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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]
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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.
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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.
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Affiliation(s)
- Michael Knoll
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring, Germany.
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Grage K, Jahns AC, Parlane N, Palanisamy R, Rasiah IA, Atwood JA, Rehm BHA. Bacterial Polyhydroxyalkanoate Granules: Biogenesis, Structure, and Potential Use as Nano-/Micro-Beads in Biotechnological and Biomedical Applications. Biomacromolecules 2009; 10:660-9. [DOI: 10.1021/bm801394s] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katrin Grage
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Anika C. Jahns
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Natalie Parlane
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Rajasekaran Palanisamy
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Indira A. Rasiah
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Jane A. Atwood
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Bernd H. A. Rehm
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand and Hopkirk Research Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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56
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Polyhydroxyalkanoate granules are complex subcellular organelles (carbonosomes). J Bacteriol 2009; 191:3195-202. [PMID: 19270094 DOI: 10.1128/jb.01723-08] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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de Eugenio L, García J, García P, Prieto M, Sanz J. Comparative Analysis of the Physiological and Structural Properties of a Medium Chain Length Polyhydroxyalkanoate Depolymerase from Pseudomonas putida KT2442. Eng Life Sci 2008. [DOI: 10.1002/elsc.200700057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Ruth K, Roo GD, Egli T, Ren Q. Identification of Two Acyl-CoA Synthetases from Pseudomonas putida GPo1: One is Located at the Surface of Polyhydroxyalkanoates Granules. Biomacromolecules 2008; 9:1652-9. [DOI: 10.1021/bm8001655] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katinka Ruth
- Laboratory for Biomaterials, Swiss Federal Laboratories for Materials Testing and Research (Empa), CH-9014 St. Gallen, Switzerland, Synthon BV, Post Office Box 7071, 6503 GN Nijmegen, The Netherlands, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, CH-8092 Zurich, Switzerland, and Swiss Federal Institute of Aquatic Science and Technology (Eawag), Post Office Box 6100, CH-8600 Dübendorf, Switzerland
| | - Guy de Roo
- Laboratory for Biomaterials, Swiss Federal Laboratories for Materials Testing and Research (Empa), CH-9014 St. Gallen, Switzerland, Synthon BV, Post Office Box 7071, 6503 GN Nijmegen, The Netherlands, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, CH-8092 Zurich, Switzerland, and Swiss Federal Institute of Aquatic Science and Technology (Eawag), Post Office Box 6100, CH-8600 Dübendorf, Switzerland
| | - Thomas Egli
- Laboratory for Biomaterials, Swiss Federal Laboratories for Materials Testing and Research (Empa), CH-9014 St. Gallen, Switzerland, Synthon BV, Post Office Box 7071, 6503 GN Nijmegen, The Netherlands, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, CH-8092 Zurich, Switzerland, and Swiss Federal Institute of Aquatic Science and Technology (Eawag), Post Office Box 6100, CH-8600 Dübendorf, Switzerland
| | - Qun Ren
- Laboratory for Biomaterials, Swiss Federal Laboratories for Materials Testing and Research (Empa), CH-9014 St. Gallen, Switzerland, Synthon BV, Post Office Box 7071, 6503 GN Nijmegen, The Netherlands, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, CH-8092 Zurich, Switzerland, and Swiss Federal Institute of Aquatic Science and Technology (Eawag), Post Office Box 6100, CH-8600 Dübendorf, Switzerland
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Campisano A, Overhage J, Rehm BH. The polyhydroxyalkanoate biosynthesis genes are differentially regulated in planktonic- and biofilm-grown Pseudomonas aeruginosa. J Biotechnol 2008; 133:442-52. [DOI: 10.1016/j.jbiotec.2007.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 10/31/2007] [Accepted: 11/12/2007] [Indexed: 10/22/2022]
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Poly(3-hydroxybutyrate) (PHB) depolymerase PhaZa1 is involved in mobilization of accumulated PHB in Ralstonia eutropha H16. Appl Environ Microbiol 2007; 74:1058-63. [PMID: 18156336 DOI: 10.1128/aem.02342-07] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recently finished genome sequence of Ralstonia eutropha H16 harbors nine genes that are thought to encode functions for intracellular depolymerization (mobilization) of storage poly(3-hydroxybutyrate) (PHB). Based on amino acid similarities, the gene products belong to four classes (PhaZa1 to PhaZa5, PhaZb, PhaZc, and PhaZd1/PhaZd2). However, convincing direct evidence for the in vivo roles of the gene products is poor. In this study, we selected four candidate genes (phaZa1, phaZb, phaZc, and phaZd1) representing the four classes and investigated the physiological function of the gene products (i) with recombinant Escherichia coli strains and (ii) with R. eutropha null mutants. Evidence for weak but significant PHB depolymerase activity was obtained only for PhaZa1. The physiological roles of the other potential PHB depolymerases remain uncertain.
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Uchino K, Saito T, Gebauer B, Jendrossek D. Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA. J Bacteriol 2007; 189:8250-6. [PMID: 17720797 PMCID: PMC2168675 DOI: 10.1128/jb.00752-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly(3-hydroxybutyrate) (PHB) granules isolated in native form (nPHB granules) from Ralstonia eutropha catalyzed formation of PHB from (14)C-labeled acetyl coenzyme A (CoA) in the presence of NADPH and concomitantly released CoA, revealing that PHB biosynthetic proteins (acetoacetyl-CoA thiolase, acetoacetyl-CoA reductase, and PHB synthase) are present and active in isolated nPHB granules in vitro. nPHB granules also catalyzed thiolytic cleavage of PHB in the presence of added CoA, resulting in synthesis of 3-hydroxybutyryl-CoA (3HB-CoA) from PHB. Synthesis of 3HB-CoA was also shown by incubation of artificial (protein-free) PHB with CoA and PhaZa1, confirming that PhaZa1 is a PHB depolymerase catalyzing the thiolysis reaction. Acetyl-CoA was the major product detectable after incubation of nPHB granules in the presence of NAD(+), indicating that downstream mobilizing enzyme activities were also present and active in isolated nPHB granules. We propose that intracellular concentrations of key metabolites (CoA, acetyl-CoA, 3HB-CoA, NAD(+)/NADH) determine whether a cell accumulates or degrades PHB. Since the degradation product of PHB is 3HB-CoA, the cells do not waste energy by synthesis and degradation of PHB. Thus, our results explain the frequent finding of simultaneous synthesis and breakdown of PHB.
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Affiliation(s)
- Keiichi Uchino
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
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Jendrossek D. Peculiarities of PHA granules preparation and PHA depolymerase activity determination. Appl Microbiol Biotechnol 2007; 74:1186-96. [PMID: 17318541 DOI: 10.1007/s00253-007-0860-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 01/22/2007] [Accepted: 01/24/2007] [Indexed: 11/26/2022]
Abstract
An extensive amount of knowledge on biochemistry of poly(3-hydroxyalkanoic acid) (PHA) synthesis and on its biodegradation has accumulated during the last two decades. Numerous genes encoding enzymes involved in the formation of PHA and in PHA degradation (PHA depolymerases) were cloned and characterized from many microorganisms. A large variety of methods exists for determination of PHA depolymerase activity and for preparation of the polymeric substrate (PHA). Unfortunately, results obtained with these different methods cannot be compared directly because they highly depend on the assay method applied and on the history of PHA granules preparation. In this contribution, the peculiarities, advantages, disadvantages and limitations of existing PHA depolymerase assay methods are described.
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Affiliation(s)
- Dieter Jendrossek
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany.
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Wang L, Armbruster W, Jendrossek D. Production of medium-chain-length hydroxyalkanoic acids from Pseudomonas putida in pH stat. Appl Microbiol Biotechnol 2007; 75:1047-53. [PMID: 17401563 DOI: 10.1007/s00253-007-0920-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/01/2007] [Accepted: 03/02/2007] [Indexed: 10/23/2022]
Abstract
Pseudomonas putida GP01 cells that had accumulated medium-chain-length polyhydroxyalkanoates (PHA(MCL)) secreted 3-hydroxyoctanoate and 3-hydroxyhexanoate when incubated in alkaline buffers. The release of acids strongly decreased the pH resulting in less efficient secretion of 3HA(MCL) at neutral pH. To increase the yield of secreted MCL-hydroxyalkanoates, experiments at constant pH in a pH stat apparatus were performed. High acid releasing rates were recorded for the wild type GP01 at pH 9.2 (0.60 mmol acid h(-1) g(-1) cellular dry weight [cdw]). At more alkaline constant pH values (pH 9.3-11), the initial acid secretion rates were even higher but rapidly decreased by time. When acid secretion of PHA depolymerase mutant GPo500 was tested (pH 9.2), considerably lower rates compared to wild type were recorded (0.18 mmol acid h(-1) g(-1) cdw). Determination of dissolved oxygen during acid release indicated different respiratoric activity in wild type (low) and mutant (high). Acid release of mutant, but not of the wild type, could be enhanced by aeration. Determination of PHA content of cells after alkaline incubation showed that the wild type had lost most of its accumulated PHA, whereas the PHA content of the depolymerase mutant was not significantly reduced. Considerable amounts of 3HA(MCL) were secreted by the wild type, but only little 3HA(MCL) were found for the depolymerase mutant. In summary, 3HA(MCL) can be more efficiently produced at constant high pH than by incubation without pH control. High PHA depolymerase activity enabled the wild type to compensate for the high external pH by secretion of PHA hydrolysis products, whereas production of protons at aerobic conditions presumably was responsible for the major portion of the observed acid releasing rates in the depolymerase mutant.
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Affiliation(s)
- Lei Wang
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550, Stuttgart, Germany
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