1
|
Anjulal H, Singhvi M, Zinjarde S. Insights into the biodegradation of polyhydroxyalkanoates by the tropical marine isolate, Nocardiopsis dassonvillei NCIM 5124. 3 Biotech 2024; 14:240. [PMID: 39310033 PMCID: PMC11415560 DOI: 10.1007/s13205-024-04079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
In the current study, the ability of an indigenous marine Actinomycete Nocardiopsis dassonvillei (NCIM 5124) to degrade poly(3-hydroxybutyrate)-PHB was examined. From the whole genome sequencing data of the organism, information regarding the PHB depolymerase gene and amino acid sequence (Accession number: MCK9871921.1) was retrieved. In silico studies indicated the presence of a signal peptide characteristic of extracellular enzymes. ProtParam tool predicted that the protein had a molecular mass of 42.46 kDa with an isoelectric point of 4.51. Aliphatic and instability index values suggested that the protein was stable and the observed GARVY value indicated its hydrophilic nature. 3D structure prediction and multiple sequence alignments revealed the presence of Type I catalytic domain [including the oxyanion histidine towards the N terminal, the catalytic triad with serine (as a part of GLSAG pentapeptide), aspartate and histidine], substrate binding and linker domain. The organism was able to grow on PHB in solid and liquid media and effectively degrade it. Maximum enzyme activity (1.8 U/mL/min) was observed after 5 d of incubation in Bushnell Hass Medium containing 0.1% PHB, 1.5% sodium chloride, at 30 °C, pH 7.5 with agitation at 130 rpm. Application of the organism in disintegrating films of PHB and its copolymers was successfully demonstrated on the basis of weight loss and scanning electron microscope analysis. To the best of our knowledge, this is the first report on production of PHB depolymerase with high efficiency by N. dassonvillei, an organism that holds promise in degrading PHB-derived waste material. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04079-3.
Collapse
Affiliation(s)
- H. Anjulal
- Department of Biotechnology with Jointly Merged Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007 India
| | - Mamata Singhvi
- Department of Biotechnology with Jointly Merged Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007 India
| | - Smita Zinjarde
- Department of Biotechnology with Jointly Merged Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007 India
| |
Collapse
|
2
|
Serrano‐Aguirre L, Prieto MA. Can bioplastics always offer a truly sustainable alternative to fossil-based plastics? Microb Biotechnol 2024; 17:e14458. [PMID: 38568795 PMCID: PMC10990045 DOI: 10.1111/1751-7915.14458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
Bioplastics, comprised of bio-based and/or biodegradable polymers, have the potential to play a crucial role in the transition towards a sustainable circular economy. The use of biodegradable polymers not only leads to reduced greenhouse gas emissions but also might address the problem of plastic waste persisting in the environment, especially when removal is challenging. Nevertheless, biodegradable plastics should not be considered as substitutes for proper waste management practices, given that their biodegradability strongly depends on environmental conditions. Among the challenges hindering the sustainable implementation of bioplastics in the market, the development of effective downstream recycling routes is imperative, given the increasing production volumes of these materials. Here, we discuss about the most advisable end-of-life scenarios for bioplastics. Various recycling strategies, including mechanical, chemical or biological (both enzymatic and microbial) approaches, should be considered. Employing enzymes as biocatalysts emerges as a more selective and environmentally friendly alternative to chemical recycling, allowing the production of new bioplastics and added value and high-quality products. Other pending concerns for industrial implementation of bioplastics include misinformation among end users, the lack of a standardised bioplastic labelling, unclear life cycle assessment guidelines and the need for higher financial investments. Although further research and development efforts are essential to foster the sustainable and widespread application of bioplastics, significant strides have already been made in this direction.
Collapse
Affiliation(s)
- Lara Serrano‐Aguirre
- Polymer Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Group, Department of Plant and Microbial Biotechnology, Biological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
| |
Collapse
|
3
|
Ebu SM, Ray L, Panda AN, Gouda SK. De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain. J Genet Eng Biotechnol 2023; 21:132. [PMID: 37991636 PMCID: PMC10665291 DOI: 10.1186/s43141-023-00578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported. RESULTS From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons. CONCLUSIONS This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.
Collapse
Affiliation(s)
- Seid Mohammed Ebu
- Department of Applied Biology, SoANS, Adama Science and Technology University, Oromia, Ethiopia.
| | - Lopamudra Ray
- School of Law, Campus -16 Adjunct Faculty, School of Biotech, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ananta N Panda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Sudhansu K Gouda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| |
Collapse
|
4
|
Satoh T. New prebiotics by ketone donation. Trends Endocrinol Metab 2023:S1043-2760(23)00091-7. [PMID: 37271711 DOI: 10.1016/j.tem.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023]
Abstract
Integrity of the microbiome is an essential element for human gut health. 3-Hydroxybutyrate (3HB) secreted into the gut lumen has gained attention as a regulator of gut physiology, including stem cell expansion. In this opinion, I propose new prebiotics leading to gut health by use of a ketone (3HB) donor. When exogenous 3HB is supplied through ketone donation, it has the potential to markedly improve gut health by altering the gut microbiome and systemic metabolic status. Poly-hydroxybutyrate (PHB) donates 3HB and primarily influences microbiota, making it an effective prebiotic for improving the gut environment. Thus, exogenous 3HB donation to the lumen of the gut may aid gut health by maintaining the integrity of microbiome.
Collapse
Affiliation(s)
- Takumi Satoh
- Department of Antiaging Food Research, School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji 192-0982, Japan.
| |
Collapse
|
5
|
Lai J, Huang H, Lin M, Xu Y, Li X, Sun B. Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics. Front Microbiol 2023; 13:1113705. [PMID: 36713200 PMCID: PMC9878459 DOI: 10.3389/fmicb.2022.1113705] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.
Collapse
Affiliation(s)
- Jinghui Lai
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Huiqin Huang
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Mengwei Lin
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Youqiang Xu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| |
Collapse
|
6
|
Bher A, Mayekar PC, Auras RA, Schvezov CE. Biodegradation of Biodegradable Polymers in Mesophilic Aerobic Environments. Int J Mol Sci 2022; 23:12165. [PMID: 36293023 PMCID: PMC9603655 DOI: 10.3390/ijms232012165] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 08/29/2023] Open
Abstract
Finding alternatives to diminish plastic pollution has become one of the main challenges of modern life. A few alternatives have gained potential for a shift toward a more circular and sustainable relationship with plastics. Biodegradable polymers derived from bio- and fossil-based sources have emerged as one feasible alternative to overcome inconveniences associated with the use and disposal of non-biodegradable polymers. The biodegradation process depends on the environment's factors, microorganisms and associated enzymes, and the polymer properties, resulting in a plethora of parameters that create a complex process whereby biodegradation times and rates can vary immensely. This review aims to provide a background and a comprehensive, systematic, and critical overview of this complex process with a special focus on the mesophilic range. Activity toward depolymerization by extracellular enzymes, biofilm effect on the dynamic of the degradation process, CO2 evolution evaluating the extent of biodegradation, and metabolic pathways are discussed. Remarks and perspectives for potential future research are provided with a focus on the current knowledge gaps if the goal is to minimize the persistence of plastics across environments. Innovative approaches such as the addition of specific compounds to trigger depolymerization under particular conditions, biostimulation, bioaugmentation, and the addition of natural and/or modified enzymes are state-of-the-art methods that need faster development. Furthermore, methods must be connected to standards and techniques that fully track the biodegradation process. More transdisciplinary research within areas of polymer chemistry/processing and microbiology/biochemistry is needed.
Collapse
Affiliation(s)
- Anibal Bher
- School of Packaging, Michigan State University, East Lansing, MI 48824, USA
- Instituto de Materiales de Misiones, CONICET-UNaM, Posadas 3300, Misiones, Argentina
| | - Pooja C. Mayekar
- School of Packaging, Michigan State University, East Lansing, MI 48824, USA
| | - Rafael A. Auras
- School of Packaging, Michigan State University, East Lansing, MI 48824, USA
| | - Carlos E. Schvezov
- Instituto de Materiales de Misiones, CONICET-UNaM, Posadas 3300, Misiones, Argentina
| |
Collapse
|
7
|
|
8
|
Satti SM, Shah AA. Polyester-based biodegradable plastics: an approach towards sustainable development. Lett Appl Microbiol 2020; 70:413-430. [PMID: 32086820 DOI: 10.1111/lam.13287] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/29/2022]
Abstract
Non-degradability of conventional plastics, filling of landfill sites, raising water and land pollution and rapid depletion of fossil resources have raised the environmental issues and global concerns. The current demand and production of plastics is putting immense pressure on fossil resources, consuming about 6% of the global oil and is expected to grow up to 20%. The polyester-based biodegradable plastics (BPs) are considered as a remedy to the issue of plastics waste in the environment. BPs appear to manage the overflow of plastics by providing new means of waste management system and help in securing the non-renewable resources of nature. This review comprehensively presents the environmental burdens due to conventional plastics as well as production of polyester-based BPs as an alternative to conventional commodity plastics. The diversity of micro-organisms and their enzymes that degrade various polyester-based BPs (PLA, PCL, PHB/PHBV and PET) has also been described in detail. Moreover, the impact of plastics degradation products on soil ecology and ecosystem functions has critically been discussed. The report ends with special focus on future recommendations for the development of sustainable waste management strategies to control pollution due to plastics waste. SIGNIFICANCE AND IMPACT OF THE STUDY: Polyester-based BPs considered as a solution to current plastic waste problem as well as leading polymers in terms of biodegradability and sustainability has been critically discussed. The role of microorganisms and their enzymes involved in the biodegradation of these polymers and ecotoxicological impact of degradation products of BPs on soil microbial community and biogeochemical cycles has also been described. This report will provide an insight on the key research areas to bridge the gap for development of simulated systems as an effective and emerging strategy to divert the overflow of plastic in the environment as well as for the greener solution to the plastic waste management problems.
Collapse
Affiliation(s)
- S M Satti
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - A A Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
9
|
Martínez-Tobón DI, Waters B, Elias AL, Sauvageau D. Streamlined production, purification, and characterization of recombinant extracellular polyhydroxybutyrate depolymerases. Microbiologyopen 2020; 9:e1001. [PMID: 32087608 PMCID: PMC7142370 DOI: 10.1002/mbo3.1001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 01/06/2023] Open
Abstract
Heterologous production of extracellular polyhydroxybutyrate (PHB) depolymerases (PhaZs) has been of interest for over 30 years, but implementation is sometimes difficult and can limit the scope of research. With the constant development of tools to improve recombinant protein production in Escherichia coli, we propose a method that takes characteristics of PhaZs from different bacterial strains into account. Recombinant His‐tagged versions of PhaZs (rPhaZ) from Comamonas testosteroni 31A, Cupriavidus sp. T1, Marinobacter algicola DG893, Pseudomonas stutzeri, and Ralstonia sp. were successfully produced with varying expression, solubility, and purity levels. PhaZs from C. testosteroni and P. stutzeri were more amenable to heterologous expression in all aspects; however, using the E. coli Rosetta‐gami B(DE3) expression strain and establishing optimal conditions for expression and purification (variation of IPTG concentration and use of size exclusion columns) helped circumvent low expression and purity for the other PhaZs. Degradation activity of the rPhaZs was compared using a simple PHB plate‐based method, adapted to test for various pH and temperatures. rPhaZ from M. algicola presented the highest activity at 15°C, and rPhaZs from Cupriavidus sp. T1 and Ralstonia sp. had the highest activity at pH 5.4. The methods proposed herein can be used to test the production of soluble recombinant PhaZs and to perform preliminary evaluation for applications that require PHB degradation.
Collapse
Affiliation(s)
- Diana I Martínez-Tobón
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Brennan Waters
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Anastasia L Elias
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
10
|
Biochemical properties and biotechnological applications of microbial enzymes involved in the degradation of polyester-type plastics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140315. [DOI: 10.1016/j.bbapap.2019.140315] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/07/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023]
|
11
|
Priyadarshini S, Pradhan SK, Ray P. Production, characterization and application of thermostable, alkaline α-amylase (AA11) from Bacillus cereus strain SP-CH11 isolated from Chilika Lake. Int J Biol Macromol 2019; 145:804-812. [PMID: 31758985 DOI: 10.1016/j.ijbiomac.2019.11.149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
An alkaliphile bacterial strain designated as CH11 was isolated from the sediments of Chilika Lake, Odisha. The isolate showed stupendous growth and production of α-amylase at pH 10.0. Through 16S rRNA gene based molecular technique this isolate was identified as Bacillus cereus strain SP-CH11 having GenBank Accession No. KT992791. Homogenous ~55 kDa extracellular α-amylase was extracted with 241.304, 26.26 and 3.2-fold acceleration in specific activity, purification fold and yield respectively. The alkaline α-amylase AA11 was further characterized. At pH 9.0 the purified enzyme AA11 was highly stable while retaining 88-100% functional viability at temperature range from 35 to 65 °C, confirming its thermostability nature. It showed stability with powdered and liquid detergents at 7 mg/mL and 100-fold dilutions respectively. AA11 efficiently removed the starch stain from cotton fabrics. The findings of this study indicate that the isolate CH11 is a source of novel alkaline α-amylase that has promising application in food and detergent industries.
Collapse
Affiliation(s)
- Sonali Priyadarshini
- Department of Microbiology, C.B.S.H, Orissa University of Agriculture and Technology, Unit 7, Surya Nagar, Bhubaneshwar, Odisha 751003, India.
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Centre for Post Graduate Studies, Orissa University of Agriculture and Technology, Surya Nagar, Bhubaneswar, 751 003, Odisha, India
| | - Pratima Ray
- Department of Microbiology, C.B.S.H, Orissa University of Agriculture and Technology, Unit 7, Surya Nagar, Bhubaneshwar, Odisha 751003, India
| |
Collapse
|
12
|
Priyadarshini S, Ray P. Exploration of detergent-stable alkaline α-amylase AA7 from Bacillus sp strain SP-CH7 isolated from Chilika Lake. Int J Biol Macromol 2019; 140:825-832. [DOI: 10.1016/j.ijbiomac.2019.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 11/25/2022]
|
13
|
Garcia-Garcia D, Ferri JM, Montanes N, Lopez-Martinez J, Balart R. Plasticization effects of epoxidized vegetable oils on mechanical properties of poly(3-hydroxybutyrate). POLYM INT 2016. [DOI: 10.1002/pi.5164] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Garcia-Garcia
- Instituto de Tecnología de Materiales (ITM); Universitat Politècnica de València (UPV); Plaza Ferrándiz y Carbonell 1 03801 Alcoy Alicante Spain
| | - Jose M Ferri
- Instituto de Tecnología de Materiales (ITM); Universitat Politècnica de València (UPV); Plaza Ferrándiz y Carbonell 1 03801 Alcoy Alicante Spain
| | - Nestor Montanes
- Instituto de Tecnología de Materiales (ITM); Universitat Politècnica de València (UPV); Plaza Ferrándiz y Carbonell 1 03801 Alcoy Alicante Spain
| | - Juan Lopez-Martinez
- Instituto de Tecnología de Materiales (ITM); Universitat Politècnica de València (UPV); Plaza Ferrándiz y Carbonell 1 03801 Alcoy Alicante Spain
| | - Rafael Balart
- Instituto de Tecnología de Materiales (ITM); Universitat Politècnica de València (UPV); Plaza Ferrándiz y Carbonell 1 03801 Alcoy Alicante Spain
| |
Collapse
|
14
|
Wang Z, Gao J, Li L, Jiang H. Purification and characterization of an extracellular poly(3-hydroxybutyrate-co-3-hydroxyvalerate) depolymerase from Acidovorax sp. HB01. World J Microbiol Biotechnol 2012; 28:2395-402. [DOI: 10.1007/s11274-012-1048-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
|
15
|
Gong Y, Li M, Xu D, Wang H, He J, Wu D, Chen D, Qiu N, Bao Q, Sun M, Yu Z. Comparative proteomic analysis revealed metabolic changes and the translational regulation of Cry protein synthesis in Bacillus thuringiensis. J Proteomics 2012; 75:1235-46. [DOI: 10.1016/j.jprot.2011.10.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/29/2011] [Accepted: 10/31/2011] [Indexed: 01/15/2023]
|
16
|
Identification and characterization of a novel class of extracellular poly(3-hydroxybutyrate) depolymerase from Bacillus sp. strain NRRL B-14911. Appl Environ Microbiol 2011; 77:7924-32. [PMID: 21948827 DOI: 10.1128/aem.06069-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The catalytic, linker, and denatured poly(3-hydroxybutyrate) (dPHB)-binding domains of bacterial extracellular PHB depolymerases (PhaZs) are classified into several different types. We now report a novel class of extracellular PHB depolymerase from Bacillus sp. strain NRRL B-14911. Its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to them. Instead, this putative linker region can be divided into two distinct linker domains of novel types: LD1 and LD2. LD1 shows significant amino acid sequence similarity to certain regions of a large group of PHB depolymerase-unrelated proteins. LD2 and its homologs are present in a small group of PhaZs. The remaining C-terminal portion of this PhaZ can be further divided into two distinct domains: SBD1 and SBD2. Each domain showed strong binding to dPHB, and there is no significant sequence similarity between them. Each domain neither possesses the sequence features of the two known types of dPHB-binding domains nor shows significant amino acid sequence similarity to them. These unique features indicate the presence of two novel and distinct types of dPHB-binding domains. Homologs of these novel domains also are present in the extracellular PhaZ of Bacillus megaterium and the putative extracellular PhaZs of Bacillus pseudofirmus and Bacillus sp. strain SG-1. The Bacillus sp. NRRL B-14911 PhaZ appears to be a representative of a novel class of extracellular PHB depolymerases.
Collapse
|
17
|
Volova TG, Boyandin AN, Vasil’ev AD, Karpov VA, Kozhevnikov IV, Prudnikova SV, Rudnev VP, Xuån BB, Dũng VV, Gitel’zon II. Biodegradation of polyhydroxyalkanoates (PHAs) in the South China Sea and identification of PHA-degrading bacteria. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711020184] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
18
|
Sznajder A, Jendrossek D. Biochemical characterization of a new type of intracellular PHB depolymerase from Rhodospirillum rubrum with high hydrolytic activity on native PHB granules. Appl Microbiol Biotechnol 2011; 89:1487-95. [DOI: 10.1007/s00253-011-3096-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/04/2010] [Accepted: 11/05/2010] [Indexed: 11/29/2022]
|
19
|
Biodegradation of polyhydroxyalkanoates (PHAs) in tropical coastal waters and identification of PHA-degrading bacteria. Polym Degrad Stab 2010. [DOI: 10.1016/j.polymdegradstab.2010.08.023] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Degradation of Natural and Artificial Poly[(R)-3-hydroxyalkanoate]s: From Biodegradation to Hydrolysis. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-3-642-03287-5_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
21
|
Identification and characterization of a novel intracellular poly(3-hydroxybutyrate) depolymerase from Bacillus megaterium. Appl Environ Microbiol 2009; 75:5290-9. [PMID: 19561190 DOI: 10.1128/aem.00621-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene that codes for a novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase, designated PhaZ1, has been identified in the genome of Bacillus megaterium. A native PHB (nPHB) granule-binding assay showed that purified soluble PhaZ1 had strong affinity for nPHB granules. Turbidimetric analyses revealed that PhaZ1 could rapidly degrade nPHB granules in vitro without the need for protease pretreatment of the granules to remove surface proteins. Notably, almost all the final hydrolytic products produced from the in vitro degradation of nPHB granules by PhaZ1 were 3-hydroxybutyric acid (3HB) monomers. Unexpectedly, PhaZ1 could also hydrolyze denatured semicrystalline PHB, with the generation of 3HB monomers. The disruption of the phaZ1 gene significantly affected intracellular PHB mobilization during the PHB-degrading stage in B. megaterium, as demonstrated by transmission electron microscopy and the measurement of the PHB content. These results indicate that PhaZ1 is functional in intracellular PHB mobilization in vivo. Some of these features, which are in striking contrast with those of other known nPHB granule-degrading PhaZs, may provide an advantage for B. megaterium PhaZ1 in fermentative production of the biotechnologically valuable chiral compound (R)-3HB.
Collapse
|
22
|
Knoll M, Hamm TM, Wagner F, Martinez V, Pleiss J. The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases. BMC Bioinformatics 2009; 10:89. [PMID: 19296857 PMCID: PMC2666664 DOI: 10.1186/1471-2105-10-89] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 03/18/2009] [Indexed: 01/16/2023] Open
Abstract
Background Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common α/β-hydrolase fold and a catalytic triad, which is also found in other α/β-hydrolases. Results The PHA Depolymerase Engineering Database (DED, ) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated. Conclusion The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.
Collapse
Affiliation(s)
- Michael Knoll
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring, Germany.
| | | | | | | | | |
Collapse
|
23
|
Microbial degradation and physico-chemical alteration of polyhydroxyalkanoates by a thermophilic Streptomyces sp. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0050-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
24
|
Phithakrotchanakoon C, Daduang R, Thamchaipenet A, Wangkam T, Srikhirin T, Eurwilaichitr L, Champreda V. Heterologous expression of polyhydroxyalkanoate depolymerase from Thermobifida sp. in Pichia pastoris and catalytic analysis by surface plasmon resonance. Appl Microbiol Biotechnol 2009; 82:131-40. [DOI: 10.1007/s00253-008-1754-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 10/13/2008] [Accepted: 10/18/2008] [Indexed: 11/30/2022]
|
25
|
Shah AA, Hasan F, Hameed A, Ahmed S. Biological degradation of plastics: a comprehensive review. Biotechnol Adv 2008; 26:246-65. [PMID: 18337047 DOI: 10.1016/j.biotechadv.2007.12.005] [Citation(s) in RCA: 983] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Revised: 12/31/2007] [Accepted: 12/31/2007] [Indexed: 10/22/2022]
Abstract
Lack of degradability and the closing of landfill sites as well as growing water and land pollution problems have led to concern about plastics. With the excessive use of plastics and increasing pressure being placed on capacities available for plastic waste disposal, the need for biodegradable plastics and biodegradation of plastic wastes has assumed increasing importance in the last few years. Awareness of the waste problem and its impact on the environment has awakened new interest in the area of degradable polymers. The interest in environmental issues is growing and there are increasing demands to develop material which do not burden the environment significantly. Biodegradation is necessary for water-soluble or water-immiscible polymers because they eventually enter streams which can neither be recycled nor incinerated. It is important to consider the microbial degradation of natural and synthetic polymers in order to understand what is necessary for biodegradation and the mechanisms involved. This requires understanding of the interactions between materials and microorganisms and the biochemical changes involved. Widespread studies on the biodegradation of plastics have been carried out in order to overcome the environmental problems associated with synthetic plastic waste. This paper reviews the current research on the biodegradation of biodegradable and also the conventional synthetic plastics and also use of various techniques for the analysis of degradation in vitro.
Collapse
Affiliation(s)
- Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
| | | | | | | |
Collapse
|