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Vivek K, Sandhia GS, Subramaniyan S. Extremophilic lipases for industrial applications: A general review. Biotechnol Adv 2022; 60:108002. [PMID: 35688350 DOI: 10.1016/j.biotechadv.2022.108002] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 06/02/2022] [Indexed: 01/10/2023]
Abstract
With industrialization and development in modern science enzymes and their applications increased widely. There is always a hunt for new proficient enzymes with novel properties to meet specific needs of various industrial sectors. Along with the high efficiency, the green and eco-friendly side of enzymes attracts human attention, as they form a true answer to counter the hazardous and toxic conventional industrial catalyst. Lipases have always earned industrial attention due to the broad range of hydrolytic and synthetic reactions they catalyse. When these catalytic properties get accompanied by features like temperature stability, pH stability, and solvent stability lipases becomes an appropriate tool for use in many industrial processes. Extremophilic lipases offer the same, thermostable: hot and cold active thermophilic and psychrophilic lipases, acid and alkali resistant and active acidophilic and alkaliphilic lipases, and salt tolerant halophilic lipases form excellent biocatalyst for detergent formulations, biofuel synthesis, ester synthesis, food processing, pharmaceuticals, leather, and paper industry. An interesting application of these lipases is in the bioremediation of lipid waste in harsh environments. The review gives a brief account on various extremophilic lipases with emphasis on thermophilic, psychrophilic, halophilic, alkaliphilic, and acidophilic lipases, their sources, biochemical properties, and potential applications in recent decades.
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Affiliation(s)
- K Vivek
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India
| | - G S Sandhia
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India
| | - S Subramaniyan
- Postgraduate Department of Botany and Research Centre (University of Kerala), University College, Thiruvananthapuram 695034, India.
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2
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Sandi J, Mata-Araya I, Aguilar F. Diversity of Lipase-Producing Microorganisms from Tropical Oilseeds Elaeis guineensis, Ricinus communis, and Jatropha curcas L. from Costa Rica. Curr Microbiol 2020; 77:943-952. [PMID: 31982967 DOI: 10.1007/s00284-020-01886-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
Tropical oleaginous seeds are an unexplored source for the discovery of novel lipolytic microorganisms, which could be applied to the bioremediation of agro-industrial oily wastes and solve numerous environmental issues. Such wastes hold potential to be revalorized towards a variety of products through microbial bioremediation. In this study, we investigate the microbial diversity and lipase activity from bacterial and fungal isolates obtained from the oil seeds of Elaeis guineensis, Ricinus communis, and Jatropha curcas L. from Costa Rica. A total of 27 strains were confirmed as lipase-producing strains via fluorogenic and colorimetric agar plate assays. The diversity of the isolates comprises 12 fungal ascomycetes from the genera Aspergillus and Fusarium and 15 bacterial isolates classified into four genera: Serratia, Proteus, Pseudomonas, and Bacillus. Microbial isolates from E. guineensis showed the highest diversity of lipolytic microorganisms (6 genera) followed by J. curcas (4 genera) and R. communis (2 genera). Isolates showing the highest activity in agar plates were tested further by submerged fermentation and the specific lipase activity was measured with 4-nitrophenyl laurate as substrate. Accordingly, the highest specific lipase activity was demonstrated by Bacillus pumilus B5 (24.98 U mg-1), Serratia marcescens B10 (17.65 U mg-1), Pseudomonas mendocina B16 (8.62 U mg-1), and Bacillus pumilus B1 (5.72 U mg-1) in submerged fermentation. These findings indicate the presence of a specialized microbial diversity in tropical oil seeds and highlight their potential to be applied in the bioremediation of agro-industrial oily wastes.
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Affiliation(s)
- Javier Sandi
- School of Biology, Costa Rican Institute of Technology, Cartago, Costa Rica
| | - Iray Mata-Araya
- Bioprocess Unit, National Center for Biotechnological Innovations of Costa Rica - CENIBiot, San José, Costa Rica
| | - Francisco Aguilar
- Bioprocess Unit, National Center for Biotechnological Innovations of Costa Rica - CENIBiot, San José, Costa Rica.
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Heater BS, Chan WS, Lee MM, Chan MK. Directed evolution of a genetically encoded immobilized lipase for the efficient production of biodiesel from waste cooking oil. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:165. [PMID: 31297153 PMCID: PMC6598307 DOI: 10.1186/s13068-019-1509-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/19/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND We have recently developed a one-step, genetically encoded immobilization approach based on fusion of a target enzyme to the self-crystallizing protein Cry3Aa, followed by direct production and isolation of the fusion crystals from Bacillus thuringiensis. Using this approach, Bacillus subtilis lipase A was genetically fused to Cry3Aa to produce a Cry3Aa-lipA catalyst capable of the facile conversion of coconut oil into biodiesel over 10 reaction cycles. Here, we investigate the fusion of another lipase to Cry3Aa with the goal of producing a catalyst suitable for the conversion of waste cooking oil into biodiesel. RESULTS Genetic fusion of the Proteus mirabilis lipase (PML) to Cry3Aa allowed for the production of immobilized lipase crystals (Cry3Aa-PML) directly in bacterial cells. The fusion resulted in the loss of PML activity, however, and so taking advantage of its genetically encoded immobilization, directed evolution was performed on Cry3Aa-PML directly in its immobilized state in vivo. This novel strategy allowed for the selection of an immobilized PML mutant with 4.3-fold higher catalytic efficiency and improved stability. The resulting improved Cry3Aa-PML catalyst could be used to catalyze the conversion of waste cooking oil into biodiesel for at least 15 cycles with minimal loss in conversion efficiency. CONCLUSIONS The genetically encoded nature of our Cry3Aa-fusion immobilization platform makes it possible to perform both directed evolution and screening of immobilized enzymes directly in vivo. This work is the first example of the use of directed evolution to optimize an enzyme in its immobilized state allowing for identification of a mutant that would unlikely have been identified from screening of its soluble form. We demonstrate that the resulting Cry3Aa-PML catalyst is suitable for the recyclable conversion of waste cooking oil into biodiesel.
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Affiliation(s)
- Bradley S. Heater
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Wai Shan Chan
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Marianne M. Lee
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Michael K. Chan
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, SAR China
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Shao H, Hu X, Sun L, Zhou W. Gene cloning, expression in E. coli, and in vitro refolding of a lipase from Proteus sp. NH 2-2 and its application for biodiesel production. Biotechnol Lett 2018; 41:159-169. [PMID: 30446859 DOI: 10.1007/s10529-018-2625-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/12/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To obtain active lipases for biodiesel production by refolding Proteus sp. lipase inclusion bodies expressed in E. coli. RESULTS A lipase gene lipPN1 was cloned from Proteus sp. NH 2-2 and expressed in E. coli BL21(DE3). Non-reducing SDS-PAGE revealed that recombinant LipPN1(rLipPN1) were prone to form inclusion bodies as disulfide-linked dimers in E. coli. Site-directed mutagenesis confirmed that Cys85 in LipPN1 was involved in the dimer formation. After optimizing the inclusion body refolding conditions, the maximum lipase activity reached 1662 U/L. The refolded rLipPN1 exhibited highest activity toward p-nitrophenyl butyrate at pH 9.0 and 40 °C. It could be activated by Ca2+ with moderate tolerance to organic solvents. It could also convert soybean oil into biodiesel at a conversion ratio of 91.5%. CONCLUSION Preventing the formation of disulfide bond could enhance the refolding efficiency of rLipPN1 inclusion bodies.
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Affiliation(s)
- Hua Shao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, People's Republic of China.
| | - Xianmei Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, People's Republic of China
| | - Liping Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, People's Republic of China
| | - Wenshan Zhou
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, People's Republic of China
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5
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High-level expression and characterization of solvent-tolerant lipase. J Biosci Bioeng 2018; 125:23-29. [DOI: 10.1016/j.jbiosc.2017.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 11/18/2022]
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6
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Gao B, Jiang S, Wang L, Zhang L, Wei D. Energy and conformation determine the enantioselectivity of enzyme. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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Production of itaconate by whole-cell bioconversion of citrate mediated by expression of multiple cis-aconitate decarboxylase (cadA) genes in Escherichia coli. Sci Rep 2017; 7:39768. [PMID: 28051098 PMCID: PMC5209708 DOI: 10.1038/srep39768] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022] Open
Abstract
Itaconate, a C5 unsaturated dicarboxylic acid, is an important chemical building block that is used in manufacturing high-value products, such as latex and superabsorbent polymers. Itaconate is produced by fermentation of sugars by the filamentous fungus Aspergillus terreus. However, fermentation by A. terreus involves a long fermentation period and the formation of various byproducts, resulting in high production costs. E. coli has been developed as an alternative for producing itaconate. However, fermentation of glucose gives low conversion yields and low productivity. Here, we report the whole-cell bioconversion of citrate to itaconate with enhanced aconitase and cis-aconitate decarboxylase activities by controlling the expression of multiple cadA genes. In addition, this bioconversion system does not require the use of buffers, which reduces the production cost and the byproducts released during purification. Using this whole-cell bioconversion system, we were able to catalyze the conversion of 319.8 mM of itaconate (41.6 g/L) from 500 mM citrate without any buffer system or additional cofactors, with 64.0% conversion in 19 h and a productivity of 2.19 g/L/h. Our bioconversion system suggests very high productivity for itaconate production.
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Yan J, Yan Y, Madzak C, Han B. Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway. Crit Rev Biotechnol 2015; 37:26-36. [DOI: 10.3109/07388551.2015.1104531] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zhuang S, Fu J, Powell C, Huang J, Xia Y, Yan R. Production of medium-chain volatile flavour esters in Pichia pastoris whole-cell biocatalysts with extracellular expression of Saccharomyces cerevisiae acyl-CoA:ethanol O-acyltransferase Eht1 or Eeb1. SPRINGERPLUS 2015; 4:467. [PMID: 26357598 PMCID: PMC4556718 DOI: 10.1186/s40064-015-1195-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/29/2015] [Indexed: 11/10/2022]
Abstract
Medium-chain volatile flavour esters are important molecules since they have extensive applications in food, fragrance, cosmetic, paint and coating industries, which determine different characteristics of aroma or taste in commercial products. Biosynthesis of these compounds by alcoholysis is catalyzed by acyl-CoA:ethanol O-acyltransferases Eht1 or Eeb1 in Saccharomyces cerevisiae. In this study, these two yeast enzymes were selected to explore their preparations as the form of whole cell biocatalysts for the production of volatile flavour esters. Here, the novel whole cell biocatalysts Pichia pastoris yeasts with functional extracellular expression of Eht1 or Eeb1 were constructed. Flavour production was established through an integrated process with coupled enzyme formation and ester biosynthesis in the recombinant yeasts in one pot, leading to the formation of volatile C6–C14 methyl and ethyl esters from wort medium. Interestingly, there is no significant difference between P. pastoris-EHT1 and P. pastoris-EEB1 in substrate preference during flavour biosynthesis, indicating a similar role of Eht1 and Eeb1 in P. pastoris cells, in contradiction with previous findings in S. cerevisiae to some extent. Consequently the study not only provides a greater understanding of these two enzymes in a heterogeneous host, but also demonstrated the positive effect of the recombinant Eht1 and Eeb1 in ester formation by P. pastoris live cells, potentially paving the way towards achieving efficient production of volatile flavour by an integrated biocatalytic system composed of recombinant enzyme production and flavour biosynthesis.
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Affiliation(s)
- Shiwen Zhuang
- School of Life Sciences, Tianjin University, Tianjin, China.,National Food Institute, Technical University of Denmark, 2800 Kg. Lyngby, Denmark
| | - Junshu Fu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Chris Powell
- Division of Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottinghamshire, UK
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yihe Xia
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruixiang Yan
- School of Life Sciences, Tianjin University, Tianjin, China
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11
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Borrelli GM, Trono D. Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications. Int J Mol Sci 2015; 16:20774-840. [PMID: 26340621 PMCID: PMC4613230 DOI: 10.3390/ijms160920774] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/17/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022] Open
Abstract
Lipases and phospholipases are interfacial enzymes that hydrolyze hydrophobic ester linkages of triacylglycerols and phospholipids, respectively. In addition to their role as esterases, these enzymes catalyze a plethora of other reactions; indeed, lipases also catalyze esterification, transesterification and interesterification reactions, and phospholipases also show acyltransferase, transacylase and transphosphatidylation activities. Thus, lipases and phospholipases represent versatile biocatalysts that are widely used in various industrial applications, such as for biodiesels, food, nutraceuticals, oil degumming and detergents; minor applications also include bioremediation, agriculture, cosmetics, leather and paper industries. These enzymes are ubiquitous in most living organisms, across animals, plants, yeasts, fungi and bacteria. For their greater availability and their ease of production, microbial lipases and phospholipases are preferred to those derived from animals and plants. Nevertheless, traditional purification strategies from microbe cultures have a number of disadvantages, which include non-reproducibility and low yields. Moreover, native microbial enzymes are not always suitable for biocatalytic processes. The development of molecular techniques for the production of recombinant heterologous proteins in a host system has overcome these constraints, as this allows high-level protein expression and production of new redesigned enzymes with improved catalytic properties. These can meet the requirements of specific industrial process better than the native enzymes. The purpose of this review is to give an overview of the structural and functional features of lipases and phospholipases, to describe the recent advances in optimization of the production of recombinant lipases and phospholipases, and to summarize the information available relating to their major applications in industrial processes.
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Affiliation(s)
- Grazia M Borrelli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura, S.S. 673 Km 25, 200-71122 Foggia, Italy.
| | - Daniela Trono
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura, S.S. 673 Km 25, 200-71122 Foggia, Italy.
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Reconstitution of the In Vitro Activity of the Cyclosporine-Specific P450 Hydroxylase from Sebekia benihana and Development of a Heterologous Whole-Cell Biotransformation System. Appl Environ Microbiol 2015; 81:6268-75. [PMID: 26150455 DOI: 10.1128/aem.01353-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/27/2015] [Indexed: 01/09/2023] Open
Abstract
The cytochrome P450 enzyme CYP-sb21 from Sebekia benihana is capable of catalyzing the site-specific hydroxylation of the immunosuppressant cyclosporine (CsA), leading to the single product γ-hydroxy-N-methyl-l-Leu4-CsA (CsA-4-OH). Unlike authentic CsA, this hydroxylated CsA shows significantly reduced immunosuppressive activity while it retains a side effect of CsA, the hair growth stimulation effect. Although CYP-sb21 was previously identified to be responsible for CsA-specific hydroxylation in vivo, the in vitro activity of CYP-sb21 has yet to be established for a deeper understanding of this P450 enzyme and further reaction optimization. In this study, we reconstituted the in vitro activity of CYP-sb21 by using surrogate redox partner proteins of bacterial and cyanobacterial origins. The highest CsA site-specific hydroxylation activity by CYP-sb21 was observed when it was partnered with the cyanobacterial redox system composed of seFdx and seFdR from Synechococcus elongatus PCC 7942. The best bioconversion yields were obtained in the presence of 10% methanol as a cosolvent and an NADPH regeneration system. A heterologous whole-cell biocatalyst using Escherichia coli was also constructed, and the permeability problem was solved by using N-cetyl-N,N,N-trimethylammonium bromide (CTAB). This work provides a useful example for reconstituting a hybrid P450 system and developing it into a promising biocatalyst for industrial application.
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Production of phenylpyruvic acid from l-phenylalanine using an l-amino acid deaminase from Proteus mirabilis: comparison of enzymatic and whole-cell biotransformation approaches. Appl Microbiol Biotechnol 2015; 99:8391-402. [DOI: 10.1007/s00253-015-6757-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/12/2022]
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14
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Garcia RAM, Pereira MR, Maester TC, de Macedo Lemos EG. Investigation, expression, and molecular modeling of ORF2, a metagenomic lipolytic enzyme. Appl Biochem Biotechnol 2015; 175:3875-87. [PMID: 25764223 DOI: 10.1007/s12010-015-1556-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/22/2015] [Indexed: 11/27/2022]
Abstract
One clone exhibiting lipolytic activity was selected among 30 positives from a metagenomic library of a microbe consortium specialized in petroleum hydrocarbon degradation. From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it was possible to identify a potential ORF that encodes a lipolytic enzyme, denoted ORF2. This ORF is composed of 1035-bp 345 amino acids and displayed 98 % identity with an alpha/beta hydrolase from Pseudomonas nitroreducens (accession number WP024765380.1). When analyzed against a metagenome database, ORF2 also showed 76 % of sequence identity with a hypothetical protein from a marine metagenome (accession number ECT55726.1). The ProtParam analyses indicated that the recombinant protein ORF2 has a molecular mass approximately 39 kDa, as expected from its amino acid sequence, and based on phylogenetic analysis and molecular modeling, it was possible to suggest that ORF2 is a new member from family V. This enzyme exhibits the catalytic triad and conserved motifs typical from this family, wherein the serine residue is located in the central position of the conserved motif GASMGG. The orf2 gene was cloned in the expression vector pET28a, and the recombinant protein was superexpressed in Escherichia coli BL21(DE3) cells. The lipolytic activity of protein bands presented in a SDS-PAGE gel was confirmed by zymogram analyses, indicating ORF2 activity. These discoveries raise the possibility of employing this protein in biotechnological applications, such as bioremediation.
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Affiliation(s)
- Rosmeriana Afnis Marioto Garcia
- Departamento de Tecnologia, UNESP-Univ Estadual Paulista, Faculdade de Ciências Agrárias eVeterinárias, Rod. Prof. Paulo Donato Castellane km 5, CEP, Jaboticabal, SP, 18884-900, Brazil,
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Wang D, Ni K, Ren Y, Wei D. Site-directed modification of genetically engineered Proteus sp. lipase K107 variants with a polyethylene glycol derivative. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1183-92. [DOI: 10.1016/j.bbapap.2014.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/16/2014] [Accepted: 02/24/2014] [Indexed: 11/18/2022]
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Brault G, Shareck F, Hurtubise Y, Lépine F, Doucet N. Short-chain flavor ester synthesis in organic media by an E. coli whole-cell biocatalyst expressing a newly characterized heterologous lipase. PLoS One 2014; 9:e91872. [PMID: 24670408 PMCID: PMC3966760 DOI: 10.1371/journal.pone.0091872] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/16/2014] [Indexed: 11/18/2022] Open
Abstract
Short-chain aliphatic esters are small volatile molecules that produce fruity and pleasant aromas and flavors. Most of these esters are artificially produced or extracted from natural sources at high cost. It is, however, possible to 'naturally' produce these molecules using biocatalysts such as lipases and esterases. A gene coding for a newly uncovered lipase was isolated from a previous metagenomic study and cloned into E. coli BL21 (DE3) for overexpression using the pET16b plasmid. Using this recombinant strain as a whole-cell biocatalyst, short chain esters were efficiently synthesized by transesterification and esterification reactions in organic media. The recombinant lipase (LipIAF5-2) showed good affinity toward glyceryl trioctanoate and the highest conversion yields were obtained for the transesterification of glyceryl triacetate with methanol. Using a simple cetyl-trimethylammonium bromide pretreatment increased the synthetic activity by a six-fold factor and the whole-cell biocatalyst showed the highest activity at 40°C with a relatively high water content of 10% (w/w). The whole-cell biocatalyst showed excellent tolerance to alcohol and short-chain fatty acid denaturation. Substrate affinity was equally effective with all primary alcohols tested as acyl acceptors, with a slight preference for methanol. The best transesterification conversion of 50 mmol glyceryl triacetate into isoamyl acetate (banana fragrance) provided near 100% yield after 24 hours using 10% biocatalyst loading (w/w) in a fluidized bed reactor, allowing recycling of the biocatalyst up to five times. These results show promising potential for an industrial approach aimed at the biosynthesis of short-chain esters, namely for natural flavor and fragrance production in micro-aqueous media.
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Affiliation(s)
- Guillaume Brault
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - François Shareck
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Yves Hurtubise
- Innu-Science Canada, Inc., Local 119, Trois-Rivières, Québec, Canada
| | - François Lépine
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
- PROTEO, the Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
- GRASP, Groupe de Recherche Axé sur la Structure des Protéines, Québec, Canada
- * E-mail:
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Yan J, Zheng X, Li S. A novel and robust recombinant Pichia pastoris yeast whole cell biocatalyst with intracellular overexpression of a Thermomyces lanuginosus lipase: preparation, characterization and application in biodiesel production. BIORESOURCE TECHNOLOGY 2014; 151:43-48. [PMID: 24189383 DOI: 10.1016/j.biortech.2013.10.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 06/02/2023]
Abstract
A novel and robust recombinant Pichia pastoris yeast whole cell catalyst (WCC) with functional intracellular expression of Thermomyces lanuginosus lipase (Tll) was constructed and characterized for biodiesel production from waste cooking oils. This permeabilized WCC was able to convert waste cooking oils to biodiesel with 82% yield within 84 h at 6% dosage whole cells. The WCC showed two fold catalytic activity of 0.73 U/mg DCW compared to its commercial counterpart Lipozyme TLIM (immobilized Tll). Short chain alcohol tolerance of this WCC was significantly improved compared to Lipozyme TLIM. This beneficial property enabled it to catalyze biodiesel production efficiently with one step addition of methanol. The reusability of this biocatalyst retained 78% activity after three batch cycles. This easily prepared and cost-effective WCC showed better catalytic performance than Lipozyme TLIM with respect to biodiesel yield and productivity, thus suggesting a promising cost-effective biocatalyst for biodiesel production.
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Affiliation(s)
- Jinyong Yan
- Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China.
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Zhang L, Tang X, Cui D, Yao Z, Gao B, Jiang S, Yin B, Yuan YA, Wei D. A method to rationally increase protein stability based on the charge-charge interaction, with application to lipase LipK107. Protein Sci 2013; 23:110-6. [PMID: 24353171 DOI: 10.1002/pro.2388] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/14/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022]
Abstract
We report a suite of enzyme redesign protocol based on the surface charge-charge interaction calculation, which is potentially applied to improve the stability of an enzyme without compromising its catalytic activity. Together with the experimental validation, we have released a suite of enzyme redesign algorithm Enzyme Thermal Stability System, written based on our model, for open access to meet the needs in wet labs. Lipk107, a lipase of a versatile industrial use, was chosen to test our software. Our calculation determined that four residues, D113, D149, D213, and D253, located on the surface of LipK107 were critical to the stability of the enzyme. The model was validated with mutagenesis at these four residues followed by stability and activity tests. LipK107 mutants D113A and D149K were more resistant to thermal inactivation with ∼10°C higher half-inactivation temperature than wild-type LipK107. Moreover, mutant D149K exhibited significant retention in residual activity under constant heat, showing a 14-fold increase in the half-inactivation time at 50°C. Activity tests showed that these mutants retained the equal or higher specific activity, among which noteworthy was the mutant D253A with as much as 20% higher activity. We suggest that our protocol could be used as a general guideline to redesign protein enzymes with increased stabilities and enhanced activities.
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Affiliation(s)
- Lujia Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing, Jiangsu 211800, People's Republic of China
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Korman TP, Sahachartsiri B, Charbonneau DM, Huang GL, Beauregard M, Bowie JU. Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:70. [PMID: 23648063 PMCID: PMC3670234 DOI: 10.1186/1754-6834-6-70] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/01/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Biodiesels are methyl esters of fatty acids that are usually produced by base catalyzed transesterification of triacylglyerol with methanol. Some lipase enzymes are effective catalysts for biodiesel synthesis and have many potential advantages over traditional base or acid catalyzed transesterification. Natural lipases are often rapidly inactivated by the high methanol concentrations used for biodiesel synthesis, however, limiting their practical use. The lipase from Proteus mirabilis is a particularly promising catalyst for biodiesel synthesis as it produces high yields of methyl esters even in the presence of large amounts of water and expresses very well in Escherichia coli. However, since the Proteus mirabilis lipase is only moderately stable and methanol tolerant, these properties need to be improved before the enzyme can be used industrially. RESULTS We employed directed evolution, resulting in a Proteus mirabilis lipase variant with 13 mutations, which we call Dieselzyme 4. Dieselzyme 4 has greatly improved thermal stability, with a 30-fold increase in the half-inactivation time at 50°C relative to the wild-type enzyme. The evolved enzyme also has dramatically increased methanol tolerance, showing a 50-fold longer half-inactivation time in 50% aqueous methanol. The immobilized Dieselzyme 4 enzyme retains the ability to synthesize biodiesel and has improved longevity over wild-type or the industrially used Brukholderia cepacia lipase during many cycles of biodiesel synthesis. A crystal structure of Dieselzyme 4 reveals additional hydrogen bonds and salt bridges in Dieselzyme 4 compared to the wild-type enzyme, suggesting that polar interactions may become particularly stabilizing in the reduced dielectric environment of the oil and methanol mixture used for biodiesel synthesis. CONCLUSIONS Directed evolution was used to produce a stable lipase, Dieselzyme 4, which could be immobilized and re-used for biodiesel synthesis. Dieselzyme 4 outperforms the industrially used lipase from Burkholderia cepacia and provides a platform for still further evolution of desirable biodiesel production properties.
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Affiliation(s)
- Tyler P Korman
- Department of Chemistry and Biochemisty, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
| | - Bobby Sahachartsiri
- Department of Chemistry and Biochemisty, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
| | - David M Charbonneau
- Département de chimie-biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Grace L Huang
- Department of Chemistry and Biochemisty, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
| | - Marc Beauregard
- Département de chimie-biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - James U Bowie
- Department of Chemistry and Biochemisty, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, USA
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Crystal structure of Proteus mirabilis lipase, a novel lipase from the Proteus/psychrophilic subfamily of lipase family I.1. PLoS One 2012; 7:e52890. [PMID: 23300806 PMCID: PMC3530535 DOI: 10.1371/journal.pone.0052890] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/23/2012] [Indexed: 12/29/2022] Open
Abstract
Bacterial lipases from family I.1 and I.2 catalyze the hydrolysis of triacylglycerol between 25-45°C and are used extensively as biocatalysts. The lipase from Proteus mirabilis belongs to the Proteus/psychrophilic subfamily of lipase family I.1 and is a promising catalyst for biodiesel production because it can tolerate high amounts of water in the reaction. Here we present the crystal structure of the Proteus mirabilis lipase, a member of the Proteus/psychrophilic subfamily of I.1lipases. The structure of the Proteus mirabilis lipase was solved in the absence and presence of a bound phosphonate inhibitor. Unexpectedly, both the apo and inhibitor bound forms of P. mirabilis lipase were found to be in a closed conformation. The structure reveals a unique oxyanion hole and a wide active site that is solvent accessible even in the closed conformation. A distinct mechanism for Ca²⁺ coordination may explain how these lipases can fold without specific chaperones.
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Yan J, Li A, Xu Y, Ngo TPN, Phua S, Li Z. Efficient production of biodiesel from waste grease: one-pot esterification and transesterification with tandem lipases. BIORESOURCE TECHNOLOGY 2012; 123:332-337. [PMID: 22940338 DOI: 10.1016/j.biortech.2012.07.103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 06/01/2023]
Abstract
A novel concept and efficient method for producing biodiesel (FAME) from grease (15-40wt% free fatty acid, FFA) were developed by using tandem lipases for one-pot esterification of FFA and transesterification of triglyceride with methanol in a solvent-free system. Combining immobilized Candida antarctica lipase B (CALB) (Novozyme 435) favoring the esterification and immobilized Thermomyces lanuginosus lipase (TLL) (Lipozyme TLIM) preferring the transesterification at 2:8 (wt/wt) gave FAME in 80% yield, being better than that with Novozyme 435 or Lipozyme TLIM. Recombinant Escherichia coli (Calb/Tll) co-expressing CALB and TLL was engineered as a more efficient tandem-lipases system. Using wet or dry cells (4wt%) gave FAME in 87% or 95% yield, which is much better than that with E. coli cells expressing either CALB or TLL alone. Cells of E. coli (Calb/Tll) were recycled for five times and retained 75% productivity, thus being practical for producing biodiesel from grease.
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Affiliation(s)
- Jinyong Yan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
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Huffer S, Roche CM, Blanch HW, Clark DS. Escherichia coli for biofuel production: bridging the gap from promise to practice. Trends Biotechnol 2012; 30:538-45. [DOI: 10.1016/j.tibtech.2012.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 02/04/2023]
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Brault G, Shareck F, Hurtubise Y, Lépine F, Doucet N. Isolation and characterization of EstC, a new cold-active esterase from Streptomyces coelicolor A3(2). PLoS One 2012; 7:e32041. [PMID: 22396747 PMCID: PMC3292560 DOI: 10.1371/journal.pone.0032041] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/18/2012] [Indexed: 12/02/2022] Open
Abstract
The genome sequence of Streptomyces coelicolor A3(2) contains more than 50 genes coding for putative lipolytic enzymes. Many studies have shown the capacity of this actinomycete to store important reserves of intracellular triacylglycerols in nutrient depletion situations. In the present study, we used genome mining of S. coelicolor to identify genes coding for putative, non-secreted esterases/lipases. Two genes were cloned and successfully overexpressed in E. coli as His-tagged fusion proteins. One of the recombinant enzymes, EstC, showed interesting cold-active esterase activity with a strong potential for the production of valuable esters. The purified enzyme displayed optimal activity at 35°C and was cold-active with retention of 25% relative activity at 10°C. Its optimal pH was 8.5-9 but the enzyme kept more than 75% of its maximal activity between pH 7.5 and 10. EstC also showed remarkable tolerance over a wide range of pH values, retaining almost full residual activity between pH 6-11. The enzyme was active toward short-chain p-nitrophenyl esters (C2-C12), displaying optimal activity with the valerate (C5) ester (k(cat)/K(m) = 737±77 s(-1) mM(-1)). The enzyme was also very active toward short chain triglycerides such as triacetin (C2:0) and tributyrin (C4:0), in addition to showing good primary alcohol and organic solvent tolerance, suggesting it could function as an interesting candidate for organic synthesis of short-chain esters such as flavors.
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Affiliation(s)
- Guillaume Brault
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - François Shareck
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Yves Hurtubise
- Innu-Science Canada, Inc., Trois-Rivières, Québec, Canada
| | - François Lépine
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
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Lin J, Shen H, Tan H, Zhao X, Wu S, Hu C, Zhao ZK. Lipid production by Lipomyces starkeyi cells in glucose solution without auxiliary nutrients. J Biotechnol 2011; 152:184-8. [DOI: 10.1016/j.jbiotec.2011.02.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 01/23/2011] [Accepted: 02/23/2011] [Indexed: 10/18/2022]
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Gao B, Xu T, Lin J, Zhang L, Su E, Jiang Z, Wei D. Improving the catalytic activity of lipase LipK107 from Proteus sp. by site-directed mutagenesis in the lid domain based on computer simulation. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Prospects for microbial biodiesel production. Biotechnol J 2011; 6:277-85. [PMID: 21328544 DOI: 10.1002/biot.201000117] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/03/2011] [Accepted: 01/14/2011] [Indexed: 01/25/2023]
Abstract
As the demand for biofuels for transportation is increasing, it is necessary to develop technologies that will allow for low-cost production of biodiesel. Conventional biodiesel is mainly produced from vegetable oil by chemical transesterification. This production, however, has relatively low land-yield and is competing for agricultural land that can be used for food production. Therefore, there is an increasing interest in developing microbial fermentation processes for production of biodiesel as this will allow for the use of a wide range of raw-materials, including sugar cane, corn, and biomass. Production of biodiesel by microbial fermentation can be divided into two different approaches, (1) indirect biodiesel production from oleaginous microbes by in vitro transesterification, and (2) direct biodiesel production from redesigned cell factories. This work reviews both microbial approaches for renewable biodiesel production and evaluates the existing challenges in these two strategies.
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Affiliation(s)
- Shuobo Shi
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Li Q, Li G, Ma F, Zhang Z, Zheng B, Feng Y. Highly efficient ring-opening polymerization of ɛ-caprolactone catalyzed by a recombinant Escherichia coli whole-cell biocatalyst. Process Biochem 2011. [DOI: 10.1016/j.procbio.2010.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sequential optimization of production of a thermostable and organic solvent tolerant lipase by recombinant Escherichia coli. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0170-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Template-based modeling of a psychrophilic lipase: Conformational changes, novel structural features and its application in predicting the enantioselectivity of lipase catalyzed transesterification of secondary alcohols. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:2183-90. [DOI: 10.1016/j.bbapap.2010.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 08/24/2010] [Accepted: 08/27/2010] [Indexed: 11/21/2022]
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Increasing unsaturated fatty acid contents in Escherichia coli by coexpression of three different genes. Appl Microbiol Biotechnol 2010; 87:271-80. [DOI: 10.1007/s00253-009-2377-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 11/19/2009] [Accepted: 11/20/2009] [Indexed: 11/26/2022]
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Bajaj A, Lohan P, Jha PN, Mehrotra R. Biodiesel production through lipase catalyzed transesterification: An overview. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.09.018] [Citation(s) in RCA: 366] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Röttig A, Wenning L, Bröker D, Steinbüchel A. Fatty acid alkyl esters: perspectives for production of alternative biofuels. Appl Microbiol Biotechnol 2009; 85:1713-33. [DOI: 10.1007/s00253-009-2383-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 12/01/2022]
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Xu T, Zhang L, Wang X, Wei D, Li T. Structure-based substrate screening for an enzyme. BMC Bioinformatics 2009; 10:257. [PMID: 19695105 PMCID: PMC2745390 DOI: 10.1186/1471-2105-10-257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 08/21/2009] [Indexed: 11/10/2022] Open
Abstract
Background Nowadays, more and more novel enzymes can be easily found in the whole enzyme pool with the rapid development of genetic operation. However, experimental work for substrate screening of a new enzyme is laborious, time consuming and costly. On the other hand, many computational methods have been widely used in lead screening of drug design. Seeing that the ligand-target protein system in drug design and the substrate-enzyme system in enzyme applications share the similar molecular recognition mechanism, we aim to fulfill the goal of substrate screening by in silico means in the present study. Results A computer-aided substrate screening (CASS) system which was based on the enzyme structure was designed and employed successfully to help screen substrates of Candida antarctica lipase B (CALB). In this system, restricted molecular docking which was derived from the mechanism of the enzyme was applied to predict the energetically favorable poses of substrate-enzyme complexes. Thereafter, substrate conformation, distance between the oxygen atom of the alcohol part of the ester (in some compounds, this oxygen atom was replaced by nitrogen atom of the amine part of acid amine or sulfur atom of the thioester) and the hydrogen atom of imidazole of His224, distance between the carbon atom of the carbonyl group of the compound and the oxygen atom of hydroxyl group of Ser105 were used sequentially as the criteria to screen the binding poses. 223 out of 233 compounds were identified correctly for the enzyme by this screening system. Such high accuracy guaranteed the feasibility and reliability of the CASS system. Conclusion The idea of computer-aided substrate screening is a creative combination of computational skills and enzymology. Although the case studied in this paper is tentative, high accuracy of the CASS system sheds light on the field of computer-aided substrate screening.
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Affiliation(s)
- Tao Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, PR China.
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Uthoff S, Bröker D, Steinbüchel A. Current state and perspectives of producing biodiesel-like compounds by biotechnology. Microb Biotechnol 2009; 2:551-65. [PMID: 21255288 PMCID: PMC3815363 DOI: 10.1111/j.1751-7915.2009.00139.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The global demand for crude oil is expected to continue to rise in future while simultaneously oil production is currently reaching its peak. Subsequently, rising oil prices and their negative impacts on economy, together with an increased environmental awareness of our society, directed the focus also on the biotechnological production of fuels. Although a wide variety of such fuels has been suggested, only the production of ethanol and biodiesel has reached a certain economic feasibility and volume, yet. This review focuses on the current state and perspectives of biotechnological production of biodiesel‐like compounds. At present by far most of the produced biodiesel is obtained by chemical transesterification reactions, which cannot meet the demands of a totally ‘green’ fuel production. Therefore, also several biotechnological biodiesel production processes are currently being developed. Biotechnological production can be achieved by purified enzymes in the soluble state, which requires cost‐intensive protein preparation. Alternatively, enzymes could be immobilized on an appropriate matrix, enabling a reuse of the enzyme, although the formation of by‐products may provide difficulties to maintain the enzyme activity. Processes in presence of organic solvents like t‐butanol have been developed, which enhance by‐product solubility and therefore prevent loss of enzyme activity. As another approach the application of whole‐cell catalysis for the production of fatty acid ethyl esters, which is also referred to as ‘microdiesel’, by recombinant microorganisms has recently been suggested.
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Affiliation(s)
- Stefan Uthoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Connor MR, Liao JC. Microbial production of advanced transportation fuels in non-natural hosts. Curr Opin Biotechnol 2009; 20:307-15. [DOI: 10.1016/j.copbio.2009.04.002] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 11/16/2022]
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