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Chen J, Cui Y, Zhang S, Wu B, Han J, Xiang H. Unveiling the repressive mechanism of a PPS-like regulator (PspR) in polyhydroxyalkanoates biosynthesis network. Appl Microbiol Biotechnol 2024; 108:265. [PMID: 38498113 PMCID: PMC10948481 DOI: 10.1007/s00253-024-13100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024]
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a type of polyhydroxyalkanoates (PHA) that exhibits numerous outstanding properties and is naturally synthesized and elaborately regulated in various microorganisms. However, the regulatory mechanism involving the specific regulator PhaR in Haloferax mediterranei, a major PHBV production model among Haloarchaea, is not well understood. In our previous study, we showed that deletion of the phosphoenolpyruvate (PEP) synthetase-like (pps-like) gene activates the cryptic phaC genes in H. mediterranei, resulting in enhanced PHBV accumulation. In this study, we demonstrated the specific function of the PPS-like protein as a negative regulator of phaR gene expression and PHBV synthesis. Chromatin immunoprecipitation (ChIP), in situ fluorescence reporting system, and in vitro electrophoretic mobility shift assay (EMSA) showed that the PPS-like protein can bind to the promoter region of phaRP. Computational modeling revealed a high structural similarity between the rifampin phosphotransferase (RPH) protein and the PPS-like protein, which has a conserved ATP-binding domain, a His domain, and a predicted DNA-binding domain. Key residues within this unique DNA-binding domain were subsequently validated through point mutation and functional evaluations. Based on these findings, we concluded that PPS-like protein, which we now renamed as PspR, has evolved into a repressor capable of regulating the key regulator PhaR, and thereby modulating PHBV synthesis. This regulatory network (PspR-PhaR) for PHA biosynthesis is likely widespread among haloarchaea, providing a novel approach to manipulate haloarchaea as a production platform for high-yielding PHA. KEY POINTS: • The repressive mechanism of a novel inhibitor PspR in the PHBV biosynthesis was demonstrated • PspR is widespread among the PHA accumulating haloarchaea • It is the first report of functional conversion from an enzyme to a trans-acting regulator in haloarchaea.
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Affiliation(s)
- Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yinglu Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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2
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Sander K, Abel AJ, Friedline S, Sharpless W, Skerker J, Deutschbauer A, Clark DS, Arkin AP. Eliminating genes for a two-component system increases PHB productivity in Cupriavidus basilensis 4G11 under PHB suppressing, nonstress conditions. Biotechnol Bioeng 2024; 121:139-156. [PMID: 37638652 DOI: 10.1002/bit.28532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
Species of bacteria from the genus Cupriavidus are known, in part, for their ability to produce high amounts of poly-hydroxybutyrate (PHB) making them attractive candidates for bioplastic production. The native synthesis of PHB occurs during periods of metabolic stress, and the process regulating the initiation of PHB accumulation in these organisms is not fully understood. Screening an RB-TnSeq transposon library of Cupriavidus basilensis 4G11 allowed us to identify two genes of an apparent, uncharacterized two-component system, which when omitted from the genome enable increased PHB productivity in balanced, nonstress growth conditions. We observe average increases in PHB productivity of 56% and 41% relative to the wildtype parent strain upon deleting each gene individually from the genome. The increased PHB phenotype disappears, however, in nitrogen-free unbalanced growth conditions suggesting the phenotype is specific to fast-growing, replete, nonstress growth. Bioproduction modeling suggests this phenotype could be due to a decreased reliance on metabolic stress induced by nitrogen limitation to initiate PHB production in the mutant strains. Due to uncertainty in the two-component system's input signal and regulon, the mechanism by which these genes impart this phenotype remains unclear. Such strains may allow for the use of single-stage, continuous bioreactor systems, which are far simpler than many PHB bioproduction schemes used previously, given a similar product yield to batch systems in such a configuration. Bioproductivity modeling suggests that omitting this regulation in the cells may increase PHB productivity up to 24% relative to the wildtype organism when using single-stage continuous systems. This work expands our understanding of the regulation of PHB accumulation in Cupriavidus, in particular the initiation of this process upon transition into unbalanced growth regimes.
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Affiliation(s)
- Kyle Sander
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Anthony J Abel
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Skyler Friedline
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - William Sharpless
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
| | - Jeffrey Skerker
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Douglas S Clark
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Adam P Arkin
- Center for the Utilization of Biological Engineering in Space, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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3
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Martínez-Herrera RE, Alemán-Huerta ME, Rutiaga-Quiñones OM, de Luna-Santillana EJ, Elufisan TO. A comprehensive view of Bacillus cereus as a polyhydroxyalkanoate (PHA) producer: A promising alternative to Petroplastics. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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4
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Genome Analysis of Halomonas elongata Strain 153B and Insights Into Polyhydroxyalkanoate Synthesis and Adaptive Mechanisms to High Saline Environments. Curr Microbiol 2022; 80:18. [PMID: 36460760 DOI: 10.1007/s00284-022-03115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Species of the Halomonas genus are gram-negative, aerobic, moderately halophilic bacteria that synthesize polyhydroxyalkanoates (PHAs) and other high-value products that have a wide range of potential uses in the food, feed, cosmetics, pharmaceutical, and chemical sectors. Genome sequencing studies allow for the description and comparison of genetic traits with other strains and species, allowing for the exploration of the organism's potential, necessary to further biotechnology applications. Here, the genome of Halomonas elongata strain 153B was sequenced, its features compared to 5 other strains and 7 species, and a description of features for adaptations to hypersaline environments and bioproducts synthesis was done. Whole-genome analysis showed H. elongata 153B has more similar features to the reference strain H. elongata DSM 2581 compared to 4 other reported strains. Comparative genomics showed 2064 core genomic clusters between the strains and 666 singletons for strain 153B. Several genes in transport and signaling, osmoregulation, and oxidative stress that have roles in adaptation to environments with high osmolarity were also revealed. These appear to form an intricate network of overlapping systems carefully coordinated to bring about adaptation. H. elongata 153B genes for the synthesis of PHAs, ectoine, vitamins, and the degradation of drugs and aromatic compounds were described. The results will aid in the study of halophile physiology, provide a mine for valuable enzymes, and help speed up research for other biotechnology applications.
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Molecular Mechanisms and Applications of N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Bacteria. Molecules 2022; 27:molecules27217584. [PMID: 36364411 PMCID: PMC9654057 DOI: 10.3390/molecules27217584] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial biodiversity includes biotic and abiotic components that support all life forms by adapting to environmental conditions. Climate change, pollution, human activity, and natural calamities affect microbial biodiversity. Microbes have diverse growth conditions, physiology, and metabolism. Bacteria use signaling systems such as quorum sensing (QS) to regulate cellular interactions via small chemical signaling molecules which also help with adaptation under undesirable survival conditions. Proteobacteria use acyl-homoserine lactone (AHL) molecules as autoinducers to sense population density and modulate gene expression. The LuxI-type enzymes synthesize AHL molecules, while the LuxR-type proteins (AHL transcriptional regulators) bind to AHLs to regulate QS-dependent gene expression. Diverse AHLs have been identified, and the diversity extends to AHL synthases and AHL receptors. This review comprehensively explains the molecular diversity of AHL signaling components of Pseudomonas aeruginosa, Chromobacterium violaceum, Agrobacterium tumefaciens, and Escherichia coli. The regulatory mechanism of AHL signaling is also highlighted in this review, which adds to the current understanding of AHL signaling in Gram-negative bacteria. We summarize molecular diversity among well-studied QS systems and recent advances in the role of QS proteins in bacterial cellular signaling pathways. This review describes AHL-dependent QS details in bacteria that can be employed to understand their features, improve environmental adaptation, and develop broad biomolecule-based biotechnological applications.
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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7
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Liu X, Li D, Yan X, Zhang Z, Zheng S, Zhang J, Huang W, Wu F, Li F, Chen GQ. Rapid Quantification of Polyhydroxyalkanoates Accumulated in Living Cells Based on Green Fluorescence Protein-Labeled Phasins: The qPHA Method. Biomacromolecules 2022; 23:4153-4166. [PMID: 35786865 DOI: 10.1021/acs.biomac.2c00624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are microbial polyesters that have the potential to replace nonbiodegradable petroplastics. A real-time in situ PHA quantification method has long been awaited to replace the traditional method, which is time- and labor-consuming. Quantification of PHA in living cells was finally developed from fluorescence intensities generated from the green fluorescence protein (GFP) fused with the Halomonas bluephagenesis phasin proteins. Phasins PhaP1 and PhaP2 were used to fuse with GFP, which reflected PHA accumulation with an R-square of over 0.9. Also, a standard correlation was established to calculate PHA contents based on the fluorescence and cell density recorded via a microplate reader with an R-square of over 0.95 when grown on various substrates. The PhaP2-GFP containing H. bluephagenesis was applied successfully to quantify PHA synthesis in a 7.5 L fermenter with high precision. Moreover, the method was found to be feasible in non-natural PHA producers such as Escherichia coli, demonstrating its broad applicability.
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Affiliation(s)
- Xu Liu
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dianjie Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Xu Yan
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zonghao Zhang
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuang Zheng
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingpeng Zhang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Wuzhe Huang
- PhaBuilder Biotech Co., Ltd., Shunyi District, Zhaoquanying, Beijing 101309, China
| | - Fuqing Wu
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangting Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Lab for Industrial Biocatalysis, Department Chemical Engineering, Tsinghua University, Beijing 100084, China
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8
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Yasmin H, Bano A, Wilson NL, Nosheen A, Naz R, Hassan MN, Ilyas N, Saleem MH, Noureldeen A, Ahmad P, Kennedy I. Drought-tolerant Pseudomonas sp. showed differential expression of stress-responsive genes and induced drought tolerance in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2022; 174:e13497. [PMID: 34245030 DOI: 10.1111/ppl.13497] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/01/2021] [Accepted: 07/01/2021] [Indexed: 05/07/2023]
Abstract
The growth and persistence of rhizobacteria in soils are highly impacted by moisture stress. In this study, we report the first transcript analysis of four Pseudomonas strains (PS1, PS2, PS3, and PS4) isolated from the root-soil interface of rice and maize associated with different moisture levels during water deprivation. Filtered Pseudomonas sp. cells incubated at low (RH10%) and high (RH85%) relative humidity showed decreased survival of all Pseudomonas sp. at RH10% when compared with RH85%. RT-PCR showed differential expression of treS (trehalose synthase), rpoS (sigma factor), mucA (alginate regulatory gene), and fliM (flagellar motor switch protein gene) in response to exposure to RH10%. However, molecular fingerprinting and nutrient assimilation profile of Pseudomonas strains demonstrated genetic and physiological variation between the four strains irrespective of water regime and host. In vitro testing of these strains showed ACC deaminase activity and gibberellic acid, abscisic acid, indole acetic acid, and exopolysaccharide production. We determined that 50 μl of 1.2 × 103 CFU ml-1 of these Pseudomonas strains was enough to protect Arabidopsis plants against drought stress in a pot experiment. Inoculated plants increased their root colonization ability and biomass; however, PS2 showed higher survival (95%), relative water content (59%), chlorophyll (30%), glycine betaine (38%), proline (23%), and reduced MDA (43%) in shoots than irrigated control under induced water deprivation. It can be concluded that all Pseudomonas strains were effective in mitigating drought stress, however, PS2 appears to impart more resistance to drought than the other strains by upregulating key defense mechanisms.
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Affiliation(s)
- Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Asghari Bano
- Department of Biosciences, University of Wah, Wah Cantt, Pakistan
| | - Neil L Wilson
- Department of Agricultural Chemistry and Soil Science, University of Sydney, Sydney, New South Wales, Australia
| | - Asia Nosheen
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Rabia Naz
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | | | - Noshin Ilyas
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Hamzah Saleem
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ahmed Noureldeen
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Parvaiz Ahmad
- Department of Botany, S. P. College Srinagar, Jammu and Kashmir, India
| | - Ivan Kennedy
- Department of Agricultural Chemistry and Soil Science, University of Sydney, Sydney, New South Wales, Australia
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9
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Dudun AA, Akoulina EA, Zhuikov VA, Makhina TK, Voinova VV, Belishev NV, Khaydapova DD, Shaitan KV, Bonartseva GA, Bonartsev AP. Competitive Biosynthesis of Bacterial Alginate Using Azotobacter vinelandii 12 for Tissue Engineering Applications. Polymers (Basel) 2021; 14:polym14010131. [PMID: 35012152 PMCID: PMC8747204 DOI: 10.3390/polym14010131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
This study investigated the effect of various cultivation conditions (sucrose/phosphate concentrations, aeration level) on alginate biosynthesis using the bacterial producing strain Azotobacter vinelandii 12 by the full factorial design (FFD) method and physicochemical properties (e.g., rheological properties) of the produced bacterial alginate. We demonstrated experimentally the applicability of bacterial alginate for tissue engineering (the cytotoxicity testing using mesenchymal stem cells (MSCs)). The isolated synthesis of high molecular weight (Mw) capsular alginate with a high level of acetylation (25%) was achieved by FFD method under a low sucrose concentration, an increased phosphate concentration, and a high aeration level. Testing the viscoelastic properties and cytotoxicity showed that bacterial alginate with a maximal Mw (574 kDa) formed the densest hydrogels (which demonstrated relatively low cytotoxicity for MSCs in contrast to bacterial alginate with low Mw). The obtained data have shown promising prospects in controlled biosynthesis of bacterial alginate with different physicochemical characteristics for various biomedical applications including tissue engineering.
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Affiliation(s)
- Andrei A. Dudun
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Elizaveta A. Akoulina
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Vsevolod A. Zhuikov
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Tatiana K. Makhina
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Vera V. Voinova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Nikita V. Belishev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Dolgor D. Khaydapova
- Department of Soil Physics and Reclamation, Soil Science Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia;
| | - Konstantin V. Shaitan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
| | - Garina A. Bonartseva
- Research Center of Biotechnology of the Russian Academy of Sciences Leninsky Ave, 33, Bld. 2, 119071 Moscow, Russia; (A.A.D.); (V.A.Z.); (T.K.M.); (G.A.B.)
| | - Anton P. Bonartsev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; (E.A.A.); (V.V.V.); (N.V.B.); (K.V.S.)
- Correspondence: ; Tel.: +7-4959306306
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10
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Mitra R, Xu T, Chen GQ, Xiang H, Han J. An updated overview on the regulatory circuits of polyhydroxyalkanoates synthesis. Microb Biotechnol 2021; 15:1446-1470. [PMID: 34473895 PMCID: PMC9049629 DOI: 10.1111/1751-7915.13915] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are a promising and sustainable alternative to the petroleum‐based synthetic plastics. Regulation of PHA synthesis is receiving considerable importance as engineering the regulatory factors might help developing strains with improved PHA‐producing abilities. PHA synthesis is dedicatedly regulated by a number of regulatory networks. They tightly control the PHA content, granule size and their distribution in cells. Most PHA‐accumulating microorganisms have multiple regulatory networks that impart a combined effect on PHA metabolism. Among them, several factors ranging from global to specific regulators, have been identified and characterized till now. This review is an attempt to categorically summarize the diverse regulatory circuits that operate in some important PHA‐producing microorganisms. However, in several organisms, the detailed mechanisms involved in the regulation of PHA synthesis is not well‐explored and hence further research is needed. The information presented in this review might help researcher to identify the prevailing research gaps in PHA regulation.
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Affiliation(s)
- Ruchira Mitra
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,International College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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11
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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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12
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Sindhu R, Madhavan A, Arun KB, Pugazhendhi A, Reshmy R, Awasthi MK, Sirohi R, Tarafdar A, Pandey A, Binod P. Metabolic circuits and gene regulators in polyhydroxyalkanoate producing organisms: Intervention strategies for enhanced production. BIORESOURCE TECHNOLOGY 2021; 327:124791. [PMID: 33579565 DOI: 10.1016/j.biortech.2021.124791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Worldwide worries upsurge concerning environmental pollutions triggered by the accumulation of plastic wastes. Biopolymers are promising candidates for resolving these difficulties by replacing non-biodegradable plastics. Among biopolymers, polyhydroxyalkanoates (PHAs), are natural polymers that are synthesized and accumulated in a range of microorganisms, are considered as promising biopolymers since they have biocompatibility, biodegradability, and other physico-chemical properties comparable to those of synthetic plastics. Consequently, considerable research have been attempted to advance a better understanding of mechanisms related to the metabolic synthesis and characteristics of PHAs and to develop native and recombinant microorganisms that can proficiently produce PHAs comprising desired monomers with high titer and productivity for industrial applications. Recent developments in metabolic engineering and synthetic biology applied to enhance PHA synthesis include, promoter engineering, ribosome-binding site (RBS) engineering, development of synthetic constructs etc. This review gives a brief overview of metabolic routes and regulators of PHA production and its intervention strategies.
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Affiliation(s)
- Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ranjna Sirohi
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263 145, India
| | - Ayon Tarafdar
- Divison of Livestock Production and Management, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow 226 001, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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Borrero-de Acuña JM, Rohde M, Saldias C, Poblete-Castro I. Fed-Batch mcl- Polyhydroxyalkanoates Production in Pseudomonas putida KT2440 and Δ phaZ Mutant on Biodiesel-Derived Crude Glycerol. Front Bioeng Biotechnol 2021; 9:642023. [PMID: 33796510 PMCID: PMC8007980 DOI: 10.3389/fbioe.2021.642023] [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: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel industry. Pseudomonas bacteria metabolize the polyol into several biopolymers, including alginate and medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs). Although P. putida is a suited platform to derive these polyoxoesters from crude glycerol, the attained concentrations in batch and fed-batch cultures are still low. In this study, we employed P. putida KT2440 and the hyper-PHA producer ΔphaZ mutant in two different fed-batch modes to synthesize mcl-PHAs from raw glycerol. Initially, the cells grew in a batch phase (μmax 0.21 h–1) for 22 h followed by a carbon-limiting exponential feeding, where the specific growth rate was set at 0.1 (h–1), resulting in a cell dry weight (CDW) of nearly 50 (g L–1) at 40 h cultivation. During the PHA production stage, we supplied the substrate at a constant rate of 50 (g h–1), where the KT2440 and the ΔphaZ produced 9.7 and 12.7 gPHA L–1, respectively, after 60 h cultivation. We next evaluated the PHA production ability of the P. putida strains using a DO-stat approach under nitrogen depletion. Citric acid was the main by-product secreted by the cells, accumulating in the culture broth up to 48 (g L–1) under nitrogen limitation. The mutant ΔphaZ amassed 38.9% of the CDW as mcl-PHA and exhibited a specific PHA volumetric productivity of 0.34 (g L–1 h–1), 48% higher than the parental KT2440 under the same growth conditions. The biosynthesized mcl-PHAs had average molecular weights ranging from 460 to 505 KDa and a polydispersity index (PDI) of 2.4–2.6. Here, we demonstrated that the DO-stat feeding approach in high cell density cultures enables the high yield production of mcl-PHA in P. putida strains using the industrial crude glycerol, where the fed-batch process selection is essential to exploit the superior biopolymer production hallmarks of engineered bacterial strains.
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Affiliation(s)
- José Manuel Borrero-de Acuña
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility of Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cesar Saldias
- Departamento de Química Física, Facultad de Química y Farmacia, Pontificia Universidad Católica de Chile, Macul, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Faculty of Life Sciences, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
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14
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Investigation of the Physiology of the Obligate Alkaliphilic Bacillus marmarensis GMBE 72 T Considering Its Alkaline Adaptation Mechanism for Poly(3-hydroxybutyrate) Synthesis. Microorganisms 2021; 9:microorganisms9020462. [PMID: 33672214 PMCID: PMC7926669 DOI: 10.3390/microorganisms9020462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/25/2022] Open
Abstract
The novel extreme obligate alkaliphilic Bacillus marmarensis DSM 21297 is known to produce polyhydroxybutyrate (PHB). However, the detailed mechanism of PHB synthesis in B. marmarensis is still unknown. Here, we investigated which metabolic pathways and metabolic enzymes are responsible for PHB synthesis in order to understand the regulatory pathway and optimize PHB synthesis in B. marmarensis. In accordance with the fact that beta-galactosidase, 3-hydroxyacyl-CoA dehydrogenase, and Enoyl-CoA hydratase together with acyl-CoA dehydrogenase and lipase were annotated in B. marmarensis according to the RAST server, we used glucose, lactose, and olive oil to understand the preferred metabolic pathway for the PHB synthesis. It was found that B. marmarensis produces PHB from glucose, lactose, and olive oil. However, the highest PHB titer and the highest amount of PHB synthesized per dry cell mass (YP/X) were achieved in the presence of lactose, as compared to glucose and olive oil. Additionally, in the absence of peptone, the amount of PHB synthesized is reduced for each carbon source. Interestingly, none of the carbon sources studied yielded an efficient PHB synthesis, and supplementation of the medium with potassium ions did not enhance PHB synthesis. According to these experimental results and the presence of annotated metabolic enzymes based on the RAST server, PHB accumulation in the cells of B. marmarensis could be improved by the level of the expression of 3-hydroxybutyryl-CoA dehydrogenase (1.1.1.157), which increases the production of NADPH. Additionally, the accumulation of 3-hydroxyacyl-CoA could enhance the production of PHB in B. marmarensis in the presence of fatty acids. To our knowledge, this is the first report investigating the regulatory system involved in the control of PHB metabolism of B. marmarensis.
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