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Chen J, Cui Y, Zhang S, Wu B, Han J, Xiang H. Unveiling the repressive mechanism of a PPS-like regulator (PspR) in polyhydroxyalkanoates biosynthesis network. Appl Microbiol Biotechnol 2024; 108:265. [PMID: 38498113 PMCID: PMC10948481 DOI: 10.1007/s00253-024-13100-x] [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: 12/04/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024]
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a type of polyhydroxyalkanoates (PHA) that exhibits numerous outstanding properties and is naturally synthesized and elaborately regulated in various microorganisms. However, the regulatory mechanism involving the specific regulator PhaR in Haloferax mediterranei, a major PHBV production model among Haloarchaea, is not well understood. In our previous study, we showed that deletion of the phosphoenolpyruvate (PEP) synthetase-like (pps-like) gene activates the cryptic phaC genes in H. mediterranei, resulting in enhanced PHBV accumulation. In this study, we demonstrated the specific function of the PPS-like protein as a negative regulator of phaR gene expression and PHBV synthesis. Chromatin immunoprecipitation (ChIP), in situ fluorescence reporting system, and in vitro electrophoretic mobility shift assay (EMSA) showed that the PPS-like protein can bind to the promoter region of phaRP. Computational modeling revealed a high structural similarity between the rifampin phosphotransferase (RPH) protein and the PPS-like protein, which has a conserved ATP-binding domain, a His domain, and a predicted DNA-binding domain. Key residues within this unique DNA-binding domain were subsequently validated through point mutation and functional evaluations. Based on these findings, we concluded that PPS-like protein, which we now renamed as PspR, has evolved into a repressor capable of regulating the key regulator PhaR, and thereby modulating PHBV synthesis. This regulatory network (PspR-PhaR) for PHA biosynthesis is likely widespread among haloarchaea, providing a novel approach to manipulate haloarchaea as a production platform for high-yielding PHA. KEY POINTS: • The repressive mechanism of a novel inhibitor PspR in the PHBV biosynthesis was demonstrated • PspR is widespread among the PHA accumulating haloarchaea • It is the first report of functional conversion from an enzyme to a trans-acting regulator in haloarchaea.
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Affiliation(s)
- Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yinglu Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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Quelas JI, Cabrera JJ, Díaz-Peña R, Sánchez-Schneider L, Jiménez-Leiva A, Tortosa G, Delgado MJ, Pettinari MJ, Lodeiro AR, del Val C, Mesa S. Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism. Int J Mol Sci 2024; 25:2157. [PMID: 38396833 PMCID: PMC10888616 DOI: 10.3390/ijms25042157] [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: 12/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this bacterium. To deeply uncover the function of PhaR, we applied a multipronged approach, including the expression profile of a phaR mutant at the transcriptional and protein levels under microaerobic conditions, and the identification of direct targets and of proteins associated with PHA granules. Our results confirmed a pleiotropic function of PhaR, affecting several phenotypes, in addition to PHA cycle control. These include growth deficiency, regulation of carbon and nitrogen allocation, and bacterial motility. Interestingly, PhaR may also modulate the microoxic-responsive regulatory network by activating the expression of fixK2 and repressing nifA, both encoding two transcription factors relevant for microaerobic regulation. At the molecular level, two PhaR-binding motifs were predicted and direct control mediated by PhaR determined by protein-interaction assays revealed seven new direct targets for PhaR. Finally, among the proteins associated with PHA granules, we found PhaR, phasins, and other proteins, confirming a dual function of PhaR in microoxia.
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Affiliation(s)
- Juan I. Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- YPF Tecnología S.A. (Y-TEC), Avenida. del Petróleo Argentino s/n (1923), Berisso 1923, Argentina
| | - Juan J. Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Rocío Díaz-Peña
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Lucía Sánchez-Schneider
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - María J. Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - M. Julia Pettinari
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Aníbal R. Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- Cátedra de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Coral del Val
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
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3
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Sander K, Abel AJ, Friedline S, Sharpless W, Skerker J, Deutschbauer A, Clark DS, Arkin AP. Eliminating genes for a two-component system increases PHB productivity in Cupriavidus basilensis 4G11 under PHB suppressing, nonstress conditions. Biotechnol Bioeng 2024; 121:139-156. [PMID: 37638652 DOI: 10.1002/bit.28532] [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: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
Species of bacteria from the genus Cupriavidus are known, in part, for their ability to produce high amounts of poly-hydroxybutyrate (PHB) making them attractive candidates for bioplastic production. The native synthesis of PHB occurs during periods of metabolic stress, and the process regulating the initiation of PHB accumulation in these organisms is not fully understood. Screening an RB-TnSeq transposon library of Cupriavidus basilensis 4G11 allowed us to identify two genes of an apparent, uncharacterized two-component system, which when omitted from the genome enable increased PHB productivity in balanced, nonstress growth conditions. We observe average increases in PHB productivity of 56% and 41% relative to the wildtype parent strain upon deleting each gene individually from the genome. The increased PHB phenotype disappears, however, in nitrogen-free unbalanced growth conditions suggesting the phenotype is specific to fast-growing, replete, nonstress growth. Bioproduction modeling suggests this phenotype could be due to a decreased reliance on metabolic stress induced by nitrogen limitation to initiate PHB production in the mutant strains. Due to uncertainty in the two-component system's input signal and regulon, the mechanism by which these genes impart this phenotype remains unclear. Such strains may allow for the use of single-stage, continuous bioreactor systems, which are far simpler than many PHB bioproduction schemes used previously, given a similar product yield to batch systems in such a configuration. Bioproductivity modeling suggests that omitting this regulation in the cells may increase PHB productivity up to 24% relative to the wildtype organism when using single-stage continuous systems. This work expands our understanding of the regulation of PHB accumulation in Cupriavidus, in particular the initiation of this process upon transition into unbalanced growth regimes.
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Affiliation(s)
- Kyle Sander
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Anthony J Abel
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Skyler Friedline
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - William Sharpless
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
| | - Jeffrey Skerker
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Douglas S Clark
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Adam P Arkin
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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4
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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: 0] [Impact Index Per Article: 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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5
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Aghaali Z, Naghavi MR. Biotechnological Approaches for Enhancing Polyhydroxyalkanoates (PHAs) Production: Current and Future Perspectives. Curr Microbiol 2023; 80:345. [PMID: 37731015 DOI: 10.1007/s00284-023-03452-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/19/2023] [Indexed: 09/22/2023]
Abstract
The benefits of biotechnology are not limited to genetic engineering, but it also displays its great impact on industrial uses of crops (e.g., biodegradable plastics). Polyhydroxyalkanoates (PHAs) make a diverse class of bio-based and biodegradable polymers naturally synthesized by numerous microorganisms. However, several C3 and C4 plants have also been genetically engineered to produce PHAs. The highest production yield of PHAs was obtained with a well-known C3 plant, Arabidopsis thaliana, upto 40% of the dry weight of the leaf. This review summarizes all biotechnological mechanisms that have been adopted with the goal of increasing PHAs production in bacteria and plant species alike. Moreover, the possibility of using some methods that have not been applied in bioplastic science are discussed with special attention to plants. These include producing PHAs in transgenic hairy roots and cell suspension cultures, making transformed bacteria and plants via transposons, constructing an engineered metabolon, and overexpressing of phaP and the ABC operon concurrently. Taken together, that biotechnology will be highly beneficial for reducing plastic pollution through the implementation of biotechnological strategies is taken for granted.
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Affiliation(s)
- Zahra Aghaali
- Department of Genetic and Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Reza Naghavi
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj, Iran.
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6
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Dong H, Yang X, Shi J, Xiao C, Zhang Y. Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges. Polymers (Basel) 2023; 15:polym15102333. [PMID: 37242908 DOI: 10.3390/polym15102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.
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Affiliation(s)
- Huaming Dong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chunqiao Xiao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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7
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Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes. Appl Environ Microbiol 2023; 89:e0142822. [PMID: 36541797 PMCID: PMC9888253 DOI: 10.1128/aem.01428-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The number of genes encoding β-oxidation enzymes in Cupriavidus necator H16 (synonym, Ralstonia eutropha H16) is high, but only the operons A0459-A0464 and A1526-A1531, each encoding four genes for β-oxidation enzymes, were expressed during growth with long-chain-length fatty acids (LCFAs). However, we observed that C. necator ΔA0459-A0464 ΔA1526-A1531 and C. necator H16 showed the same growth behavior during growth with decanoic acid and shorter FAs. The negative effect of the deletion of these two operons increased with an increasing chain length of the utilized FAs. Transcriptome sequencing (RNA-Seq) revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16. Operon A0459-A0464 was expressed only during growth with nonanoic acid, whereas operon A1526-A1531 was highly expressed during growth with octanoic and nonanoic acid. The gene clusters B1187-B1192 and B0751-B0759 showed a log2 fold change in expression of up to 4.29 and 4.02, respectively, during growth with octanoic acid and up to 8.82 and 5.50, respectively, with nonanoic acid compared to sodium gluconate-grown cells. Several acyl-CoA ligases catalyze the activation of MCFAs with coenzyme A (CoA), but fadD3 (A3288), involved in activation of LCFAs, was not detected. The expression profiles of C. necator strain ΔA0459-A0464 ΔA1526-A1531 showed that the growth with nonanoic acid resulted in the expression of further β-oxidation enzyme-encoding genes. Additional insights into the transport of FAs in C. necator H16 revealed the complexity and putative involvement of the DegV-like protein encoded by A0463 in the transport of odd-chain-length FAs and of siderophore biosynthesis in the transport mechanism. IMPORTANCE Although Cupriavidus necator H16 has been used in several studies to produce polyhydroxyalkanoates from various lipids, the fatty acid metabolism is poorly understood. The β-oxidation of long-chain-length FAs has been investigated, but the tremendous number of homologous genes encoding β-oxidation enzymes hides the potential for variances in the expressed genes for catabolism of shorter FAs. The catabolism of medium-chain-length FAs and connected pathways has not been investigated yet. As more sustainable substrates such as lipids and the production of fatty acids and fatty acid derivates become more critical with the dependency on fossil-based substances, understanding the complex metabolism in this highly diverse workhorse for biotechnology, C. necator, is inevitable. For further metabolic engineering and construction of production strains, we investigated the metabolism during growth on medium-chain-length FAs by RNA-Seq.
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Schäfer L, Mikowsky N, Meinert-Berning C, Steinbüchel A. Unveiling steps of the TDP degradation pathway in Variovorax paradoxus TBEA6. Enzyme Microb Technol 2022; 160:110095. [PMID: 35810625 DOI: 10.1016/j.enzmictec.2022.110095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Since the role of biobased plastics increases every year, the search for alternatives to petrol-based polymers is very important. Variovorax paradoxus TBEA6 is able to grow with 3,3'-thiodipropionic acid (TDP) as sole source for carbon and energy. TDP can be used as a precursor substrate for the synthesis of polythioesters (PTE). To increase the feasibility of PTE synthesis, a good understanding of the degradation pathway of TDP in V. paradoxus TBEA6 is essential. Therefore, two putative 3-hydroxyisobutyryl-CoA hydrolases (VPARA_03110 & VPARA_05510) and two putative 3-hydroxypropionate dehydrogenases (VPARA_41140 & VPARA_54550) were investigated in this study. The deletion mutant V. paradoxus ∆VPARA_05510 showed a TDP-negative phenotype during growth experiments. The ability to grow with TDP as sole carbon source was successfully restored by complementation. Supernatant analysis revealed that the deletion mutant did not metabolize TDP or 3MP anymore. A specific enzyme activity up to 0.032 U/mg for the purified 3-hydroxyisobutyryl-CoA hydrolase VPARA_05510 was determined. A shift in the proteins (VPARA_54550) melting temperature of 6 °C with 2000 µM 3HP in comparison to protein without ligand was observed during thermal shift assays with the putative 3-hydroxypropionate dehydrogenase.
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Affiliation(s)
- Lukas Schäfer
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Nadine Mikowsky
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany; Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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Liu X, Li D, Yan X, Zhang Z, Zheng S, Zhang J, Huang W, Wu F, Li F, Chen GQ. Rapid Quantification of Polyhydroxyalkanoates Accumulated in Living Cells Based on Green Fluorescence Protein-Labeled Phasins: The qPHA Method. Biomacromolecules 2022; 23:4153-4166. [PMID: 35786865 DOI: 10.1021/acs.biomac.2c00624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are microbial polyesters that have the potential to replace nonbiodegradable petroplastics. A real-time in situ PHA quantification method has long been awaited to replace the traditional method, which is time- and labor-consuming. Quantification of PHA in living cells was finally developed from fluorescence intensities generated from the green fluorescence protein (GFP) fused with the Halomonas bluephagenesis phasin proteins. Phasins PhaP1 and PhaP2 were used to fuse with GFP, which reflected PHA accumulation with an R-square of over 0.9. Also, a standard correlation was established to calculate PHA contents based on the fluorescence and cell density recorded via a microplate reader with an R-square of over 0.95 when grown on various substrates. The PhaP2-GFP containing H. bluephagenesis was applied successfully to quantify PHA synthesis in a 7.5 L fermenter with high precision. Moreover, the method was found to be feasible in non-natural PHA producers such as Escherichia coli, demonstrating its broad applicability.
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Affiliation(s)
- Xu Liu
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dianjie Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Xu Yan
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zonghao Zhang
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuang Zheng
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingpeng Zhang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Wuzhe Huang
- PhaBuilder Biotech Co., Ltd., Shunyi District, Zhaoquanying, Beijing 101309, China
| | - Fuqing Wu
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangting Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Lab for Industrial Biocatalysis, Department Chemical Engineering, Tsinghua University, Beijing 100084, China
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10
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Strittmatter CS, Eggers J, Biesgen V, Pauels I, Becker F, Steinbüchel A. The reliance of glycerol utilization by Cupriavidus necator on CO 2 fixation and improved glycerol catabolism. Appl Microbiol Biotechnol 2022; 106:2541-2555. [PMID: 35325274 DOI: 10.1007/s00253-022-11842-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022]
Abstract
While crude glycerol is a cheap carbon source for industrial-scale cultivation of microorganisms, its application relies on fast growth and conversion. The biopolymer producing Cupriavidus necator H16 (synonym: Ralstonia eutropha H16) grows poorly on glycerol. The heterologous expression of glycerol facilitator glpF, glycerol kinase glpK, and glycerol dehydrogenase glpD from E. coli accelerated the growth considerably. The naturally occurring glycerol utilization is inhibited by low glycerol kinase activity. A limited heterotrophic growth promotes the dependency on autotrophic growth by carbon dioxide (CO2) fixation and refixation. As mixotrophic growth occurs in the wildtype due to low consumption rates of glycerol, CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle is essential. The deletion of both cbbX copies encoding putative RuBisCO-activases (AAA + ATPase) resulted in a sharp slowdown of growth and glycerol consumption. Activase activity is necessary for functioning carboxylation by RuBisCO. Each of the two copies compensates for the loss of the other, as suggested by observed expression levels. The strong tendency towards autotrophy supports previous investigations of glycerol growth and emphasizes the versatility of the metabolism of C. necator H16. Mixotrophy with glycerol-utilization and CO2 fixation with a high dependence on the CBB is automatically occurring unless transportation and degradation of glycerol are optimized. Parallel engineering of CO2 fixation and glycerol degradation is suggested towards application for value-added production from crude glycerol. KEY POINTS: • Growth on glycerol is highly dependent on efficient carbon fixation via CBB cycle. • CbbX is essential for the efficiency of RuBisCO in C. necator H16. • Expression of glycerol degradation pathway enzymes accelerates glycerol utilization.
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Affiliation(s)
- Carl Simon Strittmatter
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Jessica Eggers
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Vanessa Biesgen
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Inga Pauels
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Florian Becker
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany. .,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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11
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Insights in the Degradation of Medium-Chain Length Dicarboxylic Acids in Cupriavidus necator H16 reveal Differences in β-Oxidation between Dicarboxylic Acids and Fatty Acids. Appl Environ Microbiol 2021; 88:e0187321. [PMID: 34731045 DOI: 10.1128/aem.01873-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many homologous genes encoding β-oxidation enzymes were found in the genome of Cupriavidus necator H16 (synonym: Ralstonia eutropha H16). By proteome analysis, the degradation of adipic acid was investigated and showed differences to the degradation of hexanoic acid. During β-oxidation of adipic acid, activation with coenzyme A (CoA) is catalyzed by the two-subunit acyl-CoA ligase encoded by B0198 and B0199. The operon is completed by B0200 encoding a thiolase catalyzing the cleavage of acetyl-CoA at the end of the β-oxidation cycle. Strain C. necator ΔB0198-B0200 showed improved growth on adipic acid. Potential substitutes are B1239 for B0198-B0199 and A0170 as well as A1445 for B0200. A deletion mutant without all three thiolases showed diminished growth. The deletion of detected acyl-CoA dehydrogenase encoded by B2555 has an altered phenotype grown with sebacic acid but not adipic acid. With hexanoic acid, acyl-CoA dehydrogenase encoded by B0087 was detected on 2D gels. Both enzymes are active with adipoyl-CoA and hexanoyl-CoA as substrates, but specific activity indicates a higher activity of B2555 with adipoyl-CoA. 2D gels, growth experiments and enzyme assays suggest the specific expression of B2555 for the degradation of dicarboxylic acids. In C. necator H16 the degradation of carboxylic acids potentially changes with an increasing chain length. Two operons involved in growth with long-chain fatty acids seem to be replaced during growth on medium-chain carboxylic acids. Only two deletion mutants showed diminished growth. Replacement of deleted genes with one of the numerous homologous is likely. Importance The biotechnologically interesting bacterium Cupriavidus necator H16 was thoroughly investigated. Fifteen years ago, it was sequenced entirely and annotated (Pohlmann et al., 2006). Nevertheless, the degradation of monocarboxylic fatty acids and dicarboxylic acids has not been elucidated completely. C. necator is used to produce value-added products from affordable substrates. One of our investigations ' primary targets is the biotechnological production of organic acids with different and specific chain lengths. The versatile metabolism of carboxylic acids recommends C. necator H16 as a candidate for producing value-added organic products. Therefore, the metabolism of these compounds is of interest, and for different applications in industry, understanding such central metabolic pathways is crucial.
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12
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The over-expression of phasin and regulator genes promoting the synthesis of polyhydroxybutyrate in Cupriavidus necator H16 under non-stress conditions. Appl Environ Microbiol 2021; 88:e0145821. [PMID: 34731058 DOI: 10.1128/aem.01458-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cupriavidus necator H16 is an ideal strain for polyhydroxybutyrate (PHB) production from CO2. Low-oxygen-stress can induce PHB synthesis in C. necator H16 while reducing bacterial growth under chemoautotrophic culture. The optimum growth and PHB synthesis of C. necator H16 cannot be achieved simultaneously, which restricts PHB production. The present study was initiated to address the issue through comparative transcriptome and gene function analysis. Firstly, the comparative transcriptome of C. necator H16 chemoautotrophically cultured under low-oxygen-stress and non-stress conditions was studied. Three types of transcription different genes were discovered: PHB enzymatic synthesis, PHB granulation, and regulators. Under low-oxygen-stress condition, acetoacetyl-CoA reductase gene phaB2, PHB synthase gene phaC2, phasins genes phaP1 and phaP2, regulators genes uspA and rpoN were up-regulated 3.0, 2.5, 1.8, 2.7, 3.5, 1.6 folds, respectively. Secondly, the functions of up-regulated genes and their applications in PHB synthesis were further studied. It was found that the over-expression of phaP1, phaP2, uspA, and rpoN can induce PHB synthesis under non-stress condition, while phaB2 and phaC2 have no significant effect. Under the optimum condition, PHB percentage content in C. necator H16 was respectively increased by 37.2%, 28.4%, 15.8%, and 41.0% with the over-expression of phaP1, phaP2, uspA, and rpoN, and the corresponding PHB production increased by 49.8%, 42.9%, 47.0%, and 77.5% under non-stress chemoautotrophic conditions. Similar promotion by phaP1, phaP2, uspA, and rpoN was observed in heterotrophically cultured C. necator H16. The PHB percentage content and PHB production were respectively increased by 54.4% and 103.1% with the over-expression of rpoN under non-stress heterotrophic conditions. Importance Microbial fixation of CO2 is an effective way to reduce greenhouse gases. Some microbes such as C. necator H16 usually accumulate PHB when they grow under stress. Low-oxygen-stress can induce PHB synthesis when C. necator H16 is autotrophically cultured with CO2, H2, and O2, while under stress, growth is restricted and total PHB yield is reduced. Achieving the optimal bacterial growth and PHB synthesis at the same time is an ideal condition for transforming CO2 into PHB by C. necator H16. The present study was initiated to clarify the molecular basis of low-oxygen-stress promoting PHB accumulation and to realize the optimal PHB production by C. necator H16. Genes up-regulated under non-stress conditions were identified through comparative transcriptome analysis and over-expression of phasin and regulator genes were demonstrated to promote PHB synthesis in C. necator H16.
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13
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Lee HS, Lee HJ, Kim SH, Cho JY, Suh MJ, Ham S, Bhatia SK, Gurav R, Kim YG, Lee EY, Yang YH. Novel phasins from the Arctic Pseudomonas sp. B14-6 enhance the production of polyhydroxybutyrate and increase inhibitor tolerance. Int J Biol Macromol 2021; 190:722-729. [PMID: 34506862 DOI: 10.1016/j.ijbiomac.2021.08.236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/18/2021] [Accepted: 08/31/2021] [Indexed: 01/17/2023]
Abstract
Phasin (PhaP), one of the polyhydroxyalkanoate granule-associated protein, enhances cell growth and polyhydroxybutyrate (PHB) biosynthesis by regulating the number and size of PHB granules. However, few studies have applied phasins to various PHB production conditions. In this study, we identified novel phasin genes from the genomic data of Arctic soil bacterium Pseudomonas sp. B14-6 and determined the role of phaP1Ps under different PHB production conditions. Transmission electron microscopy and gel permeation chromatography revealed small PHB granules with high-molecular weight, while differential scanning calorimetry showed that the extracted PHB films had similar thermal properties. The phasin protein derived from Pseudomonas sp. B14-6 revealed higher PHB production and exhibited higher tolerance to several lignocellulosic biosugar-based inhibitors than the phasin protein of Ralstonia eutropha H16 in a recombinant Escherichia coli strain. The increased tolerance to propionate, temperature, and other inhibitors was attributed to the introduction of phaP1Ps, which increased PHB production from lignocellulosic hydrolysate (2.39-fold) in the phaP1Ps strain. However, a combination of phasin proteins isolated from two different sources did not increase PHB production. These findings suggest that phasin could serve as a powerful means to increase robustness and PHB production in heterologous strains.
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Affiliation(s)
- Hye Soo Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Min Ju Suh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea.
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea.
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14
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Mitra R, Xu T, Chen GQ, Xiang H, Han J. An updated overview on the regulatory circuits of polyhydroxyalkanoates synthesis. Microb Biotechnol 2021; 15:1446-1470. [PMID: 34473895 PMCID: PMC9049629 DOI: 10.1111/1751-7915.13915] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are a promising and sustainable alternative to the petroleum‐based synthetic plastics. Regulation of PHA synthesis is receiving considerable importance as engineering the regulatory factors might help developing strains with improved PHA‐producing abilities. PHA synthesis is dedicatedly regulated by a number of regulatory networks. They tightly control the PHA content, granule size and their distribution in cells. Most PHA‐accumulating microorganisms have multiple regulatory networks that impart a combined effect on PHA metabolism. Among them, several factors ranging from global to specific regulators, have been identified and characterized till now. This review is an attempt to categorically summarize the diverse regulatory circuits that operate in some important PHA‐producing microorganisms. However, in several organisms, the detailed mechanisms involved in the regulation of PHA synthesis is not well‐explored and hence further research is needed. The information presented in this review might help researcher to identify the prevailing research gaps in PHA regulation.
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Affiliation(s)
- Ruchira Mitra
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,International College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Three-dimensional label-free visualization and quantification of polyhydroxyalkanoates in individual bacterial cell in its native state. Proc Natl Acad Sci U S A 2021; 118:2103956118. [PMID: 34312231 DOI: 10.1073/pnas.2103956118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable polyesters that are intracellularly accumulated as distinct insoluble granules by various microorganisms. PHAs have attracted much attention as sustainable substitutes for petroleum-based plastics. However, the formation of PHA granules and their characteristics, such as localization, volume, weight, and density of granules, in an individual live bacterial cell are not well understood. Here, we report the results of three-dimensional (3D) quantitative label-free analysis of PHA granules in individual live bacterial cells through measuring the refractive index distributions by optical diffraction tomography (ODT). The formation and growth of PHA granules in the cells of Cupriavidus necator, the best-studied native PHA producer, and recombinant Escherichia coli harboring C. necator poly(3-hydroxybutyrate) (PHB) biosynthesis pathway are comparatively examined. Through the statistical ODT analyses of the bacterial cells, the distinctive characteristics for density and localization of PHB granules in vivo could be observed. The PHB granules in recombinant E. coli show higher density and localization polarity compared with those of C. necator, indicating that polymer chains are more densely packed and granules tend to be located at the cell poles, respectively. The cells were investigated in more detail through real-time 3D analyses, showing how differently PHA granules are processed in relation to the cell division process in native and nonnative PHA-producing strains. We also show that PHA granule-associated protein PhaM of C. necator plays a key role in making these differences between C. necator and recombinant E. coli strains. This study provides spatiotemporal insights into PHA accumulation inside the native and recombinant bacterial cells.
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16
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Lim H, Chuah JA, Chek MF, Tan HT, Hakoshima T, Sudesh K. Identification of regions affecting enzyme activity, substrate binding, dimer stabilization and polyhydroxyalkanoate (PHA) granule morphology in the PHA synthase of Aquitalea sp. USM4. Int J Biol Macromol 2021; 186:414-423. [PMID: 34246679 DOI: 10.1016/j.ijbiomac.2021.07.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/23/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biopolyesters synthesized by microorganisms as intracellular energy reservoirs under stressful environmental conditions. PHA synthase (PhaC) is the key enzyme responsible for PHA biosynthesis, but the importance of its N- and C-terminal ends still remains elusive. Six plasmid constructs expressing truncation variants of Aquitalea sp. USM4 PhaC (PhaC1As) were generated and heterologously expressed in Cupriavidus necator PHB-4. Removal of the first six residues at the N-terminus enabled the modulation of PHA composition without altering the PHA content in cells. Meanwhile, deletion of 13 amino acids from the C-terminus greatly affected the catalytic activity of PhaC1As, retaining only 1.1-7.4% of the total activity. Truncation(s) at the N- and/or C-terminus of PhaC1As gradually diminished the incorporation of comonomer units, and revealed that the N-terminal region is essential for PhaC1As dimerization whereas the C-terminal region is required for stabilization. Notably, transmission electron microscopy analysis showed that PhaC modification affected the morphology of intracellular PHA granules, which until now is only known to be regulated by phasins. This study provided substantial evidence and highlighted the significance of both the N- and C-termini of PhaC1As in regulating intracellular granule morphology, activity, substrate specificity, dimerization and stability of the synthase.
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Affiliation(s)
- Hui Lim
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jo-Ann Chuah
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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17
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Reddy MV, Steinbüchel A. 3,3'-Thiodipropionic acid (TDP), a possible precursor for the synthesis of polythioesters: identification of TDP transport proteins in Variovorax paradoxus TBEA6. Appl Microbiol Biotechnol 2021; 105:3733-3743. [PMID: 33900422 PMCID: PMC8102459 DOI: 10.1007/s00253-021-11294-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/21/2021] [Accepted: 04/12/2021] [Indexed: 11/26/2022]
Abstract
3,3'-Thiodipropionic acid (TDP) is an antioxidant, which can be used as precursor carbon source to synthesize polythioesters. The bacterium Variovorax paradoxus TBEA6 strain can use TDP as a single source of carbon and energy. In the present study, experiments were carried out to identify proteins involved in the transport of TDP into the cells of strain TBEA6. Hence, eight putative tctC genes, which encode for the TctC proteins, were amplified from genomic DNA of TBEA6 strain using polymerase chain reaction and expressed in E. coli BL21 cells. Cells were grown in auto-induction medium, and protein purification was done using His Spin Trap affinity columns. Purity and molecular weight of each protein were confirmed by SDS-PAGE analysis. Protein-ligand interactions were monitored in thermoshift assays using the real-time PCR system. Two TctC proteins (locus tags VPARA-44430 and VPARA-01760) out of eight proteins showed a significant shift in their melting temperatures when they interact with the ligand (TDP or gluconate). The responsible genes were deleted in the genome of TBEA6 using suicide plasmid pJQ200mp18Tc, and single deletion mutants of the two candidate genes were subsequently generated. Finally, growth of the wild-type strain (TBEA6) and the two mutant strains (ΔVPARA-44430 and ΔVPARA-01760) were monitored and compared using TDP or gluconate as carbon sources. Wild type strains were successfully grown with TDP or gluconate. From the two mutant strains, one (ΔVPARA-44430) was unable to grow with TDP indicating that the tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP.Key Points• Putative tctC genes from V. paradoxus TBEA6 were heterologously expressed in E. coli.• Protein-ligand interactions monitored in thermoshift assays using the real-time PCR.• tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP.
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Affiliation(s)
- M Venkateswar Reddy
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany.
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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18
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Eggers J, Strittmatter CS, Küsters K, Biller E, Steinbüchel A. Biotin Synthesis in Ralstonia eutropha H16 Utilizes Pimeloyl Coenzyme A and Can Be Regulated by the Amount of Acceptor Protein. Appl Environ Microbiol 2020; 86:e01512-20. [PMID: 32680858 PMCID: PMC7480372 DOI: 10.1128/aem.01512-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/20/2022] Open
Abstract
The biotin metabolism of the Gram-negative facultative chemolithoautotrophic bacterium Ralstonia eutropha (syn. Cupriavidus necator), which is used for biopolymer production in industry, was investigated. A biotin auxotroph mutant lacking bioF was generated, and biotin depletion in the cells and the minimal biotin demand of a biotin-auxotrophic R. eutropha strain were determined. Three consecutive cultivations in biotin-free medium were necessary to prevent growth of the auxotrophic mutant, and 40 ng/ml biotin was sufficient to promote cell growth. Nevertheless, 200 ng/ml biotin was necessary to ensure growth comparable to that of the wild type, which is similar to the demand of biotin-auxotrophic mutants among other prokaryotic and eukaryotic microbes. A phenotypic complementation of the R. eutropha ΔbioF mutant was only achieved by homologous expression of bioF of R. eutropha or heterologous expression of bioF of Bacillus subtilis but not by bioF of Escherichia coli Together with the results from bioinformatic analysis of BioFs, this leads to the assumption that the intermediate of biotin synthesis in R. eutropha is pimeloyl-CoA instead of pimeloyl-acyl carrier protein (ACP) like in the Gram-positive B. subtilis Internal biotin content was enhanced by homologous expression of accB, whereas homologous expression of accB and accC2 in combination led to decreased biotin concentrations in the cells. Although a DNA-binding domain of the regulator protein BirA is missing, biotin synthesis seemed to be influenced by the amount of acceptor protein present.IMPORTANCERalstonia eutropha is applied in industry for the production of biopolymers and serves as a research platform for the production of diverse fine chemicals. Due to its ability to grow on hydrogen and carbon dioxide as the sole carbon and energy source, R. eutropha is often utilized for metabolic engineering to convert inexpensive resources into value-added products. The understanding of the metabolic pathways in this bacterium is mandatory for further bioengineering of the strain and for the development of new strategies for biotechnological production.
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Affiliation(s)
- Jessica Eggers
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Carl Simon Strittmatter
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kira Küsters
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Emre Biller
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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19
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Pu N, Wang MR, Li ZJ. Characterization of polyhydroxyalkanoate synthases from the marine bacterium Neptunomonas concharum JCM17730. J Biotechnol 2020; 319:69-73. [PMID: 32526261 DOI: 10.1016/j.jbiotec.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/19/2022]
Abstract
Neptunomonas concharum JCM17730 was isolated from an ark clam sample and characterized as a mesophilic bacterium. The genome of N. concharum JCM17730 contains thirteen genes related to polyhydroxyalkanoates (PHA) metabolism. Three PHA synthase encoding genes were identified, and phylogenetic analysis of enzyme sequences suggested the presence of two class I PHA synthases and one class III PHA synthase. The PHA synthases of N. concharum were heterologously expressed with acetyl-CoA acetyltransferase and acetoacetyl-CoA reductase in Escherichia coli to confirm the catalytic activity of each PHA synthase. Recombinants harboring different PHA synthase exhibit important distinctions in poly-3-hydroxybutyrate synthesis ability under various temperatures. Decreased cultivation temperature (≤30 °C) significantly improved PHB titer and content. This is the first report on characterization of PHA synthases from the marine genus Neptunomonas and would provide molecular basis for PHA production using Neptunomonas species.
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Affiliation(s)
- Nan Pu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Meng-Ru Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zheng-Jun Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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20
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Velázquez-Sánchez C, Espín G, Peña C, Segura D. The Modification of Regulatory Circuits Involved in the Control of Polyhydroxyalkanoates Metabolism to Improve Their Production. Front Bioeng Biotechnol 2020; 8:386. [PMID: 32426348 PMCID: PMC7204398 DOI: 10.3389/fbioe.2020.00386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/07/2020] [Indexed: 11/13/2022] Open
Abstract
Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a nutrient is growth-limiting while there is still enough carbon source in the medium. On the other side, the accumulated polymer is mobilized under conditions of nutrient accessibility or by limitation of the carbon source. Thus, it is well known that the accumulation of PHAs is affected by the availability of nutritional resources and this knowledge has been used to establish culture conditions favoring high productivities. In addition to this effect of the metabolic status on PHAs accumulation, several genetic regulatory networks have been shown to drive PHAs metabolism, so the expression of the PHAs genes is under the influence of global or specific regulators. These regulators are thought to coordinate PHAs synthesis and mobilization with the rest of bacterial physiology. While the metabolic and biochemical knowledge related to the biosynthesis of these polymers has led to the development of processes in bioreactors for high-level production and also to the establishment of strategies for metabolic engineering for the synthesis of modified biopolymers, the use of knowledge related to the regulatory circuits controlling PHAs metabolism for strain improvement is scarce. A better understanding of the genetic control systems involved could serve as the foundation for new strategies for strain modification in order to increase PHAs production or to adjust the chemical structure of these biopolymers. In this review, the regulatory systems involved in the control of PHAs metabolism are examined, with emphasis on those acting at the level of expression of the enzymes involved and their potential modification for strain improvement, both for higher titers, or manipulation of polymer properties. The case of the PHAs producer Azotobacter vinelandii is taken as an example of the complexity and variety of systems controlling the accumulation of these interesting polymers in response to diverse situations, many of which could be engineered to improve PHAs production.
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Affiliation(s)
- Claudia Velázquez-Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos Peña
- Departamento Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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21
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Lundquist PK, Shivaiah KK, Espinoza-Corral R. Lipid droplets throughout the evolutionary tree. Prog Lipid Res 2020; 78:101029. [PMID: 32348789 DOI: 10.1016/j.plipres.2020.101029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/11/2020] [Accepted: 04/18/2020] [Indexed: 12/11/2022]
Abstract
Intracellular lipid droplets are utilized for lipid storage and metabolism in organisms as evolutionarily diverse as animals, fungi, plants, bacteria, and archaea. These lipid droplets demonstrate great diversity in biological functions and protein and lipid compositions, yet fundamentally share common molecular and ultrastructural characteristics. Lipid droplet research has been largely fragmented across the diversity of lipid droplet classes and sub-classes. However, we suggest that there is great potential benefit to the lipid community in better integrating the lipid droplet research fields. To facilitate such integration, we survey the protein and lipid compositions, functional roles, and mechanisms of biogenesis across the breadth of lipid droplets studied throughout the natural world. We depict the big picture of lipid droplet biology, emphasizing shared characteristics and unique differences seen between different classes. In presenting the known diversity of lipid droplets side-by-side it becomes necessary to offer for the first time a consistent system of categorization and nomenclature. We propose a division into three primary classes that reflect their sub-cellular location: i) cytoplasmic lipid droplets (CYTO-LDs), that are present in the eukaryotic cytoplasm, ii) prokaryotic lipid droplets (PRO-LDs), that exist in the prokaryotic cytoplasm, and iii) plastid lipid droplets (PL-LDs), that are found in plant plastids, organelles of photosynthetic eukaryotes. Within each class there is a remarkable array of sub-classes displaying various sizes, shapes and compositions. A more integrated lipid droplet research field will provide opportunities to better build on discoveries and accelerate the pace of research in ways that have not been possible.
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Affiliation(s)
- Peter K Lundquist
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Kiran-Kumar Shivaiah
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Roberto Espinoza-Corral
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
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Utsunomia C, Ren Q, Zinn M. Poly(4-Hydroxybutyrate): Current State and Perspectives. Front Bioeng Biotechnol 2020; 8:257. [PMID: 32318554 PMCID: PMC7147479 DOI: 10.3389/fbioe.2020.00257] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
By the end of 1980s, for the first time polyhydroxyalkanoate (PHA) copolymers with incorporated 4-hydroxybutyrate (4HB) units were produced in the bacterium Cupriavidus necator (formally Ralstonia eutropha) from structurally related carbon sources. After that, production of PHA copolymers composed of 3-hydroxybutyrate (3HB) and 4HB [P(3HB-co-4HB)] was demonstrated in diverse wild-type bacteria. The P4HB homopolymer, however, was hardly synthesized because existing bacterial metabolism on 4HB precursors also generate and incorporate 3HB. The resulting material assumes the properties of thermoplastics and elastomers depending on the 4HB fraction in the copolyester. Given the fact that P4HB is biodegradable and yield 4HB, which is a normal compound in the human body and proven to be biocompatible, P4HB has become a prospective material for medical applications, which is the only FDA approved PHA for medical applications since 2007. Different from other materials used in similar applications, high molecular weight P4HB cannot be produced via chemical synthesis. Thus, aiming at the commercial production of this type of PHA, genetic engineering was extensively applied resulting in various production strains, with the ability to convert unrelated carbon sources (e.g., sugars) to 4HB, and capable of producing homopolymeric P4HB. In 2001, Metabolix Inc. filed a patent concerning genetically modified and stable organisms, e.g., Escherichia coli, producing P4HB and copolymers from inexpensive carbon sources. The patent is currently hold by Tepha Inc., the only worldwide producer of commercial P4HB. To date, numerous patents on various applications of P4HB in the medical field have been filed. This review will comprehensively cover the historical evolution and the most recent publications on P4HB biosynthesis, material properties, and industrial and medical applications. Finally, perspectives for the research and commercialization of P4HB will be presented.
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Affiliation(s)
- Camila Utsunomia
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), Sion, Switzerland
| | - Qun Ren
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis), Sion, Switzerland
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Moreno S, Castellanos M, Bedoya-Pérez LP, Canales-Herrerías P, Espín G, Muriel-Millán LF. Outer membrane protein I is associated with poly-β-hydroxybutyrate granules and is necessary for optimal polymer accumulation in Azotobacter vinelandii on solid medium. Microbiology (Reading) 2019; 165:1107-1116. [DOI: 10.1099/mic.0.000837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Mildred Castellanos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Department of Biochemistry and Molecular Biology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Leidy Patricia Bedoya-Pérez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Pablo Canales-Herrerías
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
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Martínez-Martínez MDLA, González-Pedrajo B, Dreyfus G, Soto-Urzúa L, Martínez-Morales LJ. Phasin PhaP1 is involved in polyhydroxybutyrate granules morphology and in controlling early biopolymer accumulation in Azospirillum brasilense Sp7. AMB Express 2019; 9:155. [PMID: 31555910 PMCID: PMC6761214 DOI: 10.1186/s13568-019-0876-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/09/2019] [Indexed: 11/10/2022] Open
Abstract
Phasins are amphiphilic proteins involved in the regulation of the number and size of polyhydroxybutyrate (PHB) granules. The plant growth promoting bacterium Azospirillum brasilense Sp7 accumulates high quantities of bioplastic PHB as carbon and energy source. By analyzing the genome, we identified six genes that code for proteins with a Phasin_2 domain. To understand the role of A. brasilense Sp7 PhaP1 (PhaP1Abs) on PHB synthesis, the phaP1 gene (AMK58_RS17065) was deleted. The morphology of the PHB granules was analyzed by transmission electron microscopy (TEM) and the PHB produced was quantified under three different C:N ratios in cultures subjected to null or low-oxygen transfer. The results showed that PhaP1Abs is involved in PHB granules morphology and in controlling early biopolymer accumulation. Using RT-PCR it was found that phasin genes, except phaP4, are transcribed in accordance with the C:N ratio used for the growth of A. brasilense. phaP1, phaP2 and phaP3 genes were able to respond to the growth conditions tested. This study reports the first analysis of a phasin protein in A. brasilense Sp7.
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Coordinated Regulation of the Size and Number of Polyhydroxybutyrate Granules by Core and Accessory Phasins in the Facultative Microsymbiont Sinorhizobium fredii NGR234. Appl Environ Microbiol 2019; 85:AEM.00717-19. [PMID: 31375484 DOI: 10.1128/aem.00717-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
The exact roles of various granule-associated proteins (GAPs) of polyhydroxybutyrate (PHB) are poorly investigated, particularly for bacteria associated with plants. In this study, four structural GAPs, named phasins PhaP1 to PhaP4, were identified and demonstrated as true phasins colocalized with PHB granules in Sinorhizobium fredii NGR234, a facultative microsymbiont of Vigna unguiculata and many other legumes. The conserved PhaP2 dominated in regulation of granule size under both free-living and symbiotic conditions. PhaP1, another conserved phasin, made a higher contribution than accessory phasins PhaP4 and PhaP3 to PHB biosynthesis at stationary phase. PhaP3, with limited phyletic distribution on the symbiosis plasmid of Sinorhizobium, was more important than PhaP1 in regulating PHB biosynthesis in V. unguiculata nodules. Under the test conditions, no significant symbiotic defects were observed for mutants lacking individual or multiple phaP genes. The mutant lacking two PHB synthases showed impaired symbiotic performance, while mutations in individual PHB synthases or a PHB depolymerase yielded no symbiotic defects. This phenomenon is not related to either the number or size of PHB granules in test mutants within nodules. Distinct metabolic profiles and cocktail pools of GAPs of different phaP mutants imply that core and accessory phasins can be differentially involved in regulating other cellular processes in the facultative microsymbiont S. fredii NGR234.IMPORTANCE Polyhydroxybutyrate (PHB) granules are a store of carbon and energy in bacteria and archaea and play an important role in stress adaptation. Recent studies have highlighted distinct roles of several granule-associated proteins (GAPs) in regulating the size, number, and localization of PHB granules in free-living bacteria, though our knowledge of the role of GAPs in bacteria associated with plants is still limited. Here we report distinct roles of core and accessory phasins associated with PHB granules of Sinorhizobium fredii NGR234, a broad-host-range microsymbiont of diverse legumes. Core phasins PhaP2 and PhaP1 are conserved major phasins in free-living cells. PhaP2 and accessory phasin PhaP3, encoded by an auxiliary gene on the symbiosis plasmid, are major phasins in nitrogen-fixing bacteroids in cowpea nodules. GAPs and metabolic profiles can vary in different phaP mutants. Contrasting symbiotic performances between mutants lacking PHB synthases, depolymerase, or phasins were revealed.
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Wu YW, Yang SH, Hwangbo M, Chu KH. Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system. PLoS One 2019; 14:e0222143. [PMID: 31513626 PMCID: PMC6742469 DOI: 10.1371/journal.pone.0222143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/22/2019] [Indexed: 01/25/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.
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Affiliation(s)
- Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Shih-Hung Yang
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
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Schäfer L, Meinert-Berning C, Wübbeler JH, Steinbüchel A. A tripartite tricarboxylate transporter (MIM_c39170-MIM_c39210) of Advenella mimigardefordensis DPN7 T is involved in citrate uptake. Int Microbiol 2019; 22:461-470. [PMID: 31098825 DOI: 10.1007/s10123-019-00073-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 01/30/2023]
Abstract
To date, tripartite tricarboxylate transport (TTT) systems are not well characterized in most organisms. To investigate which carbon sources are transported by the TTT system of A. mimigardefordensis DPN7T, single deletion mutants were generated lacking either completely both sets of genes encoding for these transport systems tctABCDE1 and tctABDE2 in the organism or the two genes encoding for the regulatory components of the third chosen TTT system, tctDE3. Deletion of tctABCDE1 (MIM_c39170-MIM_c39210) in Advenella mimigardefordensis strain DPN7T led to inhibition of growth of the cells with citrate indicating that TctABCDE1 is the transport system for the uptake of citrate. Because of the negative phenotype, it was concluded that this deletion cannot be substituted by other transporters encoded in the genome of strain DPN7T. A triple deletion mutant of A. mimigardefordensis lacking both complete TTT transport systems and the regulatory components of the third chosen system (ΔTctABCDE1 ΔTctABDE2 ΔTctDE3) showed a leaky growth with α-ketoglutarate in comparison with the wild type. The other investigated TTT (TctABDE3, MIM_c17190-MIM_c17220) is most probably involved in the transport of α-ketoglutarate. Additionally, thermoshift assays with TctC1 (MIM_c39190) showed a significant shift in the melting temperature of the protein in the presence of citrate whereas no shift occurred with α-ketoglutarate. A dissociation constant Kd for citrate of 41.7 μM was determined. Furthermore, alternative α-ketoglutarate transport was investigated via in silico analysis.
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Affiliation(s)
- Lukas Schäfer
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany. .,Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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Shen R, Ning ZY, Lan YX, Chen JC, Chen GQ. Manipulation of polyhydroxyalkanoate granular sizes in Halomonas bluephagenesis. Metab Eng 2019; 54:117-126. [PMID: 30959245 DOI: 10.1016/j.ymben.2019.03.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/20/2019] [Accepted: 03/31/2019] [Indexed: 10/27/2022]
Abstract
Bacterial polyhydroxyalkanoates (PHA) are a family of intracellular polyester granules with sizes ranging from 100 to 500 nm. Due to their small sizes, it has been very difficult to separate the PHA granules from the bacterial broths. This study aims to engineer the PHA size control mechanism to obtain large PHA granular sizes beneficial for the separation. It has been reported that phasin (PhaP) is an amphiphilic protein located on the surface of PHA granules functioning to regulate sizes and numbers of PHA granules in bacterial cells, deletions on PhaPs result in reduced PHA granule number and enhanced granule sizes. Three genes phaP1, phaP2 and phaP3 encoding three PhaP proteins were deleted in various combinations in halophilic bacterium Halomonas bluephagenesis TD01. The phaP1-knockout strain generated much larger PHA granules with almost the same size as their producing cells without significantly affecting the PHA accumulation yet with a reduced PHA molecular weights. In contrast, the phaP2- and phaP3-knockout strains produced slightly larger sizes of PHA granules with increased PHA molecular weights. While PHA accumulation by phaP3-knockout strains showed a significant reduction. All of the PhaP deletion efforts could not form PHA granules larger than a normal size of H. bluephagenesis TD01. It appears that the PHA granular sizes could be limited by bacterial cell sizes. Therefore, genes minC and minD encoding proteins that block formation of cell fission rings (Z-rings) were over-expressed in various phaP deleted H. bluephagenesis TD01, resulting in large cell sizes of H. bluephagenesis TD01 containing PHA granules with sizes of up to 10 μm that has never been observed previously. It can be concluded that PHA granule sizes are limited by the cell sizes. By engineering a large cell morphology large PHA granules can be produced by PhaP deleted mutants.
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Affiliation(s)
- Rui Shen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhi-Yu Ning
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu-Xuan Lan
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Lab of Industrial Biocatalysis, Dept of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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Heine V, Meinert-Berning C, Lück J, Mikowsky N, Voigt B, Riedel K, Steinbüchel A. The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis. PLoS One 2019; 14:e0211876. [PMID: 30742653 PMCID: PMC6370202 DOI: 10.1371/journal.pone.0211876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Variovorax paradoxus strain TBEA6 is one of the few organisms known to utilize 3,3'-thiodipropionate (TDP) as the only source of carbon and energy. It cleaves TDP to 3-mercaptopropionate (3MP), which is a direct precursor for polythioester synthesis. To establish this process in V. paradoxus TBEA6, it is crucial to unravel its TDP metabolism. Therefore, a proteomic approach with subsequent deletion of interesting genes in the bacterium was chosen. Cells were cultivated with D-gluconate, TDP or 3-sulfinopropionate as the only carbon sources. Proteins with high abundances in gels of cells cultivated with either of the organic sulfur compounds were analyzed further. Thereby, we did not only confirm parts of the already postulated TDP metabolism, but also eight new protein candidates for TDP degradation were detected. Deletions of the corresponding genes (two enoyl-CoA hydratases (Ech-20 and Ech-30), an FK506-binding protein, a putative acetolactate synthase, a carnitinyl-CoA dehydratase, and a putative crotonase family protein) were obtained. Only the deletions of both Ech-20 and Ech-30 led to a TDP negative phenotype. The deletion mutant of VPARA_05510, which encodes the putative crotonase family protein showed reduced growth with TDP. The three genes are located in one cluster with genes proven to be involved in TDP metabolism. Thermal shift assays showed an increased stability of Ech-20 with TDP-CoA but not with TDP. These results indicate that Ech-20 uses TDP-CoA as a substrate instead of TDP. Hence, we postulate a new putative pathway for TDP metabolism. Ech-30 interacts with neither TDP-CoA nor TDP but might interact with other CoA-activated intermediates of the proposed pathway. Further enzyme characterization is necessary to unravel the complete pathway from TDP to 3MP.
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Affiliation(s)
- Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Janina Lück
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Nadine Mikowsky
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Long JY, Song KL, He X, Zhang B, Cui XF, Song CF. Mutagenesis of PhaR, a Regulator Gene of Polyhydroxyalkanoate Biosynthesis of Xanthomonas oryzae pv. oryzae Caused Pleiotropic Phenotype Changes. Front Microbiol 2018; 9:3046. [PMID: 30619137 PMCID: PMC6304360 DOI: 10.3389/fmicb.2018.03046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/27/2018] [Indexed: 01/04/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are intracellular carbon and energy storage materials produced in various microorganisms under nutrient-limited conditions. PhaR is a regulatory protein involved in PHA synthesis. Xanthomonas oryzae pv. oryzae (Xoo) is one of the most important bacterial pathogens in rice and has PHA biosynthesis genes in its genome, but the biological function of phaR in Xoo is unknown. In this study, we investigated the effects of the mutagenesis of phaR gene in Xoo strain PXO99A. Compared to the wildtype, the PhaR gene knock-out mutant PXO99ΔphaR was hypermotile and showed decreased growth rates in both rich and limited nutrient media. PXO99ΔphaR also showed almost 75% decrease in extracellular polysaccharide (EPS) production. When inoculated in rice leaves by leaf-clipping method, PXO99ΔphaR displayed reduced virulence in terms of lesion length and bacterial multiplication compared with the wildtype strain. PXO99ΔphaR also showed enhanced hypersensitive response (HR) induction in the leaves of non-host Nicotiana benthamiana with elevated hpa1 gene expression. Introduction of a cosmid containing the phaR coding sequence restored the phenotypes of the mutant to those of the wildtype strain. These results suggest that PhaR gene is an important gene that affects multiple bacterial characteristics, including EPS production, growth rate, defense response induced harpin production and motility, related to its virulence in plant.
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Affiliation(s)
| | | | | | | | | | - Cong-Feng Song
- Department of Plant Pathology, College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
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Nishihata S, Kondo T, Tanaka K, Ishikawa S, Takenaka S, Kang CM, Yoshida KI. Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation. BMC Microbiol 2018; 18:156. [PMID: 30355296 PMCID: PMC6201568 DOI: 10.1186/s12866-018-1317-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulation is orchestrated by not only the enzymes for PHB synthesis but also PHB-binding phasin proteins (PhaPs) stabilizing the PHB granules. The transcription factor PhaR controls the phaP genes. Results Inactivation of phaR led to decreases in PHB accumulation, less cell yield, increases in exopolysaccharide (EPS) production, some improvement in heat stress tolerance, and slightly better growth under microaerobic conditions. Changes in the transcriptome upon phaR inactivation were analyzed. PhaR appeared to be involved in the repression of various target genes, including some PHB-degrading enzymes and others involved in EPS production. Furthermore, in vitro gel shift analysis demonstrated that PhaR bound to the promoter regions of representative targets. For the phaP1 and phaP4 promoter regions, PhaR-binding sites were determined by DNase I footprinting, allowing us to deduce a consensus sequence for PhaR-binding as TGCRNYGCASMA (R: A or G, Y: C or T, S: C or G, M: A or C). We searched for additional genes associated with a PhaR-binding sequence and found that some genes involved in central carbon metabolism, such as pdhA for pyruvate dehydrogenase and pckA for phosphoenolpyruvate carboxykinase, may be regulated positively and directly by PhaR. Conclusions These results suggest that PhaR could regulate various genes not only negatively but also positively to coordinate metabolism holistically in response to PHB accumulation. Electronic supplementary material The online version of this article (10.1186/s12866-018-1317-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shogo Nishihata
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Takahiko Kondo
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan
| | - Choong-Min Kang
- Department of Biological Science, California State University, Stanislaus, Turlock, CA, 95382, USA
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501, Japan.
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Martla M, Umsakul K, Sudesh K. Production and recovery of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from biodiesel liquid waste (BLW). J Basic Microbiol 2018; 58:977-986. [DOI: 10.1002/jobm.201800279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/04/2018] [Accepted: 07/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Mananya Martla
- Faculty of Science; Department of Microbiology; Prince of Songkla University; Hatyai Songkhla Thailand
| | - Kamontam Umsakul
- Faculty of Science; Department of Microbiology; Prince of Songkla University; Hatyai Songkhla Thailand
| | - Kumar Sudesh
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
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Kutralam-Muniasamy G, Peréz-Guevara F. Genome characteristics dictate poly-R-(3)-hydroxyalkanoate production in Cupriavidus necator H16. World J Microbiol Biotechnol 2018; 34:79. [DOI: 10.1007/s11274-018-2460-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 11/28/2022]
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Burkholderia xenovorans LB400 possesses a functional polyhydroxyalkanoate anabolic pathway encoded by the pha genes and synthesizes poly(3-hydroxybutyrate) under nitrogen-limiting conditions. Int Microbiol 2018; 21:47-57. [DOI: 10.1007/s10123-018-0004-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 10/16/2022]
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Kutralam-Muniasamy G, Corona-Hernandez J, Narayanasamy RK, Marsch R, Pérez-Guevara F. Phylogenetic diversification and developmental implications of poly-(R)-3-hydroxyalkanoate gene cluster assembly in prokaryotes. FEMS Microbiol Lett 2018; 364:3888817. [PMID: 28655209 DOI: 10.1093/femsle/fnx135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Many polyhydroxyalkanoates (PHAs) system genes, such as phaC, phaA, phaB, phaR, phaP and phaZ, are often found to be organised in the form of operon-like clusters. In this study, a genome survey was performed to identify such clustered PHA systems among 256 prokaryotic organisms. These data were then used to generate a comprehensive 16S rRNA species tree depicting the phylogenetic distribution of the observed clusters with diverse gene arrangements. In addition, the gene occurrences and physical linkages between PHA system genes were quantitatively estimated. From this, we identified a centrally connected hub gene, i.e. the phaC gene of PHA. Furthermore, a comparative investigation was performed between the clusters of PHA and glycogen, which decoded the role of the hub gene in the cluster organisation of both systems. Together, these findings suggest that the highly connected hub gene might contribute substantively towards the organisation and maintenance of the gene network connectivity in the clusters, particularly in the storage reserve systems.
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Affiliation(s)
- Gurusamy Kutralam-Muniasamy
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Juan Corona-Hernandez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Ravi-Kumar Narayanasamy
- Department of Infectomics y Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Rodolfo Marsch
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Fermín Pérez-Guevara
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México.,Nanoscience and Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
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Kutralam-Muniasamy G, Perez-Guevara F. Recombinant surface engineering to enhance and expand the potential of biologically produced nanoparticles: A review. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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38
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PhaR, a Negative Regulator of PhaP, Modulates the Colonization of a Burkholderia Gut Symbiont in the Midgut of the Host Insect, Riptortus pedestris. Appl Environ Microbiol 2017; 83:AEM.00459-17. [PMID: 28341680 DOI: 10.1128/aem.00459-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/21/2017] [Indexed: 12/20/2022] Open
Abstract
Five genes encoding PhaP family proteins and one phaR gene have been identified in the genome of Burkholderia symbiont strain RPE75. PhaP proteins function as the surface proteins of polyhydroxyalkanoate (PHA) granules, and the PhaR protein acts as a negative regulator of PhaP biosynthesis. Recently, we characterized one phaP gene to understand the molecular cross talk between Riptortus insects and Burkholderia gut symbionts. In this study, we constructed four other phaP gene-depleted mutants (ΔphaP1, ΔphaP2, ΔphaP3, and ΔphaP4 mutants), one phaR gene-depleted mutant, and a phaR-complemented mutant (ΔphaR/phaR mutant). To address the biological roles of four phaP family genes and the phaR gene during insect-gut symbiont interaction, these Burkholderia mutants were fed to the second-instar nymphs, and colonization ability and fitness parameters were examined. In vitro, the ΔphaP3 and ΔphaR mutants cannot make a PHA granule normally in a stressful environment. Furthermore, the ΔphaR mutation decreased the colonization ability in the host midgut and negatively affected the host insect's fitness compared with wild-type Burkholderia-infected insects. However, other phaP family gene-depleted mutants colonized well in the midgut of the fifth-instar nymph insects. However, in the case of females, the colonization rate of the ΔphaP3 mutant was decreased and the host's fitness parameters were decreased compared with the wild-type-infected host, suggesting that the environment of the female midgut may be more hostile than that of the male midgut. These results demonstrate that PhaR plays an important role in the biosynthesis of PHA granules and that it is significantly related to the colonization of the Burkholderia gut symbiont in the host insects' midgut.IMPORTANCE Bacterial polyhydroxyalkanoate (PHA) biosynthesis is a complex process requiring several enzymes. The biological roles of PHA granule synthesis enzymes and the surface proteins of PHA granules during host-gut symbiont interactions are not fully understood. Here, we report the effects on colonization ability in the host midguts and the fitness of host insects after feeding Burkholderia mutant cells (four phaP-depleted mutants and one phaR-depleted mutant) to the host insects. Analyses of both synthesized PHA granule amounts and CFU numbers suggest that the phaR gene is closely related to synthesis of the PHA granule and the colonization of the Burkholderia gut symbiont in the host insect's midgut. Like our previous report, this study also supports the idea that the environment of the host midgut may not be favorable to symbiotic Burkholderia cells and that PHA granules may be required to adapt in the host midgut.
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Meinert C, Senger J, Witthohn M, Wübbeler JH, Steinbüchel A. Carbohydrate uptake in Advenella mimigardefordensis strain DPN7 T is mediated by periplasmic sugar oxidation and a TRAP-transport system. Mol Microbiol 2017; 104:916-930. [PMID: 28407382 DOI: 10.1111/mmi.13692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2017] [Indexed: 11/28/2022]
Abstract
In this study, we investigated an SBP (DctPAm ) of a tripartite ATP-independent periplasmic transport system (TRAP) in Advenella mimigardefordensis strain DPN7T . Deletion of dctPAm as well as of the two transmembrane compounds of the tripartite transporter, dctQ and dctM, impaired growth of A. mimigardefordensis strain DPN7T , if cultivated on mineral salt medium supplemented with d-glucose, d-galactose, l-arabinose, d-fucose, d-xylose or d-gluconic acid, respectively. The wild type phenotype was restored during complementation studies of A. mimigardefordensis ΔdctPAm using the broad host vector pBBR1MCS-5::dctPAm . Furthermore, an uptake assay with radiolabeled [14 C(U)]-d-glucose clearly showed that the deletion of dctPAm , dctQ and dctM, respectively, disabled the uptake of this aldoses in cells of either mutant strain. Determination of KD performing thermal shift assays showed a shift in the melting temperature of DctPAm in the presence of d-gluconic acid (KD 11.76 ± 1.3 µM) and the corresponding aldonic acids to the above-mentioned carbohydrates d-galactonate (KD 10.72 ± 1.4 µM), d-fuconic acid (KD 13.50 ± 1.6 µM) and d-xylonic acid (KD 8.44 ± 1.0 µM). The sugar (glucose) dehydrogenase activity (E.C.1.1.5.2) in the membrane fraction was shown for all relevant sugars, proving oxidation of the molecules in the periplasm, prior to transport.
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Affiliation(s)
- Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Jana Senger
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Marco Witthohn
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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40
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Meinert C, Brandt U, Heine V, Beyert J, Schmidl S, Wübbeler JH, Voigt B, Riedel K, Steinbüchel A. Proteomic analysis of organic sulfur compound utilisation in Advenella mimigardefordensis strain DPN7T. PLoS One 2017; 12:e0174256. [PMID: 28358882 PMCID: PMC5373536 DOI: 10.1371/journal.pone.0174256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/06/2017] [Indexed: 01/07/2023] Open
Abstract
2-Mercaptosuccinate (MS) and 3,3´-ditiodipropionate (DTDP) were discussed as precursor substance for production of polythioesters (PTE). Therefore, degradation of MS and DTDP was investigated in Advenella mimigardefordensis strain DPN7T, applying differential proteomic analysis, gene deletion and enzyme assays. Protein extracts of cells cultivated with MS, DTDP or 3-sulfinopropionic acid (SP) were compared with those cultivated with propionate (P) and/or succinate (S). The chaperone DnaK (ratio DTDP/P 9.2, 3SP/P 4.0, MS/S 6.1, DTDP/S 6.2) and a Do-like serine protease (DegP) were increased during utilization of all organic sulfur compounds. Furthermore, a putative bacterioferritin (locus tag MIM_c12960) showed high abundance (ratio DTDP/P 5.3, 3SP/P 3.2, MS/S 4.8, DTDP/S 3.9) and is probably involved in a thiol-specific stress response. The deletion of two genes encoding transcriptional regulators (LysR (MIM_c31370) and Xre (MIM_c31360)) in the close proximity of the relevant genes of DTDP catabolism (acdA, mdo and the genes encoding the enzymes of the methylcitric acid cycle; prpC,acnD, prpF and prpB) showed that these two regulators are essential for growth of A. mimigardefordensis strain DPN7T with DTDP and that they most probably regulate transcription of genes mandatory for this catabolic pathway. Furthermore, proteome analysis revealed a high abundance (ratio MS/S 10.9) of a hypothetical cupin-2-domain containing protein (MIM_c37420). This protein shows an amino acid sequence similarity of 60% to a newly identified MS dioxygenase from Variovorax paradoxus strain B4. Deletion of the gene and the adjacently located transcriptional regulator LysR, as well as heterologous expression of MIM_c37420, the putative mercaptosuccinate dioxygenase (Msdo) from A. mimigardefordensis, showed that this protein is the key enzyme of MS degradation in A. mimigardefordensis strain DPN7T (KM 0.2 mM, specific activity 17.1 μmol mg-1 min-1) and is controlled by LysR (MIM_c37410).
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Affiliation(s)
- Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Ulrike Brandt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Jessica Beyert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Sina Schmidl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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41
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Vadlja D, Koller M, Novak M, Braunegg G, Horvat P. Footprint area analysis of binary imaged Cupriavidus necator cells to study PHB production at balanced, transient, and limited growth conditions in a cascade process. Appl Microbiol Biotechnol 2016; 100:10065-10080. [PMID: 27695913 PMCID: PMC5102984 DOI: 10.1007/s00253-016-7844-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/21/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022]
Abstract
Statistical distribution of cell and poly[3-(R)-hydroxybutyrate] (PHB) granule size and number of granules per cell are investigated for PHB production in a five-stage cascade (5CSTR). Electron microscopic pictures of cells from individual cascade stages (R1-R5) were converted to binary pictures to visualize footprint areas for polyhydroxyalkanoate (PHA) and non-PHA biomass. Results for each stage were correlated to the corresponding experimentally determined kinetics (specific growth rate μ and specific productivity π). Log-normal distribution describes PHA granule size dissimilarity, whereas for R1 and R4, gamma distribution best reflects the situation. R1, devoted to balanced biomass synthesis, predominately contains cells with rather small granules, whereas with increasing residence time τ, maximum and average granule sizes by trend increase, approaching an upper limit determined by the cell's geometry. Generally, an increase of intracellular PHA content and ratio of granule to cell area slow down along the cascade. Further, the number of granules per cell decreases with increasing τ. Data for μ and π obtained by binary picture analysis correlate well with the experimental results. The work describes long-term continuous PHA production under balanced, transient, and nutrient-deficient conditions, as well as their reflection on the granules size, granule number, and cell structure on the microscopic level.
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Affiliation(s)
- Denis Vadlja
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Martin Koller
- Office of Research Management and Service, c/o Institute of Chemistry, NAWI Graz, University of Graz, Heinrichstrasse 28/III, 8010, Graz, Austria. .,ARENA Arbeitsgemeinschaft für Ressourcenschonende & Nachhaltige Technologien, Inffeldgasse 21b, 8010, Graz, Austria.
| | - Mario Novak
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Gerhart Braunegg
- ARENA Arbeitsgemeinschaft für Ressourcenschonende & Nachhaltige Technologien, Inffeldgasse 21b, 8010, Graz, Austria
| | - Predrag Horvat
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
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Parlane NA, Gupta SK, Rubio-Reyes P, Chen S, Gonzalez-Miro M, Wedlock DN, Rehm BHA. Self-Assembled Protein-Coated Polyhydroxyalkanoate Beads: Properties and Biomedical Applications. ACS Biomater Sci Eng 2016; 3:3043-3057. [PMID: 33445349 DOI: 10.1021/acsbiomaterials.6b00355] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biological polyesters that can be naturally produced by a range of bacteria as water-insoluble inclusions composed of a PHA core coated with PHA synthesis, structural, and regulatory proteins. These naturally self-assembling shell-core particles have been recently conceived as biomaterials that can be bioengineered as biologically active beads for medical applications. Protein engineering of PHA-associated proteins enabled the production of PHA-protein assemblies exhibiting biologically active protein-based functions relevant for applications as vaccines or diagnostics. Here we provide an overview of the recent advances in bioengineering of PHA particles toward the display of biomedically relevant protein functions such as selected disease-specific antigens as diagnostic tools or for the design of particulate subunit vaccines against infectious diseases such as tuberculosis, meningitis, pneumonia, and hepatitis C.
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Affiliation(s)
- Natalie A Parlane
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Sandeep K Gupta
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Patricia Rubio-Reyes
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Shuxiong Chen
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Majela Gonzalez-Miro
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - D Neil Wedlock
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Bernd H A Rehm
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Kelburn Parade, Wellington 6140, New Zealand
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Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens. Appl Environ Microbiol 2016; 82:4299-4308. [PMID: 27208130 DOI: 10.1128/aem.00757-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/02/2016] [Indexed: 02/06/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is a carbon and energy reserve polymer in various prokaryotic species. We determined that, when grown with mannitol as the sole carbon source, Bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (PHB). Conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of PHB, which was observed as cytoplasmic granules. To study the regulation of PHB synthesis, we generated mutations in the regulator gene phaR and the phasin genes phaP1 and phaP4 Under permissive conditions, mutation of phaR impaired PHB accumulation, and a phaP1 phaP4 double mutant produced more PHB than the wild type, which was accumulated in a single, large cytoplasmic granule. Moreover, PhaR negatively regulated the expression of phaP1 and phaP4 as well as the expression of phaA1 and phaA2 (encoding a 3-ketoacyl coenzyme A [CoA] thiolases), phaC1 and phaC2 (encoding PHB synthases), and fixK2 (encoding a cyclic AMP receptor protein [CRP]/fumarate and nitrate reductase regulator [FNR]-type transcription factor of genes for microoxic lifestyle). In addition to the depressed PHB cycling, phaR mutants accumulated more extracellular polysaccharides and promoted higher plant shoot dry weight and competitiveness for nodulation than the wild type, in contrast to the phaC1 mutant strain, which is defective in PHB synthesis. These results suggest that phaR not only regulates PHB granule formation by controlling the expression of phasins and biosynthetic enzymes but also acts as a global regulator of excess carbon allocation and symbiosis by controlling fixK2 IMPORTANCE: In this work, we investigated the regulation of polyhydroxybutyrate synthesis in the soybean-nodulating bacterium Bradyrhizobium diazoefficiens and its influence in bacterial free-living and symbiotic lifestyles. We uncovered a new interplay between the synthesis of this carbon reserve polymer and the network responsible for microoxic metabolism through the interaction between the gene regulators phaR and fixK2 These results contribute to the understanding of the physiological conditions required for polyhydroxybutyrate biosynthesis. The interaction between these two main metabolic pathways is also reflected in the symbiotic phenotypes of soybeans inoculated with phaR mutants, which were more competitive for nodulation and enhanced dry matter production by the plants. Therefore, this knowledge may be applied to the development of superior strains to be used as improved inoculants for soybean crops.
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Alves LPS, Teixeira CS, Tirapelle EF, Donatti L, Tadra-Sfeir MZ, Steffens MBR, de Souza EM, de Oliveira Pedrosa F, Chubatsu LS, Müller-Santos M. Backup Expression of the PhaP2 Phasin Compensates for phaP1 Deletion in Herbaspirillum seropedicae, Maintaining Fitness and PHB Accumulation. Front Microbiol 2016; 7:739. [PMID: 27242754 PMCID: PMC4873508 DOI: 10.3389/fmicb.2016.00739] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022] Open
Abstract
Phasins are important proteins controlling poly-3-hydroxybutyrate (PHB) granules formation, their number into the cell and stability. The genome sequencing of the endophytic and diazotrophic bacterium Herbaspirillum seropedicae SmR1 revealed two homologous phasin genes. To verify the role of the phasins on PHB accumulation in the parental strain H. seropedicae SmR1, isogenic strains defective in the expression of phaP1, phaP2 or both genes were obtained by gene deletion and characterized in this work. Despite of the high sequence similarity between PhaP1 and PhaP2, PhaP1 is the major phasin in H. seropedicae, since its deletion reduced PHB accumulation by ≈50% in comparison to the parental and ΔphaP2. Upon deletion of phaP1, the expression of phaP2 was sixfold enhanced in the ΔphaP1 strain. The responsive backup expression of phaP2 partially rescued the ΔphaP1 mutant, maintaining about 50% of the parental PHB level. The double mutant ΔphaP1.2 did not accumulate PHB in any growth stage and showed a severe reduction of growth when glucose was the carbon source, a clear demonstration of negative impact in the fitness. The co-occurrence of phaP1 and phaP2 homologous in bacteria relatives of H. seropedicae, including other endophytes, indicates that the mechanism of phasin compensation by phaP2 expression may be operating in other organisms, showing that PHB metabolism is a key factor to adaptation and efficiency of endophytic bacteria.
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Affiliation(s)
- Luis P S Alves
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Cícero S Teixeira
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Evandro F Tirapelle
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Lucélia Donatti
- Functional Morphology and Comparative Ecophysiology Laboratory, Cell Biology Department, Federal University of Paraná Curitiba, Brazil
| | - Michelle Z Tadra-Sfeir
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Maria B R Steffens
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Emanuel M de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Leda S Chubatsu
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná Curitiba, Brazil
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Wübbeler JH, Hiessl S, Meinert C, Poehlein A, Schuldes J, Daniel R, Steinbüchel A. The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3'-thiodipropionic acid and hence the production of polythioesters. J Biotechnol 2015; 209:85-95. [PMID: 26073999 DOI: 10.1016/j.jbiotec.2015.06.390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/01/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
Abstract
The betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3'-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn5::mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse.
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany; Faculty of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.
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Hokamura A, Fujino K, Isoda Y, Arizono K, Shiratsuchi H, Matsusaki H. Characterization and identification of the proteins bound to two types of polyhydroxyalkanoate granules in Pseudomonas sp. 61-3. Biosci Biotechnol Biochem 2015; 79:1369-77. [PMID: 25971301 DOI: 10.1080/09168451.2015.1023250] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Pseudomonas sp. 61-3 accumulates two types of polyhydroxyalkanoates (PHAs), poly(3-hydroxybutyrate) [P(3HB)], and poly(3HB-co-3-hydroxyalkanoates) [P(3HB-co-3HA)], and some proteins associated with their PHA granules have been identified. To date, PhaFPs (GA36) and PhaIPs (GA18) were identified from P(3HB-co-3HA) granules. In this study, the gene encoding GA24 associated with P(3HB) granule was identified as phbPPs. PhbPPs was composed of 192 amino acids with a calculated molecular mass of 20.4 kDa and was assumed to be a phasin. phbFPs gene and unknown ORF were also found on phb locus. PhbFPs was anticipated to be the transcriptional repressor of phbPPs gene. PhbPPs was bound to the P(3HB-co-3HA) granules with 3HB composition of more than 87 mol%, and PhaIPs and PhaFPs were bound to the P(3HB-co-3HA) granules with 3HA (C6-C12) composition of more than 13 mol% in the producing cells, suggesting that localization of these proteins is attributed to the monomer compositions of the copolymers.
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Affiliation(s)
- Ayaka Hokamura
- a Faculty of Environmental and Symbiotic Sciences, Department of Food and Health Sciences , Prefectural University of Kumamoto , Kumamoto , Japan
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Linares-Pastén JA, Sabet-Azad R, Pessina L, Sardari RRR, Ibrahim MHA, Hatti-Kaul R. Efficient poly(3-hydroxypropionate) production from glycerol using Lactobacillus reuteri and recombinant Escherichia coli harboring L. reuteri propionaldehyde dehydrogenase and Chromobacterium sp. PHA synthase genes. BIORESOURCE TECHNOLOGY 2015; 180:172-176. [PMID: 25600014 DOI: 10.1016/j.biortech.2014.12.099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/27/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
Poly(3-hydroxypropionate), P(3HP), is a polymer combining good biodegradability with favorable material properties. In the present study, a production system for P(3HP) was designed, comprising conversion of glycerol to 3-hydroxypropionaldehyde (3HPA) as equilibrium mixture with 3HPA-hydrate and -dimer in aqueous system (reuterin) using resting cells of native Lactobacillus reuteri in a first stage followed by transformation of the 3HPA to P(3HP) using recombinant Escherichia coli strain co-expressing highly active coenzyme A-acylating propionaldehyde dehydrogenase (PduP) from L. reuteri and polyhydroxyalkanoate synthase (PhaCcs) from Chromobacterium sp. P(3HP) content of up to 40% (w/w) cell dry weight was reached, and the yield with respect to the reuterin consumed by the cells was 78%. Short biotransformation period (4.5h), lack of additives or expensive cofactors, and use of a cheap medium for cultivation of the recombinant strain, provides a new efficient and potentially economical system for P(3HP) production.
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Affiliation(s)
- Javier A Linares-Pastén
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ramin Sabet-Azad
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Laura Pessina
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Roya R R Sardari
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mohammad H A Ibrahim
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; Chemistry of Natural and Microbial Products Department, National Research Centre, Al-Bohoos St., 12622 Cairo, Egypt
| | - Rajni Hatti-Kaul
- Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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48
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Eggers J, Steinbüchel A. Impact of Ralstonia eutropha's poly(3-Hydroxybutyrate) (PHB) Depolymerases and Phasins on PHB storage in recombinant Escherichia coli. Appl Environ Microbiol 2014; 80:7702-9. [PMID: 25281380 PMCID: PMC4249218 DOI: 10.1128/aem.02666-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/29/2014] [Indexed: 11/20/2022] Open
Abstract
The model organism for polyhydroxybutyrate (PHB) biosynthesis, Ralstonia eutropha H16, possesses multiple isoenzymes of granules coating phasins as well as of PHB depolymerases, which degrade accumulated PHB under conditions of carbon limitation. In this study, recombinant Escherichia coli BL21(DE3) strains were used to study the impact of selected PHB depolymerases of R. eutropha H16 on the growth behavior and on the amount of accumulated PHB in the absence or presence of phasins. For this purpose, 20 recombinant E. coli BL21(DE3) strains were constructed, which harbored a plasmid carrying the phaCAB operon from R. eutropha H16 to ensure PHB synthesis and a second plasmid carrying different combinations of the genes encoding a phasin and a PHB depolymerase from R. eutropha H16. It is shown in this study that the growth behavior of the respective recombinant E. coli strains was barely affected by the overexpression of the phasin and PHB depolymerase genes. However, the impact on the PHB contents was significantly greater. The strains expressing the genes of the PHB depolymerases PhaZ1, PhaZ2, PhaZ3, and PhaZ7 showed 35% to 94% lower PHB contents after 30 h of cultivation than the control strain. The strain harboring phaZ7 reached by far the lowest content of accumulated PHB (only 2.0% [wt/wt] PHB of cell dry weight). Furthermore, coexpression of phasins in addition to the PHB depolymerases influenced the amount of PHB stored in cells of the respective strains. It was shown that the phasins PhaP1, PhaP2, and PhaP4 are not substitutable without an impact on the amount of stored PHB. In particular, the phasins PhaP2 and PhaP4 seemed to limit the degradation of PHB by the PHB depolymerases PhaZ2, PhaZ3, and PhaZ7, whereas almost no influence of the different phasins was observed if phaZ1 was coexpressed. This study represents an extensive analysis of the impact of PHB depolymerases and phasins on PHB accumulation and provides a deeper insight into the complex interplay of these enzymes.
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Affiliation(s)
- Jessica Eggers
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität Münster, Münster, Germany Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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49
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A novel DNA-binding protein, PhaR, plays a central role in the regulation of polyhydroxyalkanoate accumulation and granule formation in the haloarchaeon Haloferax mediterranei. Appl Environ Microbiol 2014; 81:373-85. [PMID: 25344243 DOI: 10.1128/aem.02878-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are synthesized and assembled as PHA granules that undergo well-regulated formation in many microorganisms. However, this regulation remains unclear in haloarchaea. In this study, we identified a PHA granule-associated regulator (PhaR) that negatively regulates the expression of both its own gene and the granule structural gene phaP in the same operon (phaRP) in Haloferax mediterranei. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assays demonstrated a significant interaction between PhaR and the phaRP promoter in vivo. Scanning mutagenesis of the phaRP promoter revealed a specific cis-element as the possible binding position of the PhaR. The haloarchaeal homologs of the PhaR contain a novel conserved domain that belongs to a swapped-hairpin barrel fold family found in AbrB-like proteins. Amino acid substitution indicated that this AbrB-like domain is critical for the repression activity of PhaR. In addition, the phaRP promoter had a weaker activity in the PHA-negative strains, implying a function of the PHA granules in titration of the PhaR. Moreover, the H. mediterranei strain lacking phaR was deficient in PHA accumulation and produced granules with irregular shapes. Interestingly, the PhaR itself can promote PHA synthesis and granule formation in a PhaP-independent manner. Collectively, our results demonstrated that the haloarchaeal PhaR is a novel bifunctional protein that plays the central role in the regulation of PHA accumulation and granule formation in H. mediterranei.
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50
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Kohlmann Y, Pohlmann A, Schwartz E, Zühlke D, Otto A, Albrecht D, Grimmler C, Ehrenreich A, Voigt B, Becher D, Hecker M, Friedrich B, Cramm R. Coping with Anoxia: A Comprehensive Proteomic and Transcriptomic Survey of Denitrification. J Proteome Res 2014; 13:4325-38. [DOI: 10.1021/pr500491r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yvonne Kohlmann
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Anne Pohlmann
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Edward Schwartz
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Daniela Zühlke
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Andreas Otto
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Dirk Albrecht
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Christina Grimmler
- Forschungsstelle für Nahrungsmittelqualität der Universität Bayreuth, 95326 Kulmbach, Germany
| | - Armin Ehrenreich
- Lehrstuhl
für Mikrobiologie, Technische Universität München, Emil-Ramann-Straße
4, 85354 Freising, Germany
| | - Birgit Voigt
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Dörte Becher
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Michael Hecker
- Institut
für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Friedrich-Ludwig-Jahn-Straße
15, 17489 Greifswald, Germany
| | - Bärbel Friedrich
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
| | - Rainer Cramm
- Institut
für Biologie, Humboldt-Universität zu Berlin, Chausseestraße
117, 10115 Berlin, Germany
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