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Mohammed Y, Ye D, He M, Wang H, Zhu Z, Sun Y. Production of Astaxanthin by Animal Cells via Introduction of an Entire Astaxanthin Biosynthetic Pathway. Bioengineering (Basel) 2023; 10:1073. [PMID: 37760175 PMCID: PMC10525450 DOI: 10.3390/bioengineering10091073] [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: 07/18/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Astaxanthin is a fascinating molecule with powerful antioxidant activity, synthesized exclusively by specific microorganisms and higher plants. To expand astaxanthin production, numerous studies have employed metabolic engineering to introduce and optimize astaxanthin biosynthetic pathways in microorganisms and plant hosts. Here, we report the metabolic engineering of animal cells in vitro to biosynthesize astaxanthin. This was accomplished through a two-step study to introduce the entire astaxanthin pathway into human embryonic kidney cells (HEK293T). First, we introduced the astaxanthin biosynthesis sub-pathway (Ast subp) using several genes encoding β-carotene ketolase and β-carotene hydroxylase enzymes to synthesize astaxanthin directly from β-carotene. Next, we introduced a β-carotene biosynthesis sub-pathway (β-Car subp) with selected genes involved in Ast subp to synthesize astaxanthin from geranylgeranyl diphosphate (GGPP). As a result, we unprecedentedly enabled HEK293T cells to biosynthesize free astaxanthin from GGPP with a concentration of 41.86 µg/g dry weight (DW), which represented 66.19% of the total ketocarotenoids (63.24 µg/g DW). Through optimization steps using critical factors in the astaxanthin biosynthetic process, a remarkable 4.14-fold increase in total ketocarotenoids (262.10 µg/g DW) was achieved, with astaxanthin constituting over 88.82%. This pioneering study holds significant implications for transgenic animals, potentially revolutionizing the global demand for astaxanthin, particularly within the aquaculture sector.
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Affiliation(s)
- Yousef Mohammed
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding Ye
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mudan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houpeng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.M.); (D.Y.); (M.H.); (H.W.); (Z.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
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Filluelo O, Ferrando J, Picart P. Metabolic engineering of Bacillus subtilis toward the efficient and stable production of C 30-carotenoids. AMB Express 2023; 13:38. [PMID: 37119332 PMCID: PMC10148934 DOI: 10.1186/s13568-023-01542-x] [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: 02/05/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023] Open
Abstract
Commercial carotenoid production is dominated by chemical synthesis and plant extraction, both of which are unsustainable and can be detrimental to the environment. A promising alternative for the mass production of carotenoids from both an ecological and commercial perspective is microbial synthesis. To date, C30 carotenoid production in Bacillus subtilis has been achieved using plasmid systems for the overexpression of biosynthetic enzymes. In the present study, we employed a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system to develop an efficient, safe, and stable C30 carotenoid-producing B. subtilis strain, devoid of plasmids and antibiotic selection markers. To this end, the expression levels of crtM (dehydrosqualene synthase) and crtN (dehydrosqualene desaturase) genes from Staphylococcus aureus were upregulated by the insertion of three gene copies into the chromosome of B. subtilis. Subsequently, the supply of the C30 carotenoid precursor farnesyl diphosphate (FPP), which is the substrate for CrtMN enzymes, was enhanced by expressing chromosomally integrated Bacillus megaterium-derived farnesyl diphosphate synthase (FPPS), a key enzyme in the FPP pathway, and abolishing the expression of farnesyl diphosphate phosphatase (YisP), an enzyme responsible for the undesired conversion of FPP to farnesol. The consecutive combination of these features resulted in a stepwise increased production of C30 carotenoids. For the first time, a B. subtilis strain that can endogenously produce C30 carotenoids has been constructed, which we anticipate will serve as a chassis for further metabolic engineering and fermentation optimization aimed at developing a commercial scale bioproduction process.
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Affiliation(s)
- Oriana Filluelo
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Jordi Ferrando
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain.
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Casas A, Bultelle M, Motraghi C, Kitney R. PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies. ACS Synth Biol 2022; 11:1272-1291. [PMID: 35261238 PMCID: PMC8938949 DOI: 10.1021/acssynbio.1c00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We present here a
newly developed workflow—which we have
called PASIV—designed to provide a solution to a practical
problem with design of experiments (DoE) methodology: i.e., what can
be done if the scoping phase of the DoE cycle is severely hampered
by burden and toxicity issues (caused by either the metabolite or
an intermediary), making it unreliable or impossible to proceed to
the screening phase? PASIV—standing for pooled approach, screening,
identification, and visualization—was designed so the (viable)
region of interest can be made to appear through an interplay between
biology and software. This was achieved by combining multiplex construction
in a pooled approach (one-pot reaction) with a viability assay and
with a range of bioinformatics tools (including a novel construct
matching tool). PASIV was tested on the exemplar of the lycopene pathway—under
stressful constitutive expression—yielding a region of interest
with comparatively stronger producers.
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Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
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López GD, Álvarez-Rivera G, Carazzone C, Ibáñez E, Leidy C, Cifuentes A. Bacterial Carotenoids: Extraction, Characterization, and Applications. Crit Rev Anal Chem 2021; 53:1239-1262. [PMID: 34915787 DOI: 10.1080/10408347.2021.2016366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.
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Affiliation(s)
- Gerson-Dirceu López
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | | | - Chiara Carazzone
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | - Chad Leidy
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
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López GD, Suesca E, Álvarez-Rivera G, Rosato AE, Ibáñez E, Cifuentes A, Leidy C, Carazzone C. Carotenogenesis of Staphylococcus aureus: New insights and impact on membrane biophysical properties. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158941. [PMID: 33862238 DOI: 10.1016/j.bbalip.2021.158941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Staphyloxanthin (STX) is a saccharolipid derived from a carotenoid in Staphylococcus aureus involved in oxidative-stress tolerance and antimicrobial peptide resistance. STX influences the biophysical properties of the bacterial membrane and has been associated to the formation of lipid domains in the regulation of methicillin-resistance. In this work, a targeted metabolomics and biophysical characterization study was carried out to investigate the biosynthetic pathways of carotenoids, and their impact on the membrane biophysical properties. Five different S. aureus strains were investigated, including three wild-type strains containing the crtM gene related to STX biosynthesis, a crtM-deletion mutant, and a crtMN plasmid-complemented variant. LC-DAD-MS/MS analysis of extracts allowed the identification of 34 metabolites related to carotenogenesis in S. aureus at different growth phases (8, 24 and 48 h), showing the progression of these metabolites as the bacteria advances into the stationary phase. For the first time, 22 members of a large family of carotenoids were identified, including STX and STX-homologues, as well as Dehydro-STX and Dehydro-STX-homologues. Moreover, thermotropic behavior of the CH2 stretch of lipid acyl chains in live cells by FTIR, show that the presence of STX increases acyl chain order at the bacterial growth temperature. Indeed, the cooperative melting event of the bacterial membrane, which occurs around 15 °C in the native strains, shifts with increased carotenoid content. These results show the diversity biosynthetic of carotenoids in S. aureus, and their influence on membrane biophysical properties.
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Affiliation(s)
- Gerson-Dirceu López
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá D.C., Colombia; Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia; Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Elizabeth Suesca
- Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia
| | | | - Adriana E Rosato
- Molecular Microbiology Diagnostics-Research, Riverside University Health System, Professor Loma Linda University, Moreno Valley, CA, USA
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Chad Leidy
- Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá D.C., Colombia.
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Hartz P, Gehl M, König L, Bernhardt R, Hannemann F. Development and application of a highly efficient CRISPR-Cas9 system for genome engineering in Bacillus megaterium. J Biotechnol 2021; 329:170-179. [PMID: 33600891 DOI: 10.1016/j.jbiotec.2021.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/11/2021] [Accepted: 02/10/2021] [Indexed: 12/26/2022]
Abstract
Bacillus megaterium has become increasingly important for the biotechnological production of valuable compounds of industrial and pharmaceutical importance. Despite recent advances in rational strain design of B. megaterium, these studies have been largely impaired by the lack of molecular tools that are not state-of-the-art for comprehensive genome engineering approaches. In the current work, we describe the adaptation of the CRISPR-Cas9 vector pJOE8999 to enable efficient genome editing in B. megaterium. Crucial modifications comprise the exchange of promoter elements and associated ribosomal binding sites as well as the implementation of a 5-fluorouracil based counterselection system to facilitate proper plasmid curing. In addition, the functionality and performance of the new CRISPR-Cas9 vector pMOE was successfully evaluated by chromosomal disruption studies of the endogenous β-galactosidase gene (BMD_2126) and demonstrated an outstanding efficiency of 100 % based on combinatorial pheno- and genotype analyses. Furthermore, pMOE was applied for the genomic deletion of a steroid esterase gene (BMD_2256) that was identified among several other candidates as the gene encoding the esterase, which prevented accumulation of pharmaceutically important glucocorticoid esters. Recombinant expression of the bacterial chloramphenicol acetyltransferase 1 gene (cat1) in the resulting esterase deficient B. megaterium strain ultimately yielded C21-acetylated as well as novel C21-esterified derivates of cortisone.
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Affiliation(s)
- Philip Hartz
- Department of Biochemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany
| | - Manuel Gehl
- Department of Biochemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany; Present address: Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Lisa König
- Department of Biochemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany
| | - Frank Hannemann
- Department of Biochemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany.
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Deciphering Pathways for Carotenogenesis in Haloarchaea. Molecules 2020; 25:molecules25051197. [PMID: 32155882 PMCID: PMC7179442 DOI: 10.3390/molecules25051197] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/20/2020] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Bacterioruberin and its derivatives have been described as the major carotenoids produced by haloarchaea (halophilic microbes belonging to the Archaea domain). Recently, different works have revealed that some haloarchaea synthetize other carotenoids at very low concentrations, like lycopene, lycopersene, cis- and trans-phytoene, cis- and trans-phytofluene, neo-β-carotene, and neo-α-carotene. However, there is still controversy about the nature of the pathways for carotenogenesis in haloarchaea. During the last decade, the number of haloarchaeal genomes fully sequenced and assembled has increased significantly. Although some of these genomes are not fully annotated, and many others are drafts, this information provides a new approach to exploring the capability of haloarchaea to produce carotenoids. This work conducts a deeply bioinformatic analysis to establish a hypothetical metabolic map connecting all the potential pathways involved in carotenogenesis in haloarchaea. Special interest has been focused on the synthesis of bacterioruberin in members of the Haloferax genus. The main finding is that in almost all the genus analyzed, a functioning alternative mevalonic acid (MVA) pathway provides isopentenyl pyrophosphate (IPP) in haloarchaea. Then, the main branch to synthesized carotenoids proceeds up to lycopene from which β-carotene or bacterioruberin (and its precursors: monoanhydrobacterioriberin, bisanhydrobacterioruberin, dihydrobisanhydrobacteriuberin, isopentenyldehydrorhodopsin, and dihydroisopenthenyldehydrorhodopsin) can be made.
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Nascimento FX, Hernández AG, Glick BR, Rossi MJ. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 25:e00406. [PMID: 31886139 PMCID: PMC6920507 DOI: 10.1016/j.btre.2019.e00406] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/05/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022]
Abstract
In this work, the stress-resistant Bacillus megaterium STB1 is characterized and its ability to promote plant growth under normal and stress conditions is demonstrated. The genomic sequence of this bacterium, and a detailed analysis of the genes involved in facilitating its stress resistance and plant growth-promoting activities is also reported. The B. megaterium STB1 genome is rich in genetic elements involved in multiple stress resistance, xenobiotic degradation, pathogen antagonistic activities, and other traits related to soil and rhizosphere colonization. Moreover, genes participating in the biosynthesis of auxins and cytokinins, the modulation of polyamines, GABA, brassinosteroids and ethylene levels were also found. Ultimately, this study brings new insights into the role of B. megaterium as a plant growth-promoting bacterium and opens new opportunities for the development of novel strategies for agriculture and biotechnology.
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Affiliation(s)
- Francisco X. Nascimento
- IBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, 2780-157, Portugal
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Anabel G. Hernández
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Márcio J. Rossi
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
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High-yield C11-oxidation of hydrocortisone by establishment of an efficient whole-cell system in Bacillus megaterium. Metab Eng 2019; 55:59-67. [DOI: 10.1016/j.ymben.2019.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/31/2019] [Accepted: 06/14/2019] [Indexed: 11/18/2022]
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Expanding the promoter toolbox of Bacillus megaterium. J Biotechnol 2019; 294:38-48. [DOI: 10.1016/j.jbiotec.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 02/02/2023]
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