases but did not exhibit β-lactamase activity. Guided by molecular docking analysis, EstM2 was shown to hydrolyze a wide range of di- and monoesters of alkyl-, aryl- and benzyl-substituted phthalates. Thus, EstM2 displays an atypical hydrolytic potential of biotechnological significance within family VIII esterases. CONCLUSIONS This study has led to the discovery of a new member of family VIII esterases. To the best of our knowledge, this is the first phthalate hydrolase (EstM2), isolated from a soil metagenomic library that belongs to a family possessing β-lactamase like catalytic triad. Based on its catalytic potential towards hydrolysis of both phthalate diesters and phthalate monoesters, this enzyme may find use to counter the growing pollution caused by phthalate-based plasticizers in diverse geological environment and in other aspects of biotechnological applications.
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Affiliation(s)
- Jayita Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Arindam Dutta
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Piyali Pal Chowdhury
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Joydeep Chakraborty
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India.
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17
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Bioprospection of Enzymes and Microorganisms in Insects to Improve Second-Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2019. [DOI: 10.1089/ind.2019.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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18
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Almeida JM, Alnoch RC, Souza EM, Mitchell DA, Krieger N. Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140320. [PMID: 31756433 DOI: 10.1016/j.bbapap.2019.140320] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
In recent years, metagenomic strategies have been widely used to isolate and identify new enzymes from uncultivable components of microbial communities. Among these enzymes, various lipases have been obtained from metagenomic libraries from different environments and characterized. Although many of these lipases have characteristics that could make them interesting for application in biocatalysis, relatively little work has been done to evaluate their potential to catalyze industrially important reactions. In the present article, we highlight the latest research on lipases obtained through metagenomic tools, focusing on studies of activity and stability and investigations of application in biocatalysis. We also discuss the challenges of metagenomic approaches for the bioprospecting of new lipases.
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Affiliation(s)
- Janaina Marques Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Robson Carlos Alnoch
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Emanuel Maltempi Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - David Alexander Mitchell
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil
| | - Nadia Krieger
- Departamento de Química, Universidade Federal do Paraná, Cx.P. 19032 Centro Politécnico, Curitiba 81531-980, Paraná, Brazil.
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Pasqualetti M, Barghini P, Giovannini V, Fenice M. High Production of Chitinolytic Activity in Halophilic Conditions by a New Marine Strain of Clonostachys rosea. Molecules 2019; 24:E1880. [PMID: 31100818 PMCID: PMC6571954 DOI: 10.3390/molecules24101880] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022] Open
Abstract
Twenty-eight fungal strains have been isolated from different natural marine substrates and plate screened for their production of chitinolytic activity. The two apparent best producers, Trichoderma lixii IG127 and Clonostachys rosea IG119, were screened in shaken cultures in media containing 1% colloidal chitin, 1% yeast nitrogen base and 38‰ NaCl, for their ability to produce chitinolytic enzymes under halophilic conditions. In addition, they were tested for optimal growth conditions with respect to pH, salinity and temperature. The Trichoderma strain appeared to be a slight halotolerant fungus, while C. rosea IG119 clearly showed to be a halophilic marine fungus, its optimal growth conditions being very coherent for life in the marine environment (i.e., pH 8.0, salinity 38‰). Due to its high and relatively fast activity (258 U/L after 192 h of growth) accompanied by its halophilic behaviour (growth from 0 to 160‰ of salinity), C. rosea was selected for further studies. In view of possible industrial applications, its medium for chitinolytic enzyme production was optimized by Response Surface Methodology using 1% colloidal chitin and different concentrations of corn step liquor and yeast nitrogen base (0-0.5%). Time course of growth under optimized condition showed that maximum activity (394 U/L) was recorded after 120 h on medium containing Corn Steep Liquor 0.47% and Yeast Nitrogen Base 0.37%. Maximum of productivity (3.3 U/Lh) was recorded at the same incubation time. This was the first study that demonstrated high chitinolytic activity in a marine strain of C. rosea.
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Affiliation(s)
- Marcella Pasqualetti
- Dipartimento di Scienze Ecologiche e Biologiche, University of Tuscia, 01100 Viterbo, Italy.
- Laboratorio di Ecologia dei Funghi Marini, CoNISMa, University of Tuscia, 01100 Viterbo, Italy.
| | - Paolo Barghini
- Dipartimento di Scienze Ecologiche e Biologiche, University of Tuscia, 01100 Viterbo, Italy.
| | - Valeria Giovannini
- Dipartimento di Scienze Ecologiche e Biologiche, University of Tuscia, 01100 Viterbo, Italy.
| | - Massimiliano Fenice
- Dipartimento di Scienze Ecologiche e Biologiche, University of Tuscia, 01100 Viterbo, Italy.
- Laboratorio di Microbiologia Marina Applicata, CoNISMa, University of Tuscia, 01100 Viterbo, Italy.
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Torres M, Hong KW, Chong TM, Reina JC, Chan KG, Dessaux Y, Llamas I. Genomic analyses of two Alteromonas stellipolaris strains reveal traits with potential biotechnological applications. Sci Rep 2019; 9:1215. [PMID: 30718637 PMCID: PMC6361997 DOI: 10.1038/s41598-018-37720-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/27/2018] [Indexed: 11/08/2022] Open
Abstract
The Alteromonas stellipolaris strains PQQ-42 and PQQ-44, previously isolated from a fish hatchery, have been selected on the basis of their strong quorum quenching (QQ) activity, as well as their ability to reduce Vibrio-induced mortality on the coral Oculina patagonica. In this study, the genome sequences of both strains were determined and analyzed in order to identify the mechanism responsible for QQ activity. Both PQQ-42 and PQQ-44 were found to degrade a wide range of N-acylhomoserine lactone (AHL) QS signals, possibly due to the presence of an aac gene which encodes an AHL amidohydrolase. In addition, the different colony morphologies exhibited by the strains could be related to the differences observed in genes encoding cell wall biosynthesis and exopolysaccharide (EPS) production. The PQQ-42 strain produces more EPS (0.36 g l-1) than the PQQ-44 strain (0.15 g l-1), whose chemical compositions also differ. Remarkably, PQQ-44 EPS contains large amounts of fucose, a sugar used in high-value biotechnological applications. Furthermore, the genome of strain PQQ-42 contained a large non-ribosomal peptide synthase (NRPS) cluster with a previously unknown genetic structure. The synthesis of enzymes and other bioactive compounds were also identified, indicating that PQQ-42 and PQQ-44 could have biotechnological applications.
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Affiliation(s)
- Marta Torres
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, France
| | - Kar-Wai Hong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teik-Min Chong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - José Carlos Reina
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, France.
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
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Schiffer J, Mael LE, Prather KA, Amaro RE, Grassian VH. Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry. ACS CENTRAL SCIENCE 2018; 4:1617-1623. [PMID: 30648145 PMCID: PMC6311946 DOI: 10.1021/acscentsci.8b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 05/25/2023]
Abstract
Atmospheric aerosols have long been known to alter climate by scattering incoming solar radiation and acting as seeds for cloud formation. These processes have vast implications for controlling the chemistry of our environment and the Earth's climate. Sea spray aerosol (SSA) is emitted over nearly three-quarters of our planet, yet precisely how SSA impacts Earth's radiation budget remains highly uncertain. Over the past several decades, studies have shown that SSA particles are far more complex than just sea salt. Ocean biological and physical processes produce individual SSA particles containing a diverse array of biological species including proteins, enzymes, bacteria, and viruses and a diverse array of organic compounds including fatty acids and sugars. Thus, a new frontier of research is emerging at the nexus of chemistry, biology, and atmospheric science. In this Outlook article, we discuss how current and future aerosol chemistry research demands a tight coupling between experimental (observational and laboratory studies) and computational (simulation-based) methods. This integration of approaches will enable the systematic interrogation of the complexity within individual SSA particles at a level that will enable prediction of the physicochemical properties of real-world SSA, ultimately illuminating the detailed mechanisms of how the constituents within individual SSA impact climate.
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Affiliation(s)
- Jamie
M. Schiffer
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Liora E. Mael
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Kimberly A. Prather
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Vicki H. Grassian
- Department of Chemistry and Biochemistry and Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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Ranjan R, Yadav MK, Suneja G, Sharma R. Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes. Int J Biol Macromol 2018; 119:572-581. [PMID: 30059741 DOI: 10.1016/j.ijbiomac.2018.07.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022]
Abstract
Esterases are an important group of biocatalysts for synthetic organic chemistry. Functional metagenomics allows discovery of novel biocatalysts by providing access to the gene pool of the microbial community of a habitat. Two metagenomic libraries representing the gene pool of sea sediment and hot spring microbial mat were constructed. Functional screening of these libraries resulted in the isolation of total 8 clones with tributyrin hydrolytic activity. Sequence analysis revealed 10 putative lipolytic proteins with 42-99% homology to the protein sequences in the databases, nine of which represented six known esterase families. Four of the encoded proteins represented Family V and amongst others, one each represented the Family VIII, pectin acetylesterase, enterobactin esterase, G-D-S-L family and OsmC domain containing esterase. One unusual lipolytic protein possessed poly-(3-hydroxybutyrate) depolymerase domain fused to lipase/esterase domain. Two phylogenetically related esterases (MLC3 and SLC5) belonging to family V were expressed and purified to homogeneity. The enzymes exhibited environment-adapted temperature optimum and thermostability. MLC3 was able to stereoselectively hydrolyze R-methyl mandelate to produce R-mandelic acid, an important chiral building block, which suggests MLC3 has potential commercial application.
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Affiliation(s)
- Ravi Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India
| | - Manish Kumar Yadav
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India
| | - Garima Suneja
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Mathura Road, New Delhi 110025, India.
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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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Razzaghi M, Homaei A, Mosaddegh E. Penaeus vannamei protease stabilizing process of ZnS nanoparticles. Int J Biol Macromol 2018; 112:509-515. [PMID: 29382577 DOI: 10.1016/j.ijbiomac.2018.01.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/24/2022]
Abstract
The protease enzyme purified from the Penaeus vannamei shrimp has unique properties, so improving the stability of this enzyme can improve their practical applications. In this study, ZnS nanoparticles, which have special properties for enzyme immobilization, were synthesized using a chemical precipitation method, and Penaeus vannamei protease was successfully immobilized on them. The size, structure, and morphology of the ZnS nanoparticles, and the immobilization of the protease were studied, using Transmission Electron Microscopy (TEM), Fourier Transform Infrared (FT-IR) spectroscopy, UV-Vis spectroscopy and Dynamic Light Scattering (DLS) analysis. We show that the immobilized enzyme has improved functionality at high temperatures, extreme pH conditions (pH3 and 12), and during storage. Immobilization increased the optimum temperature range of the enzyme, but did not change the pH optimum, which remained at pH7. Immobilization of P. vannamei protease enzyme increased the Km and decreased kcat/Km. These results indicate that P. vannamei protease immobilized on ZnS nanoparticles, has improved properties due to its high stability and unique properties, can be used for biotechnology applications.
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Affiliation(s)
- Mozhgan Razzaghi
- Department of Marine Biology, Faculty of Science, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Biochemistry, Faculty of Science, University of Hormozgan, Bandar Abbas, Iran.
| | - Elaheh Mosaddegh
- Department of New Materials, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, PO Box 76315-117, Kerman, Iran
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Foong CP, Lakshmanan M, Abe H, Taylor TD, Foong SY, Sudesh K. A novel and wide substrate specific polyhydroxyalkanoate (PHA) synthase from unculturable bacteria found in mangrove soil. JOURNAL OF POLYMER RESEARCH 2017. [DOI: 10.1007/s10965-017-1403-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology. In this work we briefly introduce the theoretical formulation behind CBMM and then review the most recent and effective case studies of CBMM of marine microbes and communities. Also, the emerging challenges and possibilities in the use of such methodologies in the context of marine microbiology/biotechnology are discussed. As the potential applications of CBMM have a very broad range, the topics presented in this review span over a large plethora of fields such as ecology, biotechnology and evolution.
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Affiliation(s)
- Marco Fondi
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy.
| | - Renato Fani
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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Yaniv K, Golberg K, Kramarsky-Winter E, Marks R, Pushkarev A, Béjà O, Kushmaro A. Functional marine metagenomic screening for anti-quorum sensing and anti-biofilm activity. BIOFOULING 2017; 33:1-13. [PMID: 27882771 DOI: 10.1080/08927014.2016.1253684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
Quorum sensing (QS), a cell-to-cell communication process, entails the production of signaling molecules that enable synchronized gene expression in microbial communities to regulate myriad microbial functions, including biofilm formation. QS disruption may constitute an innovative approach to the design of novel antifouling and anti-biofilm agents. To identify novel quorum sensing inhibitors (QSI), 2,500 environmental bacterial artificial chromosomes (BAC) from uncultured marine planktonic bacteria were screened for QSI activity using soft agar overlaid with wild type Chromobacterium violaceum as an indicator. Of the BAC library clones, 7% showed high QSI activity (>40%) against the indicator bacterium, suggesting that QSI is common in the marine environment. The most active compound, eluted from BAC clone 14-A5, disrupted QS signaling pathways and reduced biofilm formation in both Pseudomonas aeruginosa and Acinetobacter baumannii. The mass spectra of the active BAC clone (14-A5) that had been visualized by thin layer chromatography was dominated by a m/z peak of 362.1.
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Affiliation(s)
- Karin Yaniv
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Karina Golberg
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Esti Kramarsky-Winter
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Robert Marks
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
- b The Ilse Katz Center for Meso and Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Alina Pushkarev
- c Faculty of Biology , Technion-Israel Institute of Technology , Haifa , Israel
| | - Oded Béjà
- c Faculty of Biology , Technion-Israel Institute of Technology , Haifa , Israel
| | - Ariel Kushmaro
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
- b The Ilse Katz Center for Meso and Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer-Sheva , Israel
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31
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Fernandes P. Enzymes in Fish and Seafood Processing. Front Bioeng Biotechnol 2016; 4:59. [PMID: 27458583 PMCID: PMC4935696 DOI: 10.3389/fbioe.2016.00059] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/24/2016] [Indexed: 11/15/2022] Open
Abstract
Enzymes have been used for the production and processing of fish and seafood for several centuries in an empirical manner. In recent decades, a growing trend toward a rational and controlled application of enzymes for such goals has emerged. Underlying such pattern are, among others, the increasingly wider array of enzyme activities and enzyme sources, improved enzyme formulations, and enhanced requirements for cost-effective and environmentally friendly processes. The better use of enzyme action in fish- and seafood-related application has had a significant impact on fish-related industry. Thus, new products have surfaced, product quality has improved, more sustainable processes have been developed, and innovative and reliable analytical techniques have been implemented. Recent development in these fields are presented and discussed, and prospective developments are suggested.
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Affiliation(s)
- Pedro Fernandes
- Department of Bioengineering, Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Faculdade de Engenharia, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
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32
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Zhao F, Bajic VB. The Value and Significance of Metagenomics of Marine Environments. Preface. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:271-4. [PMID: 26607677 PMCID: PMC4678774 DOI: 10.1016/j.gpb.2015.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 10/31/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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