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Roccor R, Wolf ME, Liu J, Eltis LD. The catabolism of ethylene glycol by Rhodococcus jostii RHA1 and its dependence on mycofactocin. Appl Environ Microbiol 2024:e0041624. [PMID: 38837369 DOI: 10.1128/aem.00416-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and also generated in the degradation of plastics such as polyethylene terephthalate. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1's tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams.IMPORTANCEEthylene glycol (EG), a two-carbon (C2) alcohol, is produced in high volumes for use in a wide variety of applications. There is burgeoning interest in understanding and engineering the bacterial catabolism of EG, in part to establish circular economic routes for its use. This study identifies an EG catabolic pathway in Rhodococcus, a genus of bacteria well suited for biocatalysis. This pathway is responsible for the catabolism of methanol, a C1 feedstock, in related bacteria. Finally, we describe strategies to increase the rate of degradation of EG by increasing the transformation of glycolaldehyde, a toxic metabolic intermediate. This work advances the development of biocatalytic strategies to transform C2 feedstocks.
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Affiliation(s)
- Raphael Roccor
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Megan E Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
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Wolf ME, Lalande AT, Newman BL, Bleem AC, Palumbo CT, Beckham GT, Eltis LD. The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1. Appl Environ Microbiol 2024; 90:e0215523. [PMID: 38380926 PMCID: PMC10952524 DOI: 10.1128/aem.02155-23] [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: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.
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Affiliation(s)
- Megan E. Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anne T. Lalande
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Brianne L. Newman
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Chad T. Palumbo
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
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Wang L, Hou J, Yang K, Yu H, Zhang B, Liu Z, Zheng Y. Development of synthetic small regulatory RNA for Rhodococcus erythropolis. Biotechnol J 2024; 19:e2400022. [PMID: 38528342 DOI: 10.1002/biot.202400022] [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: 01/09/2024] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/27/2024]
Abstract
Rhodococci have been regarded as ideal chassis for biotransformation, biodegradation, and biosynthesis for their unique environmental persistence and robustness. However, most species of Rhodococcus are still difficult to metabolically engineer due to the lack of genetic tools and techniques. In this study, synthetic sRNA strategy was exploited for gene repression in R. erythropolis XP. The synthetic sRNA based on the RhlS scaffold from Pseudomonas aeruginosa functions better in repressing sfgfp expression than those based on E. coli MicC, SgrS, and P. aeruginosa PrrF1-2 scaffold. The RhlS-based sRNAs were applied to study the influence of sulfur metabolism on biodesulfurization (BDS) efficiency in R. erythropolis XP and successfully identified two genes involved in sulfur metabolism that affect the BDS efficiency significantly. The RhlS-based synthetic sRNAs show promise in the metabolic engineering of Rhodococcus and promote the industrial applications of Rhodococcus in environmental remediation and biosynthesis.
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Affiliation(s)
- Lijuan Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Jie Hou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, P.R. China
| | - Kun Yang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Haonan Yu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Zhiqiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P.R. China
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Sun W, Shahrajabian MH, Soleymani A. The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems. PLANTS (BASEL, SWITZERLAND) 2024; 13:613. [PMID: 38475460 DOI: 10.3390/plants13050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/17/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.
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Affiliation(s)
- Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali Soleymani
- Department of Agronomy and Plant Breeding, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan 81551-39998, Iran
- Plant Improvement and Seed Production Research Center, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan 81551-39998, Iran
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Pang AP, Wang Y, Zhang T, Gao F, Shen JD, Huang L, Zhou J, Zhang B, Liu ZQ, Zheng YG. Highly efficient production of rhamnolipid in P. putida using a novel sacB-based system and mixed carbon source. BIORESOURCE TECHNOLOGY 2024; 394:130220. [PMID: 38109979 DOI: 10.1016/j.biortech.2023.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Pseudomonas putida KT2440, a GRAS strain, has been used for synthesizing bulk and fine chemicals. However, the gene editing tool to metabolically engineer KT2440 showed low efficiency. In this study, a novel sacB-based system pK51mobsacB was established to improve the efficiency for marker-free gene disruption. Then the rhamnolipid synthetic pathway was introduced in KT2440 and genes of the competitive pathways were deleted to lower the metabolic burden based on pK51mobsacB. A series of endogenous and synthetic promoters were used for fine tuning rhlAB expression. The limited supply of dTDP-L-rhamnose was enhanced by heterologous rmlBDAC expression. Cell growth and rhamnolipid production were well balanced by using glucose/glycerol as mixed carbon sources. The final strain produced 3.64 g/L at shake-flask and 19.77 g/L rhamnolipid in a 5 L fermenter, the highest obtained among metabolically engineered KT2440, which implied the potential of KT2440 as a promising microbial cell factory for industrial rhamnolipid production.
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Affiliation(s)
- Ai-Ping Pang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Yun Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Teng Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Feng Gao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Ji-Dong Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Lianggang Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Junping Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [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: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [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: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Xue L, Zhao Y, Li L, Rao X, Chen X, Ma F, Yu H, Xie S. A key O-demethylase in the degradation of guaiacol by Rhodococcus opacus PD630. Appl Environ Microbiol 2023; 89:e0052223. [PMID: 37800939 PMCID: PMC10617553 DOI: 10.1128/aem.00522-23] [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: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 10/07/2023] Open
Abstract
Rhodococcus opacus PD630 is a high oil-producing strain with the ability to convert lignin-derived aromatics to high values, but limited research has been done to elucidate its conversion pathway, especially the upper pathways. In this study, we focused on the upper pathways and demethylation mechanism of lignin-derived aromatics metabolism by R. opacus PD630. The results of the aromatic carbon resource utilization screening showed that R. opacus PD630 had a strong degradation capacity to the lignin-derived methoxy-containing aromatics, such as guaiacol, 3,4-veratric acid, anisic acid, isovanillic acid, and vanillic acid. The gene of gcoAR, which encodes cytochrome P450, showed significant up-regulation when R. opacus PD630 grew on diverse aromatics. Deletion mutants of gcoAR and its partner protein gcoBR resulted in the strain losing the ability to grow on guaiacol, but no significant difference to the other aromatics. Only co-complementation alone of gcoAR and gcoBR restored the strain's ability to utilize guaiacol, demonstrating that both genes were equally important in the utilization of guaiacol. In vitro assays further revealed that GcoAR could convert guaiacol and anisole to catechol and phenol, respectively, with the production of formaldehyde as a by-product. The study provided robust evidence to reveal the molecular mechanism of R. opacus PD630 on guaiacol metabolism and offered a promising study model for dissecting the demethylation process of lignin-derived aromatics in microbes.IMPORTANCEAryl-O-demethylation is believed to be the key rate-limiting step in the catabolism of heterogeneous lignin-derived aromatics in both native and engineered microbes. However, the mechanisms of O-demethylation in lignin-derived aromatic catabolism remain unclear. Notably, guaiacol, the primary component unit of lignin, lacks in situ demonstration and illustration of the molecular mechanism of guaiacol O-demethylation in lignin-degrading bacteria. This is the first study to illustrate the mechanism of guaiacol metabolism by R. opacus PD630 in situ as well as characterize the purified key O-demethylase in vitro. This study provided further insight into the lignin metabolic pathway of R. opacus PD630 and could guide the design of an efficient biocatalytic system for lignin valorization.
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Affiliation(s)
- Le Xue
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiquan Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinran Rao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinjie Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fuying Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shangxian Xie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol 2023; 75:102353. [PMID: 37413959 DOI: 10.1016/j.mib.2023.102353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) technologies brought a transformative change in the way bacterial genomes are edited, and a plethora of studies contributed to developing multiple tools based on these approaches. Prokaryotic biotechnology benefited from the implementation of such genome engineering strategies, with an increasing number of non-model bacterial species becoming genetically tractable. In this review, we summarize the recent trends in engineering non-model microbes using CRISPR-Cas technologies, discussing their potential in supporting cell factory design towards biotechnological applications. These efforts include, among other examples, genome modifications as well as tunable transcriptional regulation (both positive and negative). Moreover, we examine how CRISPR-Cas toolkits for engineering non-model organisms enabled the exploitation of emergent biotechnological processes (e.g. native and synthetic assimilation of one-carbon substrates). Finally, we discuss our slant on the future of bacterial genome engineering for domesticating non-model organisms in light of the most recent advances in the ever-expanding CRISPR-Cas field.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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10
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Grechishnikova EG, Shemyakina AO, Novikov AD, Lavrov KV, Yanenko AS. Rhodococcus: sequences of genetic parts, analysis of their functionality, and development prospects as a molecular biology platform. Crit Rev Biotechnol 2023; 43:835-850. [PMID: 35786136 DOI: 10.1080/07388551.2022.2091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/19/2022] [Accepted: 05/12/2022] [Indexed: 12/19/2022]
Abstract
Rhodococcus bacteria are a fast-growing platform for biocatalysis, biodegradation, and biosynthesis, but not a platform for molecular biology. That is, Rhodococcus are not convenient for genetic engineering. One major issue for the engineering of Rhodococcus is the absence of a publicly available, curated, and commented collection of sequences of genetic parts that are functional in biotechnologically relevant species of Rhodococcus (R. erythropolis, R. rhodochrous, R. ruber, and R. jostii). Here, we present a collection of genetic parts for Rhodococcus (vector replicons, promoter regions, regulators, markers, and reporters) supported by a thorough analysis of their functionality. We also highlight and discuss the gaps in Rhodococcus-related genetic parts and techniques, which should be filled in order to make these bacteria a full-fledged molecular biology platform independent of Escherichia coli. We conclude that all major types of required genetic parts for Rhodococcus are available now, except multicopy replicons. As for model Rhodococcus strains, there is a particular shortage of strains with high electrocompetence levels and strains designed for solving specific genetic engineering tasks. We suggest that these obstacles are surmountable in the near future due to an intensification of research work in the field of genetic techniques for non-conventional bacteria.
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Affiliation(s)
- Elena G Grechishnikova
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Anna O Shemyakina
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Andrey D Novikov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Konstantin V Lavrov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Alexander S Yanenko
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
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11
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Zulfiqar U, Haider FU, Maqsood MF, Mohy-Ud-Din W, Shabaan M, Ahmad M, Kaleem M, Ishfaq M, Aslam Z, Shahzad B. Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil. PLANTS (BASEL, SWITZERLAND) 2023; 12:3147. [PMID: 37687393 PMCID: PMC10490184 DOI: 10.3390/plants12173147] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- University of Chinese Academy of Sciences, Beijing 100039, China
| | | | - Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan;
- Department of Soil and Environmental Sciences, Ghazi University, D. G. Khan 32200, Pakistan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Muhammad Shabaan
- Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan;
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
| | - Muhammad Kaleem
- Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Muhammad Ishfaq
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; (M.A.); (M.I.)
- Department of Agriculture, Extension, Azad Jammu & Kashmir, Pakistan
| | - Zoya Aslam
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Babar Shahzad
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
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12
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Zhang L, Zhao S, Chang C, Wang J, Yang C, Cheng Z. N-terminal loops at the tetramer interface of nitrile hydratase act as "hooks" determining resistance to high amide concentrations. Int J Biol Macromol 2023; 245:125531. [PMID: 37355073 DOI: 10.1016/j.ijbiomac.2023.125531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Nitrile hydratase (NHase) has been extensively utilized in industrial acrylamide production. However, the vulnerability to high concentrations of acrylamide limits its further application. Herein, we redesigned the N-terminal loop at the tetramer interface of a thermophilic NHase from Pseudonocardia thermophila JCM3095 (PtNHase), and its catalytic activity, resistance to high acrylamide concentrations, and thermostability were improved. Amino acid residues located in the N-terminal loop of the tetramer interface that are responsible for enhancing the resistance to high acrylamide concentrations were identified via static structural analysis and molecular dynamics simulations. A variant library was used to fine-tune the tetramer interface. Variant αL6T exhibited 3.5-fold greater resistance to 50% (v/v) acrylamide, whereas its activity was 1.2-fold higher than that of the wild-type (WT) enzyme, revealing no activity-stability trade-off. Compared to the use of Escherichia coli harboring the WT enzyme, the use of E. coli harboring αL6T increased the acrylamide concentration from 398.1 g/L to 500 g/L. Crystal structure-guided analysis of αL6T and molecular dynamics simulations revealed that increased enzyme surface hydration and the introduction of positive cross-correlation into the N-terminal loop of the tetramer interface caused the two loop regions to hook to each other, thus improving the resistance to high acrylamide concentrations.
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Affiliation(s)
- Leyi Zhang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shiyue Zhao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Cheng Chang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianan Wang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
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13
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [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: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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14
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Huang S, Xue Y, Zhou C, Ma Y. An efficient
CRISPR
/Cas9‐based genome editing system for alkaliphilic
Bacillus
sp.
N16
‐5 and application in engineering xylose utilization for
D
‐lactic acid production. Microb Biotechnol 2022; 15:2730-2743. [DOI: 10.1111/1751-7915.14131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Shiyong Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing China
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15
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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16
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Jiang W, Gao H, Sun J, Yang X, Jiang Y, Zhang W, Jiang M, Xin F. Current status, challenges and prospects for lignin valorization by using Rhodococcus sp. Biotechnol Adv 2022; 60:108004. [PMID: 35690272 DOI: 10.1016/j.biotechadv.2022.108004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022]
Abstract
Lignin represents the most abundant renewable aromatics in nature, which has complicated and heterogeneous structure. The rapid development of biotransformation technology has brought new opportunities to achieve the complete lignin valorization. Especially, Rhodococcus sp. possesses excellent capabilities to metabolize aromatic hydrocarbons degraded from lignin. Furthermore, it can convert these toxic compounds into high value added bioproducts, such as microbial lipids, polyhydroxyalkanoate and carotenoid et al. Accordingly, this review will discuss the potentials of Rhodococcus sp. as a cell factory for lignin biotransformation, including phenol tolerance, lignin depolymerization and lignin-derived aromatic hydrocarbon metabolism. The detailed metabolic mechanism for lignin biotransformation and bioproducts spectrum of Rhodococcus sp. will be comprehensively discussed. The available molecular tools for the conversion of lignin by Rhodococcus sp. will be reviewed, and the possible direction for lignin biotransformation in the future will also be proposed.
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Affiliation(s)
- Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Haiyan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Jingxiang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Xinyi Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
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17
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Wang X, Lu H, Li Q, Zhou Y, Zhou J. Comparative genome and transcriptome of Rhodococcus pyridinivorans GF3 for analyzing the detoxification mechanism of anthraquinone compounds. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113545. [PMID: 35453018 DOI: 10.1016/j.ecoenv.2022.113545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Anthraquinone compounds (ACs) could be efficiently degraded and detoxified by bacteria. However, the molecular mechanism of bacterial degradation and detoxification of ACs remains unclear. In this study, 1-aminoanthraquinone-2-sulfonate (ASA-2) was used as a model anthraquinone compound, the response mechanism of Rhodococcus pyridinivorans GF3 to ASA-2 using genomics and transcriptomics techniques was investigated. Comparative genome analysis showed that strain GF3 owned an especial gene region (Genes 1337-1399) containing the genes encoding cytochrome P450, monooxygenase, dehydrogenase and oxidoreductase, which did not commonly exist in Rhodococcus genus. The amino acid sequences of these genes were similar to those of the cleavage enzymes of anthraquinone ring in Aspergillus genus. Moreover, the transcriptions of Genes 1392-1394 (cytochrome 450 gene cluster) displayed 1.8-3.1-fold up-regulation under ASA-2 exposure. Meanwhile, as an intermediate product of ASA-2, catechol was degraded to acetyl-CoA, succinyl-CoA and pyruvate, resulting in the enhanced tricarboxylic acid cycle and ATP generation. This process also promoted the up-regulation of the genes encoding resistance, efflux, transporter and anti-oxidation pressure proteins, which were involved in resisting ASA-2 and maintaining the homeostasis of cells. These results provided us with a further understanding of the molecular mechanism of degradation and detoxification of ACs.
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Affiliation(s)
- Xiaolei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Qiansheng Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yang Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China; School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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18
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CRISPR-based metabolic engineering in non-model microorganisms. Curr Opin Biotechnol 2022; 75:102698. [PMID: 35217297 DOI: 10.1016/j.copbio.2022.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
Non-model microorganisms possess unique and versatile metabolic characteristics, offering great opportunities as cell factories for biosynthesis of target products. However, lack of efficient genetic tools for pathway engineering represents a big challenge to unlock the full production potential of these microbes. Over the past years, CRISPR systems have been extensively developed and applied to domesticate non-model microorganisms. In this paper, we summarize the current significant advances in designing and constructing CRISPR-mediated genetic modification systems in non-model microorganisms, such as bacteria, fungi and cyanobacteria. We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools. Moreover, the current barriers and future perspectives on improving the editing efficiency of CRISPR systems in non-model microorganisms are also discussed.
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19
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Abstract
Schism is the new normal for the bioeconomy concept. Since its proliferation in governments, the concept has been adapted to fit national or regional exigencies. Earlier this century the knowledge-based bioeconomy (KBBE) in Europe was seen as a technical and knowledge fix in the evolving sustainability landscape. At the OECD, the concept was further honed by imagining a future where biotechnologies contribute significantly to economic growth and development. Countries started to make national bioeconomy strategies. Some countries have diverged and made the bioeconomy both much larger and more general, involving a wide variety of sectors, such as industry, energy, healthcare, agriculture, aquaculture, forestry and fishing. Whatever the approach, what seems to be consistent is the need to reconcile environmental, social and economic sustainability. This paper attempts to establish one schism that could have ramifications for the future development of the bioeconomy. Some countries, including some of the largest economies but not exclusively so, are clearly following a biotechnology model, whereas others are clearly not. In the wake of the COVID-19 pandemic, biotechnologies offer outstanding potential in healthcare, although this sector is by no means included in all bioeconomy strategies. The paper also attempts to clarify how biotechnologies can address the grand challenges and the United Nations Sustainable Development Goals. The communities of scientists seem to have no difficulty with this, but citizens and governments find it more difficult. In fact, some biotechnologies are already well established, whereas others are emerging and more controversial.
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20
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Round JW, Robeck LD, Eltis LD. An Integrative Toolbox for Synthetic Biology in Rhodococcus. ACS Synth Biol 2021; 10:2383-2395. [PMID: 34428025 DOI: 10.1021/acssynbio.1c00292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.
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Affiliation(s)
- James W. Round
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Logan D. Robeck
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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21
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Liang Y, Wei Y, Jiao S, Yu H. A CRISPR/Cas9-based single-stranded DNA recombineering system for genome editing of Rhodococcus opacus PD630. Synth Syst Biotechnol 2021; 6:200-208. [PMID: 34430726 PMCID: PMC8365321 DOI: 10.1016/j.synbio.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
Genome engineering of Rhodococcus opacus PD630, an important microorganism used for the bioconversion of lignin, is currently dependent on inefficient homologous recombination. Although a CRISPR interference procedure for gene repression has previously been developed for R. opacus PD630, a CRISPR/Cas9 system for gene knockout has yet to be reported for the strain. In this study, we found that the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks (DSBs) were the major causes of the failure of conventional CRISPR/Cas9 technologies in R. opacus, even when augmented with the recombinases Che9c60 and Che9c61. We successfully developed an efficient single-stranded DNA (ssDNA) recombineering system coupled with CRISPR/Cas9 counter-selection, which facilitated rapid and scarless editing of the R. opacus genome. A two-plasmid system, comprising Cas9 driven by a weak Rhodococcus promoter Pniami, designed to prevent cytotoxicity, and a single-guide RNA (sgRNA) under the control of a strong constitutive promoter, was proven to be appropriate with respect to cleavage function. A novel recombinase, RrRecT derived from a Rhodococcus ruber prophage, was identified for the first time, which facilitated recombination of short ssDNA donors (40–80 nt) targeted to the lagging strand and enabled us to obtain a recombination efficiency up to 103-fold higher than that of endogenous pathways. Finally, by incorporating RrRecT and Cas9 into a single plasmid and then co-transforming cells with sgRNA plasmids and short ssDNA donors, we efficiently achieved gene disruption and base mutation in R. opacus, with editing efficiencies ranging from 22 % to 100 %. Simultaneous disruption of double genes was also confirmed, although at a lower efficiency. This effective genome editing tool will accelerate the engineering of R. opacus metabolism.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China
| | - Yuwen Wei
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China
| | - Song Jiao
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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22
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Alvarez HM, Hernández MA, Lanfranconi MP, Silva RA, Villalba MS. Rhodococcus as Biofactories for Microbial Oil Production. Molecules 2021; 26:molecules26164871. [PMID: 34443455 PMCID: PMC8401914 DOI: 10.3390/molecules26164871] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
Bacteria belonging to the Rhodococcus genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.
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23
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Shen JD, Cai X, Wang M, Liu ZQ, Zheng YG. Proposed mechanism for post-translational self-modification of Co-NHase based on Co 2+ diffusion limitation. Biotechnol J 2021; 16:e2100103. [PMID: 34363653 DOI: 10.1002/biot.202100103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Nitrile hydratase (NHase), was an excellent biocatalyst for the synthesis of amide compounds. NHase was typical heterodimeric metalloprotein, required of the assistance of activator for active expressions. In this work, we found a special Co-NHase HBA from Caldalkalibacillus thermarum, which had the ability of post-translational self-modification and could incorporate Co2+ into the catalytic center in the absence of activator. METHOD AND RESULTS We simulated the movement of Co2+ in silico and established a hypothetical model to predict the Co2+ incorporation efficiency (XCo ) of NHases. According to the simulation results, NHase mutants with different positive charge distribution were constructed. Compared with wild-type, the Co2+ incorporation efficiency of K1 (M10K) was increased by 2.1-fold from 0.36 to 0.76, and the specific activity was increased by 3.2-fold from 136.3 to 432.0 U/mg, while mutant K1H1 (M10K, D11H) and K2H2 (M10K, D11H, E20K, N21H) lost the ability of post-translation self-modification. CONCLUSIONS AND IMPLICATIONS The interactions of positively charged residues near the catalytic center, such as lysine with strong electrostatic repulsive interaction, arginine with weak electrostatic repulsive interaction and histidine with metal affinity, could limit the free diffusion of Co2+ in NHase and affect the efficiency of post-translational self-modification. This work also provided an effective strategy for protein engineering of NHases and other metalloenzymes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ji-Dong Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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24
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Donini E, Firrincieli A, Cappelletti M. Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes. Folia Microbiol (Praha) 2021; 66:701-713. [PMID: 34215934 PMCID: PMC8449775 DOI: 10.1007/s12223-021-00892-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/12/2021] [Indexed: 11/04/2022]
Abstract
Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique adaptation capacities to several stress conditions such as the presence of toxic compounds and environmental fluctuations. Additionally, the capability of Rhodococcus spp. strains to produce high value-added products has received considerable attention, mostly in relation to lipid accumulation. In relation with this, several works carried out omic studies and genome comparative analyses to investigate the genetic and genomic basis of these anabolic capacities, frequently in association with the bioconversion of renewable resources and low-cost substrates into triacylglycerols. This review is focused on these omic analyses and the genetic and metabolic approaches used to improve the biosynthetic and bioconversion performance of Rhodococcus. In particular, this review summarizes the works that applied heterologous expression of specific genes and adaptive laboratory evolution approaches to manipulate anabolic performance. Furthermore, recent molecular toolkits for targeted genome editing as well as genome-based metabolic models are described here as novel and promising strategies for genome-scaled rational design of Rhodococcus cells for efficient biosynthetic processes application.
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Affiliation(s)
- Eva Donini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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25
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Li N, Wang M, Yu S, Zhou J. Optimization of CRISPR-Cas9 through promoter replacement and efficient production of L-homoserine in Corynebacterium glutamicum. Biotechnol J 2021; 16:e2100093. [PMID: 34018325 DOI: 10.1002/biot.202100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Corynebacterium glutamicum is an important chassis for industrial applications. The low efficiency of commonly used genome editing methods for C. glutamicum limits the rapid multiple engineering of the bacterium. MAIN METHODS AND MAJOR RESULTS In this study, chromosome-borne expression of cas9 and recET from Escherichia coli K12-MG1655 was achieved to avoid toxicity to the strain, increase the probability of homologous recombination, and reduce loss of viability caused by double-strand breaks. Constitutive strong promoters, such as P45 , Ptrc , and PH36 , were used to replace PglyA and to expand the application of the CRISPR-Cas9 system. By using this system, a C. glutamicum strain producing L-homoserine to 22.1 g per L in a 5-L bioreactor after 96 h was obtained. CONCLUSIONS AND IMPLICATIONS Through the application of visualized fluorescent protein, the process of plasmid curing was optimized, obtain a continuous and rapid CRISPR-Cas9 genome editing system. The method described here could be useful to construct C. glutamicum mutant rapidly.
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Affiliation(s)
- Ning Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Miao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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26
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Lin Z, Li H, He L, Jing Y, Pistolozzi M, Wang T, Ye Y. Efficient genome editing for Pseudomonas aeruginosa using CRISPR-Cas12a. Gene 2021; 790:145693. [PMID: 33961975 DOI: 10.1016/j.gene.2021.145693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The CRISPR-Cas12a system has been demonstrated as an attractive tool for bacterial genome engineering. In particular, FnCas12a recognizes protospacer-adjacent motif (PAM) sites with medium or low GC content, which complements the Cas9-based systems. Here we explored Francisella novicida Cas12a (FnCas12a) for genome editing in Pseudomonas aeruginosa. By using a two-plasmid system expressing the constitutive FnCas12a nuclease, the inducible λRed recombinase, a CRISPR RNA (crRNA), we achieved gene deletion, insertion and replacement with high efficiency (in most cases > 75%), including the deletion of large DNA fragments up to 15 kb and the serial deletion of duplicate gene clusters. This work should provide a useful and complementary addition to the genome engineering toolbox for the study of P. aeruginosa biology and physiology.
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Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Huanhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Lan He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yanyun Jing
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Marco Pistolozzi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Tingting Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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27
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Dorado‐Morales P, Martínez I, Rivero‐Buceta V, Díaz E, Bähre H, Lasa I, Solano C. Elevated c-di-GMP levels promote biofilm formation and biodesulfurization capacity of Rhodococcus erythropolis. Microb Biotechnol 2021; 14:923-937. [PMID: 33128507 PMCID: PMC8085952 DOI: 10.1111/1751-7915.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022] Open
Abstract
Bacterial biofilms provide high cell density and a superior adaptation and protection from stress conditions compared to planktonic cultures, making them a very promising approach for bioremediation. Several Rhodococcus strains can desulfurize dibenzothiophene (DBT), a major sulphur pollutant in fuels, reducing air pollution from fuel combustion. Despite multiple efforts to increase Rhodococcus biodesulfurization activity, there is still an urgent need to develop better biocatalysts. Here, we implemented a new approach that consisted in promoting Rhodococcus erythropolis biofilm formation through the heterologous expression of a diguanylate cyclase that led to the synthesis of the biofilm trigger molecule cyclic di-GMP (c-di-GMP). R. erythropolis biofilm cells displayed a significantly increased DBT desulfurization activity when compared to their planktonic counterparts. The improved biocatalyst formed a biofilm both under batch and continuous flow conditions which turns it into a promising candidate for the development of an efficient bioreactor for the removal of sulphur heterocycles present in fossil fuels.
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Affiliation(s)
- Pedro Dorado‐Morales
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Igor Martínez
- Department of Systems BiologyCentro Nacional de BiotecnologíaAgencia Estatal Consejo Superior de Investigaciones CientíficasDarwin 3Madrid28049Spain
| | - Virginia Rivero‐Buceta
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Heike Bähre
- Research Core Unit MetabolomicsHannover Medical SchoolCarl‐Neuberg‐Straße 1Hannover30625Germany
| | - Iñigo Lasa
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Cristina Solano
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
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28
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Liang Y, Yu H. Genetic toolkits for engineering Rhodococcus species with versatile applications. Biotechnol Adv 2021; 49:107748. [PMID: 33823269 DOI: 10.1016/j.biotechadv.2021.107748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023]
Abstract
Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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29
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Singh R, Chandel S, Ghosh A, Dey D, Chakravarti R, Roy S, Ravichandiran V, Ghosh D. Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules. Mol Biotechnol 2021; 63:459-476. [PMID: 33774733 DOI: 10.1007/s12033-021-00310-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/14/2021] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas protein technology area is rapidly growing technique for genome editing and modulation of transcription of several microbes. Successful engineering in microbes requires an emphasis on the aspect of efficiency and targeted aiming, which can be employed using CRISPR/Cas system. Hence, this type of system is used to modify the genome of several microbes such as yeast and bacteria. In recent years, CRISPR/Cas systems have been chosen for metabolic engineering in microbes due to their specificity, orthogonality, and efficacy. Therefore, we need to review the scheme which was acquired for the execution of the CRISPR/Cas system for the modification and metabolic engineering in yeast and bacteria. In this review, we highlighted the application of the CRISPR/Cas system which has been used for the production of small molecules in the microbial system that is chemically and biologically important.
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Affiliation(s)
- Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Arijit Ghosh
- Department of Chemistry, University of Calcutta, Kolkata, 700009, India
| | - Dhritiman Dey
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Syamal Roy
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - V Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India.
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30
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Shemyakina AO, Grechishnikova EG, Novikov AD, Asachenko AF, Kalinina TI, Lavrov KV, Yanenko AS. A Set of Active Promoters with Different Activity Profiles for Superexpressing Rhodococcus Strain. ACS Synth Biol 2021; 10:515-530. [PMID: 33605147 DOI: 10.1021/acssynbio.0c00508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Rhodococcus bacteria are a promising platform for biodegradation, biocatalysis, and biosynthesis, but the use of rhodococci is hampered by the insufficient number of both platform strains for expression and promoters that are functional and thoroughly studied in these strains. To expand the list of such strains and promoters, we studied the expression capability of the Rhodococcus rhodochrous M33 strain, and the functioning of a set of recombinant promoters in it. We showed that the strain supports superexpression of the target enzyme (nitrile hydratase) using alternative inexpensive feedings-acetate and urea-without growth factor supplementation, thus being a suitable expression platform. The promoter set included Ptuf (elongation factor Tu) and Psod (superoxide dismutase) from Corynebacterium glutamicum ATCC13032, Pcpi (isocitrate lyase) from Rhodococcus erythropolis PR4, and Pnh (nitrile hydratase) from R. rhodochrous M8. Activity levels, regulation possibilities, and growth-phase-dependent activity profiles of these promoters were studied in derivatives of the M33 strain. The activities of the promoters were significantly different (Pcpi < Psod ≪ Ptuf < Pnh), covering 103-fold range, and the most active Pnh and Ptuf produced up to a 30-50% portion of target protein in soluble intracellular proteins. On the basis of the mRNA quantification and amount of target protein, the production level of Pnh was positioned close to the theoretical upper limit of expression in a bacterial cell. A selection method for the laboratory evolution of such active promoters directly in Rhodococcus was also proposed. Concerning regulation, Ptuf could not be regulated (2-fold change), while others were tunable (6-fold for Psod, 79-fold for Pnh, and 44-fold for Pcpi). The promoters possessed four different activity profiles, including three with peak of activity at different growth phases and one with constant activity throughout the growth phases. Ptuf and Pcpi did not change their activity profile under different growth conditions, whereas the Psod and Pnh profiles changed depending on the growth media. The results allow flexible construction of Rhodococcus strains using the studied promoters, and demonstrate a valuable approach for complex characterization of promoters intended for biotechnological strain construction.
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Affiliation(s)
- Anna O. Shemyakina
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Elena G. Grechishnikova
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Andrey D. Novikov
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Andrey F. Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences, Leninsky prospect 29, Moscow, 119991, Russia
| | - Tatyana I. Kalinina
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Konstantin V. Lavrov
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Alexander S. Yanenko
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
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31
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Heng E, Tan LL, Zhang MM, Wong FT. CRISPR-Cas strategies for natural product discovery and engineering in actinomycetes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Singhi D, Parwin S, Srivastava P. Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA. Microbiology (Reading) 2021; 167. [DOI: 10.1099/mic.0.001028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Several genome engineering methods have been developed for
Rhodococcus
. However, they suffer from limitations such as extensive cloning, multiple steps, successful expression of heterologous genes via plasmid etc. Here, we report a rapid method for performing genomic deletions/disruptions in
Rhodococcus
spp. using heterologous linear DNA. The method is cost effective and less labour intensive. The applicability of the method was demonstrated by successful disruption of rodA and orphan parA. None of the disrupted genes were found to be essential for the viability of the cell. Disruption of orphan parA and rodA resulted in elongated cells and short rods, respectively. This is the first report demonstrating disruption of rodA and orphan parA genes by electroporation of heterologous linear DNA in
Rhodococcus
spp.
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Affiliation(s)
- Divya Singhi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Shabnam Parwin
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
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33
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Abdullah, Jiang Z, Hong X, Zhang S, Yao R, Xiao Y. CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants. Synth Syst Biotechnol 2020; 5:277-292. [PMID: 32954022 PMCID: PMC7481536 DOI: 10.1016/j.synbio.2020.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA double-strand break (DSB), triggering cellular repair systems mainly Non-homologous end-joining (NHEJ, imprecise repair) or Homology-directed repair (HDR, precise repair). However, DSB typically leads to unexpected DNA changes and lethality in some organisms. The establishment of bacteria and plants into major bio-production platforms require efficient and precise editing tools. Hence, in this review, we focus on the non-DSB and template-free genome editing, i.e., base editing (BE) and prime editing (PE) in bacteria and plants. We first highlight the development of base and prime editors and summarize their studies in bacteria and plants. We then discuss current and future applications of BE/PE in synthetic biology, crop improvement, evolutionary engineering, and metabolic engineering. Lastly, we critically consider the challenges and prospects of BE/PE in PAM specificity, editing efficiency, off-targeting, sequence specification, and editing window.
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Affiliation(s)
- Abdullah
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengzheng Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xulin Hong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shun Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
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Liu H, Luo J, Shukla P. Effluents detoxification from pulp and paper industry using microbial engineering and advanced oxidation techniques. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122998. [PMID: 32502804 DOI: 10.1016/j.jhazmat.2020.122998] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Due to the high demand of paper and related items, pulp and paper industry is flourishing day by day. With increased production, come the hazards associated with the toxic elements present in the effluents. Various microorganisms are currently employed in the remediation of these toxic effluents. In addition, various techniques like ozonation, electrocoagulation, UV treatment, Fenton's reagent, and photo-Fenton based techniques are used in advanced oxidation processes to reduce these toxins from effluents. This review highlights various above mentioned advanced techniques and innovative processes along with the biological remediation of these toxic effluents with the help of some potential microbial consortia or their combinatory effects. Moreover, the present review will also disclose the ideas on utilizing the tools of metabolic engineering, systems biology, and artificial intelligence towards microbial engineering for relatively better bioremediation processes. In the future, these techniques might be helpful in increasing the capability of microbial consortia towards detoxification of effluents to make them environmentally safe. Finally, this review gives well-synchronized approaches to get more insights into these innovative methodologies and techniques and their use for various industrial applications.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Cappelletti M, Presentato A, Piacenza E, Firrincieli A, Turner RJ, Zannoni D. Biotechnology of Rhodococcus for the production of valuable compounds. Appl Microbiol Biotechnol 2020; 104:8567-8594. [PMID: 32918579 PMCID: PMC7502451 DOI: 10.1007/s00253-020-10861-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022]
Abstract
Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. KEY POINTS: • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance. Graphical abstract.
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Affiliation(s)
- Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), Florence, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Raymond J Turner
- Department of Biological Sciences, Calgary University, Calgary, AB, Canada
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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Luo JM, Cui HL, Jia HC, Li F, Cheng HJ, Shen YB, Wang M. Identification, Biological Characteristics, and Active Site Residues of 3-Ketosteroid Δ 1-Dehydrogenase Homologues from Arthrobacter simplex. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9496-9512. [PMID: 32786835 DOI: 10.1021/acs.jafc.0c03360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenase (KsdD) is the key enzyme responsible for Δ1-dehydrogenation, which is one of the most valuable reactions for steroid catabolism. Arthrobacter simplex has been widely used in the industry due to its superior bioconversion efficiency, but KsdD information is not yet fully clear. Here, five KsdD homologues were identified in A. simplex CGMCC 14539. Bioinformatic analysis indicated their distinct properties and structures. Each KsdD was functionally confirmed by transcriptional response, overexpression, and heterologous expression. The substantial difference in substrate profiles might be related to the enzyme loop structure. Two promising enzymes (KsdD3 and KsdD5) were purified and characterized, exhibiting strong organic solvent tolerance and clear preference for 4-ene-3-oxosteroids. KsdD5 seemed to be more versatile due to good activity on substrates with or without a substituent at C11 and high optimal temperature and also possessed unique residues. It is the first time that KsdDs have been comprehensively disclosed in the A. simplex industrial strain.
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Affiliation(s)
- Jian-Mei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Nankai University, Tianjin 300071, P. R. China
| | - Hui-Lin Cui
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Chen Jia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Fang Li
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Jin Cheng
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Yan-Bing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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Novel Chaperones RrGroEL and RrGroES for Activity and Stability Enhancement of Nitrilase in Escherichia coli and Rhodococcus ruber. Molecules 2020; 25:molecules25041002. [PMID: 32102340 PMCID: PMC7070999 DOI: 10.3390/molecules25041002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/15/2020] [Accepted: 02/21/2020] [Indexed: 12/15/2022] Open
Abstract
For large-scale bioproduction, thermal stability is a crucial property for most industrial enzymes. A new method to improve both the thermal stability and activity of enzymes is of great significance. In this work, the novel chaperones RrGroEL and RrGroES from Rhodococcus ruber, a nontypical actinomycete with high organic solvent tolerance, were evaluated and applied for thermal stability and activity enhancement of a model enzyme, nitrilase. Two expression strategies, namely, fusion expression and co-expression, were compared in two different hosts, E. coli and R. ruber. In the E. coli host, fusion expression of nitrilase with either RrGroES or RrGroEL significantly enhanced nitrilase thermal stability (4.8-fold and 10.6-fold, respectively) but at the expense of enzyme activity (32-47% reduction). The co-expression strategy was applied in R. ruber via either a plasmid-only or genome-plus-plasmid method. Through integration of the nitrilase gene into the R. ruber genome at the site of nitrile hydratase (NHase) gene via CRISPR/Cas9 technology and overexpression of RrGroES or RrGroEL with a plasmid, the engineered strains R. ruber TH3 dNHase::RrNit (pNV18.1-Pami-RrNit-Pami-RrGroES) and TH3 dNHase::RrNit (pNV18.1-Pami-RrNit-Pami-RrGroEL) were constructed and showed remarkably enhanced nitrilase activity and thermal stability. In particular, the RrGroEL and nitrilase co-expressing mutant showed the best performance, with nitrilase activity and thermal stability 1.3- and 8.4-fold greater than that of the control TH3 (pNV18.1-Pami-RrNit), respectively. These findings are of great value for production of diverse chemicals using free bacterial cells as biocatalysts.
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Jiao S, Li F, Yu H, Shen Z. Advances in acrylamide bioproduction catalyzed with Rhodococcus cells harboring nitrile hydratase. Appl Microbiol Biotechnol 2019; 104:1001-1012. [DOI: 10.1007/s00253-019-10284-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023]
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