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Rajacharya GH, Sharma A, Yazdani SS. Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli. Sci Rep 2024; 14:12271. [PMID: 38806637 PMCID: PMC11133349 DOI: 10.1038/s41598-024-63148-y] [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: 03/12/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
The impact of recombinant protein production (RPP) on host cells and the metabolic burden associated with it undermine the efficiency of the production system. This study utilized proteomics to investigate the dynamics of parent and recombinant cells induced at different time points for RPP. The results revealed significant changes in both transcriptional and translational machinery that may have impacted the metabolic burden, growth rate of the culture and the RPP. The timing of protein synthesis induction also played a critical role in the fate of the recombinant protein within the host cell, affecting protein and product yield. The study identified significant differences in the expression of proteins involved in fatty acid and lipid biosynthesis pathways between two E. coli host strains (M15 and DH5⍺), with the E. coli M15 strain demonstrating superior expression characteristics for the recombinant protein. Overall, these findings contribute to the knowledge base for rational strain engineering for optimized recombinant protein production.
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Affiliation(s)
- Girish H Rajacharya
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Interdisciplinary Research (SIRe), Indian Institute of Technology, New Delhi, India
| | - Ashima Sharma
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Life Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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Han J, Asano K, Matsumoto T, Yamada R, Ogino H. Engineering acyl-ACP reductase with fusion tags enhances alka(e)ne synthesis in Escherichia coli. Enzyme Microb Technol 2023; 168:110262. [PMID: 37224590 DOI: 10.1016/j.enzmictec.2023.110262] [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: 11/25/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Alka(e)nes are high-value chemicals with a potentially broad range of industrial applications because of their following advantages: (1) chemical and structural resemblance to petroleum hydrocarbons and (2) higher energy density and hydrophobicity than those of other biofuels. The low yield of bio-alka(e)nes, however, hinders their commercial application. The activity and solubility of acyl carrier protein (ACP) reductase (AAR) affect alka(e)ne biosynthesis in cyanobacteria. The enhancement of the activity and concentration of soluble AAR through genetic and process engineering can improve bio-alka(e)ne yield. Although fusion tags are used to enhance the expression or solubility of recombinant proteins, their effectiveness in improving the production of bio-alka(e)nes has not yet been reported. Fusion tags can be used to improve the amount or activity of soluble AAR in Escherichia coli and to increase the yield of alka(e)nes in E. coli cells co-expressing aldehyde deformylating oxygenase (ADO). Hence, in the present study, histidine (His6/His12), thioredoxin (Trx), maltose-binding protein (MBP), and N-utilization substance (NusA) were used as AAR fusion tags. The strain expressing SeAAR with His12 tag and NpADO showed a 7.2-fold higher yield of alka(e)nes than the strain expressing AAR without fusion tag and NpADO. The highest titer of alka(e)nes (194.78 mg/L) was achieved with the His12 tag.
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Affiliation(s)
- Jiahu Han
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Koki Asano
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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Hayashi Y, Arai M. Recent advances in the improvement of cyanobacterial enzymes for bioalkane production. Microb Cell Fact 2022; 21:256. [PMID: 36503511 PMCID: PMC9743570 DOI: 10.1186/s12934-022-01981-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
The use of biologically produced alkanes has attracted considerable attention as an alternative energy source to petroleum. In 2010, the alkane synthesis pathway in cyanobacteria was found to include two small globular proteins, acyl-(acyl carrier protein [ACP]) reductase (AAR) and aldehyde deformylating oxygenase (ADO). AAR produces fatty aldehydes from acyl-ACPs/CoAs, which are then converted by ADO to alkanes/alkenes equivalent to diesel oil. This discovery has paved the way for alkane production by genetically modified organisms. Since then, many studies have investigated the reactions catalyzed by AAR and ADO. In this review, we first summarize recent findings on structures and catalytic mechanisms of AAR and ADO. We then outline the mechanism by which AAR and ADO form a complex and efficiently transfer the insoluble aldehyde produced by AAR to ADO. Furthermore, we describe recent advances in protein engineering studies on AAR and ADO to improve the efficiency of alkane production in genetically engineered microorganisms such as Escherichia coli and cyanobacteria. Finally, the role of alkanes in cyanobacteria and future perspectives for bioalkane production using AAR and ADO are discussed. This review provides strategies for improving the production of bioalkanes using AAR and ADO in cyanobacteria for enabling the production of carbon-neutral fuels.
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Affiliation(s)
- Yuuki Hayashi
- grid.26999.3d0000 0001 2151 536XDepartment of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902 Japan ,grid.26999.3d0000 0001 2151 536XEnvironmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033 Japan
| | - Munehito Arai
- grid.26999.3d0000 0001 2151 536XDepartment of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902 Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902 Japan
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Pramanik U, Khamari L, Rai S, Mahato P, Nandy A, Yadav R, Agrawal S, Mukherjee S. Macrocyclic Cavitand β-Cyclodextrin Inhibits the Alcohol-induced Trypsin Aggregation. Chemphyschem 2022; 23:e202200155. [PMID: 35608331 DOI: 10.1002/cphc.202200155] [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: 03/08/2022] [Revised: 05/24/2022] [Indexed: 11/09/2022]
Abstract
Trypsin, the most abundant pancreatic protein, aids in protein digestion by hydrolysis and exhibits aggregation propensity in presence of alcohol which can further lead to pancreatitis and eventually pancreatic cancer. Herein, by several experimental and theoretical approaches, we unearth the inhibition of alcohol-induced aggregation of Trypsin by macrocyclic cavitand, β-cyclodextrin (β-CD). β-CD interacts with the native protein and shows inhibitory effect in a dose dependent manner. Moreover, the secondary structures and morphologies of Trypsin in presence of β-CD also clearly emphasize the inhibition of fibril formation. From Fluorescence Correlation Spectroscopy, we observed an enhancement in diffusion time of Nile Red with ~ 2.5 times increase in hydrodynamic radius, substantiating the presence of fibrillar structure. Trypsin also shows reduction in its functional activity due to alcohol-induced aggregation. Our simulation data reports the probable residues responsible for fibril formation which was validated by molecular docking studies.
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Affiliation(s)
- Ushasi Pramanik
- IISER Bopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Laxmikanta Khamari
- IISER Bhopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Saurabh Rai
- IISER Bhopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Paritosh Mahato
- IISER Bopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Atanu Nandy
- IISER Bhopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Rahul Yadav
- IISER Bhopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Sameeksha Agrawal
- IISER Bopal: Indian Institute of Science Education and Research Bhopal, Chemistry, INDIA
| | - Saptarshi Mukherjee
- Indian Institute of Science Education and Research Bhopal, Chemistry, Indore By-Pass Road, Bhauri, 462066, Bhopal, INDIA
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Parveen H, Yazdani SS. Insights into cyanobacterial alkane biosynthesis. J Ind Microbiol Biotechnol 2022; 49:kuab075. [PMID: 34718648 PMCID: PMC9118987 DOI: 10.1093/jimb/kuab075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022]
Abstract
Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels. Though biological production of alkanes has been reported in various microorganisms, the reports citing photosynthetic cyanobacteria as natural producers have been the most consistent for the long-chain alkanes and alkenes (C15-C19). However, the production of alkane in cyanobacteria is low, leading to its extraction being uneconomical for commercial purposes. In order to make alkane production economically feasible from cyanobacteria, the titre and yield need to be increased by several orders of magnitude. In the recent past, efforts have been made to enhance alkane production, although with a little gain in yield, leaving space for much improvement. Genetic manipulation in cyanobacteria is considered challenging, but recent advancements in genetic engineering tools may assist in manipulating the genome in order to enhance alkane production. Further, advancement in a basic understanding of metabolic pathways and gene functioning will guide future research for harvesting the potential of these tiny photosynthetically efficient factories. In this review, our focus would be to highlight the current knowledge available on cyanobacterial alkane production, and the potential aspects of developing cyanobacterium as an economical source of biofuel. Further insights into different metabolic pathways and hosts explored so far, and possible challenges in scaling up the production of alkanes will also be discussed.
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Affiliation(s)
- Humaira Parveen
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [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] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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