Hitarth B. Bhatt
Rajesh K. Sani
Mohammad Ali Amoozegar
Satya P. Singh- 1Department of Microbiology, Faculty of Science, Atmiya University, Rajkot, Gujarat, India
- 2Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- 3Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- 4Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India
Editorial on the Research Topic
Extremozymes: characteristics, structure, protein engineering and applications
Enzymes are indispensable biological catalysts that play pivotal roles in myriad physiological processes. They accelerate chemical reactions without being consumed in the process (Liu and Kokare, 2023). Overall, the versatility and efficiency of enzymes make them indispensable in diverse fields, concerning processes, products, and cellular and environmental sustainability.
Extremozymes are obtained from organisms that thrive in extreme environmental conditions, including high or low temperatures, acidic or alkaline pH levels, and high salinity (Sarmiento et al., 2015). These enzymes exhibit unique characteristics of stability and function in harsh conditions, which make them invaluable in various applications and industrial processes (Ghattavi and Homaei, 2023; Kikani et al., 2023; Rai et al., 2024). Extremozymes have diverse application avenues, including bioremediation, pharmaceuticals, detergents, food and beverage, and biofuel production (Mesbah, 2022).
To harness extremozymes for sustainable industrial processes, it is crucial to delve deeper into the microbial diversity of different extreme environments and uncover novel enzymes having combinations of unique properties (Bhatt and Singh, 2022). With the increasing focus on sustainability, extremozymes offer a promising route to efficient biocatalysis in harsh conditions, minimizing energy use, waste, and environmental harm. Furthermore, advances in X-ray crystallography and cryo-electron microscopy are key for detailing extremozyme structures at atomic levels. Techniques like directed evolution and rational design have improved extremozymes' stability and efficiency (Nakhaee et al., 2018; Rigoldi et al., 2018; Liu et al., 2019). An interdisciplinary approach incorporating bioinformatics, synthetic biology, and materials science will further enhance the application of extremozymes in addressing global challenges.
This Research Topic aimed to delve into emerging insights regarding the structure and function of extremozymes. For this Research Topic, seven articles reflecting diverse aspects of the theme were published. These involved identifying enzymes capable of operating in extreme conditions, unraveling their adaptation mechanisms and structure-function relationships, and enhancing catalytic properties through protein engineering and innovative applications.
Shi et al. present a thorough examination of thermostable DNA ligases sourced from hyperthermophilic bacteria and archaea, spotlighting their structural and biochemical characteristics. The review delves into a comparative analysis between thermostable DNA ligases and their non-thermostable counterparts, elucidating the differences between bacterial and archaeal variants. Despite significant progress, the intricate structures of thermostable DNA ligases continue to pose challenges. The manuscript also explores potential pathways for enhancing the features and applications of thermostable DNA ligases through modification.
Karthik et al. unveiled the potential bioactive compounds from Streptomyces tauricus of mangrove ecosystems, and their impact on inhibiting prostate cancer PC3 cells. After optimized growth conditions for S. tauricus, the intracellular extract was purified and analyzed by GCMS and LCMS revealing low molecular weight peptides including Tryprostatin B, Fumonisin B1, Microcystin LR, and Surfactin C. The findings suggest the capacity of S. tauricus to generate bioactive peptides with dual antimicrobial and anticancer properties.
In another contribution by Røyseth et al., characteristics of the novel C11 protease globulin from uncultivated Archaeoglobales in the Soria Moria hydrothermal vent system on the Arctic Mid-Ocean Ridge have been described. The sequence comparison in the MEROPS-MPRO database revealed its correlation with C11-like proteases of the human gut bacteria. Through recombinant expression in Escherichia coli, they evaluated the wild-type zymogen and 13 mutant variants to reveal the maturation and function of the enzyme. Globupain stands out for its high thermostability and activity in low pH, and high reducing conditions, establishing its suitability in industrial and biotechnological applications.
The potential applications of TrLipE, a thermophilic lipase from Thermomicrobium roseum, have been constrained by its relatively low enzymatic activity. In their manuscript, Fang et al. detail the creation of 18 chimeras through lid swapping, which displayed higher expression levels than the wildtype TrLipE. Molecular dynamics (MD) simulations revealed increased flexibility in these chimeras. Moreover, these variants exhibited enhanced thermostability and resilience across a broad pH range compared to other thermostable lipases. Significantly, variants with single, double, or tripe substitutions demonstrated 2-3-fold faster catalysis than the wild TrL17.
Similarly, processed thermostable lipase from Brevibacillus sp. SHI-160 using an alcohol-salt-based aqueous two-phase system has been described by Leykun et al. The versatility of the enzyme reflected by the optimal activity at 65°C and stability in polar solvents, offers potential application prospects. Its efficient recovery, immobilization, and performance in non-aqueous media highlight its potential for cost-effective synthesis of valuable compounds.
Sun et al. have described an innovative approach, combining droplet-based microfluidics with conventional CSR for polymerase mutant site screening for enhanced salt tolerance. Substituting regular sites with conserved amino acids was projected as an effective strategy. SZ_A emerged as the most promising variant, offering improved salt tolerance, processivity, and exonuclease deficiency, ideal for nanopore sequencing. This methodology not only enhances polymerase activity for salt tolerance but also introduces a novel sequence design strategy through amino acid substitution, paving the way for biotechnological advancements and new applications.
Hu et al. successfully identified and modified the enzyme motion pathway of an α-amylase from Geobacillus stearothermophilus. The mutants exhibited enhanced characteristics. Particularly, the P44E mutation enhanced hydrolytic activity by 95% and catalytic efficiency by 93.8%, with an optimal temperature of 90°C. It was revealed that amino acids located in the central region of the conformational motion pathway serve as critical “hinge” positions, crucial for structural stability. It facilitated substrate entry and exit from the catalytic center. The strategic designing of the pivotal amino acids could modify enzymes with significantly improved activities and stability.
In conclusion, the research featured in this topic signifies significant advancements in biotechnology and enzyme engineering. It includes the exploration of thermostable DNA ligases, identification of bioactive compounds with potential anticancer properties, introduction of a novel protease, engineering of lipase variants for improved catalysis, and presentation of innovative approaches for polymerase activity enhancement. These studies offer valuable insights and drive progress in biotechnological research, particularly in the pursuit of novel extremozymes and refining existing properties through molecular evolution techniques.
Author contributions
HB: Conceptualization, Writing—original draft, Writing—review & editing. RS: Writing—review & editing. MA: Writing—review & editing. SS: Conceptualization, Writing—original draft, Writing—review & editing.
Funding
The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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References
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Ghattavi, S., and Homaei, A. (2023). Marine enzymes: classification and application in various industries. Int. J. Biol. Macromol. 230:123136. doi: 10.1016/j.ijbiomac.2023.123136
Kikani, B., Patel, R., Thumar, J., Bhatt, H., Rathore, D. S., Koladiya, G. A., and Singh, S. P. (2023). Solvent tolerant enzymes in extremophiles: adaptations and applications. Int. J. Biol. Macromol. 12:4051. doi: 10.1016/j.ijbiomac.2023.124051
Liu, Q., Xun, G., and Feng, Y. (2019). The state-of-the-art strategies of protein engineering for enzyme stabilization. Biotechnol. Adv. 37, 530–537. doi: 10.1016/j.biotechadv.2018.10.011
Liu, X., and Kokare, C. (2023). “Microbial enzymes of use in industry,” in Biotechnology of Microbial Enzymes (Cambridge: Academic Press), 405–444.
Mesbah, N. M. (2022). Industrial biotechnology based on enzymes from extreme environments. Front. Bioeng. Biotechnol. 10:870083. doi: 10.3389/fbioe.2022.870083
Nakhaee, N., Asad, S., Khajeh, K., Arab, S. S., and Amoozegar, M. A. (2018). Improving the thermal stability of azoreductase from Halomonas elongata by introducing a disulfide bond via site-directed mutagenesis. Biotechnol. Appl. Biochem. 65, 883–891. doi: 10.1002/bab.1688
Rai, R., Samanta, D., Goh, K. M., Chadha, B. S., and Sani, R. K. (2024). Biochemical unravelling of the endoxylanase activity in a bifunctional GH39 enzyme cloned and expressed from thermophilic Geobacillus sp. WSUCF1. Int. J. Biol. Macromol. 257:128679. doi: 10.1016/j.ijbiomac.2023.128679
Rigoldi, F., Donini, S., Redaelli, A., Parisini, E., and Gautieri, A. (2018). Engineering of thermostable enzymes for industrial applications. APL Bioeng. 2:1. doi: 10.1063/1.4997367
Keywords: extremophiles, extremozymes, enzyme engineering, structure-function relationship, enzyme optimization, enzyme purification and characterization, enzyme applications, enzyme immobilization
Citation: Bhatt HB, Sani RK, Amoozegar MA and Singh SP (2024) Editorial: Extremozymes: characteristics, structure, protein engineering and applications. Front. Microbiol. 15:1423463. doi: 10.3389/fmicb.2024.1423463
Received: 25 April 2024; Accepted: 30 April 2024;
Published: 08 May 2024.
Edited and reviewed by: Andreas Teske, University of North Carolina at Chapel Hill, United States
Copyright © 2024 Bhatt, Sani, Amoozegar and Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Satya P. Singh, c2F0eWFwc2luZ2gmI3gwMDA0MDt5YWhvby5jb20=; Hitarth B. Bhatt, aGl0YXJ0aF9iaGF0dCYjeDAwMDQwO3lhaG9vLmNvLmlu