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Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria. Appl Microbiol Biotechnol 2021; 105:8805-8822. [PMID: 34716462 DOI: 10.1007/s00253-021-11659-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.
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Kashiyama Y, Ishizuka Y, Terauchi I, Matsuda T, Maeda Y, Yoshino T, Matsumoto M, Yabuki A, Bowler C, Tanaka T. Engineered chlorophyll catabolism conferring predator resistance for microalgal biomass production. Metab Eng 2021; 66:79-86. [PMID: 33862197 DOI: 10.1016/j.ymben.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/27/2020] [Accepted: 03/27/2021] [Indexed: 01/27/2023]
Abstract
Production of valuable compounds including biofuels and pharmaceutical precursors derived from microalgae has garnered significant interest. Stable production of algal biomass is essential to make the microalgal industry commercially feasible. However, one of the largest issues is severe biological contamination by predators grazing the algal biomass, resulting in the crash of outdoor cultures. In the present study, we propose a novel engineering strategy for microalgae to cope with predators. The overexpression of plant chlorophyllase (CLH) in a microalga resulted in the enhancement of resistance to the predator. This result supported our hypothesis that CLH promotes chlorophyll breakdown in the chloroplasts of the microalgae when they are digested by the predator, generating the phototoxic catabolite chlorophyllide that damages the predator. To the best of our knowledge, this is the first study to establish predator-resistant microalgae by enhancing the CLH activity.
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Affiliation(s)
- Yuichiro Kashiyama
- Department of Applied Science and Engineering, Graduate School of Engineering, Fukui University of Technology, 3-6-1, Gakuen, Fukui, Fukui, 910-8505, Japan
| | - Yuki Ishizuka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Issei Terauchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Toshiki Matsuda
- Department of Applied Science and Engineering, Graduate School of Engineering, Fukui University of Technology, 3-6-1, Gakuen, Fukui, Fukui, 910-8505, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Mitsufumi Matsumoto
- Biotechnology Laboratory, Electric Power Development Co., Ltd, 1, Yanagisaki-machi, Wakamatsu-ku, Kitakyusyu, Fukuoka, 808-0111, Japan
| | - Akinori Yabuki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Sharafi E, Dehestani A, Farmani J, Parizi AP, Taheri‐Kafrani A. Chlorophyllase‐Catalyzed Chlorophyll Removal from Vegetable Oils Using Recombinant Eukaryotic and Prokaryotic Enzymes. J AM OIL CHEM SOC 2021. [DOI: 10.1002/aocs.12465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ebrahim Sharafi
- Genetics and Agricultural Biotechnology Institute of Tabarestan Sari Agricultural Sciences and Natural Resources University 578 Sari Iran
| | - Ali Dehestani
- Genetics and Agricultural Biotechnology Institute of Tabarestan Sari Agricultural Sciences and Natural Resources University 578 Sari Iran
| | - Jamshid Farmani
- Department of Food Science and Technology, Faculty of Agricultural Engineering Sari Agricultural Sciences and Natural Resources University 578 Sari Iran
| | - Ali Pakdin Parizi
- Genetics and Agricultural Biotechnology Institute of Tabarestan Sari Agricultural Sciences and Natural Resources University 578 Sari Iran
| | - Asghar Taheri‐Kafrani
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies University of Isfahan Isfahan 81746‐73441 Iran
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Gu S, Dai X, Xu Z, Niu Q, Jiang J, Liu Y. Molecular, structural and biochemical characterization of a novel recombinant chlorophyllase from cyanobacterium Oscillatoria acuminata PCC 6304. Microb Cell Fact 2021; 20:14. [PMID: 33430874 PMCID: PMC7802212 DOI: 10.1186/s12934-020-01507-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background
Chlorophyllase catalyzes the hydrolysis of chlorophyll and produces chlorophyllide and phytol. Cyanobacterial chlorophyllases are likely to be more highly heterologously expressed than plant chlorophyllases. A novel recombinant chlorophyllase from the cyanobacterium Oscillatoria acuminata PCC 6304 was successfully expressed in Escherichia coli BL21(DE3). Results The putative N-terminal 28-amino-acid signal peptide sequence of O. acuminata chlorophyllase (OaCLH) is essential for its activity, but may confer poor solubility on OaCLH. The C-terminal fusion of a 6 × His tag caused a partial loss of activity in recombinant OaCLH, but an N-terminal 6 × His tag did not destroy its activity. The optimal pH and temperature for recombinant OaCLH activity are 7.0 and 40 °C, respectively. Recombinant OaCLH has hydrolysis activities against chlorophyll a, chlorophyll b, bacteriochlorophyll a, and pheophytin a, but prefers chlorophyll b and chlorophyll a as substrates. The results of site-directed mutagenesis experiments indicated that the catalytic triad of OaCLH consists of Ser159, Asp226, and His258. Conclusions The high-level expression and broad substrate specificity of recombinant OaCLH make it suitable for genetically engineering and a promising biocatalyst for industrial production, with applications in vegetable oil refining and laundry detergents.
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Affiliation(s)
- Sitian Gu
- State Key Laboratory of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Jiangsu, 214122, Wuxi, People's Republic of China. .,Wilmar Biotechnology Research & Development Center Co., Ltd, 200137, Shanghai, People's Republic of China.
| | - Xiaojun Dai
- Wilmar Biotechnology Research & Development Center Co., Ltd, 200137, Shanghai, People's Republic of China
| | - Zhengjun Xu
- Wilmar Biotechnology Research & Development Center Co., Ltd, 200137, Shanghai, People's Republic of China
| | - Qiwen Niu
- Wilmar Biotechnology Research & Development Center Co., Ltd, 200137, Shanghai, People's Republic of China
| | - Jiang Jiang
- State Key Laboratory of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Jiangsu, 214122, Wuxi, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Jiangsu, 214122, Wuxi, People's Republic of China.
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