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Neoh SZ, Tan HT, Trakunjae C, Chek MF, Vaithanomsat P, Hakoshima T, Sudesh K. N-terminal truncation of PhaC BP-M-CPF4 and its effect on PHA production. Microb Cell Fact 2024; 23:52. [PMID: 38360657 PMCID: PMC10867992 DOI: 10.1186/s12934-024-02329-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation. RESULTS The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB-4 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4. CONCLUSION This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.
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Affiliation(s)
- Soon Zher Neoh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia
| | - Hua Tiang Tan
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Chanaporn Trakunjae
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Pilanee Vaithanomsat
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia.
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Kankonkar HT, Khandeparker RS. Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer. Curr Microbiol 2024; 81:53. [PMID: 38172411 DOI: 10.1007/s00284-023-03569-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.
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Affiliation(s)
- Harshada T Kankonkar
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakhee S Khandeparker
- Microbial Ecology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Raj Bhavan Road, Dona Paula, Goa, 403004, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Duangsri C, Salminen TA, Alix M, Kaewmongkol S, Akrimajirachoote N, Khetkorn W, Jittapalapong S, Mäenpää P, Incharoensakdi A, Raksajit W. Characterization and Homology Modeling of Catalytically Active Recombinant PhaC Ap Protein from Arthrospira platensis. BIOLOGY 2023; 12:biology12050751. [PMID: 37237563 DOI: 10.3390/biology12050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/30/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Polyhydroxybutyrate (PHB) is a biocompatible and biodegradable polymer that has the potential to replace fossil-derived polymers. The enzymes involved in the biosynthesis of PHB are β-ketothiolase (PhaA), acetoacetyl-CoA reductase (PhaB), and PHA synthase (PhaC). PhaC in Arthrospira platensis is the key enzyme for PHB production. In this study, the recombinant E. cloni®10G cells harboring A. platensis phaC (rPhaCAp) was constructed. The overexpressed and purified rPhaCAp with a predicted molecular mass of 69 kDa exhibited Vmax, Km, and kcat values of 24.5 ± 2 μmol/min/mg, 31.3 ± 2 µM and 412.7 ± 2 1/s, respectively. The catalytically active rPhaCAp was a homodimer. The three-dimensional structural model for the asymmetric PhaCAp homodimer was constructed based on Chromobacterium sp. USM2 PhaC (PhaCCs). The obtained model of PhaCAp revealed that the overall fold of one monomer was in the closed, catalytically inactive conformation whereas the other monomer was in the catalytically active, open conformation. In the active conformation, the catalytic triad residues (Cys151-Asp310-His339) were involved in the binding of substrate 3HB-CoA and the CAP domain of PhaCAp involved in the dimerization.
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Affiliation(s)
- Chanchanok Duangsri
- Program of Animal Health Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Tiina A Salminen
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Marion Alix
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Sarawan Kaewmongkol
- Program of Animal Health Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | | | - Wanthanee Khetkorn
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi (RMUTT), Thanyaburi, Pathumthani 12110, Thailand
| | - Sathaporn Jittapalapong
- Program of Animal Health Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Pirkko Mäenpää
- Faculty of Technology, University of Turku, 20014 Turku, Finland
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
| | - Wuttinun Raksajit
- Program of Animal Health Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
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4
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Aytar Celik P, Barut D, Enuh BM, Erdogan Gover K, Nural Yaman B, Burcin Mutlu M, Cabuk A. A novel higher polyhydroxybutyrate producer Halomonas halmophila 18H with unique cell factory attributes. BIORESOURCE TECHNOLOGY 2023; 372:128669. [PMID: 36702321 DOI: 10.1016/j.biortech.2023.128669] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
For cost-competitive biosynthesis of polyhydroxybutyrate (PHB), the screening of efficient producers and characterization of their genomic potential is fundamental. In this study, 94 newly isolated halophilic strains from Turkish salterns were screened for their polyhydroxyalkanoates (PHAs) biosynthesis capabilities through fermentation. Halomonas halmophila 18H was found to be the highest PHB producer, yielding 63.72 % of its biomass as PHB. The PHB produced by this strain was physically and chemically characterized using various techniques. Its genome was also sequenced and found to be large (6,713,657 bp) and have a GC content of 59.9 %. Halomonas halmophila 18H was also found to have several copies of PHB biosynthesis genes, as well as 20 % more protein-coding genes and 1075 singletons compared to other high PHB producers. These unique genomic features make it a promising cell factory for the simultaneous production of PHAs and other biotechnologically important secondary metabolites.
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Affiliation(s)
- Pinar Aytar Celik
- Environmental Protection and Control Program, Eskisehir Osmangazi University, 26110 Eskisehir, Turkey; Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey.
| | - Dilan Barut
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Blaise Manga Enuh
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Kubra Erdogan Gover
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Belma Nural Yaman
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey; Department of Biomedical Engineering, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Mehmet Burcin Mutlu
- Department of Biology, Faculty of Science, Eskisehir Technical University, Eskisehir, Turkey
| | - Ahmet Cabuk
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Sciences, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey; Department of Biology, Faculty of Science, Eskisehir Osmangazi University, Eskisehir, Turkey
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Máčalová D, Janalíková M, Sedlaříková J, Rektoříková I, Koutný M, Pleva P. Genotypic and Phenotypic Detection of Polyhydroxyalkanoate Production in Bacterial Isolates from Food. Int J Mol Sci 2023; 24:ijms24021250. [PMID: 36674766 PMCID: PMC9864133 DOI: 10.3390/ijms24021250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are widely used in medical and potentially in other applications due to their biocompatibility and biodegradability. Understanding PHA biosynthetic pathways may lead to the detection of appropriate conditions (substrates) for producing a particular PHA type by a specific microbial strain. The aim of this study was to establish a method enabling potentially interesting PHA bacterial producers to be found. In the study, all four classes of PHA synthases and other genes involved in PHA formation (fabG, phaA, phaB, phaG, and phaJ) were detected by PCR in 64 bacterial collection strains and food isolates. Acinetobacter, Bacillus, Cupriavidus, Escherichia, Klebsiella, Lelliottia, Lysinibacillus, Mammaliicoccus, Oceanobacillus, Pantoea, Peribacillus, Priestia, Pseudomonas, Rahnella, Staphylococcus, and Stenotrophomonas genera were found among these strains. Fructose, glucose, sunflower oil, and propionic acid were utilized as carbon sources and PHA production was detected by Sudan black staining, Nile blue staining, and FTIR methods. The class I synthase and phaA genes were the most frequently found, indicating the strains' ability to synthesize PHA from carbohydrates. Among the tested bacterial strains, the Pseudomonas genus was identified as able to utilize all tested carbon sources. The Pseudomonas extremorientalis strain was determined as a prospect for biotechnology applications.
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Affiliation(s)
- Daniela Máčalová
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
| | - Magda Janalíková
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
| | - Jana Sedlaříková
- Department of Fat, Surfactant and Cosmetics Technology, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
| | - Iveta Rektoříková
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
| | - Marek Koutný
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
| | - Pavel Pleva
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, 275 Vavreckova, 76001 Zlin, Czech Republic
- Correspondence:
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Esposito FP, Vecchiato V, Buonocore C, Tedesco P, Noble B, Basnett P, de Pascale D. Enhanced production of biobased, biodegradable, Poly(3-hydroxybutyrate) using an unexplored marine bacterium Pseudohalocynthiibacter aestuariivivens, isolated from highly polluted coastal environment. BIORESOURCE TECHNOLOGY 2023; 368:128287. [PMID: 36368485 DOI: 10.1016/j.biortech.2022.128287] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The production and disposal of plastics from limited fossil reserves, has prompted research for greener and sustainable alternatives. Polyhydroxyalkanoates (PHAs) are biocompatible, biodegradable, and thermoprocessable polyester produced by microbes. PHAs found several applications but their use is limited due to high production cost and low yields. Herein, for the first time, the isolation and characterization of Pseudohalocynthiibacter aestuariivivens P96, a marine bacterium able to produce surprising amount of PHAs is reported. In the best growth condition P96 was able to reach a maximum production of 4.73 g/L, corresponding to the 87 % of total cell dry-weight. Using scanning and transmission microscopy, lab-scale fermentation, spectroscopic techniques, and genome analysis, the production of thermoprocessable polymer Polyhydroxybutyrate P(3HB), a PHAs class, endowed with mechanical and thermal properties comparable to that of petroleum-based plastics was confirmed. This study represents a milestone toward the use of this unexplored marine bacterium for P(3HB) production.
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Affiliation(s)
- Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton 55, 80133 Naples, Italy
| | - Vittoria Vecchiato
- Sustainable Biotechnology Research Group, School of Life Sciences, University of Westminster, London W1W6UW, United Kingdom
| | - Carmine Buonocore
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton 55, 80133 Naples, Italy
| | - Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton 55, 80133 Naples, Italy
| | - Brendon Noble
- Sustainable Biotechnology Research Group, School of Life Sciences, University of Westminster, London W1W6UW, United Kingdom
| | - Pooja Basnett
- Sustainable Biotechnology Research Group, School of Life Sciences, University of Westminster, London W1W6UW, United Kingdom
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton 55, 80133 Naples, Italy.
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Sivashankari RM, Mierzati M, Miyahara Y, Mizuno S, Nomura CT, Taguchi S, Abe H, Tsuge T. Exploring Class I polyhydroxyalkanoate synthases with broad substrate specificity for polymerization of structurally diverse monomer units. Front Bioeng Biotechnol 2023; 11:1114946. [PMID: 36896015 PMCID: PMC9989198 DOI: 10.3389/fbioe.2023.1114946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Polyhydroxyalkanoate (PHA) synthases (PhaCs) are key enzymes in PHA polymerization. PhaCs with broad substrate specificity are attractive for synthesizing structurally diverse PHAs. In the PHA family, 3-hydroxybutyrate (3HB)-based copolymers are industrially produced using Class I PhaCs and can be used as practical biodegradable thermoplastics. However, Class I PhaCs with broad substrate specificities are scarce, prompting our search for novel PhaCs. In this study, four new PhaCs from the bacteria Ferrimonas marina, Plesiomonas shigelloides, Shewanella pealeana, and Vibrio metschnikovii were selected via a homology search against the GenBank database, using the amino acid sequence of Aeromonas caviae PHA synthase (PhaCAc), a Class I enzyme with a wide range of substrate specificities, as a template. The four PhaCs were characterized in terms of their polymerization ability and substrate specificity, using Escherichia coli as a host for PHA production. All the new PhaCs were able to synthesize P(3HB) in E. coli with a high molecular weight, surpassing PhaCAc. The substrate specificity of PhaCs was evaluated by synthesizing 3HB-based copolymers with 3-hydroxyhexanoate, 3-hydroxy-4-methylvalerate, 3-hydroxy-2-methylbutyrate, and 3-hydroxypivalate monomers. Interestingly, PhaC from P. shigelloides (PhaCPs) exhibited relatively broad substrate specificity. PhaCPs was further engineered through site-directed mutagenesis, and the variant resulted in an enzyme with improved polymerization ability and substrate specificity.
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Affiliation(s)
| | - Maierwufu Mierzati
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuki Miyahara
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Christopher T Nomura
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, ID, United States
| | - Seiichi Taguchi
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Hideki Abe
- Bioplastic Research Team, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
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Genome Analysis of Halomonas elongata Strain 153B and Insights Into Polyhydroxyalkanoate Synthesis and Adaptive Mechanisms to High Saline Environments. Curr Microbiol 2022; 80:18. [PMID: 36460760 DOI: 10.1007/s00284-022-03115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Species of the Halomonas genus are gram-negative, aerobic, moderately halophilic bacteria that synthesize polyhydroxyalkanoates (PHAs) and other high-value products that have a wide range of potential uses in the food, feed, cosmetics, pharmaceutical, and chemical sectors. Genome sequencing studies allow for the description and comparison of genetic traits with other strains and species, allowing for the exploration of the organism's potential, necessary to further biotechnology applications. Here, the genome of Halomonas elongata strain 153B was sequenced, its features compared to 5 other strains and 7 species, and a description of features for adaptations to hypersaline environments and bioproducts synthesis was done. Whole-genome analysis showed H. elongata 153B has more similar features to the reference strain H. elongata DSM 2581 compared to 4 other reported strains. Comparative genomics showed 2064 core genomic clusters between the strains and 666 singletons for strain 153B. Several genes in transport and signaling, osmoregulation, and oxidative stress that have roles in adaptation to environments with high osmolarity were also revealed. These appear to form an intricate network of overlapping systems carefully coordinated to bring about adaptation. H. elongata 153B genes for the synthesis of PHAs, ectoine, vitamins, and the degradation of drugs and aromatic compounds were described. The results will aid in the study of halophile physiology, provide a mine for valuable enzymes, and help speed up research for other biotechnology applications.
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Tan HT, Chek MF, Neoh SZ, Ang SL, Yoshida S, Hakoshima T, Sudesh K. Characterization of the polyhydroxyalkanoate (PHA) synthase from Ideonella sakaiensis, a bacterium that is capable of degrading and assimilating poly(ethylene terephthalate). Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Enuh BM, Nural Yaman B, Tarzi C, Aytar Çelik P, Mutlu MB, Angione C. Whole-genome sequencing and genome-scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use. Microbiologyopen 2022; 11:e1328. [PMID: 36314754 PMCID: PMC9597258 DOI: 10.1002/mbo3.1328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
Salt tolerant organisms are increasingly being used for the industrial production of high-value biomolecules due to their better adaptability compared to mesophiles. Chromohalobacter canadensis is one of the early halophiles to show promising biotechnology potential, which has not been explored to date. Advanced high throughput technologies such as whole-genome sequencing allow in-depth insight into the potential of organisms while at the frontiers of systems biology. At the same time, genome-scale metabolic models (GEMs) enable phenotype predictions through a mechanistic representation of metabolism. Here, we sequence and analyze the genome of C. canadensis 85B, and we use it to reconstruct a GEM. We then analyze the GEM using flux balance analysis and validate it against literature data on C. canadensis. We show that C. canadensis 85B is a metabolically versatile organism with many features for stress and osmotic adaptation. Pathways to produce ectoine and polyhydroxybutyrates were also predicted. The GEM reveals the ability to grow on several carbon sources in a minimal medium and reproduce osmoadaptation phenotypes. Overall, this study reveals insights from the genome of C. canadensis 85B, providing genomic data and a draft GEM that will serve as the first steps towards a better understanding of its metabolism, for novel applications in industrial biotechnology.
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Affiliation(s)
- Blaise Manga Enuh
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey
| | - Belma Nural Yaman
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey,Department of Biomedical Engineering, Faculty of Engineering and ArchitectureEskişehir Osmangazi UniversityEskişehirTurkey
| | - Chaimaa Tarzi
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK
| | - Pınar Aytar Çelik
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey,Environmental Protection and Control ProgramEskişehir Osmangazi UniversityEskişehirTurkey
| | - Mehmet Burçin Mutlu
- Department of Biology, Faculty of ScienceEskisehir Technical UniversityEskisehirTurkey
| | - Claudio Angione
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK,Centre for Digital InnovationTeesside UniversityMiddlesbroughUK,National Horizons CentreTeesside UniversityDarlingtonUK
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Biosynthesis of P(3HB-co-3HHx) Copolymers by a Newly Engineered Strain of Cupriavidus necator PHB−4/pBBR_CnPro-phaCRp for Skin Tissue Engineering Application. Polymers (Basel) 2022; 14:polym14194074. [PMID: 36236022 PMCID: PMC9570888 DOI: 10.3390/polym14194074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable polymers synthesized by certain bacteria and archaea with functions comparable to conventional plastics. Previously, our research group reported a newly PHA-producing bacterial strain, Rhodococcus pyridinivorans BSRT1-1, from the soil in Thailand. However, this strain’s PHA synthase (phaCRp) gene has not yet been characterized. Thus, this study aims to synthesize PHA using a newly engineered bacterial strain, Cupriavidus necator PHB−4/pBBR_CnPro-phaCRp, which harbors the phaCRp from strain BSRT1-1, and characterize the properties of PHA for skin tissue engineering application. To the best of our knowledge, this is the first study on the characterization of the PhaC from R. pyridinivorans species. The results demonstrated that the expression of the phaCRp in C. necator PHB−4 had developed in PHA production up to 3.1 ± 0.3 g/L when using 10 g/L of crude palm kernel oil (CPKO) as a sole carbon source. Interestingly, the engineered strain produced a 3-hydroxybutyrate (3HB) with 2 mol% of 3-hydroxyhexanoate (3HHx) monomer without adding precursor substrates. In addition, the 70 L stirrer bioreactor improved P(3HB-co-2 mol% 3HHx) yield 1.4-fold over the flask scale without altering monomer composition. Furthermore, the characterization of copolymer properties showed that this copolymer is promising for skin tissue engineering applications.
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12
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Subfunctionalization probably drives the emergence of plant growth-promoting genes. Symbiosis 2022. [DOI: 10.1007/s13199-022-00872-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Tan HT, Chek MF, Miyahara Y, Kim SY, Tsuge T, Hakoshima T, Sudesh K. Characterization of an (R)-specific enoyl-CoA hydratase from Streptomyces sp. strain CFMR 7: A metabolic tool for enhancing the production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). J Biosci Bioeng 2022; 134:288-294. [PMID: 35953354 DOI: 10.1016/j.jbiosc.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022]
Abstract
Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] has a high potential to serve as a commercial bioplastic due to its biodegradability, thermoplastic and mechanical properties. The properties of this copolymer are greatly affected by the composition of 3HHx monomer. One of the most efficient ways to modulate the composition of 3HHx monomer in P(3HB-co-3HHx) is by manipulating the (R)-3HHx-CoA monomer supply. In this study, a new (R)-specific enoyl-CoA hydratase originating from a non-PHA producer, Streptomyces sp. strain CFMR 7 (PhaJSs), was characterized and found to be effective in supplying 3HHx monomer during in vivo production of P(3HB-co-3HHx) copolymer. The P(3HB-co-3HHx) copolymer produced from the Cupriavidus necator transformant that harbors phaJSs, PHB-4/pBBR1-CBP-M-CPF4JSs, showed enhanced 3HHx incorporation of up to 11 mol% without affecting the P(3HB-co-3HHx) production when palm oil was used as the carbon source. In addition, both kcat and kcat/Km of PhaJSs were higher toward the C6 than the shorter C4 substrates, underscoring the preference for 3-hydroxyhexanoyl-CoA. These results suggest that PhaJSs has a significant ability to supply 3HHx monomers for PHA biosynthesis via β-oxidation and can be applied for metabolic engineering of robust PHA-producing strains.
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Affiliation(s)
- Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yuki Miyahara
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Sun-Yong Kim
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia.
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14
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Gao Q, Yang H, Wang C, Xie XY, Liu KX, Lin Y, Han SY, Zhu M, Neureiter M, Lin Y, Ye JW. Advances and trends in microbial production of polyhydroxyalkanoates and their building blocks. Front Bioeng Biotechnol 2022; 10:966598. [PMID: 35928942 PMCID: PMC9343942 DOI: 10.3389/fbioe.2022.966598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
With the rapid development of synthetic biology, a variety of biopolymers can be obtained by recombinant microorganisms. Polyhydroxyalkanoates (PHA) is one of the most popular one with promising material properties, such as biodegradability and biocompatibility against the petrol-based plastics. This study reviews the recent studies focusing on the microbial synthesis of PHA, including chassis engineering, pathways engineering for various substrates utilization and PHA monomer synthesis, and PHA synthase modification. In particular, advances in metabolic engineering of dominant workhorses, for example Halomonas, Ralstonia eutropha, Escherichia coli and Pseudomonas, with outstanding PHA accumulation capability, were summarized and discussed, providing a full landscape of diverse PHA biosynthesis. Meanwhile, we also introduced the recent efforts focusing on structural analysis and mutagenesis of PHA synthase, which significantly determines the polymerization activity of varied monomer structures and PHA molecular weight. Besides, perspectives and solutions were thus proposed for achieving scale-up PHA of low cost with customized material property in the coming future.
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Affiliation(s)
- Qiang Gao
- Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, QH, China
| | - Hao Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chi Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xin-Ying Xie
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Kai-Xuan Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuang-Yan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mingjun Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Markus Neureiter
- Institute for Environmental Biotechnology, Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Tulln, Austria
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
| | - Yina Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Markus Neureiter, ; Yina Lin, ; Jian-Wen Ye,
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15
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Musilova J, Kourilova X, Pernicova I, Bezdicek M, Lengerova M, Obruca S, Sedlar K. Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. Appl Microbiol Biotechnol 2022; 106:4669-4681. [PMID: 35759037 DOI: 10.1007/s00253-022-12039-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/26/2022]
Abstract
Aneurinibacillus thermoaerophilus CCM 8960 is a thermophilic bacterium isolated from compost in Brno. The bacterium accumulates polyhydroxyalkanoates (PHAs), a biodegradable and renewable alternative to petrochemical polymers. The bacterium reveals several features that make it a very interesting candidate for the industrial production of PHA. At first, due to its thermophilic character, the bacterium can be utilized in agreement with the concept of next-generation industrial biotechnology (NGIB), which relies on extremophiles. Second, the bacterium is capable of producing PHA copolymers containing a very high portion of 4-hydroxybutyrate (4HB). Such materials possess unique properties and can be advantageously used in multiple applications, including but not limited to medicine and healthcare. Therefore, this work focuses on the in-depth characterization of A. thermoaerophilus CCM 8960. In particular, we sequenced and assembled the genome of the bacterium and identified its most important genetic features, such as the presence of plasmids, prophages, CRISPR arrays, antibiotic-resistant genes, and restriction-modification (R-M) systems, which might be crucial for the development of genome editing tools. Furthermore, we focused on genes directly involved in PHA metabolism. We also experimentally studied the kinetics of glycerol and 1,4-butanediol (1,4BD) utilization as well as biomass growth and PHA production during cultivation. Based on these data, we constructed a metabolic model to reveal metabolic fluxes and nodes of glycerol and 1,4BD concerning their incorporation into the poly(3-hydroxybutyrate-co-4-hydroxybutyrate (P(3HB-co-4HB)) structure. KEY POINTS: • Aneurinibacillus sp. H1 was identified as Aneurinibacillus thermoaerophilus. • PHA metabolism pathway with associated genes was presented. • Unique monomer composition of produced PHAs was reported.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Iva Pernicova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Munich, Germany.
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16
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Hammami K, Souissi Y, Souii A, Ouertani A, El-Hidri D, Jabberi M, Chouchane H, Mosbah A, Masmoudi AS, Cherif A, Neifar M. Extremophilic Bacterium Halomonas desertis G11 as a Cell Factory for Poly-3-Hydroxybutyrate-co-3-Hydroxyvalerate Copolymer’s Production. Front Bioeng Biotechnol 2022; 10:878843. [PMID: 35677302 PMCID: PMC9168272 DOI: 10.3389/fbioe.2022.878843] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial polyhydroxyalkanoates (PHA) are biodegradable and biocompatible bio-based polyesters, which are used in various applications including packaging, medical and coating materials. In this study, an extremophilic hydrocarbonoclastic bacterium, previously isolated from saline sediment in the Tunisian desert, has been investigated for PHA production. The accumulation of intracellular PHA granules in Halomonas desertis G11 was detected by Nile blue A staining of the colonies. To achieve maximum PHA yield by the strain G11, the culture conditions were optimized through response surface methodology (RSM) employing a Box-Behnken Design (BBD) with three independent variables, namely, substrate concentration (1–5%), inoculum size (1–5%) and incubation time (5–15 days). Under optimized conditions, G11 strain produced 1.5 g/L (68% of DCW) of PHA using glycerol as a substrate. Application of NMR (1H and 13C) and FTIR spectroscopies showed that H. desertis accumulated PHA is a poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). The genome analysis revealed the presence of typical structural genes involved in PHBV metabolism including phaA, phaB, phaC, phaP, phaZ, and phaR, coding for acetyl-CoA acetyltransferase, acetoacetyl-CoA reductase, class I polyhydroxyalkanoates synthases, phasin, polyhydroxyalkanoates depolymerase and polyhydroxyalkanoates synthesis repressor, respectively. Glycerol can be metabolized to 1) acetyl-CoA through the glycolysis pathway and subsequently converted to the 3HB monomer, and 2) to propionyl-CoA via the threonine biosynthetic pathway and subsequently converted to the 3HV monomer. In silico analysis of PhaC1 from H. desertis G11 indicated that this enzyme belongs to Class I PHA synthase family with a “lipase box”-like sequence (SYCVG). All these characteristics make the extremophilic bacterium H. desertis G11 a promising cell factory for the conversion of bio-renewable glycerol to high-value PHBV.
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Affiliation(s)
- Khouloud Hammami
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Yasmine Souissi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
- Department of Engineering, German University of Technology in Oman, Muscat, Oman
| | - Amal Souii
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Awatef Ouertani
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Darine El-Hidri
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Marwa Jabberi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Habib Chouchane
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Amor Mosbah
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Ahmed Slaheddine Masmoudi
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Ameur Cherif
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
| | - Mohamed Neifar
- BVBGR-LR11ES31, Higher Institute of Biotechnology of Sidi Thabet (ISBST), University of Manouba, Ariana, Tunisia
- APVA-LR16ES20, National School of Engineers of Sfax (ENIS), University of Sfax, Sfax, Tunisia
- *Correspondence: Mohamed Neifar,
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17
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Assefa NG, Hansen H, Altermark B. A unique class I polyhydroxyalkanoate synthase (PhaC) from Brevundimonas sp. KH11J01 exists as a functional trimer: A comparative study with PhaC from Cupriavidus necator H16. N Biotechnol 2022; 70:57-66. [DOI: 10.1016/j.nbt.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
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18
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Kettner A, Noll M, Griehl C. Leptolyngbya sp. NIVA-CYA 255, a Promising Candidate for Poly(3-hydroxybutyrate) Production under Mixotrophic Deficiency Conditions. Biomolecules 2022; 12:biom12040504. [PMID: 35454093 PMCID: PMC9030801 DOI: 10.3390/biom12040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022] Open
Abstract
Cyanobacteria are a promising source for the sustainable production of biodegradable bioplastics such as poly(3-hydroxybutyrate) (PHB). The auto-phototrophic biomass formation is based on light and CO2, which is an advantage compared to heterotrophic PHB-producing systems. So far, only a handful of cyanobacterial species suitable for the high-yield synthesis of PHB have been reported. In the present study, the PHB formation, biomass, and elemental composition of Leptolyngbya sp. NIVA-CYA 255 were investigated. Therefore, a three-stage cultivation process was applied, consisting of a growth stage; an N-, P-, and NP-depleted phototrophic stage; and a subsequent mixotrophic deficiency stage, initiated by sodium acetate supplementation. The extracted cyanobacterial PHB was confirmed by FTIR- and GC-MS analyses. Furthermore, the fluorescent dyes LipidGreen2 and Nile red were used for fluorescence-based monitoring and the visualization of PHB. LipidGreen2 was well suited for PHB quantification, while the application of Nile red was limited by fluorescence emission crosstalk with phycocyanin. The highest PHB yields were detected in NP- (325 mg g−1) and N-deficiency (213 mg g−1). The glycogen pool was reduced in all cultures during mixotrophy, while lipid composition was not affected. The highest glycogen yield was formed under N-deficiency (217 mg g−1). Due to the high carbon storage capacity and PHB formation, Leptolyngbya sp. NIVA-CYA 255 is a promising candidate for PHB production. Further work will focus on upscaling to a technical scale and monitoring the formation by LipidGreen2-based fluorometry.
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Affiliation(s)
- Alexander Kettner
- Competence Center Algal Biotechnology, Department of Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Strasse 55, 06366 Koethen, Germany;
| | - Matthias Noll
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Friedrich-Streib-Str. 2, 96450 Coburg, Germany;
| | - Carola Griehl
- Competence Center Algal Biotechnology, Department of Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Strasse 55, 06366 Koethen, Germany;
- Correspondence: ; Tel.: +49-(0)-3496-67-2526
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19
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Phan HT, Hosoe Y, Guex M, Tomoi M, Tomita H, Zinn M, Matsumoto K. Directed Evolution of Sequence-Regulating Polyhydroxyalkanoate Synthase to Synthesize a Medium-Chain-Length-Short-Chain-Length (MCL-SCL) Block Copolymer. Biomacromolecules 2022; 23:1221-1231. [PMID: 34991313 DOI: 10.1021/acs.biomac.1c01480] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Sequence-regulating polyhydroxyalkanoate synthase PhaCAR is a chimeric enzyme comprising PhaCs from Aeromonas caviae and Ralstonia eutropha (Cupriavidus necator). It spontaneously synthesizes a short-chain-length (SCL, ≤C5) block copolymer poly(2-hydroxybutyrate)-b-poly(3-hydroxybutyrate) [P(2HB)-b-P(3HB)] from a mixture of monomer substrates. In this study, directed evolution of PhaCAR was performed to increase its activity toward a medium-chain-length (MCL, C6-12) monomer, 3-hydroxyhexanoyl (3HHx)-coenzyme A (CoA). Random mutagenesis and selection based on P(3HB-co-3HHx) production in Escherichia coli found that beneficial mutations N149D and F314L increase the 3HHx fraction. The site-directed saturation mutagenesis at position 314, which is adjacent to the catalytic center C315, demonstrated that F314H synthesizes the P(3HHx) homopolymer. The F314H mutant exhibited increased activity toward 3HHx-CoA compared with the parent enzyme, whereas the activity toward 3HB-CoA decreased. The predicted tertiary structure of PhaCAR by AlphaFold2 provided insight into the mechanism of the beneficial mutations. In addition, this finding enabled the synthesis of a new PHA block copolymer, P(3HHx)-b-P(2HB). Solvent fractionation indicated the presence of a covalent linkage between the polymer segments. This novel MCL-SCL block copolymer considerably expands the range of the molecular design of PHA block copolymers.
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Affiliation(s)
- Hien Thi Phan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yumi Hosoe
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Maureen Guex
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), 1950 Sion, Switzerland
| | - Masayoshi Tomoi
- Course of Applied Chemistry, Department of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hiroya Tomita
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), 1950 Sion, Switzerland
| | - Ken'ichiro Matsumoto
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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20
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Nanda S, Patra BR, Patel R, Bakos J, Dalai AK. Innovations in applications and prospects of bioplastics and biopolymers: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2022; 20:379-395. [PMID: 34867134 PMCID: PMC8629338 DOI: 10.1007/s10311-021-01334-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 05/22/2023]
Abstract
Non-biodegradable plastics are continually amassing landfills and oceans worldwide while creating severe environmental issues and hazards to animal and human health. Plastic pollution has resulted in the death of millions of seabirds and aquatic animals. The worldwide production of plastics in 2020 has increased by 36% since 2010. This has generated significant interest in bioplastics to supplement global plastic demands. Bioplastics have several advantages over conventional plastics in terms of biodegradability, low carbon footprint, energy efficiency, versatility, unique mechanical and thermal characteristics, and societal acceptance. Bioplastics have huge potential to replace petroleum-based plastics in a wide range of industries from automobiles to biomedical applications. Here we review bioplastic polymers such as polyhydroxyalkanoate, polylactic acid, poly-3-hydroxybutyrate, polyamide 11, and polyhydroxyurethanes; and cellulose-based, starch-based, protein-based and lipid-based biopolymers. We discuss economic benefits, market scenarios, chemistry and applications of bioplastic polymers.
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Affiliation(s)
- Sonil Nanda
- Titan Clean Energy Projects Corporation, Craik, SK Canada
| | - Biswa R. Patra
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
| | - Ravi Patel
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
| | - Jamie Bakos
- Titan Clean Energy Projects Corporation, Craik, SK Canada
| | - Ajay K. Dalai
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK Canada
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21
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Zher Neoh S, Fey Chek M, Tiang Tan H, Linares-Pastén JA, Nandakumar A, Hakoshima T, Sudesh K. Polyhydroxyalkanoate synthase (PhaC): The key enzyme for biopolyester synthesis. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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22
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Christensen M, Jablonski P, Altermark B, Irgum K, Hansen H. High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741 T and in silico analyses of the genus specific PhaC 2 polymerase variant. Microb Cell Fact 2021; 20:225. [PMID: 34930259 PMCID: PMC8686332 DOI: 10.1186/s12934-021-01713-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains. RESULTS Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains. CONCLUSIONS Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.
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Affiliation(s)
- Mikkel Christensen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Piotr Jablonski
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Bjørn Altermark
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Knut Irgum
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Hilde Hansen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
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23
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Rekhi P, Goswami M, Ramakrishna S, Debnath M. Polyhydroxyalkanoates biopolymers toward decarbonizing economy and sustainable future. Crit Rev Biotechnol 2021; 42:668-692. [PMID: 34645360 DOI: 10.1080/07388551.2021.1960265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polymers are synonymous with the modern way of living. However, polymers with a large carbon footprint, especially those derived from nonrenewable petrochemical sources, are increasingly perceived as detrimental to the environment and a sustainable future. Polyhydroxyalkanoate (PHA) is a microbial biopolymer and a plausible alternative for renewable sources. However, PHA in its monomeric forms has very limited applications due to its limited flexibility, tensile strength, and moldability. Herein, the life cycle of PHA molecules, from biosynthesis to commercial utilization for diverse applications is discussed. For clarity, the applications of this bioplastic biocomposite material are further segregated into two domains, namely, the industrial sector and the medical sector. The industry sectors reviewed here include food packaging, textiles, agriculture, automotive, and electronics. High-value addition of PHA for a sustainable future can be foreseen in the medical domain. Properties such as biodegradability and biocompatibility make PHA a suitable candidate for decarbonizing biomaterials during tissue repair, organ reconstruction, drug delivery, bone tissue engineering, and chemotherapeutics.
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Affiliation(s)
- Pavni Rekhi
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Moushmi Goswami
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Mousumi Debnath
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
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Vuong P, Lim DJ, Murphy DV, Wise MJ, Whiteley AS, Kaur P. Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes. Front Microbiol 2021; 12:697309. [PMID: 34322108 PMCID: PMC8312272 DOI: 10.3389/fmicb.2021.697309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Daniel J. Lim
- Department of Physics and Astronomy, Curtin University, Perth, WA, Australia
| | - Daniel V. Murphy
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Michael J. Wise
- School of Physics, Mathematics and Computing, The University of Western Australia, Perth, WA, Australia
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA, Australia
| | | | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Lim H, Chuah JA, Chek MF, Tan HT, Hakoshima T, Sudesh K. Identification of regions affecting enzyme activity, substrate binding, dimer stabilization and polyhydroxyalkanoate (PHA) granule morphology in the PHA synthase of Aquitalea sp. USM4. Int J Biol Macromol 2021; 186:414-423. [PMID: 34246679 DOI: 10.1016/j.ijbiomac.2021.07.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/23/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biopolyesters synthesized by microorganisms as intracellular energy reservoirs under stressful environmental conditions. PHA synthase (PhaC) is the key enzyme responsible for PHA biosynthesis, but the importance of its N- and C-terminal ends still remains elusive. Six plasmid constructs expressing truncation variants of Aquitalea sp. USM4 PhaC (PhaC1As) were generated and heterologously expressed in Cupriavidus necator PHB-4. Removal of the first six residues at the N-terminus enabled the modulation of PHA composition without altering the PHA content in cells. Meanwhile, deletion of 13 amino acids from the C-terminus greatly affected the catalytic activity of PhaC1As, retaining only 1.1-7.4% of the total activity. Truncation(s) at the N- and/or C-terminus of PhaC1As gradually diminished the incorporation of comonomer units, and revealed that the N-terminal region is essential for PhaC1As dimerization whereas the C-terminal region is required for stabilization. Notably, transmission electron microscopy analysis showed that PhaC modification affected the morphology of intracellular PHA granules, which until now is only known to be regulated by phasins. This study provided substantial evidence and highlighted the significance of both the N- and C-termini of PhaC1As in regulating intracellular granule morphology, activity, substrate specificity, dimerization and stability of the synthase.
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Affiliation(s)
- Hui Lim
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jo-Ann Chuah
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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Microbial cell factories for the production of polyhydroxyalkanoates. Essays Biochem 2021; 65:337-353. [PMID: 34132340 DOI: 10.1042/ebc20200142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Pollution caused by persistent petro-plastics is the most pressing problem currently, with 8 million tons of plastic waste dumped annually in the oceans. Plastic waste management is not systematized in many countries, because it is laborious and expensive with secondary pollution hazards. Bioplastics, synthesized by microorganisms, are viable alternatives to petrochemical-based thermoplastics due to their biodegradable nature. Polyhydroxyalkanoates (PHAs) are a structurally and functionally diverse group of storage polymers synthesized by many microorganisms, including bacteria and Archaea. Some of the most important PHA accumulating bacteria include Cupriavidus necator, Burkholderia sacchari, Pseudomonas sp., Bacillus sp., recombinant Escherichia coli, and certain halophilic extremophiles. PHAs are synthesized by specialized PHA polymerases with assorted monomers derived from the cellular metabolite pool. In the natural cycle of cellular growth, PHAs are depolymerized by the native host for carbon and energy. The presence of these microbial PHA depolymerases in natural niches is responsible for the degradation of bioplastics. Polyhydroxybutyrate (PHB) is the most common PHA with desirable thermoplastic-like properties. PHAs have widespread applications in various industries including biomedicine, fine chemicals production, drug delivery, packaging, and agriculture. This review provides the updated knowledge on the metabolic pathways for PHAs synthesis in bacteria, and the major microbial hosts for PHAs production. Yeasts are presented as a potential candidate for industrial PHAs production, with their high amenability to genetic engineering and the availability of industrial-scale technology. The major bottlenecks in the commercialization of PHAs as an alternative for plastics and future perspectives are also critically discussed.
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Sindhu R, Madhavan A, Arun KB, Pugazhendhi A, Reshmy R, Awasthi MK, Sirohi R, Tarafdar A, Pandey A, Binod P. Metabolic circuits and gene regulators in polyhydroxyalkanoate producing organisms: Intervention strategies for enhanced production. BIORESOURCE TECHNOLOGY 2021; 327:124791. [PMID: 33579565 DOI: 10.1016/j.biortech.2021.124791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Worldwide worries upsurge concerning environmental pollutions triggered by the accumulation of plastic wastes. Biopolymers are promising candidates for resolving these difficulties by replacing non-biodegradable plastics. Among biopolymers, polyhydroxyalkanoates (PHAs), are natural polymers that are synthesized and accumulated in a range of microorganisms, are considered as promising biopolymers since they have biocompatibility, biodegradability, and other physico-chemical properties comparable to those of synthetic plastics. Consequently, considerable research have been attempted to advance a better understanding of mechanisms related to the metabolic synthesis and characteristics of PHAs and to develop native and recombinant microorganisms that can proficiently produce PHAs comprising desired monomers with high titer and productivity for industrial applications. Recent developments in metabolic engineering and synthetic biology applied to enhance PHA synthesis include, promoter engineering, ribosome-binding site (RBS) engineering, development of synthetic constructs etc. This review gives a brief overview of metabolic routes and regulators of PHA production and its intervention strategies.
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Affiliation(s)
- Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ranjna Sirohi
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263 145, India
| | - Ayon Tarafdar
- Divison of Livestock Production and Management, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow 226 001, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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Davies CG, Reilly K, Altermann E, Hendrickson HL. PLAN-M; Mycobacteriophage Endolysins Fused to Biodegradable Nanobeads Mitigate Mycobacterial Growth in Liquid and on Surfaces. Front Microbiol 2021; 12:562748. [PMID: 33981289 DOI: 10.3389/fmicb.2021.562748] [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: 05/21/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
The Mycobacteria are a genus of Actinobacteria that include human pathogens such as Mycobacterium tuberculosis (TB). Active TB disease can spread by airborne transmission to healthcare workers and to their community. The HHMI SEA-PHAGES program has contributed to discovering bacteriophages that are able to infect M. smegmatis MC2 155, a close relative of M. tuberculosis. This collection of diverse Mycobacteriophages is an excellent resource for trialling bacteriophage-sourced enzymes in novel applications. Herein we measured the ability Mycobacteriophage endolysins to lyse their host strain when functionally fused to biodegradable polyhydroxyalkanoate (PHA) nanobeads. PHA nanobeads facilitate both the expression and the application of enzymes to surfaces and have been demonstrated to stabilize a wide array of proteins for practical applications whilst eliminating the challenges of traditional protein purification. We selected two Lysin A and six Lysin B homologs to be functionally fused to the polyhydroxyalkanoate synthase C (PhaC). Expression of these constructs resulted in functional lysins displayed on the surface of PHA nanobeads. The lysins thus directionally displayed on nanobeads lysed up to 79% of the M. smegmatis MC2 155 population using 80 mg/mL of nanobeads in pure culture. In order to determine whether the nanobeads would be effective as a protective layer in PPE we adapted a fabric-based test and observed a maximum of 1 log loss of the cell population after 5 h of exposure on a textile (91% cell lysis). Lysin B enzymes performed better than the Lysin A enzymes as a protective barrier on textiles surface assays. These results suggest that bacterial endolysins are efficient in their action when displayed on PHA nanobeads and can cause significant population mortality in as little as 45 min. Our results provide the proof-of-principle that Mycobacteriophage endolysins can be used on functionalized nanobeads where they can protect surfaces such as personal protective equipment (PPE) that routinely come into contact with aerosolised bacteria.
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Affiliation(s)
- Courtney G Davies
- Massey Phage Whānau, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | | | - Eric Altermann
- AgResearch Ltd., Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Heather L Hendrickson
- Massey Phage Whānau, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand.,Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
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Harada K, Kobayashi S, Oshima K, Yoshida S, Tsuge T, Sato S. Engineering of Aeromonas caviae Polyhydroxyalkanoate Synthase Through Site-Directed Mutagenesis for Enhanced Polymerization of the 3-Hydroxyhexanoate Unit. Front Bioeng Biotechnol 2021; 9:627082. [PMID: 33748082 PMCID: PMC7966705 DOI: 10.3389/fbioe.2021.627082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Polyhydroxyalkanoate (PHA) synthase is an enzyme that polymerizes the acyl group of hydroxyacyl-coenzyme A (CoA) substrates. Aeromonas caviae PHA synthase (PhaCAc) is an important biocatalyst for the synthesis of a useful PHA copolymer, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. Previously, a PhaCAc mutant with double mutations in asparagine 149 (replaced by serine [N149S]) and aspartate 171 (replaced by glycine [D171G]) was generated to synthesize a 3HHx-rich P(3HB-co-3HHx) and was named PhaCAc NSDG. In this study, to further increase the 3HHx fraction in biosynthesized PHA, PhaCAc was engineered based on the three-dimensional structural information of PHA synthases. First, a homology model of PhaCAc was built to target the residues for site-directed mutagenesis. Three residues, namely tyrosine 318 (Y318), serine 389 (S389), and leucine 436 (L436), were predicted to be involved in substrate recognition by PhaCAc. These PhaCAc NSDG residues were replaced with other amino acids, and the resulting triple mutants were expressed in the engineered strain of Ralstonia eutropha for application in PHA biosynthesis from palm kernel oil. The S389T mutation allowed the synthesis of P(3HB-co-3HHx) with an increased 3HHx fraction without a significant reduction in PHA yield. Thus, a new workhorse enzyme was successfully engineered for the biosynthesis of a higher 3HHx-fraction polymer.
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Affiliation(s)
- Ken Harada
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan.,Biotechnology Research Laboratories, Kaneka Corporation, Hyogo, Japan
| | - Shingo Kobayashi
- Biotechnology Research Laboratories, Kaneka Corporation, Hyogo, Japan
| | - Kanji Oshima
- Biotechnology Research Laboratories, Kaneka Corporation, Hyogo, Japan
| | - Shinichi Yoshida
- Biotechnology Research Laboratories, Kaneka Corporation, Hyogo, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Shunsuke Sato
- Biotechnology Research Laboratories, Kaneka Corporation, Hyogo, Japan
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30
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Tools for the discovery of biopolymer producing cysteine relays. Biophys Rev 2021; 13:247-258. [PMID: 33927786 DOI: 10.1007/s12551-021-00792-y] [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: 02/03/2021] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Cysteine relays, where a protein or small molecule is transferred multiple times via transthiolation, are central to the production of biological polymers. Enzymes that utilise relay mechanisms display broad substrate specificity and are readily engineered to produce new polymers. In this review, I discuss recent advances in the discovery, engineering and biophysical characterisation of cysteine relays. I will focus on eukaryotic ubiquitin (Ub) cascades and prokaryotic polyhydroxyalkanoate (PHA) synthesis. These evolutionarily distinct processes employ similar chemistry and are readily modified for biotechnological applications. Both processes have been studied intensively for decades, yet recent studies suggest we do not fully understand their mechanistic diversity or plasticity. I will discuss the important role that activity-based probes (ABPs) and other chemical tools have had in identifying and delineating Ub cysteine-relays and the potential for ABPs to be applied to PHA synthases. Finally, I will offer a personal perspective on the potential of engineering cysteine-relays for non-native polymer production.
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Suzuki M, Tachibana Y, Kasuya KI. Biodegradability of poly(3-hydroxyalkanoate) and poly(ε-caprolactone) via biological carbon cycles in marine environments. Polym J 2020. [DOI: 10.1038/s41428-020-00396-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AbstractApproximately 4.8–12.7 million tons of plastic waste has been estimated to be discharged into marine environments annually by wind and river currents. The Ellen MacArthur Foundation warns that the total weight of plastic waste in the oceans will exceed the total weight of fish in 2050 if the environmental runoff of plastic continues at the current rate. Hence, biodegradable plastics are attracting attention as a solution to the problems caused by plastic waste. Among biodegradable plastics, polyhydroxyalkanoates (PHAs) and poly(ε-caprolactone) (PCL) are particularly noteworthy because of their excellent marine biodegradability. In this review, the biosynthesis of PHA and cutin, a natural analog of PCL, and the biodegradation of PHA and PCL in carbon cycles in marine ecosystems are discussed. PHA is biosynthesized and biodegraded by various marine microbes in a wide range of marine environments, including coastal, shallow-water, and deep-sea environments. Marine cutin is biosynthesized by marine plants or obtained from terrestrial environments, and PCL and cutin are biodegraded by cutin hydrolytic enzyme-producing microbes in broad marine environments. Thus, biological carbon cycles for PHA and PCL exist in the marine environment, which would allow materials made of PHA and PCL to be quickly mineralized in marine environments.
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32
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Medeiros Garcia Alcântara J, Distante F, Storti G, Moscatelli D, Morbidelli M, Sponchioni M. Current trends in the production of biodegradable bioplastics: The case of polyhydroxyalkanoates. Biotechnol Adv 2020; 42:107582. [DOI: 10.1016/j.biotechadv.2020.107582] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022]
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Choi SY, Cho IJ, Lee Y, Kim YJ, Kim KJ, Lee SY. Microbial Polyhydroxyalkanoates and Nonnatural Polyesters. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907138. [PMID: 32249983 DOI: 10.1002/adma.201907138] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms produce diverse polymers for various purposes such as storing genetic information, energy, and reducing power, and serving as structural materials and scaffolds. Among these polymers, polyhydroxyalkanoates (PHAs) are microbial polyesters synthesized and accumulated intracellularly as a storage material of carbon, energy, and reducing power under unfavorable growth conditions in the presence of excess carbon source. PHAs have attracted considerable attention for their wide range of applications in industrial and medical fields. Since the first discovery of PHA accumulating bacteria about 100 years ago, remarkable advances have been made in the understanding of PHA biosynthesis and metabolic engineering of microorganisms toward developing efficient PHA producers. Recently, nonnatural polyesters have also been synthesized by metabolically engineered microorganisms, which opened a new avenue toward sustainable production of more diverse plastics. Herein, the current state of PHAs and nonnatural polyesters is reviewed, covering mechanisms of microbial polyester biosynthesis, metabolic pathways, and enzymes involved in biosynthesis of short-chain-length PHAs, medium-chain-length PHAs, and nonnatural polyesters, especially 2-hydroxyacid-containing polyesters, metabolic engineering strategies to produce novel polymers and enhance production capabilities and fermentation, and downstream processing strategies for cost-effective production of these microbial polyesters. In addition, the applications of PHAs and prospects are discussed.
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Affiliation(s)
- So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yeo-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- BioProcess Engineering Research Center and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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Moriya H, Takita Y, Matsumoto A, Yamahata Y, Nishimukai M, Miyazaki M, Shimoi H, Kawai SJ, Yamada M. Cobetia sp. Bacteria, Which Are Capable of Utilizing Alginate or Waste Laminaria sp. for Poly(3-Hydroxybutyrate) Synthesis, Isolated From a Marine Environment. Front Bioeng Biotechnol 2020; 8:974. [PMID: 32984275 PMCID: PMC7479843 DOI: 10.3389/fbioe.2020.00974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
We isolated the Cobetia sp. strains IU 180733JP01 (5-11-6-3) and 190790JP01 (5-25-4-2) from seaweeds and showed that both strains accumulate poly(3-hydroxybutyrate) [P(3HB)] homopolymer in a nitrogen-limiting mineral salt medium containing alginate as a sole carbon source. Genome sequence analysis of the isolated strains showed that they have putative genes which encode enzymes relevant to alginate assimilation and P(3HB) synthesis, and the putative alginate-assimilating genes formed a cluster. Investigation of the optimum culture conditions for high accumulation of P(3HB) showed that when the 5-11-6-3 strain was cultured in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and 3% (w/v) alginate as a sole carbon source for 2 days, the P(3HB) content and P(3HB) production reached 62.1 ± 3.4 wt% and 3.11 ± 0.16 g/L, respectively. When the 5-25-4-2 strain was cultured in a nitrogen-limiting mineral salt medium (pH 4.0) containing 5% NaCl and 3% (w/v) alginate for 2 days, the P(3HB) content and P(3HB) production reached 56.9 ± 2.1 wt% and 2.67 ± 0.11 g/L, respectively. Moreover, the 5-11-6-3 strain also produced P(3HB) in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and freeze-dried and crushed waste Laminaria sp., which is classified into brown algae and contains alginate abundantly. The resulting P(3HB) content and P(3HB) productivity were 13.5 ± 0.13 wt% and 3.99 ± 0.15 mg/L/h, respectively. Thus, we demonstrated the potential application of the isolated strains to a simple P(3HB) production process from seaweeds without chemical hydrolysis and enzymatic saccharification.
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Affiliation(s)
- Hiroki Moriya
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuto Takita
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Akira Matsumoto
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuki Yamahata
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Megumi Nishimukai
- Department of Animal Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Hitoshi Shimoi
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Sung-Jin Kawai
- New Field Pioneering Division, New Value Creation Center, Toyota Boshoku Corporation, Kariya, Japan
| | - Miwa Yamada
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
- Education and Research on Sanriku Fishery Industry Department, Organization for Revitalization of the Sanriku Region and Regional Development, Iwate University, Morioka, Japan
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Bacillus thermoamylovorans-Related Strain Isolated from High Temperature Sites as Potential Producers of Medium-Chain-Length Polyhydroxyalkanoate (mcl-PHA). Curr Microbiol 2020; 77:3044-3056. [DOI: 10.1007/s00284-020-02118-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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36
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Tan HT, Chek MF, Lakshmanan M, Foong CP, Hakoshima T, Sudesh K. Evaluation of BP-M-CPF4 polyhydroxyalkanoate (PHA) synthase on the production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from plant oil using Cupriavidus necator transformants. Int J Biol Macromol 2020; 159:250-257. [PMID: 32417540 DOI: 10.1016/j.ijbiomac.2020.05.064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/25/2020] [Accepted: 05/10/2020] [Indexed: 01/24/2023]
Abstract
Among the various types of polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] has a high potential to serve as commercial bioplastic due to its striking resemblance to petroleum-based plastics. In this study, five different genotypes of Cupriavidusnecator transformants harbouring the phaCBP-M-CPF4 gene (including PHB¯4/pBBR1-CBP-M-CPF4) were developed to evaluate the efficiency of 3HHx monomer incorporation. The fraction of 3-hydroxyhexanoate (3HHx) monomer that was incorporated into the PHA synthesized by these C. necator transformants using palm oil as the sole carbon source, was examined. Overall, co-expression of enoyl-CoA hydratase gene (phaJ1) from Pseudomonas aeruginosa, along with PHA synthase (PhaC), increased the 3HHx composition in the PHA copolymer. The differences in the enzyme activities of β-ketothiolase (PhaACn) and NADPH-dependent acetoacetyl-CoA reductase (PhaBCn) of the C. necator mutant hosts used in this study, were observed to alter the 3HHx composition and molecular weight of the PHA copolymer produced. The 3HHx fractions in the P(3HB-co-3HHx) produced by these C. necator transformants ranged between 1 and 18 mol%, while the weight-average molecular weight ranged from 0.7 × 106 to 1.8 × 106 Da. PhaCBP-M-CPF4 displayed a typical initial lag-phase and a relatively low synthase activity in the in vitro enzyme assay, which is thought to be the reason for the higher molecular weights of PHA obtained in this study.
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Affiliation(s)
- Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Manoj Lakshmanan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia; USM-RIKEN International Center for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia
| | - Choon Pin Foong
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia; USM-RIKEN International Center for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia.
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Chek MF, Kim SY, Mori T, Tan HT, Sudesh K, Hakoshima T. Asymmetric Open-Closed Dimer Mechanism of Polyhydroxyalkanoate Synthase PhaC. iScience 2020; 23:101084. [PMID: 32388399 PMCID: PMC7214940 DOI: 10.1016/j.isci.2020.101084] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Biodegradable polyester polyhydroxyalkanoate (PHA) is a promising bioplastic material for industrial use as a replacement for petroleum-based plastics. PHA synthase PhaC forms an active dimer to polymerize acyl moieties from the substrate acyl-coenzyme A (CoA) into PHA polymers. Here we present the crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, bound to CoA. The structure reveals an asymmetric dimer, in which one protomer adopts an open conformation bound to CoA, whereas the other adopts a closed conformation in a CoA-free form. The open conformation is stabilized by the asymmetric dimerization and enables PhaC to accommodate CoA and also to create the product egress path. The bound CoA molecule has its β-mercaptoethanolamine moiety extended into the active site with the terminal SH group close to active center Cys291, enabling formation of the reaction intermediate by acylation of Cys291. Crystal structure of PhaCCs-CAT bound to coenzyme A A unique asymmetric open-closed dimer Restructuring of the CAP subdomain provides a cleft toward the active site The cleft enables the substrate entry and the product egress
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Affiliation(s)
- Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Sun-Yong Kim
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Mori
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hua Tiang Tan
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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Thomas T, Sudesh K, Bazire A, Elain A, Tan HT, Lim H, Bruzaud S. PHA Production and PHA Synthases of the Halophilic Bacterium Halomonas sp. SF2003. Bioengineering (Basel) 2020; 7:bioengineering7010029. [PMID: 32244900 PMCID: PMC7175313 DOI: 10.3390/bioengineering7010029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 01/18/2023] Open
Abstract
Among the different tools which can be studied and managed to tailor-make polyhydroxyalkanoates (PHAs) and enhance their production, bacterial strain and carbon substrates are essential. The assimilation of carbon sources is dependent on bacterial strain’s metabolism and consequently cannot be dissociated. Both must wisely be studied and well selected to ensure the highest production yield of PHAs. Halomonas sp. SF2003 is a marine bacterium already identified as a PHA-producing strain and especially of poly-3-hydroxybutyrate (P-3HB) and poly-3-hydroxybutyrate-co-3-hydroxyvalerate (P-3HB-co-3HV). Previous studies have identified different genes potentially involved in PHA production by Halomonas sp. SF2003, including two phaC genes with atypical characteristics, phaC1 and phaC2. At the same time, an interesting adaptability of the strain in front of various growth conditions was highlighted, making it a good candidate for biotechnological applications. To continue the characterization of Halomonas sp. SF2003, the screening of carbon substrates exploitable for PHA production was performed as well as production tests. Additionally, the functionality of both PHA synthases PhaC1 and PhaC2 was investigated, with an in silico study and the production of transformant strains, in order to confirm and to understand the role of each one on PHA production. The results of this study confirm the adaptability of the strain and its ability to exploit various carbon substrates, in pure or mixed form, for PHA production. Individual expression of PhaC1 and PhaC2 synthases in a non-PHA-producing strain, Cupriavidus necator H16 PHB¯4 (DSM 541), allows obtaining PHA production, demonstrating at the same time, functionality and differences between both PHA synthases. All the results of this study confirm the biotechnological interest in Halomonas sp. SF2003.
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Affiliation(s)
- Tatiana Thomas
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne Sud (UBS), EA 3884 Lorient, France;
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne Sud (UBS), 56300 Pontivy, France;
- Correspondence: ; Tel.: +33-661-730-222
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia (USM), Penang 11800, Malaysia; (K.S.); (H.T.T.); (H.L.)
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines (LBCM), IUEM, Université de Bretagne-Sud (UBS), EA 3884 Lorient, France;
| | - Anne Elain
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne Sud (UBS), 56300 Pontivy, France;
| | - Hua Tiang Tan
- School of Biological Sciences, Universiti Sains Malaysia (USM), Penang 11800, Malaysia; (K.S.); (H.T.T.); (H.L.)
| | - Hui Lim
- School of Biological Sciences, Universiti Sains Malaysia (USM), Penang 11800, Malaysia; (K.S.); (H.T.T.); (H.L.)
| | - Stéphane Bruzaud
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne Sud (UBS), EA 3884 Lorient, France;
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Surendran A, Lakshmanan M, Chee JY, Sulaiman AM, Thuoc DV, Sudesh K. Can Polyhydroxyalkanoates Be Produced Efficiently From Waste Plant and Animal Oils? Front Bioeng Biotechnol 2020; 8:169. [PMID: 32258007 PMCID: PMC7090169 DOI: 10.3389/fbioe.2020.00169] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are a potential replacement for some petrochemical-based plastics. PHAs are polyesters synthesized and stored by various bacteria and archaea in their cytoplasm as water-insoluble inclusions. PHAs are usually produced when the microbes are cultured with nutrient-limiting concentrations of nitrogen, phosphorus, sulfur, or oxygen and excess carbon sources. Such fermentation conditions have been optimized by industry to reduce the cost of PHAs produced commercially. Industrially, these biodegradable polyesters are derived from microbial fermentation processes utilizing various carbon sources. One of the major constraints in scaling-up PHA production is the cost of the carbon source metabolized by the microorganisms. Hence, cheap and renewable carbon substrates are currently being investigated around the globe. Plant and animal oils have been demonstrated to be excellent carbon sources for high yield production of PHAs. Waste streams from oil mills or the used oils, which are even cheaper, are also used. This approach not only reduces the production cost for PHAs, but also makes a significant contribution toward the reduction of environmental pollution caused by the used oil. Advancements in the genetic and metabolic engineering of bacterial strains have enabled a more efficient utilization of various carbon sources, in achieving high PHA yields with specified monomer compositions. This review discusses recent developments in the biosynthesis and classification of various forms of PHAs produced using crude and waste oils from the oil palm and fish industries. The biodegradability of the PHAs produced from these oils will also be discussed.
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Affiliation(s)
- Arthy Surendran
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Manoj Lakshmanan
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- USM-RIKEN International Centre for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Jiun Yee Chee
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Doan Van Thuoc
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- USM-RIKEN International Centre for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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Tarrahi R, Fathi Z, Seydibeyoğlu MÖ, Doustkhah E, Khataee A. Polyhydroxyalkanoates (PHA): From production to nanoarchitecture. Int J Biol Macromol 2020; 146:596-619. [DOI: 10.1016/j.ijbiomac.2019.12.181] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/03/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023]
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Metabolic engineering for the synthesis of polyesters: A 100-year journey from polyhydroxyalkanoates to non-natural microbial polyesters. Metab Eng 2020; 58:47-81. [DOI: 10.1016/j.ymben.2019.05.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/04/2019] [Accepted: 05/26/2019] [Indexed: 11/16/2022]
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Clifton‐García B, González‐Reynoso O, Robledo‐Ortiz J, Villafaña‐Rojas J, González‐García Y. Forest soil bacteria able to produce homo and copolymers of polyhydroxyalkanoates from several pure and waste carbon sources. Lett Appl Microbiol 2020; 70:300-309. [DOI: 10.1111/lam.13272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 11/28/2022]
Affiliation(s)
- B. Clifton‐García
- Departamento de Ingeniería Química Universidad de Guadalajara Jalisco México
| | - O. González‐Reynoso
- Departamento de Ingeniería Química Universidad de Guadalajara Jalisco México
| | - J.R. Robledo‐Ortiz
- Departamento de Madera Celulosa y Papel Universidad de Guadalajara Jalisco México
| | - J. Villafaña‐Rojas
- Departamento de Química Universidad Autónoma de Guadalajara Jalisco México
| | - Y. González‐García
- Departamento de Madera Celulosa y Papel Universidad de Guadalajara Jalisco México
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Complete Genome Sequence of a Novel Polyhydroxyalkanoate (PHA) Producer, Jeongeupia sp. USM3 (JCM 19920) and Characterization of Its PHA Synthases. Curr Microbiol 2020; 77:500-508. [PMID: 31893298 DOI: 10.1007/s00284-019-01852-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
Abstract
A novel polyhydroxyalkanoate (PHA)-producing bacterium, Jeongeupia sp. USM3 (JCM 19920) was isolated from the limestone soil at Gua Tempurung, Perak, Malaysia. This is the first report on the complete genome sequence for the genus Jeongeupia. This genome consists of a circular chromosome with a size of 3,788,814 bp and contains 3557 genes. Two PHA synthase (phaC) genes encoding for the key enzyme in the polymerization of PHA monomers and other PHA-associated genes were identified from the genome. Phylogenetic analysis of the PhaC protein sequences has revealed that both PhaC1 and PhaC2 of Jeongeupia sp. USM3 are categorized as Class I PHA synthases with 56% similarity to each other. Both of the PHA synthase genes of this isolate were cloned and heterologously expressed in a PHA mutant strain Cupriavidus necator PHB-4. The ability of the transformants to accumulate PHA showed that both PhaC1 and PhaC2 were functional.
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Wang J, Tan H, Li K, Yin H. Two‐stage fermentation optimization for poly‐3‐hydroxybutyrate production from methanol by a new Methylobacterium isolate from oil fields. J Appl Microbiol 2019; 128:171-181. [DOI: 10.1111/jam.14463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- J. Wang
- Liaoning Provincial Key Laboratory of Carbohydrates Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
- College of Fisheries and Life Science Dalian Ocean University Dalian China
| | - H. Tan
- Liaoning Provincial Key Laboratory of Carbohydrates Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - K. Li
- Liaoning Provincial Key Laboratory of Carbohydrates Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - H. Yin
- Liaoning Provincial Key Laboratory of Carbohydrates Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
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Higuchi-Takeuchi M, Numata K. Marine Purple Photosynthetic Bacteria as Sustainable Microbial Production Hosts. Front Bioeng Biotechnol 2019; 7:258. [PMID: 31681740 PMCID: PMC6798066 DOI: 10.3389/fbioe.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/25/2019] [Indexed: 12/01/2022] Open
Abstract
Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. Front Microbiol 2019; 10:2104. [PMID: 31572321 PMCID: PMC6749099 DOI: 10.3389/fmicb.2019.02104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 12/02/2022] Open
Abstract
In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Harada K, Nambu Y, Mizuno S, Tsuge T. In vivo and in vitro characterization of hydrophilic protein tag-fused Ralstonia eutropha polyhydroxyalkanoate synthase. Int J Biol Macromol 2019; 138:379-385. [PMID: 31315020 DOI: 10.1016/j.ijbiomac.2019.07.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/13/2019] [Accepted: 07/13/2019] [Indexed: 01/02/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are synthesized by bacteria as an intracellular storage polyester, where PHA synthase (PhaC) catalyzes the polymerization of its substrate hydroxyacyl-coenzyme A (HA-CoA) to form PHA. When PhaC is overexpressed in Escherichia coli, most PhaC protein is produced as insoluble inclusion bodies due to its low aqueous solubility. This study aimed to improve the solubility of Ralstonia eutropha PHA synthase (PhaCRe) by fusing a hydrophilic tag, glutathione S-transferase (GST), to the protein's N-terminus. In in vivo assays, the GST tag had no obvious effect on solubility and enzymatic activity of PhaCRe. However, an in vitro assay revealed that the surface of GST-fused PhaCRe (GST-PhaCRe) had increased hydrophilicity, and tended to form correct PhaCRe dimers when added to the (R)-3-hydroxybutyryl-CoA substrate. Although GST-PhaCRe displayed a long lag phase at the start of a polymerization reaction, granule-associated GST-PhaCRe showed higher catalytic activity than PhaCRe in kinetic analysis. The results are discussed in light of the dimerization mechanisms of PhaCRe.
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Affiliation(s)
- Ken Harada
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Yuka Nambu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Shoji Mizuno
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Takeharu Tsuge
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan.
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Can biotechnology turn the tide on plastics? Curr Opin Biotechnol 2019; 57:160-166. [DOI: 10.1016/j.copbio.2019.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/30/2022]
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Chek MF, Hiroe A, Hakoshima T, Sudesh K, Taguchi S. PHA synthase (PhaC): interpreting the functions of bioplastic-producing enzyme from a structural perspective. Appl Microbiol Biotechnol 2018; 103:1131-1141. [DOI: 10.1007/s00253-018-9538-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
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50
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Teh AH, Chiam NC, Furusawa G, Sudesh K. Modelling of polyhydroxyalkanoate synthase from Aquitalea sp. USM4 suggests a novel mechanism for polymer elongation. Int J Biol Macromol 2018; 119:438-445. [DOI: 10.1016/j.ijbiomac.2018.07.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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