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Mandic M, Spasic J, Ponjavic M, Nikolic MS, Cosovic VR, O'Connor KE, Nikodinovic-Runic J, Djokic L, Jeremic S. Biodegradation of poly(ε-caprolactone) (PCL) and medium chain length polyhydroxyalkanoate (mcl-PHA) using whole cells and cell free protein preparations of Pseudomonas and Streptomyces strains grown on waste cooking oil. Polym Degrad Stab 2019. [DOI: 10.1016/j.polymdegradstab.2019.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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52
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Sharma PK, Mohanan N, Sidhu R, Levin DB. Colonization and degradation of polyhydroxyalkanoates by lipase-producing bacteria. Can J Microbiol 2019; 65:461-475. [PMID: 30897336 DOI: 10.1139/cjm-2019-0042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biodegradation of short-chain-length polyhydroxyalkanoates (scl-PHAs) and medium-chain-length polyhydroxyalkanoates (mcl-PHAs) was studied using 2 bacteria, Pseudomonas chlororaphis and Acinetobacter lwoffii, which secrete an enzyme, or enzymes, with lipase activity. These bacteria produced clear zones of depolymerization on Petri plates containing colloidal solutions of PHA polymers with different monomer compositions. Lipase activity in these bacteria was measured using p-nitrophenyl octanoate as a substrate. In liquid medium, scl-PHA (e.g., PHBV) and mcl-PHA (e.g., PHO) films were used as the sole carbon source for growth, and after 7 days, 5%-18% loss in mass of PHA films was observed. Scanning electron microscopy of these films revealed bacterial colonization of the polymers, with cracks and pitting in the film surfaces. Degradation of polymers released 3-hydroxyhexanoate, 3-hydroxyoctanoate, and 3-hydroxydecanoate monomers into the liquid medium, depending on the starting polymer. Genes encoding secretory lipases, with amino acid consensus sequences for lipase boxes and oxyanion holes, were identified in the genomes of P. chlororaphis and A. lwoffii. Although amino acid consensus sequences for lipase boxes and oxyanion holes are also present in PHA depolymerases identified in the genomes of other PHA-degrading bacteria, the P. chlororaphis and A. lwoffii lipases had low homology with these depolymerases.
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Affiliation(s)
- Parveen K Sharma
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Nisha Mohanan
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Ravinder Sidhu
- b Manitoba Institute for Materials & Faculty of Science, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - David B Levin
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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Gräff M, Buchholz PC, Stockinger P, Bommarius B, Bommarius AS, Pleiss J. The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family. Proteins 2019; 87:443-451. [DOI: 10.1002/prot.25666] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Maike Gräff
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Patrick C.F. Buchholz
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Bettina Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Andreas S. Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
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Alamgeer M. Polyhydroxyalkanoates (PHA) genes Database. Bioinformation 2019; 15:36-39. [PMID: 31359997 PMCID: PMC6651032 DOI: 10.6026/97320630015036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 11/25/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are polyesters of various hydroxyl alkanoates that are synthesized by many gram-positive and gramnegative bacteria from about 75 different genera. PHA genes database is a repository of genes and its genomic information related to PHA.It contains data on the genomic characterization of intermediates of PHA. These include CAB genes, responsible for biodegradable plastic synthesis. The genomic database provides data on PHA genes from archaeal, bacterial and eukaryotic genomes.
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Affiliation(s)
- Mohammad Alamgeer
- Department of Information Systems, King Khalid University, Kingdom of Saudi Arabia (KSA)
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Azura Azami N, Ira Aryani W, Aik-Hong T, Amirul AA. Purification and characterization of new bio-plastic degrading enzyme from Burkholderia cepacia DP1. Protein Expr Purif 2018; 155:35-42. [PMID: 30352276 DOI: 10.1016/j.pep.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 10/28/2022]
Abstract
Depolymerase is an enzyme that plays an important role in the hydrolysis of polyhydroxyalkanoates [PHAs]. In the current study, Burkholderia cepacia DP1 was obtained from Penang, Malaysia in which the enzyme was purified using ion exchange and gel filtration (Superdex-75) column chromatography. The molecular mass of the enzyme was estimated to be 53.3 kDa using SDS-PAGE. The enzyme activity was increased to 36.8 folds with the recovery of 16.3% after purification. The enzyme activity was detected between pH 6.0-10 and at 35-55 °C with pH 6.0 and 45 °C facilitating the maximum activity. Depolymerase was inactivated by Tween-20, Tween-80, SDS and PMSF, but insensitive to metal ions (Mg2+, Ca2+, K+, Na2+, Fe3+) and organic solvents (methanol, ethanol, and acetone). The apparent Km values of the purified P(3HB) depolymerase enzyme for P(3HB) and P(3HB-co-14%3HV) were 0.7 mg/ml and 0.8 mg/ml, respectively. The Vmax values of the purified enzyme were 10 mg/min and 8.89 mg/min for P(3HB) and P(3HB-co-14%3HV), respectively. The current study discovered a new extracellular poly(3-hydroxybutyrate) [P(3HB)] depolymerase enzyme from Burkholderia cepacia DP1 isolated and purified to homogeneity from the culture supernatant. To the best of our knowledge, this is the first report demonstrating the purification and biochemical characterization of P(3HB) depolymerase enzyme from genus Burkholderia.
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Affiliation(s)
| | | | | | - A A Amirul
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia; Centre for Chemical Biology, Penang, Malaysia; Malaysian Institute of Pharmaceuticals and Nutraceuticals, NIBM, Malaysia.
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Jung HW, Yang MK, Su RC. Purification, characterization, and gene cloning of an Aspergillus fumigatus polyhydroxybutyrate depolymerase used for degradation of polyhydroxybutyrate, polyethylene succinate, and polybutylene succinate. Polym Degrad Stab 2018. [DOI: 10.1016/j.polymdegradstab.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Martínez-Tobón DI, Gul M, Elias AL, Sauvageau D. Polyhydroxybutyrate (PHB) biodegradation using bacterial strains with demonstrated and predicted PHB depolymerase activity. Appl Microbiol Biotechnol 2018; 102:8049-8067. [DOI: 10.1007/s00253-018-9153-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 11/24/2022]
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Wei R, Zimmermann W. Microbial enzymes for the recycling of recalcitrant petroleum-based plastics: how far are we? Microb Biotechnol 2017; 10:1308-1322. [PMID: 28371373 PMCID: PMC5658625 DOI: 10.1111/1751-7915.12710] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 01/25/2023] Open
Abstract
Petroleum-based plastics have replaced many natural materials in their former applications. With their excellent properties, they have found widespread uses in almost every area of human life. However, the high recalcitrance of many synthetic plastics results in their long persistence in the environment, and the growing amount of plastic waste ending up in landfills and in the oceans has become a global concern. In recent years, a number of microbial enzymes capable of modifying or degrading recalcitrant synthetic polymers have been identified. They are emerging as candidates for the development of biocatalytic plastic recycling processes, by which valuable raw materials can be recovered in an environmentally sustainable way. This review is focused on microbial biocatalysts involved in the degradation of the synthetic plastics polyethylene, polystyrene, polyurethane and polyethylene terephthalate (PET). Recent progress in the application of polyester hydrolases for the recovery of PET building blocks and challenges for the application of these enzymes in alternative plastic waste recycling processes will be discussed.
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Affiliation(s)
- Ren Wei
- Department of Microbiology and Bioprocess TechnologyInstitute of BiochemistryLeipzig UniversityJohannisallee 21‐2304103LeipzigGermany
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess TechnologyInstitute of BiochemistryLeipzig UniversityJohannisallee 21‐2304103LeipzigGermany
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Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis. Appl Environ Microbiol 2017; 83:AEM.01251-17. [PMID: 28802264 DOI: 10.1128/aem.01251-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/03/2017] [Indexed: 11/20/2022] Open
Abstract
Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from Aspergillus luchuensis (AlAXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family. AlAXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from Aspergillus niger indicated that AlAXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of AlAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan.IMPORTANCE Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of thermoplastic polymers.
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60
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Laycock B, Nikolić M, Colwell JM, Gauthier E, Halley P, Bottle S, George G. Lifetime prediction of biodegradable polymers. Prog Polym Sci 2017. [DOI: 10.1016/j.progpolymsci.2017.02.004] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Azami NA, Wirjon IA, Kannusamy S, Teh AH, Abdullah AAA. Enhanced degradation of polyhydroxyalkanoates (PHAs) by newly isolated Burkholderia cepacia DP1 with high depolymerase activity. 3 Biotech 2017; 7:75. [PMID: 28452023 DOI: 10.1007/s13205-017-0716-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/30/2017] [Indexed: 11/30/2022] Open
Abstract
The contribution of microbial depolymerase has received much attention because of its potential in biopolymer degradation. In this study, the P(3HB) depolymerase enzyme of a newly isolated Burkholderia cepacia DP1 from soil in Penang, Malaysia, was optimized using response surface methodology (RSM). The factors affecting P(3HB) depolymerase enzyme production were studied using one-variable-at-a-time approach prior to optimization. Preliminary experiments revealed that the concentration of nitrogen source, concentration of carbon source, initial pH and incubation time were among the main factors influencing the enzyme productivity. An increase of 9.4 folds in enzyme production with an activity of 5.66 U/mL was obtained using optimal medium containing 0.028% N of di-ammonium hydrogen phosphate and 0.31% P(3HB-co-21%4HB) as carbon source at the initial pH of 6.8 for 38 h of incubation. Moreover, the RSM model showed great similarity between predicted and actual enzyme production indicating a successful model validation. This study warrants the ability of P(3HB) degradation by B. cepacia DP1 in producing higher enzyme activity as compared to other P(3HB) degraders being reported. Interestingly, the production of P(3HB) depolymerase was rarely reported within genus Burkholderia. Therefore, this is considered to be a new discovery in the field of P(3HB) depolymerase production.
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Affiliation(s)
- Nor Azura Azami
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
- Centre for Chemical Biology, Bayan Lepas, Penang, Malaysia
| | | | - Shantini Kannusamy
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Bayan Lepas, Penang, Malaysia
| | - Amirul Al-Ashraf Abdullah
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
- Centre for Chemical Biology, Bayan Lepas, Penang, Malaysia.
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, NIBM, Penang, Malaysia.
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Parlane NA, Gupta SK, Rubio-Reyes P, Chen S, Gonzalez-Miro M, Wedlock DN, Rehm BHA. Self-Assembled Protein-Coated Polyhydroxyalkanoate Beads: Properties and Biomedical Applications. ACS Biomater Sci Eng 2016; 3:3043-3057. [PMID: 33445349 DOI: 10.1021/acsbiomaterials.6b00355] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biological polyesters that can be naturally produced by a range of bacteria as water-insoluble inclusions composed of a PHA core coated with PHA synthesis, structural, and regulatory proteins. These naturally self-assembling shell-core particles have been recently conceived as biomaterials that can be bioengineered as biologically active beads for medical applications. Protein engineering of PHA-associated proteins enabled the production of PHA-protein assemblies exhibiting biologically active protein-based functions relevant for applications as vaccines or diagnostics. Here we provide an overview of the recent advances in bioengineering of PHA particles toward the display of biomedically relevant protein functions such as selected disease-specific antigens as diagnostic tools or for the design of particulate subunit vaccines against infectious diseases such as tuberculosis, meningitis, pneumonia, and hepatitis C.
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Affiliation(s)
- Natalie A Parlane
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Sandeep K Gupta
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Patricia Rubio-Reyes
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Shuxiong Chen
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Majela Gonzalez-Miro
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - D Neil Wedlock
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Bernd H A Rehm
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Kelburn Parade, Wellington 6140, New Zealand
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Prieto A. To be, or not to be biodegradable… that is the question for the bio-based plastics. Microb Biotechnol 2016; 9:652-7. [PMID: 27477765 PMCID: PMC4993184 DOI: 10.1111/1751-7915.12393] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/10/2016] [Indexed: 01/26/2023] Open
Abstract
Global warming, market and production capacity are being the key drivers for selecting the main players for the next decades in the market of bio‐based plastics. The drop‐in bio‐based polymers such as the bio‐based polyethylene terephtalate (PET) or polyethylene (PE), chemically identical to their petrochemical counterparts but having a component of biological origin, are in the top of the list. They are followed by new polymers such as PHA and PLA with a significant market growth rate since 2014 with projections to 2020. Research will provide improved strains designed through synthetic and systems biology approaches; furthermore, the use of low‐cost substrates will contribute to the widespread application of these bio‐ based polymers. The durability of plastics is not considered anymore as a virtue, and interesting bioprospecting strategies to isolate microorganisms for assimilating the recalcitrant plastics will pave the way for in vivo strategies for plastic mineralization. In this context, waste management of bio‐based plastic will be one of the most important issues in the near future in terms of the circular economy. There is a clear need for standardized labelling and sorting instructions, which should be regulated in a coordinated way by policymakers and material producers.
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Affiliation(s)
- Auxiliadora Prieto
- Polymer Biotechnology Lab, Centro de Investigaciones Biologicas (CIB), C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
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65
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Seghal Kiran G, Priyadharshini S, Dobson ADW, Gnanamani E, Selvin J. Degradation intermediates of polyhydroxy butyrate inhibits phenotypic expression of virulence factors and biofilm formation in luminescent Vibrio sp. PUGSK8. NPJ Biofilms Microbiomes 2016; 2:16002. [PMID: 28721241 PMCID: PMC5515267 DOI: 10.1038/npjbiofilms.2016.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/28/2016] [Accepted: 03/08/2016] [Indexed: 11/21/2022] Open
Abstract
Luminescent vibrios are ubiquitous in the marine environment and are the causative agents of vibriosis and mass mortality in many aquatic animals. In aquatic environments, treatments cannot be limited to the diseased population alone, therefore treatment of the entire aquatic system is the only possible approach. Thus, the use of antibiotics to treat part of the infected animals requires a dose based on the entire biomass, which results in the treatment of uninfected animals as well as non-target normal microbial flora. A treatment method based on anti-virulence or quorum quenching has recently been proposed as an effective treatment strategy for aquatic animals. Polyhydroxy butyrates (PHB) are bacterial storage molecules, which accumulate in cells under nutritional stress. The degradation of PHB releases short-chain β-hydroxy butyric acid, which may act as anti-infective molecule. To date, there is very limited information on the potential anti-infective and anti-virulence mechanisms involving PHB. In this study, we aim to examine the effect of PHB on inhibition of the virulence cascade of Vibrio such as biofilm formation, luminescence, motility behaviour, haemolysin and quorum sensing. A luminescent Vibrio PUGSK8, tentatively identified as Vibrio campbellii PUGSK8 was tested in vitro for production of extracellular virulence factors and then established as a potential shrimp pathogen based on in vivo challenge experiments. The ability of Vibrio PUGSK8 to form biofilms and the effect of PHB on biofilm formation was tested in a 96-well microtitre-plate assay system. The motility behaviour of Vibrio PUGSK8 was evaluated using twitching, swimming and swarming plate assays. Reporter strains such as Chromobacterium violaceum CV026 and Agrobacterium tumefaciens were used to detect quorum-sensing molecules. Gas chromatography-mass spectrometry spectral analysis was performed to elucidate the fragmentation pattern and structure of N-hexanoyl homoserine lactone. PHB depolymerase activity in Vibrio PUGSK8 was quantified as the amount of the enzyme solution to hydrolyse 1 μg of PHB per min. An in vivo challenge experiment was performed using a gnotobiotic Artemia assay. Of the 27 isolates tested, the Vibrio PUGSK8 strain was selected for target-specific assays based on the high intensity of luminescence and production of virulence factors. The virulence cascade detected in Vibrio PUGSK8 include luminescence, motility behaviour, biofilm formation, quorum sensing and haemolysin production. Thus inhibition/degradation of the virulence cascade would be an effective approach to contain Vibrio infections in aquatic animals. In this report, we demonstrate that the degradation intermediate of PHB effectively inhibits biofilm formation, luminescence, motility behaviour, haemolysin production and the N-acyl-homoserine lactone (AHL)-mediated quorum-sensing pathway in PUGSK8. Interestingly, the growth of Vibrio PUGSK8 remains unaffected in the presence of PHB, with PHB degradation being detected in the media. PHB depolymerase activity in Vibrio PUGSK8 results in the release of degradation intermediates include a short-chain β-hydroxy butyric acid, which inhibits the virulence cascade in Vibrio PUGSK8. Thus, a molecule that targets quorum sensing and the virulence cascade and which is species/strain-specific could prove to be an effective alternative to antimicrobial agents to control the pathogenesis of Vibrio, and thereby help to contain Vibrio outbreaks in aquatic systems.
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Affiliation(s)
- George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Sethu Priyadharshini
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | | | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
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Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery: The case of the polyhydroxyalkanoates. Sci Rep 2016; 6:24381. [PMID: 27087466 PMCID: PMC4834554 DOI: 10.1038/srep24381] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/22/2016] [Indexed: 02/04/2023] Open
Abstract
This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered were polyhydroxyalkanoates (PHAs) produced naturally by Pseudomonas putida and Cupriavidus necator, or by recombinant Escherichia coli strains. B. bacteriovorus with a mutated PHA depolymerase gene to prevent the unwanted breakdown of the bio-product allowed the recovery of up to 80% of that accumulated by the prey bacteria, even at high biomass concentrations. This innovative downstream process highlights how B. bacteriovorus can be used as a novel, biological lytic agent for the inexpensive, industrial scale recovery of intracellular products from different Gram-negative prey cultures.
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Fademrecht S, Scheller PN, Nestl BM, Hauer B, Pleiss J. Identification of imine reductase-specific sequence motifs. Proteins 2016; 84:600-10. [PMID: 26857686 DOI: 10.1002/prot.25008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/02/2015] [Accepted: 02/02/2016] [Indexed: 01/17/2023]
Abstract
Chiral amines are valuable building blocks for the production of a variety of pharmaceuticals, agrochemicals and other specialty chemicals. Only recently, imine reductases (IREDs) were discovered which catalyze the stereoselective reduction of imines to chiral amines. Although several IREDs were biochemically characterized in the last few years, knowledge of the reaction mechanism and the molecular basis of substrate specificity and stereoselectivity is limited. To gain further insights into the sequence-function relationships, the Imine Reductase Engineering Database (www.IRED.BioCatNet.de) was established and a systematic analysis of 530 putative IREDs was performed. A standard numbering scheme based on R-IRED-Sk was introduced to facilitate the identification and communication of structurally equivalent positions in different proteins. A conservation analysis revealed a highly conserved cofactor binding region and a predominantly hydrophobic substrate binding cleft. Two IRED-specific motifs were identified, the cofactor binding motif GLGxMGx(5 )[ATS]x(4) Gx(4) [VIL]WNR[TS]x(2) [KR] and the active site motif Gx[DE]x[GDA]x[APS]x(3){K}x[ASL]x[LMVIAG]. Our results indicate a preference toward NADPH for all IREDs and explain why, despite their sequence similarity to β-hydroxyacid dehydrogenases (β-HADs), no conversion of β-hydroxyacids has been observed. Superfamily-specific conservations were investigated to explore the molecular basis of their stereopreference. Based on our analysis and previous experimental results on IRED mutants, an exclusive role of standard position 187 for stereoselectivity is excluded. Alternatively, two standard positions 139 and 194 were identified which are superfamily-specifically conserved and differ in R- and S-selective enzymes.
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Affiliation(s)
- Silvia Fademrecht
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Philipp N Scheller
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bettina M Nestl
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Extracellular Polyhydroxyalkanoate Depolymerase by Acidovorax sp. DP5. Enzyme Res 2015; 2015:212159. [PMID: 26664741 PMCID: PMC4664802 DOI: 10.1155/2015/212159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/19/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteria capable of degrading polyhydroxyalkanoates (PHA) by secreting extracellular depolymerase enzymes were isolated from water and soil samples collected from various environments in Malaysia. A total of 8 potential degraders exhibited clear zones on poly(3-hydroxybutyrate) [P(3HB)] based agar, indicating the presence of extracellular PHA depolymerase. Among the isolates, DP5 exhibited the largest clearing zone with a degradation index of 6.0. The highest degradation activity of P(3HB) was also observed with depolymerase enzyme of DP5 in mineral salt medium containing P(3HB). Based on biochemical characterization and 16S rRNA cloning and sequencing, isolate DP5 was found to belong to the genus Acidovorax and subsequently named as Acidovorax sp. DP5. The highest extracellular depolymerase enzyme activity was achieved when 0.25% (w/v) of P(3HB) and 1 g/L of urea were used as carbon and nitrogen source, respectively, in the culture media. The most suitable assay condition of the depolymerase enzyme in response to pH and temperature was tested. The depolymerase produced by strain Acidovorax sp. DP5 showed high percentage of degradation with P(3HB) films in an alkaline condition with pH 9 and at a temperature of 40°C.
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Draft Genome Sequence of Ralstonia sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading Bacterium, Isolated from Compost. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01170-15. [PMID: 26450738 PMCID: PMC4599097 DOI: 10.1128/genomea.01170-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ralstonia sp. strain MD27, a novel biopolymer-degrading betaproteobacterium, was isolated from compost samples. This organism has been shown to utilize the biopolymer poly(3-hydroxybutyrate) [P(3HB)] as a carbon source for growth. We report the draft genome sequence of MD27 with an estimated total sequence length of 5.9 Mb.
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70
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Sun J, Matsumoto K, Tabata Y, Kadoya R, Ooi T, Abe H, Taguchi S. Molecular weight-dependent degradation of d-lactate-containing polyesters by polyhydroxyalkanoate depolymerases from Variovorax sp. C34 and Alcaligenes faecalis T1. Appl Microbiol Biotechnol 2015; 99:9555-63. [DOI: 10.1007/s00253-015-6756-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/29/2022]
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Prieto A, Escapa IF, Martínez V, Dinjaski N, Herencias C, de la Peña F, Tarazona N, Revelles O. A holistic view of polyhydroxyalkanoate metabolism inPseudomonas putida. Environ Microbiol 2015; 18:341-57. [DOI: 10.1111/1462-2920.12760] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Auxiliadora Prieto
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Isabel F. Escapa
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Virginia Martínez
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Nina Dinjaski
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Cristina Herencias
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Fernando de la Peña
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Natalia Tarazona
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Olga Revelles
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
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72
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Wang YL, Lin YT, Chen CL, Shaw GC, Liaw SH. Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase from Bacillus thuringiensis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1421-3. [PMID: 25286954 DOI: 10.1107/s2053230x14019347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/26/2014] [Indexed: 11/10/2022]
Abstract
Poly[(R)-3-hydroxybutyrate] (PHB) is a microbial biopolymer that has been commercialized as biodegradable plastics. The key enzyme for the degradation is PHB depolymerase (PhaZ). A new intracellular PhaZ from Bacillus thuringiensis (BtPhaZ) has been screened for potential applications in polymer biodegradation. Recombinant BtPhaZ was crystallized using 25% polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5 at 288 K. The crystals belonged to space group P1, with unit-cell parameters a = 42.97, b = 83.23, c = 85.50 Å, α = 73.45, β = 82.83, γ = 83.49°. An X-ray diffraction data set was collected to 1.42 Å resolution with an Rmerge of 6.4%. Unexpectedly, a molecular-replacement solution was obtained using the crystal structure of Streptomyces lividans chloroperoxidase as a template, which shares 24% sequence identity to BtPhaZ. This is the first crystal structure of an intracellular poly(3-hydroxybutyrate) depolymerase.
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Affiliation(s)
- Yung Lin Wang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yi Ting Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chia Lin Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Gwo Chyuan Shaw
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Shwu Huey Liaw
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
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73
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Catone MV, Ruiz JA, Castellanos M, Segura D, Espin G, López NI. High polyhydroxybutyrate production in Pseudomonas extremaustralis is associated with differential expression of horizontally acquired and core genome polyhydroxyalkanoate synthase genes. PLoS One 2014; 9:e98873. [PMID: 24887088 PMCID: PMC4041789 DOI: 10.1371/journal.pone.0098873] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/08/2014] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas extremaustralis produces mainly polyhydroxybutyrate (PHB), a short chain length polyhydroxyalkanoate (sclPHA) infrequently found in Pseudomonas species. Previous studies with this strain demonstrated that PHB genes are located in a genomic island. In this work, the analysis of the genome of P. extremaustralis revealed the presence of another PHB cluster phbFPX, with high similarity to genes belonging to Burkholderiales, and also a cluster, phaC1ZC2D, coding for medium chain length PHA production (mclPHA). All mclPHA genes showed high similarity to genes from Pseudomonas species and interestingly, this cluster also showed a natural insertion of seven ORFs not related to mclPHA metabolism. Besides PHB, P. extremaustralis is able to produce mclPHA although in minor amounts. Complementation analysis demonstrated that both mclPHA synthases, PhaC1 and PhaC2, were functional. RT-qPCR analysis showed different levels of expression for the PHB synthase, phbC, and the mclPHA synthases. The expression level of phbC, was significantly higher than the obtained for phaC1 and phaC2, in late exponential phase cultures. The analysis of the proteins bound to the PHA granules showed the presence of PhbC and PhaC1, whilst PhaC2 could not be detected. In addition, two phasin like proteins (PhbP and PhaI) associated with the production of scl and mcl PHAs, respectively, were detected. The results of this work show the high efficiency of a foreign gene (phbC) in comparison with the mclPHA core genome genes (phaC1 and phaC2) indicating that the ability of P. extremaustralis to produce high amounts of PHB could be explained by the different expression levels of the genes encoding the scl and mcl PHA synthases.
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Affiliation(s)
- Mariela V. Catone
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena A. Ruiz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, CONICET, Buenos Aires, Argentina
| | - Mildred Castellanos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Guadalupe Espin
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Nancy I. López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
- * E-mail:
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74
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Tan LT, Hiraishi T, Sudesh K, Maeda M. Effects of mutation at position 285 of Ralstonia pickettii T1 poly[(R)-3-hydroxybutyrate] depolymerase on its activities. Appl Microbiol Biotechnol 2014; 98:7061-8. [PMID: 24676749 DOI: 10.1007/s00253-014-5660-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 02/28/2014] [Accepted: 03/02/2014] [Indexed: 11/26/2022]
Abstract
Asn at position 285 (N285) in the catalytic domain of poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 most likely participates in the cleavage of ester bonds as revealed by our previous evolutionary engineering study using the error-prone polymerase chain reaction (PCR) method. To exhaustively examine the effects of mutations at that position, we conducted site-directed saturation mutagenesis at that position and the resultant mutant enzymes (N285X) were evaluated in p-nitrophenyl ester (pNPCn) hydrolysis and PHB degradation. Kinetic studies demonstrated that the PHB-degrading activities of N285X were reciprocally related to their pNPCn-hydrolyzing activities, with the exception of N285A and N285G, and that His residue could functionally substitute for Asn285 on PHB degradation.
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Affiliation(s)
- Liu-Tzea Tan
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
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75
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Di Martino C, Catone MV, López NI, Raiger Iustman LJ. Polyhydroxyalkanoate Synthesis Affects Biosurfactant Production and Cell Attachment to Hydrocarbons in Pseudomonas sp. KA-08. Curr Microbiol 2014; 68:735-42. [DOI: 10.1007/s00284-014-0536-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022]
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76
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García-Hidalgo J, Hormigo D, Arroyo M, de la Mata I. Novel extracellular PHB depolymerase from Streptomyces ascomycinicus: PHB copolymers degradation in acidic conditions. PLoS One 2013; 8:e71699. [PMID: 23951224 PMCID: PMC3741128 DOI: 10.1371/journal.pone.0071699] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/30/2013] [Indexed: 11/18/2022] Open
Abstract
The ascomycin-producer strain Streptomyces ascomycinicus has been proven to be an extracellular poly(R)-3-hydroxybutyrate (PHB) degrader. The fkbU gene, encoding a PHB depolymerase (PhaZSa), has been cloned in E. coli and Rhodococcus sp. T104 strains for gene expression. Gram-positive host Rhodococcus sp. T104 was able to produce and secrete to the extracellular medium an active protein form. PhaZSa was purified by two hydrophobic interaction chromatographic steps, and afterwards was biochemically as well as structurally characterized. The enzyme was found to be a monomer with a molecular mass of 48.4 kDa, and displayed highest activity at 45°C and pH 6, thus being the first PHB depolymerase from a gram-positive bacterium presenting an acidic pH optimum. The PHB depolymerase activity of PhaZSa was increased in the presence of divalent cations due to non-essential activation, and also in the presence of methyl-β-cyclodextrin and PEG 3350. Protein structure was analyzed, revealing a globular shape with an alpha-beta hydrolase fold. The amino acids comprising the catalytic triad, Ser131-Asp209-His269, were identified by multiple sequence alignment, chemical modification of amino acids and site-directed mutagenesis. These structural results supported the proposal of a three-dimensional model for this depolymerase. PhaZSa was able to degrade PHB, but also demonstrated its ability to degrade films made of PHB, PHBV copolymers and a blend of PHB and starch (7∶3 proportion wt/wt). The features shown by PhaZSa make it an interesting candidate for industrial applications involving PHB degradation.
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Affiliation(s)
- Javier García-Hidalgo
- Department of Biochemistry and Molecular Biology I. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Daniel Hormigo
- Department of Biochemistry and Molecular Biology I. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology I. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology I. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
- * E-mail:
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77
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Purification and characterization of two extracellular polyhydroxyalkanoate depolymerases from Pseudomonas mendocina. Biotechnol Lett 2013; 35:1919-24. [DOI: 10.1007/s10529-013-1288-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/24/2013] [Indexed: 11/30/2022]
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78
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Martínez V, Jurkevitch E, García JL, Prieto MA. Reward forBdellovibrio bacteriovorusfor preying on a polyhydroxyalkanoate producer. Environ Microbiol 2012; 15:1204-15. [DOI: 10.1111/1462-2920.12047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/29/2012] [Accepted: 11/03/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Virginia Martínez
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology; Faculty of Agricultural, Food and Environmental Quality Sciences; the Hebrew University of Jerusalem; Rehovot; 76100; Israel
| | - José Luis García
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
| | - María Auxiliadora Prieto
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
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79
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Verma R, Schwaneberg U, Roccatano D. Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering. Comput Struct Biotechnol J 2012; 2:e201209008. [PMID: 24688649 PMCID: PMC3962222 DOI: 10.5936/csbj.201209008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/07/2012] [Accepted: 10/12/2012] [Indexed: 12/01/2022] Open
Abstract
The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE) and the review summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this review is to provide concise information about currently available computational resources to assist the design of directed evolution based protein engineering experiment.
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Affiliation(s)
- Rajni Verma
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany ; Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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80
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Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria. Appl Environ Microbiol 2012; 78:7229-37. [PMID: 22865072 DOI: 10.1128/aem.01707-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(l-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters, Streptomyces roseolus SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and p-nitrophenyl (pNP)-alkanoates, with its maximum activity being measured with pNP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (R)-3-hydroxyoctanoate. In addition, the genes of several Actinobacteria strains, including S. roseolus SL3, were identified on the basis of the peptide de novo sequencing of the Streptomyces venezuelae SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases.
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81
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Identification and biochemical evidence of a medium-chain-length polyhydroxyalkanoate depolymerase in the Bdellovibrio bacteriovorus predatory hydrolytic arsenal. Appl Environ Microbiol 2012; 78:6017-26. [PMID: 22706067 DOI: 10.1128/aem.01099-12] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate predator Bdellovibrio bacteriovorus HD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 of B. bacteriovorus HD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZ(Bd)). The primary structure of PhaZ(Bd) suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZ(Bd) has been extracellularly produced using different hypersecretor Tol-pal mutants of Escherichia coli and Pseudomonas putida as recombinant hosts. The recombinant PhaZ(Bd) has been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZ(Bd) is an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers.
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82
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Brigham CJ, Reimer EN, Rha C, Sinskey AJ. Examination of PHB Depolymerases in Ralstonia eutropha: Further Elucidation of the Roles of Enzymes in PHB Homeostasis. AMB Express 2012; 2:26. [PMID: 22537946 PMCID: PMC3430594 DOI: 10.1186/2191-0855-2-26] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 04/26/2012] [Indexed: 11/29/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are biodegradable polymers that are attractive materials for use in tissue engineering and medical device manufacturing. Ralstonia eutropha is regarded as the model organism for PHA biosynthesis. We examined the effects of PHA depolymerase (PhaZ) expression on PHA homeostasis in R. eutropha strains. In order to analyze the impact of PhaZs on R. eutropha granule architecture, we performed electron microscopy on several phaZ knockout strains and the wild type strain grown under PHA production conditions. Analysis of the acquired micrographs was based on stereology: the ratio of granule area and cell area was determined, along with total granule count per full-size cell image. Cells bearing a phaZ2 knockout mutation alone or in conjunction with a phaZ1 mutation were found to have a high granule volume per cell volume and a higher granule count compared to wild type. A phaZ quadruple knockout strain appeared to have a low granule volume per cell volume and a low granule count per cell. Cells bearing a phaZ3 knockout were found to have a higher granule count than the wild type, whereas granule volume per cell volume was similar. Accordingly, we hypothesize that PhaZs have not only an impact on PHA degradation but also on the 3-dimensional granule architecture. Based on our data, PhaZ2 is postulated to affect granule density. This work increased our knowledge about PHA depolymerases in R. eutropha, including enzymes that had previously been uncharacterized.
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Affiliation(s)
- Christopher J Brigham
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - ChoKyun Rha
- Biomaterials Science and Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Division of Health Sciences Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Engineering Systems Division, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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83
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Rodríguez-Contreras A, Calafell-Monfort M, Marqués-Calvo MS. Enzymatic degradation of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) by commercial lipases. Polym Degrad Stab 2012. [DOI: 10.1016/j.polymdegradstab.2012.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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84
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Sirim D, Wagner F, Wang L, Schmid RD, Pleiss J. The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar006. [PMID: 21498547 PMCID: PMC3077825 DOI: 10.1093/database/bar006] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineering Database (LccED, http://www.lcced.uni-stuttgart.de) was designed to serve as a tool for a systematic sequence-based classification and analysis of the diverse multicopper oxidase protein family. More than 2200 proteins were classified into 11 superfamilies and 56 homologous families. For each family, the LccED provides multiple sequence alignments, phylogenetic trees and family-specific HMM profiles. The integration of structures for 14 different proteins allows a comprehensive comparison of sequences and structures to derive biochemical properties. Among the families, the distribution of the proteins regarding different kingdoms was investigated. The database was applied to perform a comprehensive analysis by MCO- and laccase-specific patterns. The LccED combines information of sequences and structures of MCOs. It serves as a classification tool to assign new proteins to a homologous family and can be applied to investigate sequence–structure–function relationship and to guide protein engineering. Database URL:http://www.lcced.uni-stuttgart.de
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Affiliation(s)
- Demet Sirim
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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85
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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]
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86
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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]
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87
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Arroyo M, García-Hidalgo J, Villalón M, de Eugenio L, Hormigo D, Acebal C, García JL, Prieto MA, de la Mata I. Characterization of a novel immobilized biocatalyst obtained by matrix-assisted refolding of recombinant polyhydroxyoctanoate depolymerase from Pseudomonas putida KT2442 isolated from inclusion bodies. J Ind Microbiol Biotechnol 2010; 38:1203-9. [DOI: 10.1007/s10295-010-0898-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
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88
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Widmann M, Radloff R, Pleiss J. The Thiamine diphosphate dependent Enzyme Engineering Database: a tool for the systematic analysis of sequence and structure relations. BMC BIOCHEMISTRY 2010; 11:9. [PMID: 20122171 PMCID: PMC2831816 DOI: 10.1186/1471-2091-11-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 02/01/2010] [Indexed: 01/12/2023]
Abstract
BACKGROUND Thiamine diphosphate (ThDP)-dependent enzymes form a vast and diverse class of proteins, catalyzing a wide variety of enzymatic reactions including the formation or cleavage of carbon-sulfur, carbon-oxygen, carbon-nitrogen, and especially carbon-carbon bonds. Although very diverse in sequence and domain organisation, they share two common protein domains, the pyrophosphate (PP) and the pyrimidine (PYR) domain. For the comprehensive and systematic comparison of protein sequences and structures the Thiamine diphosphate (ThDP)-dependent Enzyme Engineering Database (TEED) was established. DESCRIPTION The TEED http://www.teed.uni-stuttgart.de contains 12048 sequence entries which were assigned to 9443 different proteins and 379 structure entries. Proteins were assigned to 8 different superfamilies and 63 homologous protein families. For each family, the TEED offers multisequence alignments, phylogenetic trees, and family-specific HMM profiles. The conserved pyrophosphate (PP) and pyrimidine (PYR) domains have been annotated, which allows the analysis of sequence similarities for a broad variety of proteins. Human ThDP-dependent enzymes are known to be involved in many diseases. 20 different proteins and over 40 single nucleotide polymorphisms (SNPs) of human ThDP-dependent enzymes were identified in the TEED. CONCLUSIONS The online accessible version of the TEED has been designed to serve as a navigation and analysis tool for the large and diverse family of ThDP-dependent enzymes.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Robert Radloff
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Sirim D, Wagner F, Lisitsa A, Pleiss J. The cytochrome P450 engineering database: Integration of biochemical properties. BMC BIOCHEMISTRY 2009; 10:27. [PMID: 19909539 PMCID: PMC2779185 DOI: 10.1186/1471-2091-10-27] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 11/12/2009] [Indexed: 11/21/2022]
Abstract
Background Cytochrome P450 monooxygenases (CYPs) form a vast and diverse enzyme class of particular interest in drug development and a high biotechnological potential. Although very diverse in sequence, they share a common structural fold. For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED) was established. It was built up based on an extensible data model that enables its functions readily enhanced. Description The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families and superfamilies. To gain biochemical information on substrates and inhibitors, the CYPED was linked to the Cytochrome P450 Knowledgebase (CPK). To overcome differences in the data model and inconsistencies in the content of CYPED and CPK, a metric was established based on sequence similarity to link protein sequences as primary keys. In addition, the annotation of structurally and functionally relevant residues was extended by a reliable prediction of conserved secondary structure elements and by information on the effect of single nucleotide polymorphisms. Conclusion The online accessible version of the CYPED at http://www.cyped.uni-stuttgart.de provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties.
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Affiliation(s)
- Demet Sirim
- Institute of Technical Biochemistry, University of Stuttgart, Germany.
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