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Parrell D, Olson J, Lemke RA, Donohue TJ, Wright ER. Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy. Biomolecules 2024; 14:1006. [PMID: 39199393 PMCID: PMC11352279 DOI: 10.3390/biom14081006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/01/2024] Open
Abstract
Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.
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Affiliation(s)
- Daniel Parrell
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53706, USA; (D.P.); (J.O.)
- Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, WI 53726, USA;
- Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Joseph Olson
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53706, USA; (D.P.); (J.O.)
| | - Rachelle A. Lemke
- Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, WI 53726, USA;
- Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, WI 53726, USA;
- Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, WI 53726, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53706, USA; (D.P.); (J.O.)
- Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, WI 53726, USA;
- Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, WI 53726, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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2
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Neoh SZ, Tan HT, Trakunjae C, Chek MF, Vaithanomsat P, Hakoshima T, Sudesh K. N-terminal truncation of PhaC BP-M-CPF4 and its effect on PHA production. Microb Cell Fact 2024; 23:52. [PMID: 38360657 PMCID: PMC10867992 DOI: 10.1186/s12934-024-02329-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation. RESULTS The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB-4 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4. CONCLUSION This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.
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Affiliation(s)
- Soon Zher Neoh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia
| | - Hua Tiang Tan
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Chanaporn Trakunjae
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Pilanee Vaithanomsat
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok, 10900, Thailand
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia.
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de Koning EA, Panjalingam M, Tran J, Eckhart MR, Dahlberg PD, Shapiro L. The PHB Granule Biogenesis Pathway in Caulobacter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548030. [PMID: 37461544 PMCID: PMC10350054 DOI: 10.1101/2023.07.06.548030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
PHB granules are bacterial organelles that store excess carbohydrates in the form of water-insoluble polyhydroxybutyrate (PHB). The PHB polymerase, phasin (a small amphipathic protein), and active PHB synthesis are essential for the formation of mature PHB granules in Caulobacter crescentus. Granule formation was found to be initiated by the condensation of self-associating PHB polymerase-GFP into foci, closely followed by the recruitment and condensation of phasin-mCherry. Following the active synthesis of PHB and granule maturation, the polymerase dissociates from mature granules and the PHB depolymerase is recruited to the granule. The polymerase directly binds phasin in vitro through its intrinsically disordered N-terminal domain. Thus, granule biogenesis is initiated and controlled by the action of a PHB polymerase and an associated helper protein, phasin, that together synthesize the hydrophobic granule's content while forming the granules protein boundary.
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4
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Raturi G, Shree S, Sharma A, Panesar PS, Goswami S. Recent approaches for enhanced production of microbial polyhydroxybutyrate: Preparation of biocomposites and applications. Int J Biol Macromol 2021; 182:1650-1669. [PMID: 33992649 DOI: 10.1016/j.ijbiomac.2021.05.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022]
Abstract
In modern decades, an increase in environmental awareness has attracted the keen interest of researchers to investigate eco-sustainable, recyclable materials to minimize reliance on petroleum-based polymeric compounds. Poly (3-hydroxybutyrate) is amorphous, linear, and biodegradable bacterial polyesters that belong to the polyhydroxyalkanoates family with enormous applications in many fields. The present review provides comprehensive information on polyhydroxybutyrate production from different biomass feedstock. Various studies on PHB production by genetically engineered bacterial cells and optimization of parameters have been discussed. Recent technological innovation in processing polyhydroxybutyrate-based biocomposite through the different process has also been examined. Besides this, the potential applications of the derived competent biocomposites in the other fields have been depicted.
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Affiliation(s)
- Gaurav Raturi
- Department of Agri-Biotechnology, National Agri-food Biotechnology Institute, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shweta Shree
- Department of Biotechnology, Texas A&M University, USA
| | - Amita Sharma
- Department of Chemical Engineering, Centre of Innovative and Applied Bioprocessing, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Parmjit S Panesar
- Department of Food Engineering and Technology, Sant Longowal Institute of Engineering and Technology, Longowal 148106, Punjab, India
| | - Saswata Goswami
- Department of Chemical Engineering, Centre of Innovative and Applied Bioprocessing, Knowledge City, Sector-81, Mohali, Punjab 140306, India.
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Novel unexpected functions of PHA granules. Appl Microbiol Biotechnol 2020; 104:4795-4810. [PMID: 32303817 DOI: 10.1007/s00253-020-10568-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. KEY POINTS: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells.
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7
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Kundrat V, Matouskova P, Marova I. Facile Preparation of Porous Microfiber from Poly-3-(R)-Hydroxybutyrate and Its Application. MATERIALS 2019; 13:ma13010086. [PMID: 31877992 PMCID: PMC6981871 DOI: 10.3390/ma13010086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
In this study, we described the development of a simplified wet spinning method of the production of a novel type of porous continuous fiber based on poly-3-(R)-hydroxybutyrate (PHB). The principle of this method is precipitation of PHB dissolved in chloroform solution into the ethanol precipitation bath. The influence of various PHB concentrations and feed rates on specific surface area (measured by nitrogen absorption method) was studied. Materials were also characterized by SEM. Surface areas of fibers achieved by wet spinning were in the range of tens of m2.g-1, and the biggest surface area value was 55 m2.g-1. The average diameter of fibers was in the range of 20-120 μm and was dependent on both PHB concentration and feed rate. Optimum conditions for reaching stable fibers of high surface area were 3-5 % w.t. of PHB and feed rate 0.5-3 ml.h-1. Fibers were functionalized by adsorption of some natural plant extracts. The incorporation of active substances into fibers was confirmed by infrared spectroscopy. High antioxidant and antimicrobial effect of PHB-fibers with cloves extract was found, as well as excellent long-term stability and optimal dynamics of the release of active compounds. The newly produced material would be applicable in pharmacy, cosmetics, and wound healing.
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8
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Soda N, Rehm BHA, Sonar P, Nguyen NT, Shiddiky MJA. Advanced liquid biopsy technologies for circulating biomarker detection. J Mater Chem B 2019; 7:6670-6704. [PMID: 31646316 DOI: 10.1039/c9tb01490j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry, Physics and Mechanical Engineering, Molecular Design and Synthesis, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
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9
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Liu C, Noda I, Chase DB, Zhang Y, Qu J, Jia M, Ni C, Rabolt JF. Crystallization Retardation of Ultrathin Films of Poly[( R)-3-hydroxybutyrate] and a Random Copolymer Poly[( R)-3-hydroxybutyrate- co-( R)-3-hydroxyhexanoate] on an Aluminum Oxide Surface. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Isao Noda
- Danimer Scientific, Bainbridge 39817, Georgia, United States
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10
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Tian B, Shah M, Choi MH, Rho JK, Lee SY, Yoon SC. Calcium Involved Directional Organization of Polymer Chains in Polyester Nanogranules in Bacterial Cells. Sci Rep 2019; 9:3429. [PMID: 30837614 PMCID: PMC6401383 DOI: 10.1038/s41598-019-40097-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/06/2019] [Indexed: 12/04/2022] Open
Abstract
Soil bacteria accumulate polyesters (typically poly([R]-3-hydroxybutyrate (PHB), in which one end of the chain terminates with a carboxyl group) in the form of hydrated, amorphous nanogranules in cells. However, it is not clear what drives the structure of these biomaterials inside bacterial cells. Here, we determined that calcium guides intracellular formation of PHB nanogranules. Our systematic study using the surface zeta potential measurement and the carboxyl-specific SYTO-62 dye binding assay showed that the terminal carboxyl is not exposed to the granule surface but is buried inside native “unit-granules” comprising the mature granule. Extracellular Ca2+ was found to mediate the formation of these PHB unit-granules, with uptaken Ca2+ stored inside the granules. Comparative [Ca2+]-dependent fluorescence spectroscopy revealed that the native granules in Cupriavidus necator H16 act as a Ca2+ storage system, presumably for the regulation of its cytosolic Ca2+ level, but those from recombinant Escherichia coli do not. This study reveals intimate links between Ca2+ and native granule formation, and establishes a novel mechanism that intracellular PHB granules function as Ca2+ storage in order to relieve soil bacteria from Ca2+ stress.
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Affiliation(s)
- Baoxia Tian
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 23003, People's Republic of China
| | - Mohsin Shah
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Department of Physiology, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, 40000, Pakistan
| | - Mun Hwan Choi
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jong Kook Rho
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sang Yeol Lee
- Systems & Synthetic Agrobiotech Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sung Chul Yoon
- Nano-Biomaterials Science Laboratory, Division of Applied Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Systems & Synthetic Agrobiotech Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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11
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Mato A, Tarazona NA, Hidalgo A, Cruz A, Jiménez M, Pérez-Gil J, Prieto MA. Interfacial Activity of Phasin PhaF from Pseudomonas putida KT2440 at Hydrophobic-Hydrophilic Biointerfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:678-686. [PMID: 30580527 DOI: 10.1021/acs.langmuir.8b03036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phasins, the major proteins coating polyhydroxyalkanoate (PHA) granules, have been proposed as suitable biosurfactants for multiple applications because of their amphiphilic nature. In this work, we analyzed the interfacial activity of the amphiphilic α-helical phasin PhaF from Pseudomonas putida KT2440 at different hydrophobic-hydrophilic interfacial environments. The binding of PhaF to surfaces containing PHA or phospholipids, postulated as structural components of PHA granules, was confirmed in vitro using supported lipid bilayers and confocal microscopy, with polyhydroxyoctanoate- co-hexanoate P(HO- co-HHx) and Escherichia coli lipid extract as model systems. The surfactant-like capabilities of PhaF were determined by measuring changes in surface pressure in Langmuir devices. PhaF spontaneously adsorbed at the air-water interface, reducing the surface tension from 72 mN/m (water surface tension at 25 °C) to 50 mN/m. The differences in the adsorption of the protein in the presence of different phospholipid films showed a marked preference for phosphatidylglycerol species, such as 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphoglycerol. The PHA-binding domain of PhaF (BioF) conserved a similar surface activity to PhaF, suggesting that it is responsible for the surfactant properties of the whole protein. These new findings not only increase our knowledge about the role of phasins in the PHA machinery but also open new outlooks for the application of these proteins as biosurfactants.
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Affiliation(s)
| | | | - Alberto Hidalgo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Antonio Cruz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | | | - Jesús Pérez-Gil
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas , Universidad Complutense de Madrid , 28040 Madrid , Spain
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Involvement of polyhydroxyalkanoates in stress resistance of microbial cells: Biotechnological consequences and applications. Biotechnol Adv 2018; 36:856-870. [DOI: 10.1016/j.biotechadv.2017.12.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/24/2017] [Accepted: 12/12/2017] [Indexed: 01/30/2023]
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13
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Mohamed RA, Salleh AB, Leow ATC, Yahaya NM, Abdul Rahman MB. Ability of T1 Lipase to Degrade Amorphous P(3HB): Structural and Functional Study. Mol Biotechnol 2018; 59:284-293. [PMID: 28580552 DOI: 10.1007/s12033-017-0012-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
An enzyme with broad substrate specificity would be an asset for industrial application. T1 lipase apparently has the same active site residues as polyhydroxyalkanoates (PHA) depolymerase. Sequences of both enzymes were studied and compared, and a conserved lipase box pentapeptide region around the nucleophilic serine was detected. The alignment of 3-D structures for both enzymes showed their active site residues were well aligned with an RMSD value of 1.981 Å despite their sequence similarity of only 53.8%. Docking of T1 lipase with P(3HB) gave forth high binding energy of 5.4 kcal/mol, with the distance of 4.05 Å between serine hydroxyl (OH) group of TI lipase to the carbonyl carbon of the substrate, similar to the native PhaZ7 Pl . This suggests the possible ability of T1 lipase to bind P(3HB) in its active site. The ability of T1 lipase in degrading amorphous P(3HB) was investigated on 0.2% (w/v) P(3HB) plate. Halo zone was observed around the colony containing the enzyme which confirms that T1 lipase is indeed able to degrade amorphous P(3HB). Results obtained in this study highlight the fact that T1 lipase is a versatile hydrolase enzyme which does not only record triglyceride degradation activity but amorphous P(3HB) degradation activity as well.
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Affiliation(s)
- Rauda A Mohamed
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Adam Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Normi M Yahaya
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Narancic T, Scollica E, Cagney G, O'Connor KE. Three novel proteins co-localise with polyhydroxybutyrate (PHB) granules in Rhodospirillum rubrum S1. MICROBIOLOGY-SGM 2018; 164:625-634. [PMID: 29493489 DOI: 10.1099/mic.0.000642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Polyhydroxybutyrate (PHB), a biodegradable polymer accumulated by bacteria is deposited intracellularly in the form of inclusion bodies often called granules. The granules are supramolecular complexes harbouring a varied number of proteins on their surface, which have specific but incompletely characterised functions. By comparison with other organisms that produce biodegradable polymers, only two phasins have been described to date for Rhodosprillum rubrum, raising the possibility that more await discovery. Using a comparative proteomics strategy to compare the granules of wild-type R. rubrum with a PHB-negative mutant housing artificial PHB granules, we identified four potential PHB granules' associated proteins. These were: Q2RSI4, an uncharacterised protein; Q2RWU9, annotated as an extracellular solute-binding protein; Q2RQL4, annotated as basic membrane lipoprotein; and Q2RQ51, annotated as glucose-6-phosphate isomerase. In silico analysis revealed that Q2RSI4 harbours a Phasin_2 family domain and shares low identity with a single-strand DNA-binding protein from Sphaerochaeta coccoides. Fluorescence microscopy found that three proteins Q2RSI4, Q2EWU9 and Q2RQL4 co-localised with PHB granules. This work adds three potential new granule associated proteins to the repertoire of factors involved in bacterial storage granule formation, and confirms that proteomics screens are an effective strategy for discovery of novel granule associated proteins.
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Affiliation(s)
- Tanja Narancic
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elisa Scollica
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Sciences, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin E O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.,BEACON - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, Ireland
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15
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Bello-Gil D, Maestro B, Fonseca J, Dinjaski N, Prieto MA, Sanz JM. Poly-3-Hydroxybutyrate Functionalization with BioF-Tagged Recombinant Proteins. Appl Environ Microbiol 2018; 84:e02595-17. [PMID: 29196289 PMCID: PMC5795070 DOI: 10.1128/aem.02595-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable polyesters that accumulate in the cytoplasm of certain bacteria. One promising biotechnological application utilizes these biopolymers as supports for protein immobilization. Here, the PHA-binding domain of the Pseudomonas putida KT2440 PhaF phasin (BioF polypeptide) was investigated as an affinity tag for the in vitro functionalization of poly-3-hydroxybutyrate (PHB) particles with recombinant proteins, namely, full-length PhaF and two fusion proteins tagged to BioF (BioF-C-LytA and BioF-β-galactosidase, containing the choline-binding module C-LytA and the β-galactosidase enzyme, respectively). The protein-biopolyester interaction was strong and stable at a wide range of pHs and temperatures, and the bound protein was highly protected from self-degradation, while the binding strength could be modulated by coating with amphiphilic compounds. Finally, BioF-β-galactosidase displayed very stable enzymatic activity after several continuous activity-plus-washing cycles when immobilized in a minibioreactor. Our results demonstrate the potentialities of PHA and the BioF tag for the construction of novel bioactive materials.IMPORTANCE Our results confirm the biotechnological potential of the BioF affinity tag as a versatile tool for functionalizing PHA supports with recombinant proteins, leading to novel bioactive materials. The wide substrate range of the BioF tag presumably enables protein immobilization in vitro of virtually all natural PHAs as well as blends, copolymers, or artificial chemically modified derivatives with novel physicochemical properties. Moreover, the strength of protein adsorption may be easily modulated by varying the coating of the support, providing new perspectives for the engineering of bioactive materials that require a tight control of protein loading.
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Affiliation(s)
- Daniel Bello-Gil
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Beatriz Maestro
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Jennifer Fonseca
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Nina Dinjaski
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - Jesús M Sanz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
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Inactivation of an intracellular poly-3-hydroxybutyrate depolymerase of Azotobacter vinelandii allows to obtain a polymer of uniform high molecular mass. Appl Microbiol Biotechnol 2018; 102:2693-2707. [DOI: 10.1007/s00253-018-8806-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 01/20/2023]
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17
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Maestro B, Sanz JM. Polyhydroxyalkanoate-associated phasins as phylogenetically heterogeneous, multipurpose proteins. Microb Biotechnol 2017; 10:1323-1337. [PMID: 28425176 PMCID: PMC5658603 DOI: 10.1111/1751-7915.12718] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are natural polyesters of increasing biotechnological importance that are synthesized by many prokaryotic organisms as carbon and energy storage compounds in limiting growth conditions. PHAs accumulate intracellularly in form of inclusion bodies that are covered with a proteinaceous surface layer (granule-associated proteins or GAPs) conforming a network-like surface of structural, metabolic and regulatory polypeptides, and configuring the PHA granules as complex and well-organized subcellular structures that have been designated as 'carbonosomes'. GAPs include several enzymes related to PHA metabolism (synthases, depolymerases and hydroxylases) together with the so-called phasins, an heterogeneous group of small-size proteins that cover most of the PHA granule and that are devoid of catalytic functions but nevertheless play an essential role in granule structure and PHA metabolism. Structurally, phasins are amphiphilic proteins that shield the hydrophobic polymer from the cytoplasm. Here, we summarize the characteristics of the different phasins identified so far from PHA producer organisms and highlight the diverse opportunities that they offer in the Biotechnology field.
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Affiliation(s)
- Beatriz Maestro
- Instituto de Biología Molecular y CelularUniversidad Miguel HernándezAv. Universidad s/nElche03202Spain
| | - Jesús M. Sanz
- Instituto de Biología Molecular y CelularUniversidad Miguel HernándezAv. Universidad s/nElche03202Spain
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Thorat Gadgil BS, Killi N, Rathna GVN. Polyhydroxyalkanoates as biomaterials. MEDCHEMCOMM 2017; 8:1774-1787. [PMID: 30108887 PMCID: PMC6084198 DOI: 10.1039/c7md00252a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/23/2017] [Indexed: 12/18/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biopolymers synthesized by bacteria under unbalanced growth conditions. These biopolymers are considered as potential biomaterials for future applications because they are biocompatible, biodegradable, and easy to produce and functionalize with strong mechanical strength. Currently, PHAs are being extensively innovated for biomedical applications due to their prerequisite properties. The wide range of biomedical applications includes drug delivery systems, implants, tissue engineering, scaffolds, artificial organ constructs, etc. In this article we review the utility of PHAs in various forms (bulk/nano) for biomedical applications so as to bring about the future vision for PHAs as biomaterials for the advancement of research and technology.
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Affiliation(s)
- Bhagyashri S Thorat Gadgil
- Polymer Science and Engineering division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune , 411008 India .
| | - Naresh Killi
- Polymer Science and Engineering division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune , 411008 India .
| | - Gundloori V N Rathna
- Polymer Science and Engineering division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune , 411008 India .
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Anis SNS, Mohamad Annuar MS, Simarani K. In vivo and in vitro depolymerizations of intracellular medium-chain-length poly-3-hydroxyalkanoates produced by Pseudomonas putida Bet001. Prep Biochem Biotechnol 2017. [DOI: 10.1080/10826068.2017.1342266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Siti Nor Syairah Anis
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Khanom Simarani
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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Chloroform induces outstanding crystallization of poly(hydroxybutyrate) (PHB) vesicles within bacteria. Anal Bioanal Chem 2017; 409:2353-2361. [PMID: 28175936 DOI: 10.1007/s00216-017-0181-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/18/2016] [Accepted: 01/03/2017] [Indexed: 01/03/2023]
Abstract
Poly[(R)-3-hydroxyalkanoate]s or PHAs are aliphatic polyesters produced by numerous microorganisms. They are accumulated as energy and carbon reserve in the form of small intracellular vesicles. Poly[(R)-3-hydroxybutyrate] (PHB) is the most ubiquitous and simplest PHA. An atomic force microscope coupled with a tunable infrared laser (AFM-IR) was used to record highly spatially resolved infrared spectra of commercial purified PHB and native PHB within bacteria. For the first time, the crystallinity degree of native PHB within vesicle has been directly evaluated in situ without alteration due to the measure or extraction and purification steps of the polymer: native PHB is in crystalline state at 15% whereas crystallinity degree reaches 57% in commercial PHB. Chloroform addition on native PHB induces crystallization of the polymer within bacteria up to 60%. This possibility of probing and changing the physical state of polymer in situ could open alternative ways of production for PHB and others biopolymers. Graphical abstract An atomic force microscope coupled with a tunable infrared laser (AFM-IR) has been used to record local infrared spectra of biopolymer PHB within bacteria. Deconvolution of those spectra has allowed to determine in situ the crystallinity degree of native PHB.
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Rastogi VK, Samyn P. Synthesis of Polyhydroxybutyrate Particles with Micro-to-Nanosized Structures and Application as Protective Coating for Packaging Papers. NANOMATERIALS 2016; 7:nano7010005. [PMID: 28336839 PMCID: PMC5295195 DOI: 10.3390/nano7010005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/22/2016] [Accepted: 12/26/2016] [Indexed: 11/25/2022]
Abstract
This study reports on the development of bio-based hydrophobic coatings for packaging papers through deposition of polyhydroxybutyrate (PHB) particles in combination with nanofibrillated cellulose (NFC) and plant wax. In the first approach, PHB particles in the micrometer range (PHB-MP) were prepared through a phase-separation technique providing internally-nanosized structures. The particles were transferred as a coating by dip-coating filter papers in the particle suspension, followed by sizing with a carnauba wax solution. This approach allowed partial to almost full surface coverage of PHB-MP over the paper surface, resulting in static water contact angles of 105°–122° and 129°–144° after additional wax coating. In the second approach, PHB particles with submicron sizes (PHB-SP) were synthesized by an oil-in-water emulsion (o/w) solvent evaporation method and mixed in aqueous suspensions with 0–7 wt % NFC. After dip-coating filter papers in PHB-SP/NFC suspensions and sizing with a carnauba wax solution, static water contact angles of 112°–152° were obtained. The intrinsic properties of the particles were analyzed by scanning electron microscopy, thermal analysis and infrared spectroscopy, indicating higher crystallinity for PHB-SP than PHB-MP. The chemical interactions between the more amorphous PHB-MP particles and paper fibers were identified as an esterification reaction, while the morphology of the NFC fibrillar network was playing a key role as the binding agent in the retention of more crystalline PHB-SP at the paper surface, hence contributing to higher hydrophobicity.
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Affiliation(s)
- Vibhore Kumar Rastogi
- Freiburg Institute for Advanced Studies (FRIAS), Chair for Bio-Based Materials Engineering, Faculty for Environment and Natural Resources, University of Freiburg, Werthmannstrasse 6, 79085 Freiburg, Germany.
| | - Pieter Samyn
- Freiburg Institute for Advanced Studies (FRIAS), Chair for Bio-Based Materials Engineering, Faculty for Environment and Natural Resources, University of Freiburg, Werthmannstrasse 6, 79085 Freiburg, Germany.
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Peprah BA, Ramsay JA, Ramsay BA. Dense stable suspensions of medium-chain-length poly(3-hydroxyalkanoate) nanoparticles. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bresan S, Sznajder A, Hauf W, Forchhammer K, Pfeiffer D, Jendrossek D. Polyhydroxyalkanoate (PHA) Granules Have no Phospholipids. Sci Rep 2016; 6:26612. [PMID: 27222167 PMCID: PMC4879537 DOI: 10.1038/srep26612] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/05/2016] [Indexed: 12/11/2022] Open
Abstract
Polyhydroxybutyrate (PHB) granules, also designated as carbonosomes, are supra-molecular complexes in prokaryotes consisting of a PHB polymer core and a surface layer of structural and functional proteins. The presence of suspected phospholipids in the surface layer is based on in vitro data of isolated PHB granules and is often shown in cartoons of the PHB granule structure in reviews on PHB metabolism. However, the in vivo presence of a phospholipid layer has never been demonstrated. We addressed this topic by the expression of fusion proteins of DsRed2EC and other fluorescent proteins with the phospholipid-binding domain (LactC2) of lactadherin in three model organisms. The fusion proteins specifically localized at the cell membrane of Ralstonia eutropha but did not co-localize with PHB granules. The same result was obtained for Pseudomonas putida, a species that accumulates another type of polyhydroxyalkanoate (PHA) granules related to PHB. Notably, DsRed2EC-LactC2 expressed in Magnetospirillum gryphiswaldense was detected at the position of membrane-enclosed magnetosome chains and at the cytoplasmic membrane but not at PHB granules. In conclusion, the carbonosomes of representatives of α-proteobacteria, β-proteobacteria and γ-proteobacteria have no phospholipids in vivo and we postulate that the PHB/PHA granule surface layers in natural producers generally are free of phospholipids and consist of proteins only.
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Affiliation(s)
| | - Anna Sznajder
- Institute of Microbiology, University Stuttgart, Germany
| | - Waldemar Hauf
- Department of Organismic Interactions, Eberhard Karls Universität Tübingen, Germany
| | - Karl Forchhammer
- Department of Organismic Interactions, Eberhard Karls Universität Tübingen, Germany
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Application of a non-halogenated solvent, methyl ethyl ketone (MEK) for recovery of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(HB-co-HV)] from bacterial cells. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0546-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Kwiecień I, Bałakier T, Jurczak J, Kowalczuk M, Adamus G. Molecular architecture of novel potentially bioactive (co)oligoesters containing pesticide moieties established by electrospray ionization multistage mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:533-544. [PMID: 26160419 DOI: 10.1002/rcm.7133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/17/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Pesticides are commonly used in agriculture to ensure high crop yield; however, because of their low resistance to environmental conditions, a large amount of pesticides does not reach target pests and becomes an environmental pollutant. One of the ways to reduce these drawbacks is synthesis of polymeric systems, which allows for controlled release of pesticides for a prolonged period of time. Herein we report the synthesis and characterization of novel potentially bioactive (co)oligoesters with bioactive moieties (selected from pesticides) which are covalently linked along an oligoester backbone. METHODS The delivery systems of pesticides were prepared via anionic ring-opening polymerization of β-substituted β-lactones containing bioactive moieties as a pendant group selected from pesticides and their copolymerization with β-butyrolactone in the presence of carboxylates as initiators. Electrospray ionization multistage mass spectrometry (ESI-MS(n)) supported by (1)H NMR were applied in order to establish the structure, at a molecular level, of the new biodegradable oligomeric release system of selected pesticides. RESULTS Based on ESI-MS(n) analyses, the structures of the resulting (co)oligoesters were established at the molecular level. The ESI-MS/MS allowed to confirm the structures of end groups and to determine the composition of individual (co)oligoester molecules which contained one, two or three bioactive molecules per (co)oligomer. Additionally, it was shown that fragmentation of selected ions of potentially bioactive (co)oligoesters proceeded via random breakage of ester bonds along the oligomer chain and ester bonds of the bioactive pendant group. CONCLUSIONS An analytical method for detailed structural characterization at the molecular level of potentially bioactive (co)oligoesters has been developed. These results are important in the analysis of designed biodegradable polymeric controlled-release systems of pesticides with potential agricultural applications.
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Affiliation(s)
- Iwona Kwiecień
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 41-819, Zabrze, Poland
| | - Tomasz Bałakier
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland
| | - Janusz Jurczak
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland
| | - Marek Kowalczuk
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 41-819, Zabrze, Poland
- School of Biology, Chemistry and Forensic Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, WV1 1SB, UK
| | - Grażyna Adamus
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, 41-819, Zabrze, Poland
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Rho JK, Choi MH, Gutierrez M, Tian B, Yoo T, Baek JE, Shah M, Yoon SC. Amorphous poly(3-hydroxybutyrate) nanoparticles prepared with recombinant phasins and PHB depolymerase. J Appl Polym Sci 2014. [DOI: 10.1002/app.41074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jong Kook Rho
- Radiation Research Division for Biotechnology; Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute; 29 Geumgu-gil Jeongeup Jeonbuk 580-185 Republic of Korea
| | - Mun Hwan Choi
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
| | - Merced Gutierrez
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
| | - Baoxia Tian
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
| | - Taesik Yoo
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
| | - Jung Eun Baek
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
| | - Mohsin Shah
- Department of Biochemistry; Institute of Basic Medical Sciences, Khyber Medical University; Peshawar Pakistan
| | - Sung Chul Yoon
- Nano-Biomaterials Science Laboratory; Division of Applied Life Sciences; Graduate School, Gyeongsang National University; Jinju 660-701 Republic of Korea
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Laycock B, Halley P, Pratt S, Werker A, Lant P. The chemomechanical properties of microbial polyhydroxyalkanoates. Prog Polym Sci 2014. [DOI: 10.1016/j.progpolymsci.2013.06.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rodríguez-Contreras A, Canal C, Calafell-Monfort M, Ginebra MP, Julio-Moran G, Marqués-Calvo MS. Methods for the preparation of doxycycline-loaded phb micro- and nano-spheres. Eur Polym J 2013. [DOI: 10.1016/j.eurpolymj.2013.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Laycock B, Halley P, Pratt S, Werker A, Lant P. The chemomechanical properties of microbial polyhydroxyalkanoates. Prog Polym Sci 2013. [DOI: 10.1016/j.progpolymsci.2012.06.003] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sun X, Chen Z, Wang F, Yan S, Takahashi I. Influence of Poly(vinylphenol) Sublayer on the Crystallization Behavior of Poly(3-hydroxybutyrate) Thin Films. Macromolecules 2013. [DOI: 10.1021/ma302349a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoli Sun
- State Key Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen Chen
- State Key Laboratory of Polymer
Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China
| | - Feng Wang
- State Key Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shouke Yan
- State Key Laboratory of Chemical
Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Isao Takahashi
- School of Science and Technology, Kwansei Gakuin University, Sanda 669-1337, Japan
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Alejandra RC, Margarita CM, María Soledad MC. Enzymatic degradation of poly(3-hydroxybutyrate) by a commercial lipase. Polym Degrad Stab 2012. [DOI: 10.1016/j.polymdegradstab.2012.07.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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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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Cho M, Brigham CJ, Sinskey AJ, Stubbe J. Purification of polyhydroxybutyrate synthase from its native organism, Ralstonia eutropha: implications for the initiation and elongation of polymer formation in vivo. Biochemistry 2012; 51:2276-88. [PMID: 22369488 DOI: 10.1021/bi2013596] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class I polyhydroxybutyrate (PHB) synthase (PhaC) from Ralstonia eutropha catalyzes the formation of PHB from (R)-3-hydroxybutyryl-CoA, ultimately resulting in the formation of insoluble granules. Previous mechanistic studies of R. eutropha PhaC, purified from Escherichia coli (PhaC(Ec)), demonstrated that the polymer elongation rate is much faster than the initiation rate. In an effort to identify a factor(s) from the native organism that might prime the synthase and increase the rate of polymer initiation, an N-terminally Strep2-tagged phaC (Strep2-PhaC(Re)) was constructed and integrated into the R. eutropha genome in place of wild-type phaC. Strep2-PhaC(Re) was expressed and purified by affinity chromatography from R. eutropha grown in nutrient-rich TSB medium for 4 h (peak production PHB, 15% cell dry weight) and 24 h (PHB, 2% cell dry weight). Analysis of the purified PhaC by size exclusion chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and gel permeation chromatography revealed that it unexpectedly copurified with the phasin protein, PhaP1, and with soluble PHB (M(w) = 350 kDa) in a "high-molecular weight" (HMW) complex and in monomeric/dimeric (M/D) forms with no associated PhaP1 or PHB. Assays for monitoring the formation of PHB in the HMW complex showed no lag phase in CoA release, in contrast to M/D forms of PhaC(Re) (and PhaC(Ec)), suggesting that PhaC in the HMW fraction has been isolated in a PHB-primed form. The presence of primed and nonprimed PhaC suggests that the elongation rate for PHB formation is also faster than the initiation rate in vivo. A modified micelle model for granule genesis is proposed to accommodate the reported observations.
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Affiliation(s)
- Mimi Cho
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Growth and localization of polyhydroxybutyrate granules in Ralstonia eutropha. J Bacteriol 2011; 194:1092-9. [PMID: 22178974 DOI: 10.1128/jb.06125-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The bacterium Ralstonia eutropha forms cytoplasmic granules of polyhydroxybutyrate that are a source of biodegradable thermoplastic. While much is known about the biochemistry of polyhydroxybutyrate production, the cell biology of granule formation and growth remains unclear. Previous studies have suggested that granules form either in the inner membrane, on a central scaffold, or in the cytoplasm. Here we used electron cryotomography to monitor granule genesis and development in 3 dimensions (3-D) in a near-native, "frozen-hydrated" state in intact Ralstonia eutropha cells. Neither nascent granules within the cell membrane nor scaffolds were seen. Instead, granules of all sizes resided toward the center of the cytoplasm along the length of the cell and exhibited a discontinuous surface layer more consistent with a partial protein coating than either a lipid mono- or bilayer. Putatively fusing granules were also seen, suggesting that small granules are continually generated and then grow and merge. Together, these observations support a model of biogenesis wherein granules form in the cytoplasm coated not by phospholipid but by protein. Previous thin-section electron microscopy (EM), fluorescence microscopy, and atomic force microscopy (AFM) results to the contrary may reflect both differences in nucleoid condensation and specimen preparation-induced artifacts.
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Monitoring the in situ crystallization of native biopolyester granules in Ralstonia eutropha via infrared spectroscopy. J Microbiol Methods 2011; 87:49-55. [DOI: 10.1016/j.mimet.2011.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 06/28/2011] [Accepted: 07/06/2011] [Indexed: 11/21/2022]
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Li J, Shang G, You M, Peng S, Wang Z, Wu H, Chen GQ. Endotoxin removing method based on lipopolysaccharide binding protein and polyhydroxyalkanoate binding protein PhaP. Biomacromolecules 2011; 12:602-8. [PMID: 21261300 DOI: 10.1021/bm101230n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyhydroxyalkanoates (PHAs) granule associated protein PhaP has a strong affinity to PHA and other hydrophobic polymers. Human lipopolysaccharide binding protein (hLBP) is a natural endotoxin receptor in plasma. In this study, genes encoding hLBP fused with PhaP were expressed in Pichia pastoris GS115 for production of the fusion protein. The purified rhLBP-PhaP fusion protein was immobilized on particles of polyhydroxybutyrate (PHB), which is a member of microbial polyhydroxyalkanoates (PHA). The rhLBP-PhaP-coated PHB particles were added to endotoxin containing water and protein solutions to study their endotoxin removal and protein recovery efficiencies. The influences of ionic strengths and pH on endotoxin removal and protein recovery in different protein solutions were also studied using acidic proteins including bovine serum albumin (BSA), ovalbumin, and basic protein α-chymotrypsinogen as model proteins. The results showed that rhLBP-PhaP particles could remove endotoxin with an efficiency of over 90%. All endotoxin removal and protein recovery efficiencies were only slightly affected by ionic strengths but were drastically affected by pH changes. Our results demonstrated that rhLBP-PhaP particles with their high efficiency, ease of preparation, and nontoxicity will be a suitable system for endotoxin removal in the protein purification industry.
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Affiliation(s)
- Jian Li
- Multidisciplinary Research Center, Shantou University, Shantou 515063, Guangdong, China
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38
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Bourbonnais R, Marchessault RH. Application of Polyhydroxyalkanoate Granules for Sizing of Paper. Biomacromolecules 2010; 11:989-93. [DOI: 10.1021/bm9014667] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Bourbonnais
- Department of Chemistry, McGill University, 3420 University Street, Montreal, QC, H3A2A7 Canada
| | - Robert H. Marchessault
- Department of Chemistry, McGill University, 3420 University Street, Montreal, QC, H3A2A7 Canada
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39
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Song SJ, Park YJ, Park J, Cho MD, Kim JH, Jeong MH, Kim YS, Cho DL. Preparation of a drug-eluting stent using a TiO2 film deposited by plasma enhanced chemical vapour deposition as a drug-combining matrix. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b925409a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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40
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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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41
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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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42
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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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43
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Wang Z, Wu H, Chen J, Zhang J, Yao Y, Chen GQ. A novel self-cleaving phasin tag for purification of recombinant proteins based on hydrophobic polyhydroxyalkanoate nanoparticles. LAB ON A CHIP 2008; 8:1957-1962. [PMID: 18941699 DOI: 10.1039/b807762b] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A novel protein purification method was developed using microbial polyhydroxyalkanoates (PHA) granule-associated protein phasin, a pH-inducible self-cleaving intein and PHA nanoparticles. Genes for the target proteins to be produced and purified were fused to genes of intein and phasin, the genes were jointly over-expressed in vivo, such as in E. coli cells in this study. The fused proteins containing target protein, intein and phasin produced by the recombinant E. coli were released together with all other E. coli proteins via a bacterial lysis process. They were then adsorbed in vitro to the surfaces of the hydrophobic polymer nanoparticles incubated with the cell lysates. The nanoparticles attached with the fused proteins were concentrated via centrifugation. Then, the reasonably purified target protein was released by self-cleavage of intein and separated with nanoparticles by a simple centrifugation process. Using this system, enhanced green fluorescent protein (EGFP), maltose binding protein (MBP) and beta-galactosidase were successfully purified in their active forms with reasonable yields, respectively, demonstrating the effectiveness and reliability of this purification system. This method allows the production and purification of high value added proteins in a continuous way with low cost.
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Affiliation(s)
- Zhihui Wang
- Multidisciplinary Research Center, Shantou University, Shantou 515063, Guangdong, China
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44
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Orts WJ, Nobes GA, Kawada J, Nguyen S, Yu GE, Ravenelle F. Poly(hydroxyalkanoates): Biorefinery polymers with a whole range of applications. The work of Robert H. Marchessault. CAN J CHEM 2008. [DOI: 10.1139/v08-050] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review describes the characterization and application of poly(hydroxyalkanoates), PHAs, a remarkable family of natural polyesters with a wide array of useful properties and potential applications. It places specific emphasis on the work of Robert H. Marchessault and his many colleagues outlining how Marchessault’s body of work both shaped the field and complemented the work of his contemporaries. Particular attention will focus on the “rediscovery” of poly(β-hydroxybutyrate), PHB, the first PHA to be discovered, from the late 1950s onward, highlighting some of the historical aspects of PHA’s path toward commercial applications. It will also cover why this class of materials is so unique, including PHA structure–properties relationships, its unique crystalline behaviour, in vivo – in vitro synthesis and degradation, and PHA-graft-copolymers.Key words: poly(hydroxyalkanoate), PHA, poly(β-hydroxybutyrate), PHB, biopolymers, bacterial polyester, random copolymers, polymer single crystals, graft copolymers.
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45
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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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46
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de Eugenio LI, Garci A P, Luengo JM, Sanz JSM, Roma N JS, Garci A JL, Prieto MAA. Biochemical Evidence That phaZ Gene Encodes a Specific Intracellular Medium Chain Length Polyhydroxyalkanoate Depolymerase in Pseudomonas putida KT2442. J Biol Chem 2007; 282:4951-4962. [PMID: 17170116 DOI: 10.1074/jbc.m608119200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) can be catabolized by many microorganisms using intra- or extracellular PHA depolymerases. Most of our current knowledge of these intracellular enzyme-coding genes comes from the analysis of short chain length PHA depolymerases, whereas medium chain length PHA (mcl-PHA) intracellular depolymerization systems still remained to be characterized. The phaZ gene of some Pseudomonas putida strains has been identified only by mutagenesis and complementation techniques as putative intracellular mcl-PHA depolymerase. However, none of their corresponding encoded PhaZ enzymes have been characterized in depth. In this study the PhaZ depolymerase from P. putida KT2442 has been purified and biochemically characterized after its overexpression in Escherichia coli. To facilitate these studies we have developed a new and very sensitive radioactive method for detecting PHA hydrolysis in vitro. We have demonstrated that PhaZ is an intracellular depolymerase that is located in PHA granules and that hydrolyzes specifically mcl-PHAs containing aliphatic and aromatic monomers. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. We have modeled the three-dimensional structure of PhaZ complexed with a 3-hydroxyoctanoate dimer. Using this model, we found that the enzyme appears to be built up from a corealpha/beta hydrolase-type domain capped with a lid structure with an active site containing a catalytic triad buried near the connection between domains. All these data constitute the first biochemical characterization of PhaZ and allow us to propose this enzyme as the paradigmatic representative of intracellular endo/exo-mcl-PHA depolymerases.
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Affiliation(s)
- Laura I de Eugenio
- Departamento de Microbiologi´a Molecular, Centro de Investigaciones Biolo´gicas, Consejo Superior de Investigaciones Cienti´ficas (CSIC), C. Ramiro de Maeztu, 9, 28040 Madrid
| | - Pedro Garci A
- Departamento de Microbiologi´a Molecular, Centro de Investigaciones Biolo´gicas, Consejo Superior de Investigaciones Cienti´ficas (CSIC), C. Ramiro de Maeztu, 9, 28040 Madrid
| | - José M Luengo
- Departamento de Bioqui´mica y Biologi´a Molecular, Universidad de Leo´n, 24007 Leo´n
| | - Jesu S M Sanz
- Instituto de Biologi´a Molecular y Celular, Universidad Miguel Herna´ndez, Av. Universidad, s/n. 03202 Elche (Alicante), and the
| | - Julio San Roma N
- Instituto de Ciencia y Tecnologi´a de Poli´meros, CSIC, C. Juan de la Cierva 3, 28006 Madrid, Spain
| | - José Luis Garci A
- Departamento de Microbiologi´a Molecular, Centro de Investigaciones Biolo´gicas, Consejo Superior de Investigaciones Cienti´ficas (CSIC), C. Ramiro de Maeztu, 9, 28040 Madrid
| | - Mari A A Prieto
- Departamento de Microbiologi´a Molecular, Centro de Investigaciones Biolo´gicas, Consejo Superior de Investigaciones Cienti´ficas (CSIC), C. Ramiro de Maeztu, 9, 28040 Madrid.
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47
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Gebauer B, Jendrossek D. Assay of poly(3-hydroxybutyrate) depolymerase activity and product determination. Appl Environ Microbiol 2006; 72:6094-100. [PMID: 16957234 PMCID: PMC1563597 DOI: 10.1128/aem.01184-06] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two methods for accurate poly(3-hydroxybutyrate) (PHB) depolymerase activity determination and quantitative and qualitative hydrolysis product determination are described. The first method is based on online determination of NaOH consumption rates necessary to neutralize 3-hydroxybutyric acid (3HB) and/or 3HB oligomers produced during the hydrolysis reaction and requires a pH-stat apparatus equipped with a software-controlled microliter pump for rapid and accurate titration. The method is universally suitable for hydrolysis of any type of polyhydroxyalkanoate or other molecules with hydrolyzable ester bonds, allows the determination of hydrolysis rates of as low as 1 nmol/min, and has a dynamic capacity of at least 6 orders of magnitude. By applying this method, specific hydrolysis rates of native PHB granules isolated from Ralstonia eutropha H16 were determined for the first time. The second method was developed for hydrolysis product identification and is based on the derivatization of 3HB oligomers into bromophenacyl derivates and separation by high-performance liquid chromatography. The method allows the separation and quantification of 3HB and 3HB oligomers up to the octamer. The two methods were applied to investigate the hydrolysis of different types of PHB by selected PHB depolymerases.
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Affiliation(s)
- Birgit Gebauer
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
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48
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Abe T, Kobayashi T, Saito T. Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16. J Bacteriol 2005; 187:6982-90. [PMID: 16199568 PMCID: PMC1251622 DOI: 10.1128/jb.187.20.6982-6990.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase (PhaZd) of Wautersia eutropha (formerly Ralstonia eutropha) H16 which shows similarity with the catalytic domain of the extracellular PHB depolymerase in Ralstonia pickettii T1 was identified. The positions of the catalytic triad (Ser190-Asp266-His330) and oxyanion hole (His108) in the amino acid sequence of PhaZd deduced from the nucleotide sequence roughly accorded with those of the extracellular PHB depolymerase of R. pickettii T1, but a signal peptide, a linker domain, and a substrate binding domain were missing. The PhaZd gene was cloned and the gene product was purified from Escherichia coli. The specific activity of PhaZd toward artificial amorphous PHB granules was significantly greater than that of other known intracellular PHB depolymerase or 3-hydroxybutyrate (3HB) oligomer hydrolases of W. eutropha H16. The enzyme degraded artificial amorphous PHB granules and mainly released various 3-hydroxybutyrate oligomers. PhaZd distributed nearly equally between PHB inclusion bodies and the cytosolic fraction. The amount of PHB was greater in phaZd deletion mutant cells than the wild-type cells under various culture conditions. These results indicate that PhaZd is a novel intracellular PHB depolymerase which participates in the mobilization of PHB in W. eutropha H16 along with other PHB depolymerases.
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Affiliation(s)
- Tomoko Abe
- Laboratory of Molecular Microbiology, Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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49
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Kobayashi T, Uchino K, Abe T, Yamazaki Y, Saito T. Novel intracellular 3-hydroxybutyrate-oligomer hydrolase in Wautersia eutropha H16. J Bacteriol 2005; 187:5129-35. [PMID: 16030206 PMCID: PMC1196019 DOI: 10.1128/jb.187.15.5129-5135.2005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wautersia eutropha H16 (formerly Ralstonia eutropha) mobilizes intracellularly accumulated poly(3-hydroxybutyrate) (PHB) with intracellular poly(3-hydroxybutyrate) depolymerases. In this study, a novel intracellular 3-hydroxybutyrate-oligomer hydrolase (PhaZc) gene was cloned and overexpressed in Escherichia coli. Then PhaZc was purified and characterized. Immunoblot analysis with polyclonal antiserum against PhaZc revealed that most PhaZc is present in the cytosolic fraction and a small amount is present in the poly(3-hydroxybutyrate) inclusion bodies of W. eutropha. PhaZc degraded various 3-hydroxybutyrate oligomers at a high specific activity and artificial amorphous poly(3-hydroxybutyrate) at a lower specific activity. Native PHB granules and semicrystalline PHB were not degraded by PhaZc. A PhaZ deletion mutation enhanced the deposition of PHB in the logarithmic phase in nutrient-rich medium. PhaZc differs from the hydrolases of W. eutropha previously reported and is a novel type of intracellular 3-hydroxybutyrate-oligomer hydrolase, and it participates in the mobilization of PHB along with other hydrolases.
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Affiliation(s)
- Teruyuki Kobayashi
- Laboratory of Molecular Microbiology, Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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50
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Stubbe J, Tian J, He A, Sinskey AJ, Lawrence AG, Liu P. NONTEMPLATE-DEPENDENT POLYMERIZATION PROCESSES: Polyhydroxyalkanoate Synthases as a Paradigm. Annu Rev Biochem 2005; 74:433-80. [PMID: 15952894 DOI: 10.1146/annurev.biochem.74.082803.133013] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review focuses on nontemplate-dependent polymerases that use water-soluble substrates and convert them into water-insoluble polymers that form granules or inclusions within the cell. The initial part of the review summarizes briefly the current knowledge of polymer formation catalyzed by starch and glycogen synthases, polyphosphate kinase (a polymerase), cyanophycin synthetases, and rubber synthases. Specifically, our current understanding of their mechanisms of initiation, elongation (including granule formation), termination, remodeling, and polymer reutilization will be presented. General underlying principles that govern these types of polymerization reactions will be enumerated as a paradigm for all nontemplate-dependent polymerizations. The bulk of the review then focuses on polyhydroxyalkanoate (PHA) synthases that generate polyoxoesters. These enzymes are of interest as they generate biodegradable polymers. Our current knowledge of PHA production and utilization in vitro and in vivo as well as the contribution of many proteins to these processes will be reviewed.
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Affiliation(s)
- Joanne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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