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Kelly S, Tham JL, McKeever K, Dillon E, O'Connell D, Scholz D, Simpson JC, O'Connor K, Narancic T, Cagney G. Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin. Mol Cell Proteomics 2024; 23:100765. [PMID: 38608840 PMCID: PMC11103573 DOI: 10.1016/j.mcpro.2024.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example, low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiments. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to coordinately increase or decrease within clustered pathways. Next, we analyzed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.
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Affiliation(s)
- Siobhan Kelly
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Jia-Lynn Tham
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kate McKeever
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Eugene Dillon
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David O'Connell
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Dimitri Scholz
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Jeremy C Simpson
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; UCD Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kevin O'Connor
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland; UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Tanja Narancic
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
| | - Gerard Cagney
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
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Amir M, Bano N, Gupta A, Zaheer MR, Roohi. Purification and characterization of extracellular PHB depolymerase enzyme from Aeromonas caviae Kuk1-(34) and their biodegradation studies with polymer films. Biodegradation 2024; 35:137-153. [PMID: 37639167 DOI: 10.1007/s10532-023-10051-4] [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: 01/11/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
PHB depolymerase enzymes are able to breakdown the PHB polymers and thereby get significant economic value in the bioplastics industry and for bioremediation as well. This study shows the purification of novel extracellular PHB depolymerase enzyme from Aeromonas caviae Kuk1-(34) using dialysis followed by gel filtration and HPLC. The purification fold and yield after HPLC were 45.92 and 27.04%, respectively. HPLC data showed a single peak with a retention time of 1.937 min. GC-MS analysis reveals the presence of three compounds, of which 1-Dodecanol was found to be most significant with 54.48% area and 8.623-min retention time (RT). The molecular weight of the purified enzyme was obtained as 35 kDa with Km and apparent Vmax values of 0.769 mg/mL and 1.89 U/mL, respectively. The enzyme was moderately active at an optimum temperature of 35 °C and at pH 8.0. The stability was detected at pH 7.0-9.0 and 35-45 °C. Complete activity loss was observed with EDTA, SDS, Tween-20 at 5 mM and with 0.1% Triton X 100. A biodegradation study of commercially available biodegradable polymer films was carried out in a liquid medium and in soil separately with pure microbial culture and with purified enzyme for 7, 14, 28, and 49 consecutive days. In a liquid medium, with a pure strain of Aeromonas caviae Kuk1-(34), the maximum degradation (89%) was achieved on the PHB film, while no changes were observed with other polymer films. With purified enzyme in the soil, 71% degradation of the PHB film was noticed, and it was only 18% in the liquid medium. All such weight analysis were confirmed by SEM images where several holes, pits, grooves, crest, and surface roughness are clearly observed. Our results demonstrated the potential utility of Aeromonas caviae Kuk1-(34) as a source of extracellular PHB depolymerase capable of degrading PHB under a wide range of natural/ lab conditions.
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Affiliation(s)
- Mohd Amir
- Protein research Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Naushin Bano
- Protein research Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Anamika Gupta
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP, India
| | - Mohd Rehan Zaheer
- Department of Chemistry, R.M.P.S.P. Girls Post Graduate College, Basti, Uttar Pradesh, 272301, India
| | - Roohi
- Protein research Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, 226026, India.
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Takimoto R, Tatemichi Y, Aoki W, Kosaka Y, Minakuchi H, Ueda M, Kuroda K. A critical role of an oxygen-responsive gene for aerobic nitrogenase activity in Azotobacter vinelandii and its application to Escherichia coli. Sci Rep 2022; 12:4182. [PMID: 35264690 PMCID: PMC8907163 DOI: 10.1038/s41598-022-08007-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Since nitrogenase is irreversibly inactivated within a few minutes after exposure to oxygen, current studies on the heterologous expression of nitrogenase are limited to anaerobic conditions. This study comprehensively identified genes showing oxygen-concentration-dependent expression only under nitrogen-fixing conditions in Azotobacter vinelandii, an aerobic diazotroph. Among the identified genes, nafU, with an unknown function, was greatly upregulated under aerobic nitrogen-fixing conditions. Through replacement and overexpressing experiments, we suggested that nafU is involved in the maintenance of nitrogenase activity under aerobic nitrogenase activity. Furthermore, heterologous expression of nafU in nitrogenase-producing Escherichia coli increased nitrogenase activity under aerobic conditions by 9.7 times. Further analysis of NafU protein strongly suggested its localization in the inner membrane and raised the possibility that this protein may lower the oxygen concentration inside the cells. These findings provide new insights into the mechanisms for maintaining stable nitrogenase activity under aerobic conditions in A. vinelandii and provide a platform to advance the use of nitrogenase under aerobic conditions.
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Affiliation(s)
- Ren Takimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuki Tatemichi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuishin Kosaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | | | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
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Müller-Santos M, Koskimäki JJ, Alves LPS, de Souza EM, Jendrossek D, Pirttilä AM. The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol Rev 2021; 45:fuaa058. [PMID: 33118006 DOI: 10.1093/femsre/fuaa058] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Therefore, it is widely believed that the function of PHB is to serve as a mobilizable carbon repository when bacteria face carbon limitation, supporting their survival. However, recent findings indicate that bacteria switch from PHB synthesis to mobilization under stress conditions such as thermal and oxidative shock. The mobilization products, 3-hydroxybutyrate and its oligomers, show a protective effect against protein aggregation and cellular damage caused by reactive oxygen species and heat shock. Thus, bacteria should have an environmental monitoring mechanism directly connected to the regulation of the PHB metabolism. Here, we review the current knowledge on PHB physiology together with a summary of recent findings on novel functions of PHB in stress resistance. Potential applications of these new functions are also presented.
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Affiliation(s)
- Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Luis Paulo Silveira Alves
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
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