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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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Matarredona L, García-Bonete MJ, Guío J, Camacho M, Fillat MF, Esclapez J, Bonete MJ. Global Lrp regulator protein from Haloferax mediterranei: Transcriptional analysis and structural characterization. Int J Biol Macromol 2024; 260:129541. [PMID: 38244746 DOI: 10.1016/j.ijbiomac.2024.129541] [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: 11/24/2023] [Revised: 01/03/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Haloferax mediterranei, an extreme halophilic archaeon thriving in hypersaline environments, has acquired significant attention in biotechnological and biochemical research due to its remarkable ability to flourish in extreme salinity conditions. Transcription factors, essential in regulating diverse cellular processes, have become focal points in understanding its adaptability. This study delves into the role of the Lrp transcription factor, exploring its modulation of glnA, nasABC, and lrp gene promoters in vivo through β-galactosidase assays. Remarkably, our findings propose Lrp as the pioneering transcriptional regulator of nitrogen metabolism identified in a haloarchaeon. This study suggests its potential role in activating or repressing assimilatory pathway enzymes (GlnA and NasA). The interaction between Lrp and these promoters is analyzed using Electrophoretic Mobility Shift Assay and Differential Scanning Fluorimetry, highlighting l-glutamine's indispensable role in stabilizing the Lrp-DNA complex. Our research uncovers that halophilic Lrp forms octameric structures in the presence of l-glutamine. The study reveals the three-dimensional structure of the Lrp as a homodimer using X-ray crystallography, confirming this state in solution by Small-Angle X-ray Scattering. These findings illuminate the complex molecular mechanisms driving Hfx. mediterranei's nitrogen metabolism, offering valuable insights about its gene expression regulation and enriching our comprehension of extremophile biology.
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Affiliation(s)
- Laura Matarredona
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain
| | - María-José García-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine. University of Gothenburg, Sweden
| | - Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Mónica Camacho
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain
| | - María F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Institute for Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Julia Esclapez
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain.
| | - María-José Bonete
- Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Grupo Biotecnología de Extremófilos, Universidad de Alicante, San Vicente del Raspeig, Alicante, Spain.
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Dong H, Yang X, Shi J, Xiao C, Zhang Y. Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges. Polymers (Basel) 2023; 15:polym15102333. [PMID: 37242908 DOI: 10.3390/polym15102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.
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Affiliation(s)
- Huaming Dong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chunqiao Xiao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Analysis of the external signals driving the transcriptional regulation of the main genes involved in denitrification in Haloferax mediterranei. Front Microbiol 2023; 14:1109550. [PMID: 37007523 PMCID: PMC10062603 DOI: 10.3389/fmicb.2023.1109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
Haloferax mediterranei is the model microorganism for the study of the nitrogen cycle in haloarchaea. This archaeon not only assimilate N-species such as nitrate, nitrite, or ammonia, but also it can perform denitrification under low oxygen conditions, using nitrate or nitrite as alternative electron acceptors. However, the information currently available on the regulation of this alternative respiration in this kind of microorganism is scarce. Therefore, in this research, the study of haloarchaeal denitrification using H. mediterranei has been addressed by analyzing the promoter regions of the four main genes of denitrification (narGH, nirK, nor, and nosZ) through bioinformatics, reporter gene assays under oxic and anoxic conditions and by site-directed mutagenesis of the promoter regions. The results have shown that these four promoter regions share a common semi-palindromic motif that plays a role in the control of the expression levels of nor and nosZ (and probably nirK) genes. Regarding the regulation of the genes under study, it has been concluded that nirK, nor, and nosZ genes share some expression patterns, and therefore their transcription could be under the control of the same regulator whereas nar operon expression displays differences, such as the activation by dimethyl sulfoxide with respect to the expression in the absence of an electron acceptor, which is almost null under anoxic conditions. Finally, the study with different electron acceptors demonstrated that this haloarchaea does not need complete anoxia to perform denitrification. Oxygen concentrations around 100 μM trigger the activation of the four promoters. However, a low oxygen concentration per se is not a strong signal to activate the promoters of the main genes involved in this pathway; high activation also requires the presence of nitrate or nitrite as final electron acceptors.
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Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- *Correspondence: Carmen Pire,
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Replication Origin Deletion Enhances Poly(3-Hydroxybutyrate- co-3-Hydroxyvalerate) Synthesis in Haloarchaea. Microbiol Spectr 2022; 10:e0214922. [PMID: 36264235 PMCID: PMC9769981 DOI: 10.1128/spectrum.02149-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although the use of multiple replication origins for chromosome replication has been widely characterized in haloarchaea, whether it is possible to manipulate the chromosome copy number by their genetic engineering is not known, and how it would affect the cell functioning is poorly understood. Here, we demonstrate that deletion of the three active chromosomal origins in Haloferax mediterranei remarkably reduces its DNA amounts and ploidy numbers. Consequently, the mutant strain H. mediterranei Δ123 is more sensitive to UV and mitomycin C. Surprisingly, the cell size increases by 21.2%, and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production in shake flask culture enhances from 7.23 to 8.11 g/L in ΔEPSΔ123, although there is also a decrease in cell growth. In this mutant, the chromosomal copy number decreases, whereas the pha-encoding pHM300 megaplasmid copy number increases. Moreover, our transcriptome analysis reveals that the genes involved in primary metabolisms are significantly downregulated in ΔEPSΔ123, whereas those responsible for starch utilization and precursor supplying for PHBV monomers are upregulated. This indicates that more energy and carbon flux is redirected from primary metabolism to PHBV synthesis, thereby enhancing its PHBV accumulation. These findings may therefore provide a rational design to enhance PHBV synthesis by simply tuning the replication origins to modulate the chromosome/megaplasmid copy number ratio and subsequently influence cellular metabolism and physiological functions. IMPORTANCE The haloarchaeon Haloferax mediterranei is a potential producer of PHBV (100% biodegradable plastic) from inexpensive carbon sources. We previously reported that H. mediterranei possessed three active chromosomal origins and, when these origins were deleted, a dormant origin was activated to initiate the replication of chromosome. In this context, in the present study, we first found a close connection between replication initiation and PHBV accumulation. We describe the potential industrial advantages of the strain H. mediterranei ΔEPSΔ123, which includes the enlargement of cell volume by 21.2% and enhancement of PHBV production by 11.2%. We further reveal the possible mechanism that contributes to the greater PHBV production in the ΔEPSΔ123 strain. Overall, we provide here a conceptual advance in the field of synthetic biology by modulating chromosome replication to improve the production of bio-based chemicals.
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Miao C, Meng D, Liu Y, Wang F, Chen L, Huang Z, Fan X, Gu P, Li Q. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in metabolically recombinant Escherichia coli. Int J Biol Macromol 2021; 193:956-964. [PMID: 34751142 DOI: 10.1016/j.ijbiomac.2021.10.183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/08/2021] [Accepted: 10/23/2021] [Indexed: 11/25/2022]
Abstract
In this study, a phaCR gene encoding PHA synthase was identified in Rhodoligotrophos defluvii which was adjacent to β-ketothiolase encoded by phaAR gene and acetoacetyl-CoA reductase encoded by phaBR gene. Amino acid comparison of PhaCR showed the highest homology of 65.98% with PhaC of R. appendicifer, while its homology with typical class I PHA synthase in Cupriavidus necator was only 42.54%. PHA synthesis genes were then transformed into E. coli harboring phaCABR and phaCRABC which were cultured with 15 g/L glucose respectively, and 20.46 wt% and 16.95 wt% of CDW for poly(3-hydroxybutyrate) (PHB) were accumulated respectively. To further explore the effect of substrate specificity for PHA production, the ptsG gene was then deleted and 15 g/L glucose and 1.5 g/L propionate were co-employed as carbon sources, which enabled the synthesis of poly(3HB-co-3HV) copolymer. As a result, poly(3HB-co-3HV) was accumulated up to 24.74 wt% of CDW, and the highest content of 3-hydroxyvalerate (3HV) was 10.86 mol%. The Td5 was 260 °C, which implied that it possessed good thermal stability, and the Mw of GPC in recombinant strains were between 22 and 26 × 104 g/mol, and the highest PDI was 3.771. The structure of poly (3HB-co-3HV) copolymer was determined through 1H NMR analysis.
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Affiliation(s)
- Changfeng Miao
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Dong Meng
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuling Liu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Fang Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Lu Chen
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, China.
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, China.
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Rekhi P, Goswami M, Ramakrishna S, Debnath M. Polyhydroxyalkanoates biopolymers toward decarbonizing economy and sustainable future. Crit Rev Biotechnol 2021; 42:668-692. [PMID: 34645360 DOI: 10.1080/07388551.2021.1960265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polymers are synonymous with the modern way of living. However, polymers with a large carbon footprint, especially those derived from nonrenewable petrochemical sources, are increasingly perceived as detrimental to the environment and a sustainable future. Polyhydroxyalkanoate (PHA) is a microbial biopolymer and a plausible alternative for renewable sources. However, PHA in its monomeric forms has very limited applications due to its limited flexibility, tensile strength, and moldability. Herein, the life cycle of PHA molecules, from biosynthesis to commercial utilization for diverse applications is discussed. For clarity, the applications of this bioplastic biocomposite material are further segregated into two domains, namely, the industrial sector and the medical sector. The industry sectors reviewed here include food packaging, textiles, agriculture, automotive, and electronics. High-value addition of PHA for a sustainable future can be foreseen in the medical domain. Properties such as biodegradability and biocompatibility make PHA a suitable candidate for decarbonizing biomaterials during tissue repair, organ reconstruction, drug delivery, bone tissue engineering, and chemotherapeutics.
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Affiliation(s)
- Pavni Rekhi
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Moushmi Goswami
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Mousumi Debnath
- Department of Biosciences, Manipal University Jaipur, Jaipur, India
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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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