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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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Grzesiak J, Rogala MM, Gawor J, Kouřilová X, Obruča S. Polyhydroxyalkanoate involvement in stress-survival of two psychrophilic bacterial strains from the High Arctic. Appl Microbiol Biotechnol 2024; 108:273. [PMID: 38520566 PMCID: PMC10960890 DOI: 10.1007/s00253-024-13092-8] [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: 01/05/2024] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/25/2024]
Abstract
An ever-growing body of literature evidences the protective role of polyhydroxyalkanoates (PHAs) against a plethora of mostly physical stressors in prokaryotic cells. To date, most of the research done involved bacterial strains isolated from habitats not considered to be life-challenging or extremely impacted by abiotic environmental factors. Polar region microorganisms experience a multitude of damaging factors in combinations rarely seen in other of Earth's environments. Therefore, the main objective of this investigation was to examine the role of PHAs in the adaptation of psychrophilic, Arctic-derived bacteria to stress conditions. Arctic PHA producers: Acidovorax sp. A1169 and Collimonas sp. A2191, were chosen and their genes involved in PHB metabolism were deactivated making them unable to accumulate PHAs (ΔphaC) or to utilize them (Δi-phaZ) as a carbon source. Varying stressors were applied to the wild-type and the prepared mutant strains and their survival rates were assessed based on CFU count. Wild-type strains with a functional PHA metabolism were best suited to survive the freeze-thaw cycle - a common feature of polar region habitats. However, the majority of stresses were best survived by the ΔphaC mutants, suggesting that the biochemical imbalance caused by the lack of PHAs induced a permanent cell-wide stress response thus causing them to better withstand the stressor application. Δi-phaZ mutants were superior in surviving UV irradiation, hinting that PHA granule presence in bacterial cells is beneficial despite it being biologically inaccessible. Obtained data suggests that the ability to metabolize PHA although important for survival, probably is not the most crucial mechanism in the stress-resistance strategies arsenal of cold-loving bacteria. KEY POINTS: • PHA metabolism helps psychrophiles survive freezing • PHA-lacking psychrophile mutants cope better with oxidative and heat stresses • PHA granule presence enhances the UV resistance of psychrophiles.
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Affiliation(s)
- Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
| | - Małgorzata Marta Rogala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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3
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Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023; 13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-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: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
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Mason-Jones K, Breidenbach A, Dyckmans J, Banfield CC, Dippold MA. Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth. Nat Commun 2023; 14:2240. [PMID: 37076457 PMCID: PMC10115882 DOI: 10.1038/s41467-023-37713-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 03/28/2023] [Indexed: 04/21/2023] Open
Abstract
The concept of biomass growth is central to microbial carbon (C) cycling and ecosystem nutrient turnover. Microbial biomass is usually assumed to grow by cellular replication, despite microorganisms' capacity to increase biomass by synthesizing storage compounds. Resource investment in storage allows microbes to decouple their metabolic activity from immediate resource supply, supporting more diverse microbial responses to environmental changes. Here we show that microbial C storage in the form of triacylglycerides (TAGs) and polyhydroxybutyrate (PHB) contributes significantly to the formation of new biomass, i.e. growth, under contrasting conditions of C availability and complementary nutrient supply in soil. Together these compounds can comprise a C pool 0.19 ± 0.03 to 0.46 ± 0.08 times as large as extractable soil microbial biomass and reveal up to 279 ± 72% more biomass growth than observed by a DNA-based method alone. Even under C limitation, storage represented an additional 16-96% incorporation of added C into microbial biomass. These findings encourage greater recognition of storage synthesis as a key pathway of biomass growth and an underlying mechanism for resistance and resilience of microbial communities facing environmental change.
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Affiliation(s)
- Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany.
| | - Andreas Breidenbach
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Jens Dyckmans
- Centre for Stable Isotope Research and Analysis, Georg-August University of Göttingen, Göttingen, Germany
| | - Callum C Banfield
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, Department of Crop Sciences, Georg-August University of Göttingen, Göttingen, Germany.
- Geo-Biosphere Interactions, Department of Geosciences, University of Tübingen, Tübingen, Germany.
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Kang BJ, Jeon JM, Bhatia SK, Kim DH, Yang YH, Jung S, Yoon JJ. Two-Stage Bio-Hydrogen and Polyhydroxyalkanoate Production: Upcycling of Spent Coffee Grounds. Polymers (Basel) 2023; 15:polym15030681. [PMID: 36771983 PMCID: PMC9919241 DOI: 10.3390/polym15030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Coffee waste is an abundant biomass that can be converted into high value chemical products, and is used in various renewable biological processes. In this study, oil was extracted from spent coffee grounds (SCGs) and used for polyhydroxyalkanoate (PHA) production through Pseudomonas resinovorans. The oil-extracted SCGs (OESCGs) were hydrolyzed and used for biohydrogen production through Clostridium butyricum DSM10702. The oil extraction yield through n-hexane was 14.4%, which accounted for 97% of the oil present in the SCGs. OESCG hydrolysate (OESCGH) had a sugar concentration of 32.26 g/L, which was 15.4% higher than that of the SCG hydrolysate (SCGH) (27.96 g/L). Hydrogen production using these substrates was 181.19 mL and 136.58 mL in OESCGH and SCGH media, respectively. The consumed sugar concentration was 6.77 g/L in OESCGH and 5.09 g/L in SCGH media. VFA production with OESCGH (3.58 g/L) increased by 40.9% compared with SCGH (2.54 g/L). In addition, in a fed-batch culture using the extracted oil, cell dry weight was 5.4 g/L, PHA was 1.6 g/L, and PHA contents were 29.5% at 24 h.
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Affiliation(s)
- Beom-Jung Kang
- Green & Sustainable Materials R&D Department, Korea Institute of Industrial Technology (KITECH), Chunan-si 31056, Republic of Korea
| | - Jong-Min Jeon
- Green & Sustainable Materials R&D Department, Korea Institute of Industrial Technology (KITECH), Chunan-si 31056, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, Konkuk University, Seoul 27478, Republic of Korea
| | - Do-Hyung Kim
- Sustainable Technology and Wellness R&D Group, Korea Institute of Industrial Technology (KITECH), Jeju-si 63243, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul 27478, Republic of Korea
| | - Sangwon Jung
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Republic of Korea
| | - Jeong-Jun Yoon
- Green & Sustainable Materials R&D Department, Korea Institute of Industrial Technology (KITECH), Chunan-si 31056, Republic of Korea
- Correspondence: ; Tel.: +82-41-589-8266
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA). BIOGEOCHEMISTRY 2023; 162:359-380. [PMID: 36873379 PMCID: PMC9971093 DOI: 10.1007/s10533-022-01008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments. Graphical Abstract Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-022-01008-5.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Díaz M, Bach T, González Anta G, Agaras B, Wibberg D, Noguera F, Canciani W, Valverde C. Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. strain 1008 T. FRONTIERS IN PLANT SCIENCE 2022; 13:894985. [PMID: 35968096 PMCID: PMC9369656 DOI: 10.3389/fpls.2022.894985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Pseudomonas sp. strain 1008 was isolated from the rhizosphere of field grown wheat plants at the tillering stage in an agricultural plot near Pergamino city, Argentina. Based on its in vitro phosphate solubilizing capacity and the production of IAA, strain 1008 was formulated as an inoculant for bacterization of wheat seeds and subjected to multiple field assays within the period 2010-2017. Pseudomonas sp. strain 1008 showed a robust positive impact on the grain yield (+8% on average) across a number of campaigns, soil properties, seed genotypes, and with no significant influence of the simultaneous seed treatment with a fungicide, strongly supporting the use of this biostimulant bacterium as an agricultural input for promoting the yield of wheat. Full genome sequencing revealed that strain 1008 has the capacity to access a number of sources of inorganic and organic phosphorus, to compete for iron scavenging, to produce auxin, 2,3-butanediol and acetoin, and to metabolize GABA. Additionally, the genome of strain 1008 harbors several loci related to rhizosphere competitiveness, but it is devoid of biosynthetic gene clusters for production of typical secondary metabolites of biocontrol representatives of the Pseudomonas genus. Finally, the phylogenomic, phenotypic, and chemotaxonomic comparative analysis of strain 1008 with related taxa strongly suggests that this wheat rhizospheric biostimulant isolate is a representative of a novel species within the genus Pseudomonas, for which the name Pseudomonas pergaminensis sp. nov. (type strain 1008T = DSM 113453T = ATCC TSD-287T) is proposed.
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Affiliation(s)
- Marisa Díaz
- Rizobacter Argentina S.A., Buenos Aires, Argentina
| | - Teresa Bach
- Rizobacter Argentina S.A., Buenos Aires, Argentina
| | - Gustavo González Anta
- Escuela de Ciencias Agrarias, Exactas y Naturales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA), Buenos Aires, Argentina
- Departamento de Ciencias Naturales y Exactas, Universidad Nacional de San Antonio de Areco (UNSAdA), Buenos Aires, Argentina
- Indrasa Biotecnología S.A., Córdoba, Argentina
| | - Betina Agaras
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | | | | | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
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8
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Mechanomodulatory Biomaterials Prospects in Scar Prevention and Treatment. Acta Biomater 2022; 150:22-33. [DOI: 10.1016/j.actbio.2022.07.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/25/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022]
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Hua X, Zhang C, Han J, Xu Y. pH regulatory divergent point for the selective bio-oxidation of primary diols during resting cell catalysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:73. [PMID: 35773746 PMCID: PMC9248139 DOI: 10.1186/s13068-022-02171-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/09/2022] [Indexed: 11/12/2022]
Abstract
Background Hydroxyl acid is an important platform chemical that covers many industrial applications due to its dual functional modules. At present, the traditional technology for hydroxyl acid production mainly adopts the petroleum route with benzene, cyclohexane, butadiene and other non-renewable resources as raw materials which violates the development law of green chemistry. Conversely, it is well-known that biotechnology and bioengineering techniques possess several advantages over chemical methods, such as moderate reaction conditions, high chemical selectivity, and environmental-friendly. However, compared with chemical engineering, there are still some major obstacles in the industrial application of biotechnology. The critical issue of the competitiveness between bioengineering and chemical engineering is products titer and volume productivity. Therefore, based on the importance of hydroxyl acids in many fields, exploring a clean, practical and environmental-friendly preparation process of the hydroxyl acids is the core purpose of this study. Results To obtain high-purity hydroxyl acid, a microbiological regulation for its bioproduction by Gluconobacter oxydans was constructed. In the study, we found a critical point of chain length determine the end-products. Gluconobacter oxydans catalyzed diols with chain length ≤ 4, forming hydroxyl acids, and converting 1,5-pentylene glycol and 1,6-hexylene glycol to diacids. Based on this principle, we successfully synthesized 75.3 g/L glycolic acid, 83.2 g/L 3-hydroxypropionic acid, and 94.3 g/L 4-hydroxybutyric acid within 48 h. Furthermore, we directionally controlled the products of C5/C6 diols by adjusting pH, resulting in 102.3 g/L 5‑hydroxyvaleric acid and 48.8 g/L 6-hydroxycaproic acid instead of diacids. Combining pH regulation and cell-recycling technology in sealed-oxygen supply bioreactor, we prepared 271.4 g 5‑hydroxyvaleric acid and 129.4 g 6-hydroxycaproic acid in 6 rounds. Conclusions In this study, a green scheme of employing G. oxydans as biocatalyst for superior-quality hydroxyl acids (C2–C6) production is raised up. The proposed strategy commendably demonstrated a novel technology with simple pH regulation for high-value production of hydroxyl acids via green bioprocess developments. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02171-5.
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Affiliation(s)
- Xia Hua
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - ChenHui Zhang
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - Jian Han
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - Yong Xu
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China. .,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China. .,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China.
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10
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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11
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Jaffur N, Jeetah P, Kumar G. A review on enzymes and pathways for manufacturing polyhydroxybutyrate from lignocellulosic materials. 3 Biotech 2021; 11:483. [PMID: 34790507 DOI: 10.1007/s13205-021-03009-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
Currently, major focus in the biopolymer field is being drawn on the exploitation of plant-based resources grounded on holistic sustainability trends to produce novel, affordable, biocompatible and environmentally safe polyhydroxyalkanoate biopolymers. The global PHA market, estimated at USD 62 Million in 2020, is predicted to grow by 11.2 and 14.2% between 2020-2024 and 2020-2025 correspondingly based on market research reports. The market is primarily driven by the growing demand for PHA products by the food packaging, biomedical, pharmaceutical, biofuel and agricultural sectors. One of the key limitations in the growth of the PHA market is the significantly higher production costs associated with pure carbon raw materials as compared to traditional polymers. Nonetheless, considerations such as consumer awareness on the toxicity of petroleum-based plastics and strict government regulations towards the prohibition of the use and trade of synthetic plastics are expected to boost the market growth rate. This study throws light on the production of polyhydroxybutyrate from lignocellulosic biomass using environmentally benign techniques via enzyme and microbial activities to assess its feasibility as a green substitute to conventional plastics. The novelty of the present study is to highlight the recent advances, pretreatment techniques to reduce the recalcitrance of lignocellulosic biomass such as dilute and concentrated acidic pretreatment, alkaline pretreatment, steam explosion, ammonia fibre explosion (AFEX), ball milling, biological pretreatment as well as novel emerging pretreatment techniques notably, high-pressure homogenizer, electron beam, high hydrostatic pressure, co-solvent enhanced lignocellulosic fractionation (CELF) pulsed-electric field, low temperature steep delignification (LTSD), microwave and ultrasound technologies. Additionally, inhibitory compounds and detoxification routes, fermentation downstream processes, life cycle and environmental impacts of recovered natural biopolymers, review green procurement policies in various countries, PHA strategies in line with the United Nations Sustainable Development Goals (SDGs) along with the fate of the spent polyhydroxybutyrate are outlined.
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Affiliation(s)
- Nausheen Jaffur
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Mauritius, Réduit, 80837 Mauritius
| | - Pratima Jeetah
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Mauritius, Réduit, 80837 Mauritius
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
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Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
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Post-Transcriptional Control in the Regulation of Polyhydroxyalkanoates Synthesis. Life (Basel) 2021; 11:life11080853. [PMID: 34440597 PMCID: PMC8401924 DOI: 10.3390/life11080853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
The large production of non-degradable petrol-based plastics has become a major global issue due to its environmental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated with their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available concerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forthcoming research on riboregulation, synthetic, and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure.
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Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature. Appl Environ Microbiol 2021; 87:e0092921. [PMID: 34160268 PMCID: PMC8357295 DOI: 10.1128/aem.00929-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, Halomonas sp. 363 and Paracoccus sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of Halomonas sp. 363 carries three phaC synthase genes and transcribes genes along three PHA pathways (I to III), whereas Paracoccus sp. 392 carries only one phaC gene and transcribes genes along one pathway (I). Thus, Halomonas sp. 363 has a versatile repertoire of phaC genes and pathways enabling production of both short- and medium-chain-length PHA products. IMPORTANCE Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, Halomonas sp. 363 and Paracoccus sp. 392, are able to produce various types of PHA from inexpensive carbon sources. Halomonas sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.
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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: 42] [Impact Index Per Article: 14.0] [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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Park K, Mrsny R. Are controlled release scientists doing enough for our environment? J Control Release 2021; 332:620-622. [PMID: 33741384 DOI: 10.1016/j.jconrel.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Kinam Park
- Purdue University, West Lafayette, Indiana, United States of America
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Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. Sci Rep 2021; 11:4836. [PMID: 33649356 PMCID: PMC7921382 DOI: 10.1038/s41598-021-84286-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/15/2021] [Indexed: 12/23/2022] Open
Abstract
To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.
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Nduko JM, Taguchi S. Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks From Renewable and Waste Resources. Front Bioeng Biotechnol 2021; 8:618077. [PMID: 33614605 PMCID: PMC7889595 DOI: 10.3389/fbioe.2020.618077] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are naturally occurring biopolymers produced by microorganisms. PHAs have become attractive research biomaterials in the past few decades owing to their extensive potential industrial applications, especially as sustainable alternatives to the fossil fuel feedstock-derived products such as plastics. Among the biopolymers are the bioplastics and oligomers produced from the fermentation of renewable plant biomass. Bioplastics are intracellularly accumulated by microorganisms as carbon and energy reserves. The bioplastics, however, can also be produced through a biochemistry process that combines fermentative secretory production of monomers and/or oligomers and chemical synthesis to generate a repertoire of biopolymers. PHAs are particularly biodegradable and biocompatible, making them a part of today's commercial polymer industry. Their physicochemical properties that are similar to those of petrochemical-based plastics render them potential renewable plastic replacements. The design of efficient tractable processes using renewable biomass holds key to enhance their usage and adoption. In 2008, a lactate-polymerizing enzyme was developed to create new category of polyester, lactic acid (LA)-based polymer and related polymers. This review aims to introduce different strategies including metabolic and enzyme engineering to produce LA-based biopolymers and related oligomers that can act as precursors for catalytic synthesis of polylactic acid. As the cost of PHA production is prohibitive, the review emphasizes attempts to use the inexpensive plant biomass as substrates for LA-based polymer and oligomer production. Future prospects and challenges in LA-based polymer and oligomer production are also highlighted.
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Affiliation(s)
- John Masani Nduko
- Department of Dairy and Food Science and Technology, Faculty of Agriculture, Egerton University, Egerton, Kenya
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
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Cha D, Ha HS, Lee SK. Metabolic engineering of Pseudomonas putida for the production of various types of short-chain-length polyhydroxyalkanoates from levulinic acid. BIORESOURCE TECHNOLOGY 2020; 309:123332. [PMID: 32305015 DOI: 10.1016/j.biortech.2020.123332] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Poly(3-hydroxybutyrate), a short-chain-length polyhydroxyalkanoate (scl-PHA), is considered as a good alternative to conventional synthetic plastics. However, various biopolymers with diverse characteristics are still in demand. In this study, four different types of scl-PHA were successfully produced by engineering levulinic acid (LA) utilization metabolic pathway and expressing heterologous PHA synthase (PhaEC), acetyl-CoA acetyltransferase (PhaA), and acetyl-CoA reductase (PhaB) in Pseudomonas putida EM42. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)], poly(3-hydroxyvalerate-co-4-hydroxyvalerate) [P(3HV-co-4HV)] and poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxyvalerate) [P(3HB-co-3HV-co-4HV)] were produced by the natural LA pathway, poly(4-hydroxyvalerate) by lvaAB-deleted LA pathway, and P(3HV-co-4HV) and P(3HB-co-3HV-co-4HV) with relatively high 3HV by fadB-deleted LA pathway. PHA with different monomer fractions could be produced using different PHA synthases. Scl-PHA contents reached approximately 40% of cell dry mass under non-optimized flask culture. This demonstrates that the LA catabolic pathway may be a good alternative route to provide monomers for the production of various types of PHA.
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Affiliation(s)
- Daegeun Cha
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Hyo Seok Ha
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Sung Kuk Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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20
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Fedeson DT, Saake P, Calero P, Nikel PI, Ducat DC. Biotransformation of 2,4-dinitrotoluene in a phototrophic co-culture of engineered Synechococcus elongatus and Pseudomonas putida. Microb Biotechnol 2020; 13:997-1011. [PMID: 32064751 PMCID: PMC7264894 DOI: 10.1111/1751-7915.13544] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/28/2022] Open
Abstract
In contrast to the current paradigm of using microbial mono-cultures in most biotechnological applications, increasing efforts are being directed towards engineering mixed-species consortia to perform functions that are difficult to programme into individual strains. In this work, we developed a synthetic microbial consortium composed of two genetically engineered microbes, a cyanobacterium (Synechococcus elongatus PCC 7942) and a heterotrophic bacterium (Pseudomonas putida EM173). These microbial species specialize in the co-culture: cyanobacteria fix CO2 through photosynthetic metabolism and secrete sufficient carbohydrates to support the growth and active metabolism of P. putida, which has been engineered to consume sucrose and to degrade the environmental pollutant 2,4-dinitrotoluene (2,4-DNT). By encapsulating S. elongatus within a barium-alginate hydrogel, cyanobacterial cells were protected from the toxic effects of 2,4-DNT, enhancing the performance of the co-culture. The synthetic consortium was able to convert 2,4-DNT with light and CO2 as key inputs, and its catalytic performance was stable over time. Furthermore, cycling this synthetic consortium through low nitrogen medium promoted the sucrose-dependent accumulation of polyhydroxyalkanoate, an added-value biopolymer, in the engineered P. putida strain. Altogether, the synthetic consortium displayed the capacity to remediate the industrial pollutant 2,4-DNT while simultaneously synthesizing biopolymers using light and CO2 as the primary inputs.
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Affiliation(s)
- Derek T. Fedeson
- DOE‐MSU Plant Research LaboratoriesMichigan State UniversityEast LansingMIUSA
- Genetics ProgramMichigan State UniversityEast LansingMIUSA
| | - Pia Saake
- Heinrich‐Heine UniversitätDüsseldorfGermany
| | - Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs LyngbyDenmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs LyngbyDenmark
| | - Daniel C. Ducat
- DOE‐MSU Plant Research LaboratoriesMichigan State UniversityEast LansingMIUSA
- Genetics ProgramMichigan State UniversityEast LansingMIUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMIUSA
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21
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Biosynthesis of functional polyhydroxyalkanoates by engineered Halomonas bluephagenesis. Metab Eng 2020; 59:119-130. [DOI: 10.1016/j.ymben.2020.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/07/2020] [Accepted: 02/25/2020] [Indexed: 11/23/2022]
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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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Tribelli PM, Pezzoni M, Brito MG, Montesinos NV, Costa CS, López NI. Response to lethal UVA radiation in the Antarctic bacterium Pseudomonas extremaustralis: polyhydroxybutyrate and cold adaptation as protective factors. Extremophiles 2019; 24:265-275. [DOI: 10.1007/s00792-019-01152-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
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Kumar V, Kumar S, Singh D. Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges. Int J Biol Macromol 2019; 147:1255-1267. [PMID: 31739043 DOI: 10.1016/j.ijbiomac.2019.09.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India.
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25
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Poly hydroxyalkanoates (PHA): Role in bone scaffolds. J Oral Biol Craniofac Res 2019; 10:389-392. [PMID: 31754599 DOI: 10.1016/j.jobcr.2019.10.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are prokaryotic macromolecules accumulated within the cytoplasm as granules. Due to their suitable mechanical properties, biocompatibility, degradation time, ability to be blended, surface modified, and form copolymers, it is widely used in medical devices and as scaffolds in bone tissue engineering. This review describes in brief the production and extraction sources, physico-chemical characteristic, mechanical properties, degradation rate and applications of various PHAs and its copolymers with special emphasis to its role as scaffolds in bone tissue engineering.
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26
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Ran G, Tan D, Zhao J, Fan F, Zhang Q, Wu X, Fan P, Fang X, Lu X. Functionalized polyhydroxyalkanoate nano-beads as a stable biocatalyst for cost-effective production of the rare sugar d-allulose. BIORESOURCE TECHNOLOGY 2019; 289:121673. [PMID: 31260936 DOI: 10.1016/j.biortech.2019.121673] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
d-Allulose is a promising low-calorie sweetener especially for diabetes and obesity patients. The functionalized polyhydroxyalkanoate (PHA) nano-beads decorated with d-tagatose 3-epimerase (DTE) was produced in recombinant endotoxin-free ClearColi, whereby the expression, purification, and immobilization of the active DTE were efficiently combined into one step. The immobilized DTE exhibited remarkable enzyme activity of 649.3 U/g beads and extremely high stability at a harsh working condition (pH 7.0-8.0, 65 °C). When DTE-PHA beads were subjected to enzymatic synthesis of d-allulose, a maximum conversion rate of 33% can be achieved at pH 7.0 and 65 °C for 3 h, and DTE-PHA beads retained about 80% of its initial activity after 8 continuous cycles. Moreover, the d-allulose/d-fructose binary mixture can be simply separated by a single cation exchange resin-equipped chromatography. Taken together, DTE-PHA beads are promising and robust nano-biocatalysts that will remarkably simplify the production procedures of d-allulose, contributing to its cost-effective production.
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Affiliation(s)
- Ganqiao Ran
- Institute of Bio-Agriculture of Shannxi Province, Xi'an 710043, Shaanxi, People's Republic of China; Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Dan Tan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Jiping Zhao
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Fan Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Qiang Zhang
- Institute of Bio-Agriculture of Shannxi Province, Xi'an 710043, Shaanxi, People's Republic of China
| | - Xingjuan Wu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Peiyao Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Xinlei Fang
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China
| | - Xiaoyun Lu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, People's Republic of China.
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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28
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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29
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OxyR and the hydrogen peroxide stress response in Caulobacter crescentus. Gene 2019; 700:70-84. [PMID: 30880241 DOI: 10.1016/j.gene.2019.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/22/2022]
Abstract
Oxidative stress generated by hydrogen peroxide is faced by bacteria when encountering hostile environments. In order to define the physiological and regulatory networks controlling the oxidative stress response in the free-living bacterium Caulobacter crescentus, a whole transcriptome analysis of wild type and ΔoxyR strains in the presence of hydrogen peroxide for two different exposure times was carried out. The C. crescentus response to H2O2 includes a decrease of the assimilative sulfate reduction and a shift in the amino acid synthesis pathways into favoring the synthesis of histidine. Moreover, the expression of genes encoding enzymes for the depolymerization of polyhydroxybutyrate was increased, and the RpoH-dependent genes were severely repressed. Based on the expression pattern and sequence analysis, we postulate that OxyR is probably directly required for the induction of three genes (katG, ahpCF). The putative binding of OxyR to the ahpC regulatory region could be responsible for the use of one of two alternative promoters in response to oxidative stress. Nevertheless, OxyR is required for the expression of 103 genes in response to H2O2. Fur and part of its regulon were differentially expressed in response to hydrogen peroxide independently of OxyR. The non-coding RNA OsrA was upregulated in both strains, and an in silico analysis indicated that it may have a regulatory role. This work characterizes the physiological response to H2O2 in C. crescentus, the regulatory networks and differentially regulated genes in oxidative stress and the participation of OxyR in this process. It is proposed that besides OxyR, a second layer of regulation may be achieved by a small regulatory RNA and other transcriptional regulators.
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30
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Synthesis of polyhydroxyalkanoates through the biodegradation of poly(cis-1,4-isoprene) rubber. J Biosci Bioeng 2019; 127:360-365. [DOI: 10.1016/j.jbiosc.2018.08.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/17/2018] [Accepted: 08/29/2018] [Indexed: 11/19/2022]
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31
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Buyel JF. Plant Molecular Farming - Integration and Exploitation of Side Streams to Achieve Sustainable Biomanufacturing. FRONTIERS IN PLANT SCIENCE 2019; 9:1893. [PMID: 30713542 PMCID: PMC6345721 DOI: 10.3389/fpls.2018.01893] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/06/2018] [Indexed: 05/22/2023]
Abstract
Plants have unique advantages over other systems such as mammalian cells for the production of valuable small molecules and proteins. The benefits cited most often include safety due to the absence of replicating human pathogens, simplicity because sterility is not required during production, scalability due to the potential for open-field cultivation with transgenic plants, and the speed of transient expression potentially providing gram quantities of product in less than 4 weeks. Initially there were also significant drawbacks, such as the need to clarify feed streams with a high particle burden and the large quantities of host cell proteins, but efficient clarification is now readily achieved. Several additional advantages have also emerged reflecting the fact that plants are essentially biodegradable, single-use bioreactors. This article will focus on the exploitation of this concept for the production of biopharmaceutical proteins, thus improving overall process economics. Specifically, we will discuss the single-use properties of plants, the sustainability of the production platform, and the commercial potential of different biomass side streams. We find that incorporating these side streams through rational process integration has the potential to more than double the revenue that can currently be achieved using plant-based production systems.
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Affiliation(s)
- Johannes F. Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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32
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Durante-Rodríguez G, de Lorenzo V, Nikel PI. A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli. ACS Synth Biol 2018; 7:2686-2697. [PMID: 30346720 DOI: 10.1021/acssynbio.8b00345] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most of the current methods for controlling the formation rate of a key protein or enzyme in cell factories rely on the manipulation of target genes within the pathway. In this article, we present a novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent control of the steady-state protein level and inducible accumulation of target proteins. The FENIX device is based on the constitutive, proteasome-dependent degradation of the target polypeptide by tagging with a short synthetic, hybrid NIa/SsrA amino acid sequence in the C-terminal domain. Protein production is triggered via addition of an orthogonal inducer ( i.e., 3-methylbenzoate) to the culture medium. The system was benchmarked in Escherichia coli by tagging two fluorescent proteins (GFP and mCherry), and further exploited to completely uncouple poly(3-hydroxybutyrate) (PHB) accumulation from bacterial growth. By tagging PhaA (3-ketoacyl-CoA thiolase, first step of the route), a dynamic metabolic switch at the acetyl-coenzyme A node was established in such a way that this metabolic precursor could be effectively redirected into PHB formation upon activation of the system. The engineered E. coli strain reached a very high specific rate of PHB accumulation (0.4 h-1) with a polymer content of ca. 72% (w/w) in glucose cultures in a growth-independent mode. Thus, FENIX enables dynamic control of metabolic fluxes in bacterial cell factories by establishing post-translational synthetic switches in the pathway of interest.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Environmental Microbiology Group, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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33
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Carbon flux to growth or polyhydroxyalkanoate synthesis under microaerophilic conditions is affected by fatty acid chain-length in Pseudomonas putida LS46. Appl Microbiol Biotechnol 2018; 102:6437-6449. [PMID: 29799090 DOI: 10.1007/s00253-018-9055-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
Economical production of medium-chain length polyhydroxyalkanoates (mcl-PHA) is dependent on efficient cultivation processes. This work describes growth and mcl-PHA synthesis characteristics of Pseudomonas putida LS46 when grown on medium-chain length fatty acids (octanoic acid) and lower-cost long-chain fatty acids (LCFAs, derived from hydrolyzed canola oil) in microaerophilic environments. Growth on octanoic acid ceased when the oxygen uptake rate was limited by the oxygen transfer rate, and mcl-PHA accumulated to 61.9% of the cell dry mass. From LCFAs, production of non-PHA cell mass continued at a rate of 0.36 g L-1 h-1 under oxygen-limited conditions, while mcl-PHA accumulated simultaneously to 31% of the cell dry mass. The titer of non-PHA cell mass from LCFAs at 14 h post-inoculation was double that obtained from octanoic acid in bioreactors operated with identical feeding and aeration conditions. While the productivity for octanoic acid was higher by 14 h, prolonged cultivation on LCFAs achieved similar productivity but with twice the PHA titer. Simultaneous co-feeding of each substrate demonstrated the continued cell growth under microaerophilic conditions characteristic of LCFAs, and the resulting polymer was dominant in C8 monomers. Furthermore, co-feeding resulted in improved PHA titer and volumetric productivity compared to either substrate individually. These results suggest that LCFAs improve growth of P. putida in oxygen-limited environments and could reduce production costs since more non-PHA cell mass, the cellular factories required to produce mcl-PHA and the most oxygen-intensive cellular process, can be produced for a given oxygen transfer rate.
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34
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Mozejko-Ciesielska J, Pokoj T, Ciesielski S. Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress. J Ind Microbiol Biotechnol 2018; 45:433-446. [PMID: 29736608 PMCID: PMC6028892 DOI: 10.1007/s10295-018-2042-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/27/2018] [Indexed: 01/15/2023]
Abstract
Bacterial response to environmental stimuli is essential for survival. In response to fluctuating environmental conditions, the physiological status of bacteria can change due to the actions of transcriptional regulatory machinery. The synthesis and accumulation of polyhydroxyalkanoates (PHAs) are one of the survival strategies in harsh environments. In this study, we used transcriptome analysis of Pseudomonas putida KT2440 to gain a genome-wide view of the mechanisms of environmental-friendly biopolymers accumulation under nitrogen-limiting conditions during conversion of metabolically different carbon sources (sodium gluconate and oleic acid). Transcriptomic data revealed that phaG expression is associated with medium-chain-length-PHAs' synthesis not only on sodium gluconate but also on oleic acid, suggesting that PhaG may play a role in this process, as well. Moreover, genes involved in the β-oxidation pathway were induced in the PHAs production phase when sodium gluconate was supplied as the only carbon and energy source. The transition from exponential growth to stationary phase caused a significant expression of genes involved in nitrogen metabolism, energy supply, and transport system. In this study, several molecular mechanisms, which drive mcl-PHAs synthesis, have been investigated. The identified genes may provide valuable information to improve the efficiency of this bioprocess and make it more economically feasible.
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Affiliation(s)
- Justyna Mozejko-Ciesielska
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Tomasz Pokoj
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FDO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R, Müller-Santos M. PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Front Microbiol 2018; 9:472. [PMID: 29599762 PMCID: PMC5862806 DOI: 10.3389/fmicb.2018.00472] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.
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Affiliation(s)
- Marcelo B Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Cícero S Teixeira
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z T Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luis P S Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Glaucio Valdameri
- Department of Clinical Analysis, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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Abstract
It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel "omic" technologies have presented evidence of the presence of other important features to thrive in cold. In this work, we analyze cold-adapted bacteria, looking for strategies involving novel features, and/or activation of non-classical metabolisms for a cold lifestyle. Metabolic traits related to energy generation, compounds and mechanisms involved in stress resistance and cold adaptation, as well as characteristics of the cell envelope, are analyzed in heterotrophic cold-adapted bacteria. In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments.
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Affiliation(s)
- Paula M Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
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Kaminski MA, Furmanczyk EM, Sobczak A, Dziembowski A, Lipinski L. Pseudomonas silesiensis sp. nov. strain A3 T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence. Syst Appl Microbiol 2018; 41:13-22. [DOI: 10.1016/j.syapm.2017.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/15/2022]
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Mozejko-Ciesielska J, Dabrowska D, Szalewska-Palasz A, Ciesielski S. Medium-chain-length polyhydroxyalkanoates synthesis by Pseudomonas putida KT2440 relA/spoT mutant: bioprocess characterization and transcriptome analysis. AMB Express 2017; 7:92. [PMID: 28497290 PMCID: PMC5427061 DOI: 10.1186/s13568-017-0396-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 04/26/2017] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas putida KT2440 is a model bacteria used commonly for medium-chain-length polyhydroxyalkanoates (mcl-PHAs) production using various substrates. However, despite many studies conducted on P. putida KT2440 strain, the molecular mechanisms of leading to mcl-PHAs synthesis in reaction to environmental stimuli are still not clear. The rearrangement of the metabolism in response to environmental stress could be controlled by stringent response that modulates the transcription of many genes in order to promote survival under nutritional deprivation conditions. Therefore, in this work we investigated the relation between mcl-PHAs synthesis and stringent response. For this study, a relA/spoT mutant of P. putida KT2440, unable to induce the stringent response, was used. Additionally, the transcriptome of this mutant was analyzed using RNA-seq in order to examine rearrangements of the metabolism during cultivation. The results show that the relA/spoT mutant of P. putida KT2440 is able to accumulate mcl-PHAs in both optimal and nitrogen limiting conditions. Nitrogen starvation did not change the efficiency of mcl-PHAs synthesis in this mutant. The transition from exponential growth to stationary phase caused significant upregulation of genes involved in transport system and nitrogen metabolism. Transcriptional regulators, including rpoS, rpoN and rpoD, did not show changes in transcript abundance when entering the stationary phase, suggesting their limited role in mcl-PHAs accumulation during stationary phase.
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39
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Recent Advances and Challenges towards Sustainable Polyhydroxyalkanoate (PHA) Production. Bioengineering (Basel) 2017; 4:bioengineering4020055. [PMID: 28952534 PMCID: PMC5590474 DOI: 10.3390/bioengineering4020055] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 05/29/2017] [Accepted: 06/09/2017] [Indexed: 12/22/2022] Open
Abstract
Sustainable biofuels, biomaterials, and fine chemicals production is a critical matter that research teams around the globe are focusing on nowadays. Polyhydroxyalkanoates represent one of the biomaterials of the future due to their physicochemical properties, biodegradability, and biocompatibility. Designing efficient and economic bioprocesses, combined with the respective social and environmental benefits, has brought together scientists from different backgrounds highlighting the multidisciplinary character of such a venture. In the current review, challenges and opportunities regarding polyhydroxyalkanoate production are presented and discussed, covering key steps of their overall production process by applying pure and mixed culture biotechnology, from raw bioprocess development to downstream processing.
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40
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Sánchez-Pascuala A, de Lorenzo V, Nikel PI. Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol 2017; 6:793-805. [PMID: 28121421 PMCID: PMC5440799 DOI: 10.1021/acssynbio.6b00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
Embden–Meyerhof–Parnas (EMP) pathway is generally
considered to be the biochemical standard for glucose catabolism.
Alas, its native genomic organization and the control of gene expression
in Escherichia coli are both very intricate, which
limits the portability of the EMP pathway to other biotechnologically
important bacterial hosts that lack the route. In this work, the genes
encoding all the enzymes of the linear EMP route have been individually
recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals,
and synthesized de novo following a standard (GlucoBrick)
that enables their grouping in the form of functional modules at the
user’s will. After verifying their activity in several glycolytic
mutants of E. coli, the versatility of these
GlucoBricks was demonstrated in quantitative physiology tests and
biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous
hosts. Specific configurations of GlucoBricks were also adopted to
streamline the downward circulation of carbon from hexoses to pyruvate
in E. coli recombinants, thereby resulting in
a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose.
Refactoring whole metabolic blocks in the fashion described in this
work thus eases the engineering of biochemical processes where the
optimization of carbon traffic is facilitated by the operation of
the EMP pathway—which yields more ATP than other glycolytic
routes such as the Entner–Doudoroff pathway.
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Affiliation(s)
- Alberto Sánchez-Pascuala
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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Immobilization of alkaline polygalacturonate lyase from Bacillus subtilis on the surface of bacterial polyhydroxyalkanoate nano-granules. Appl Microbiol Biotechnol 2017; 101:3247-3258. [PMID: 28105486 DOI: 10.1007/s00253-016-8085-4] [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: 09/26/2016] [Revised: 12/18/2016] [Accepted: 12/19/2016] [Indexed: 01/30/2023]
Abstract
Alkaline polygalacturonate lyase (PGL), one of the pectinolytic enzymes, has been widely used for the bioscouring of cotton fibers, biodegumming, and biopulp production. In our study, PGL from Bacillus subtilis was successfully immobilized on the surface of polyhydroxyalkanoate (PHA) nanogranules by fusing PGL to the N-terminal of PHA synthase from Ralstonia eutropha via a designed linker. The PGL-decorated PHA beads could be simply achieved by recombinant fermentation and consequent centrifugation. The fused PGL occupied 0.985% of the total weight of purified PHA granules, which was identified by mass spectrometer-based quantitative proteomics. The activity of immobilized PGL (184.67 U/mg PGL protein) was a little lower than that of the free PGL (215.93 U/mg PGL protein). The immobilization process did not affect the optimal pH and the optimal temperature of the PGL, but it did enhance the thermostability as well as the pH stability at certain conditions, which will extend the practicability of the immobilized PGL-PHA beads in the alkaline and generally harsh bioscouring process. Furthermore, the immobilized PGL still retained more than 60% of its initial activity after 8 cycles of reuse. Our study provided a novel and promising approach for cost-efficient in vivo PGL immobilization, contributing to wider commercialization of this environmental-friendly biocatalyst.
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Jezierska S, Van Bogaert INA. Crossing boundaries: the importance of cellular membranes in industrial biotechnology. J Ind Microbiol Biotechnol 2016; 44:721-733. [PMID: 27837352 DOI: 10.1007/s10295-016-1858-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/30/2016] [Indexed: 01/04/2023]
Abstract
How small molecules cross cellular membranes is an often overlooked issue in an industrial microbiology and biotechnology context. This is to a large extent governed by the technical difficulties to study these transport systems or by the lack of knowledge on suitable efflux pumps. This review emphasizes the importance of microbial cellular membranes in industrial biotechnology by highlighting successful strategies of membrane engineering towards more resistant and hence better performing microorganisms, as well as transporter and other engineering strategies for increased efflux of primary and secondary metabolites. Furthermore, the benefits and limitations of eukaryotic subcellular compartmentalization are discussed, as well as the biotechnological potential of membrane vesicles.
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Affiliation(s)
- Sylwia Jezierska
- Laboratory for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Inge N A Van Bogaert
- Laboratory for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Millán M, Segura D, Galindo E, Peña C. Molecular mass of poly-3-hydroxybutyrate (P3HB) produced by Azotobacter vinelandii is determined by the ratio of synthesis and degradation under fixed dissolved oxygen tension. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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44
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The CreC Regulator of Escherichia coli, a New Target for Metabolic Manipulations. Appl Environ Microbiol 2015; 82:244-54. [PMID: 26497466 DOI: 10.1128/aem.02984-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/15/2015] [Indexed: 11/20/2022] Open
Abstract
The CreBC (carbon source-responsive) two-component regulation system of Escherichia coli affects a number of functions, including intermediary carbon catabolism. The impacts of different creC mutations (a ΔcreC mutant and a mutant carrying the constitutive creC510 allele) on bacterial physiology were analyzed in glucose cultures under three oxygen availability conditions. Differences in the amounts of extracellular metabolites produced were observed in the null mutant compared to the wild-type strain and the mutant carrying creC510 and shown to be affected by oxygen availability. The ΔcreC strain secreted more formate, succinate, and acetate but less lactate under low aeration. These metabolic changes were associated with differences in AckA and LdhA activities, both of which were affected by CreC. Measurement of the NAD(P)H/NAD(P)(+) ratios showed that the creC510 strain had a more reduced intracellular redox state, while the opposite was observed for the ΔcreC mutant, particularly under intermediate oxygen availability conditions, indicating that CreC affects redox balance. The null mutant formed more succinate than the wild-type strain under both low aeration and no aeration. Overexpression of the genes encoding phosphoenolpyruvate carboxylase from E. coli and a NADH-forming formate dehydrogenase from Candida boidinii in the ΔcreC mutant further increased the yield of succinate on glucose. Interestingly, the elimination of ackA and adhE did not significantly improve the production of succinate. The diverse metabolic effects of this regulator on the central biochemical network of E. coli make it a good candidate for metabolic-engineering manipulations to enhance the formation of bioproducts, such as succinate.
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